From 8366b2e8bd887b9abdb8eb7730de205e47aad83f Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 1 Nov 2022 18:27:09 -0500 Subject: [PATCH 001/150] Add user group functionality to repo load controller Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 62 ++++++++++++++++++++++++------ 1 file changed, 51 insertions(+), 11 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index eac07235ae..422ceca1a2 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -19,6 +19,7 @@ ORG_REPOS_ENDPOINT = "https://api.github.com/orgs/{}/repos?per_page=100" DEFAULT_REPO_GROUP_ID = 1 CLI_USER_ID = 1 +CLI_GROUP_ID = 1 class RepoLoadController: @@ -82,6 +83,14 @@ def is_valid_repo(self, url: str) -> bool: return True + def is_valid_user_group(self, user_id, group_id) -> bool: + + try: + self.session.query(UserRepo).filter(UserRepo.user_id == user_id, UserRepo.group_id == group_id).one() + return True + except s.orm.exc.NoResultFound: + return False + def retrieve_org_repos(self, url: str) -> List[str]: """Get the repos for an org. @@ -182,7 +191,7 @@ def add_repo_row(self, url: str, repo_group_id: int, tool_source): return result[0]["repo_id"] - def add_repo_to_user(self, repo_id, user_id=1): + def add_repo_to_user_group(self, repo_id, group_id=CLI_GROUP_ID): """Add a repo to a user in the user_repos table. Args: @@ -190,22 +199,47 @@ def add_repo_to_user(self, repo_id, user_id=1): user_id: id of user_id from users table """ - repo_user_data = { - "user_id": user_id, + repo_user_group_data = { + "group_id": group_id, "repo_id": repo_id } - repo_user_unique = ["user_id", "repo_id"] - return_columns = ["user_id", "repo_id"] + repo_user_group_unique = ["group_id", "repo_id"] + return_columns = ["group_id", "repo_id"] data = self.session.insert_data(repo_user_data, UserRepo, repo_user_unique, return_columns) - if data[0]["user_id"] == user_id and data[0]["repo_id"] == repo_id: + if data[0]["group_id"] == group_id and data[0]["repo_id"] == repo_id: return True return False - def add_frontend_repo(self, url: List[str], user_id: int): + def add_user_group(self, user_id, group_name): + + user_group_data = { + "group_name": group_id, + "user_id": repo_id + } + + # TODO Add exception for duplicate groups + group_obj = UserGroup(**user_group_data) + self.session.add(group_obj) + self.session.commit() + + return True + + def get_user_groups(self, user_id): + + return self.session.query(UserGroup).filter(UserGroup.user_id == user_id).all() + + def get_user_group_repos(self, user_id, group_id): + + repos = self.session.query(UserRepo).filter(UserGroup.user_id == user_id, UserGroup.group_id = group_id).all() + + return [repo["repo_id"] for repo in repos] + + + def add_frontend_repo(self, url: List[str], user_id: int, group_id: int, valid_group=False): """Add list of repos to a users repos. Args: @@ -216,12 +250,15 @@ def add_frontend_repo(self, url: List[str], user_id: int): if not self.is_valid_repo(url): return {"status": "Invalid repo", "repo_url": url} + if not valid_group and not self.is_valid_user_group(user_id, group_id): + return {"status": "Invalid user group", "group_id": group_id} + repo_id = self.add_repo_row(url, DEFAULT_REPO_GROUP_ID, "Frontend") if not repo_id: return {"status": "Repo insertion failed", "repo_url": url} - result = self.add_repo_to_user(repo_id, user_id) + result = self.add_repo_to_user_group(repo_id, group_id) if not result: return {"status": "repo_user insertion failed", "repo_url": url} @@ -230,7 +267,7 @@ def add_frontend_repo(self, url: List[str], user_id: int): - def add_frontend_org(self, url: List[str], user_id: int): + def add_frontend_org(self, url: List[str], user_id: int, group_id: int): """Add list of orgs and their repos to a users repos. Args: @@ -242,11 +279,14 @@ def add_frontend_org(self, url: List[str], user_id: int): if not repos: return {"status": "Invalid org", "org_url": url} + + if not self.is_valid_user_group(user_id, group_id): + return {"status": "Invalid user group", "group_id": group_id} failed_repos = [] for repo in repos: - result = self.add_frontend_repo(repo, user_id) + result = self.add_frontend_repo(repo, user_id, group_id, valid_group=True) if result["status"] != "Repo Added": failed_repos.append(repo) @@ -278,7 +318,7 @@ def add_cli_repo(self, repo_data: Dict[str, Any]): logger.warning(f"Invalid repo group id specified for {url}, skipping.") return - self.add_repo_to_user(repo_id, CLI_USER_ID) + self.add_repo_to_user_group(repo_id) def add_cli_org(self, org_name): """Add list of orgs and their repos to specified repo_groups From 75e275eb872ac49ca674bd715552e60f1171637e Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 19 Dec 2022 09:47:01 -0600 Subject: [PATCH 002/150] Add user group table Signed-off-by: Andrew Brain --- .../application/db/models/augur_operations.py | 22 +++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index a83d34b143..0af91d9d49 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -1,6 +1,7 @@ # coding: utf-8 from sqlalchemy import BigInteger, SmallInteger, Column, Index, Integer, String, Table, text, UniqueConstraint, Boolean, ForeignKey -from sqlalchemy.dialects.postgresql import TIMESTAMP +from sqlalchemy.dialects.postgresql import TIMESTAMP, UUID + from augur.application.db.models.base import Base @@ -191,6 +192,19 @@ class User(Base): ) +class UserGroup(Base): + id = Column(UUID, primary_key=True) + user_id = Column(Integer, + ForeignKey("augur_operations.users.user_id", name="user_group_user_id_fkey") + ) + name = Column(String, nullable=False) + __tablename__ = 'user_groups' + __table_args__ = ( + UniqueConstraint('user_g', name='user_group_unique'), + {"schema": "augur_operations"} + ) + + class UserRepo(Base): __tablename__ = "user_repos" @@ -200,10 +214,10 @@ class UserRepo(Base): } ) - user_id = Column( - ForeignKey("augur_operations.users.user_id"), primary_key=True, nullable=False + group_id = Column( + ForeignKey("augur_operations.user_groups.group_id", name="user_repo_group_id_fkey"), primary_key=True, nullable=False ) repo_id = Column( - ForeignKey("augur_data.repo.repo_id"), primary_key=True, nullable=False + ForeignKey("augur_data.repo.repo_id", name="user_repo_user_id_fkey"), primary_key=True, nullable=False ) From a7cd7fb47a98b1154814c7b4228dd8abf2532cbd Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 19 Dec 2022 09:49:36 -0600 Subject: [PATCH 003/150] Changes for user groups Signed-off-by: Andrew Brain --- augur/application/db/util.py | 4 +- ..._add_user_groups_table_and_update_user_.py | 85 +++++++++++++++++++ augur/util/repo_load_controller.py | 4 +- 3 files changed, 89 insertions(+), 4 deletions(-) create mode 100644 augur/application/schema/alembic/versions/2022-12-08_2_add_user_groups_table_and_update_user_.py diff --git a/augur/application/db/util.py b/augur/application/db/util.py index b310c68c10..3a5ed38e79 100644 --- a/augur/application/db/util.py +++ b/augur/application/db/util.py @@ -14,8 +14,8 @@ def catch_operational_error(func): time.sleep(240) try: return func() - except OperationalError: - pass + except OperationalError as e: + print(f"ERROR: {e}") attempts += 1 diff --git a/augur/application/schema/alembic/versions/2022-12-08_2_add_user_groups_table_and_update_user_.py b/augur/application/schema/alembic/versions/2022-12-08_2_add_user_groups_table_and_update_user_.py new file mode 100644 index 0000000000..f93f2b9f4b --- /dev/null +++ b/augur/application/schema/alembic/versions/2022-12-08_2_add_user_groups_table_and_update_user_.py @@ -0,0 +1,85 @@ +"""Add user_groups table and update user_repo + +Revision ID: 2 +Revises: 1 +Create Date: 2022-12-08 09:37:17.864281 + +""" +from alembic import op +import sqlalchemy as sa +from sqlalchemy.dialects import postgresql +from augur.application.db.session import DatabaseSession +from augur.application.db.models.augur_operations import UserGroup, UserRepo +import uuid +import logging + +# revision identifiers, used by Alembic. +revision = '2' +down_revision = '1' +branch_labels = None +depends_on = None + + +def upgrade(): + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('user_groups', + sa.Column('user_id', sa.Integer(), nullable=False), + sa.Column('group_id', postgresql.UUID(), nullable=False), + sa.Column('name', sa.String(), nullable=False), + sa.ForeignKeyConstraint(['user_id'], ['augur_operations.users.user_id'], name='user_group_user_id_fkey'), + sa.PrimaryKeyConstraint('group_id'), + schema='augur_operations' + ) + + + + logger = logging.getLogger(__name__) + + user_group_id_mapping = {} + with DatabaseSession(logger) as session: + user_id_query = sa.sql.text("""SELECT * FROM user_repos;""") + user_groups = session.fetchall_data_from_sql_text(user_id_query) + for row in user_groups: + row.update({"group_id": uuid.uuid4(), "name": "default"}) + user_group_id_mapping.update({row["user_id"]: row["group_id"]}) + del row["repo_id"] + + user_repo_query = sa.sql.text("""SELECT * FROM user_repos;""") + user_repo_data = session.fetchall_data_from_sql_text(user_repo_query) + for row in user_repo_data: + row.update({"group_id": user_group_id_mapping[row["user_id"]]}) + del row["user_id"] + + + remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") + session.execute_sql(remove_data_from_user_repos_query) + + op.add_column('user_repos', sa.Column('group_id', postgresql.UUID(), nullable=False), schema='augur_operations') + op.drop_constraint('user_repos_user_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') + op.drop_constraint('user_repos_repo_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') + op.create_foreign_key('user_repo_group_id_fkey', 'user_repos', 'user_groups', ['group_id'], ['group_id'], source_schema='augur_operations', referent_schema='augur_operations') + op.create_foreign_key('user_repo_user_id_fkey', 'user_repos', 'repo', ['repo_id'], ['repo_id'], source_schema='augur_operations', referent_schema='augur_data') + op.drop_column('user_repos', 'user_id', schema='augur_operations') + + session.insert_data(user_groups, UserGroup, ["user_id", "group_id"]) + session.insert_data(user_groups, UserRepo, ["group_id", "repo_id"]) + + + + + + # ### end Alembic commands ### + + +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### + # op.add_column('user_repos', sa.Column('user_id', sa.INTEGER(), autoincrement=False, nullable=False), schema='augur_operations') + # op.drop_constraint('user_repo_user_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') + # op.drop_constraint('user_repo_group_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') + # op.create_foreign_key('user_repos_repo_id_fkey', 'user_repos', 'repo', ['repo_id'], ['repo_id'], source_schema='augur_operations') + # op.create_foreign_key('user_repos_user_id_fkey', 'user_repos', 'users', ['user_id'], ['user_id'], source_schema='augur_operations', referent_schema='augur_operations') + # op.drop_column('user_repos', 'group_id', schema='augur_operations') + + pass + # op.drop_table('user_groups', schema='augur_operations') + # ### end Alembic commands ### diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index 387ec30908..f7d46cb272 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -184,7 +184,7 @@ def add_repo_to_user_group(self, repo_id, group_id=CLI_GROUP_ID): repo_user_group_unique = ["group_id", "repo_id"] return_columns = ["group_id", "repo_id"] - data = self.session.insert_data(repo_user_data, UserRepo, repo_user_unique, return_columns) + data = self.session.insert_data(repo_user_group_data, UserGroup, repo_user_group_unique, return_columns) if data[0]["group_id"] == group_id and data[0]["repo_id"] == repo_id: return True @@ -211,7 +211,7 @@ def get_user_groups(self, user_id): def get_user_group_repos(self, user_id, group_id): - repos = self.session.query(UserRepo).filter(UserGroup.user_id == user_id, UserGroup.group_id = group_id).all() + repos = self.session.query(UserRepo).filter(UserGroup.user_id == user_id, UserGroup.group_id == group_id).all() return [repo["repo_id"] for repo in repos] From 527394480f62f347a739fc63d3d1c0f4829b3055 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 19 Dec 2022 11:25:41 -0600 Subject: [PATCH 004/150] Start working on converting old dbs to new version Signed-off-by: Andrew Brain --- .../application/db/models/augur_operations.py | 6 +- ..._add_user_groups_table_and_update_user_.py | 85 ----------------- ...-19_632bd5da0e79_added_user_group_table.py | 93 +++++++++++++++++++ 3 files changed, 96 insertions(+), 88 deletions(-) delete mode 100644 augur/application/schema/alembic/versions/2022-12-08_2_add_user_groups_table_and_update_user_.py create mode 100644 augur/application/schema/alembic/versions/2022-12-19_632bd5da0e79_added_user_group_table.py diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index 0af91d9d49..d007ce93e0 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -193,14 +193,14 @@ class User(Base): class UserGroup(Base): - id = Column(UUID, primary_key=True) + user_group_id = Column(BigInteger, primary_key=True) user_id = Column(Integer, ForeignKey("augur_operations.users.user_id", name="user_group_user_id_fkey") ) name = Column(String, nullable=False) __tablename__ = 'user_groups' __table_args__ = ( - UniqueConstraint('user_g', name='user_group_unique'), + UniqueConstraint('user_id', 'name', name='user_group_unique'), {"schema": "augur_operations"} ) @@ -215,7 +215,7 @@ class UserRepo(Base): ) group_id = Column( - ForeignKey("augur_operations.user_groups.group_id", name="user_repo_group_id_fkey"), primary_key=True, nullable=False + ForeignKey("augur_operations.user_groups.user_group_id", name="user_repo_group_id_fkey"), primary_key=True, nullable=False ) repo_id = Column( ForeignKey("augur_data.repo.repo_id", name="user_repo_user_id_fkey"), primary_key=True, nullable=False diff --git a/augur/application/schema/alembic/versions/2022-12-08_2_add_user_groups_table_and_update_user_.py b/augur/application/schema/alembic/versions/2022-12-08_2_add_user_groups_table_and_update_user_.py deleted file mode 100644 index f93f2b9f4b..0000000000 --- a/augur/application/schema/alembic/versions/2022-12-08_2_add_user_groups_table_and_update_user_.py +++ /dev/null @@ -1,85 +0,0 @@ -"""Add user_groups table and update user_repo - -Revision ID: 2 -Revises: 1 -Create Date: 2022-12-08 09:37:17.864281 - -""" -from alembic import op -import sqlalchemy as sa -from sqlalchemy.dialects import postgresql -from augur.application.db.session import DatabaseSession -from augur.application.db.models.augur_operations import UserGroup, UserRepo -import uuid -import logging - -# revision identifiers, used by Alembic. -revision = '2' -down_revision = '1' -branch_labels = None -depends_on = None - - -def upgrade(): - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('user_groups', - sa.Column('user_id', sa.Integer(), nullable=False), - sa.Column('group_id', postgresql.UUID(), nullable=False), - sa.Column('name', sa.String(), nullable=False), - sa.ForeignKeyConstraint(['user_id'], ['augur_operations.users.user_id'], name='user_group_user_id_fkey'), - sa.PrimaryKeyConstraint('group_id'), - schema='augur_operations' - ) - - - - logger = logging.getLogger(__name__) - - user_group_id_mapping = {} - with DatabaseSession(logger) as session: - user_id_query = sa.sql.text("""SELECT * FROM user_repos;""") - user_groups = session.fetchall_data_from_sql_text(user_id_query) - for row in user_groups: - row.update({"group_id": uuid.uuid4(), "name": "default"}) - user_group_id_mapping.update({row["user_id"]: row["group_id"]}) - del row["repo_id"] - - user_repo_query = sa.sql.text("""SELECT * FROM user_repos;""") - user_repo_data = session.fetchall_data_from_sql_text(user_repo_query) - for row in user_repo_data: - row.update({"group_id": user_group_id_mapping[row["user_id"]]}) - del row["user_id"] - - - remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") - session.execute_sql(remove_data_from_user_repos_query) - - op.add_column('user_repos', sa.Column('group_id', postgresql.UUID(), nullable=False), schema='augur_operations') - op.drop_constraint('user_repos_user_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') - op.drop_constraint('user_repos_repo_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') - op.create_foreign_key('user_repo_group_id_fkey', 'user_repos', 'user_groups', ['group_id'], ['group_id'], source_schema='augur_operations', referent_schema='augur_operations') - op.create_foreign_key('user_repo_user_id_fkey', 'user_repos', 'repo', ['repo_id'], ['repo_id'], source_schema='augur_operations', referent_schema='augur_data') - op.drop_column('user_repos', 'user_id', schema='augur_operations') - - session.insert_data(user_groups, UserGroup, ["user_id", "group_id"]) - session.insert_data(user_groups, UserRepo, ["group_id", "repo_id"]) - - - - - - # ### end Alembic commands ### - - -def downgrade(): - # ### commands auto generated by Alembic - please adjust! ### - # op.add_column('user_repos', sa.Column('user_id', sa.INTEGER(), autoincrement=False, nullable=False), schema='augur_operations') - # op.drop_constraint('user_repo_user_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') - # op.drop_constraint('user_repo_group_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') - # op.create_foreign_key('user_repos_repo_id_fkey', 'user_repos', 'repo', ['repo_id'], ['repo_id'], source_schema='augur_operations') - # op.create_foreign_key('user_repos_user_id_fkey', 'user_repos', 'users', ['user_id'], ['user_id'], source_schema='augur_operations', referent_schema='augur_operations') - # op.drop_column('user_repos', 'group_id', schema='augur_operations') - - pass - # op.drop_table('user_groups', schema='augur_operations') - # ### end Alembic commands ### diff --git a/augur/application/schema/alembic/versions/2022-12-19_632bd5da0e79_added_user_group_table.py b/augur/application/schema/alembic/versions/2022-12-19_632bd5da0e79_added_user_group_table.py new file mode 100644 index 0000000000..38c69a5216 --- /dev/null +++ b/augur/application/schema/alembic/versions/2022-12-19_632bd5da0e79_added_user_group_table.py @@ -0,0 +1,93 @@ +"""Added user group table + +Revision ID: 632bd5da0e79 +Revises: 1 +Create Date: 2022-12-19 11:00:37.509132 + +""" +import logging + +from alembic import op +import sqlalchemy as sa +from augur.application.db.session import DatabaseSession + + + +# revision identifiers, used by Alembic. +revision = '632bd5da0e79' +down_revision = '1' +branch_labels = None +depends_on = None + + +def upgrade(): + + + + + + + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('user_groups', + sa.Column('user_group_id', sa.BigInteger(), nullable=False), + sa.Column('user_id', sa.Integer(), nullable=True), + sa.Column('name', sa.String(), nullable=False), + sa.ForeignKeyConstraint(['user_id'], ['augur_operations.users.user_id'], name='user_group_user_id_fkey'), + sa.PrimaryKeyConstraint('user_group_id'), + sa.UniqueConstraint('user_id', 'name', name='user_group_unique'), + schema='augur_operations' + ) + + logger = logging.getLogger(__name__) + + + with DatabaseSession(logger) as session: + user_id_query = sa.sql.text("""SELECT DISTINCT(user_id) FROM user_repos;""") + user_groups = session.fetchall_data_from_sql_text(user_id_query) + for row in user_groups: + row.update({"name": "default"}) + del row["repo_id"] + + result = session.insert_data(user_groups, UserGroup, ["user_id", "name"], return_columns=["group_id", "user_id"]) + + + user_group_id_mapping = {} + for row in result: + user_group_id_mapping[row["user_id"]] = row["group_id"] + + + user_repo_query = sa.sql.text("""SELECT * FROM user_repos;""") + user_repo_data = session.fetchall_data_from_sql_text(user_repo_query) + for row in user_repo_data: + row.update({"group_id": user_group_id_mapping[row["user_id"]]}) + del row["user_id"] + + + + # remove data from table before modifiying it + remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") + session.execute_sql(remove_data_from_user_repos_query) + + + op.add_column('user_repos', sa.Column('group_id', sa.BigInteger(), nullable=False), schema='augur_operations') + op.drop_constraint('user_repos_repo_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') + op.drop_constraint('user_repos_user_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') + op.create_foreign_key('user_repo_user_id_fkey', 'user_repos', 'repo', ['repo_id'], ['repo_id'], source_schema='augur_operations', referent_schema='augur_data') + op.create_foreign_key('user_repo_group_id_fkey', 'user_repos', 'user_groups', ['group_id'], ['user_group_id'], source_schema='augur_operations', referent_schema='augur_operations') + op.drop_column('user_repos', 'user_id', schema='augur_operations') + + + session.insert_data(user_repo_data, UserRepo, ["group_id", "repo_id"]) + # ### end Alembic commands ### + + +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('user_repos', sa.Column('user_id', sa.INTEGER(), autoincrement=False, nullable=False), schema='augur_operations') + op.drop_constraint('user_repo_group_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') + op.drop_constraint('user_repo_user_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') + op.create_foreign_key('user_repos_user_id_fkey', 'user_repos', 'users', ['user_id'], ['user_id'], source_schema='augur_operations', referent_schema='augur_operations') + op.create_foreign_key('user_repos_repo_id_fkey', 'user_repos', 'repo', ['repo_id'], ['repo_id'], source_schema='augur_operations') + op.drop_column('user_repos', 'group_id', schema='augur_operations') + op.drop_table('user_groups', schema='augur_operations') + # ### end Alembic commands ### From 4005390055e19840e7c7c5d8a3aab3717c6905bf Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 20 Dec 2022 09:22:16 -0600 Subject: [PATCH 005/150] Add script to upgrade database Signed-off-by: Andrew Brain --- .../application/db/models/augur_operations.py | 4 ++-- ...p_table.py => 2_added_user_group_table.py} | 22 ++++++++----------- 2 files changed, 11 insertions(+), 15 deletions(-) rename augur/application/schema/alembic/versions/{2022-12-19_632bd5da0e79_added_user_group_table.py => 2_added_user_group_table.py} (87%) diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index d007ce93e0..51002a84c9 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -193,7 +193,7 @@ class User(Base): class UserGroup(Base): - user_group_id = Column(BigInteger, primary_key=True) + group_id = Column(BigInteger, primary_key=True) user_id = Column(Integer, ForeignKey("augur_operations.users.user_id", name="user_group_user_id_fkey") ) @@ -215,7 +215,7 @@ class UserRepo(Base): ) group_id = Column( - ForeignKey("augur_operations.user_groups.user_group_id", name="user_repo_group_id_fkey"), primary_key=True, nullable=False + ForeignKey("augur_operations.user_groups.group_id", name="user_repo_group_id_fkey"), primary_key=True, nullable=False ) repo_id = Column( ForeignKey("augur_data.repo.repo_id", name="user_repo_user_id_fkey"), primary_key=True, nullable=False diff --git a/augur/application/schema/alembic/versions/2022-12-19_632bd5da0e79_added_user_group_table.py b/augur/application/schema/alembic/versions/2_added_user_group_table.py similarity index 87% rename from augur/application/schema/alembic/versions/2022-12-19_632bd5da0e79_added_user_group_table.py rename to augur/application/schema/alembic/versions/2_added_user_group_table.py index 38c69a5216..2be929101e 100644 --- a/augur/application/schema/alembic/versions/2022-12-19_632bd5da0e79_added_user_group_table.py +++ b/augur/application/schema/alembic/versions/2_added_user_group_table.py @@ -1,6 +1,6 @@ """Added user group table -Revision ID: 632bd5da0e79 +Revision ID: 2 Revises: 1 Create Date: 2022-12-19 11:00:37.509132 @@ -10,11 +10,12 @@ from alembic import op import sqlalchemy as sa from augur.application.db.session import DatabaseSession +from augur.application.db.models.augur_operations import UserGroup, UserRepo # revision identifiers, used by Alembic. -revision = '632bd5da0e79' +revision = '2' down_revision = '1' branch_labels = None depends_on = None @@ -22,18 +23,13 @@ def upgrade(): - - - - - - # ### commands auto generated by Alembic - please adjust! ### + ### commands auto generated by Alembic - please adjust! ### op.create_table('user_groups', - sa.Column('user_group_id', sa.BigInteger(), nullable=False), + sa.Column('group_id', sa.BigInteger(), nullable=False), sa.Column('user_id', sa.Integer(), nullable=True), sa.Column('name', sa.String(), nullable=False), sa.ForeignKeyConstraint(['user_id'], ['augur_operations.users.user_id'], name='user_group_user_id_fkey'), - sa.PrimaryKeyConstraint('user_group_id'), + sa.PrimaryKeyConstraint('group_id'), sa.UniqueConstraint('user_id', 'name', name='user_group_unique'), schema='augur_operations' ) @@ -46,7 +42,6 @@ def upgrade(): user_groups = session.fetchall_data_from_sql_text(user_id_query) for row in user_groups: row.update({"name": "default"}) - del row["repo_id"] result = session.insert_data(user_groups, UserGroup, ["user_id", "name"], return_columns=["group_id", "user_id"]) @@ -67,14 +62,15 @@ def upgrade(): # remove data from table before modifiying it remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") session.execute_sql(remove_data_from_user_repos_query) - + op.add_column('user_repos', sa.Column('group_id', sa.BigInteger(), nullable=False), schema='augur_operations') op.drop_constraint('user_repos_repo_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') op.drop_constraint('user_repos_user_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') op.create_foreign_key('user_repo_user_id_fkey', 'user_repos', 'repo', ['repo_id'], ['repo_id'], source_schema='augur_operations', referent_schema='augur_data') - op.create_foreign_key('user_repo_group_id_fkey', 'user_repos', 'user_groups', ['group_id'], ['user_group_id'], source_schema='augur_operations', referent_schema='augur_operations') + op.create_foreign_key('user_repo_group_id_fkey', 'user_repos', 'user_groups', ['group_id'], ['group_id'], source_schema='augur_operations', referent_schema='augur_operations') op.drop_column('user_repos', 'user_id', schema='augur_operations') + op.create_primary_key('user_repos_pk', 'user_repos', ['repo_id', 'group_id']) session.insert_data(user_repo_data, UserRepo, ["group_id", "repo_id"]) From 7b4556955050e2e4c6c03b50646955c209ff64a9 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 20 Dec 2022 14:24:43 -0600 Subject: [PATCH 006/150] Fix up downgrade and upgrade script Signed-off-by: Andrew Brain --- .../versions/2_added_user_group_table.py | 181 +++++++++++++----- 1 file changed, 137 insertions(+), 44 deletions(-) diff --git a/augur/application/schema/alembic/versions/2_added_user_group_table.py b/augur/application/schema/alembic/versions/2_added_user_group_table.py index 2be929101e..092f7c287f 100644 --- a/augur/application/schema/alembic/versions/2_added_user_group_table.py +++ b/augur/application/schema/alembic/versions/2_added_user_group_table.py @@ -20,70 +20,163 @@ branch_labels = None depends_on = None +logger = logging.getLogger(__name__) def upgrade(): - ### commands auto generated by Alembic - please adjust! ### - op.create_table('user_groups', - sa.Column('group_id', sa.BigInteger(), nullable=False), - sa.Column('user_id', sa.Integer(), nullable=True), - sa.Column('name', sa.String(), nullable=False), - sa.ForeignKeyConstraint(['user_id'], ['augur_operations.users.user_id'], name='user_group_user_id_fkey'), - sa.PrimaryKeyConstraint('group_id'), - sa.UniqueConstraint('user_id', 'name', name='user_group_unique'), - schema='augur_operations' - ) + with DatabaseSession(logger) as session: - logger = logging.getLogger(__name__) + print("Creating user groups table") + create_user_groups_table = """ + CREATE TABLE "augur_operations"."user_groups" ( + "group_id" BIGSERIAL NOT NULL, + "user_id" int4 NOT NULL, + "name" varchar COLLATE "pg_catalog"."default" NOT NULL, + PRIMARY KEY ("group_id"), + FOREIGN KEY ("user_id") REFERENCES "augur_operations"."users" ("user_id") ON DELETE NO ACTION ON UPDATE NO ACTION, + UNIQUE ("user_id", "name") + ); - - with DatabaseSession(logger) as session: + + ALTER TABLE "augur_operations"."user_groups" + OWNER TO "augur"; + """ + + session.execute_sql(sa.sql.text(create_user_groups_table)) + + + user_repos = [] + + print("Creating user groups") + # create user group for all the users that have repos user_id_query = sa.sql.text("""SELECT DISTINCT(user_id) FROM user_repos;""") user_groups = session.fetchall_data_from_sql_text(user_id_query) - for row in user_groups: - row.update({"name": "default"}) + if user_groups: + + result = [] + for row in user_groups: + + user_id = row["user_id"] + + user_group_insert = sa.sql.text(f"""INSERT INTO "augur_operations"."user_groups" ("user_id", "name") VALUES ({user_id}, 'default') RETURNING group_id, user_id;""") + result.append(session.fetchall_data_from_sql_text(user_group_insert)[0]) + + user_group_id_mapping = {} + for row in result: + user_group_id_mapping[row["user_id"]] = row["group_id"] + + + print("Getting users repos") + user_repo_query = sa.sql.text("""SELECT * FROM user_repos;""") + user_repo_data = session.fetchall_data_from_sql_text(user_repo_query) + for row in user_repo_data: + row.update({"group_id": user_group_id_mapping[row["user_id"]]}) + del row["user_id"] + user_repos.extend(user_repo_data) + + print("Removing data from user repos table") + # remove data from table before modifiying it + remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") + session.execute_sql(remove_data_from_user_repos_query) + + + table_changes = """ + ALTER TABLE user_repos + ADD COLUMN group_id INT, + ADD CONSTRAINT user_repos_group_id_fkey FOREIGN KEY (group_id) REFERENCES user_groups(group_id), + DROP COLUMN user_id, + ADD PRIMARY KEY (group_id, repo_id); + """ + + session.execute_sql(sa.sql.text(table_changes)) + + print(user_repos) + + print("Inserting data into user repos table") + for data in user_repos: + + group_id = data["group_id"] + repo_id = data["repo_id"] + + user_repo_insert = sa.sql.text(f"""INSERT INTO "augur_operations"."user_repos" ("group_id", "repo_id") VALUES ({group_id}, {repo_id});""") + result = session.execute_sql(user_repo_insert) + # ### end Alembic commands ### - result = session.insert_data(user_groups, UserGroup, ["user_id", "name"], return_columns=["group_id", "user_id"]) +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### - user_group_id_mapping = {} - for row in result: - user_group_id_mapping[row["user_id"]] = row["group_id"] - + print("Downgrade") - user_repo_query = sa.sql.text("""SELECT * FROM user_repos;""") - user_repo_data = session.fetchall_data_from_sql_text(user_repo_query) - for row in user_repo_data: - row.update({"group_id": user_group_id_mapping[row["user_id"]]}) - del row["user_id"] + user_group_ids = {} + group_repo_ids = {} + with DatabaseSession(logger) as session: + user_id_query = sa.sql.text("""SELECT * FROM user_groups;""") + user_groups = session.fetchall_data_from_sql_text(user_id_query) + for row in user_groups: + try: + user_group_ids[row["user_id"]].append(row["group_id"]) + except KeyError: + user_group_ids[row["user_id"]] = [row["group_id"]] + group_id_query = sa.sql.text("""SELECT * FROM user_repos;""") + group_repo_id_result = session.fetchall_data_from_sql_text(group_id_query) + for row in group_repo_id_result: + try: + group_repo_ids[row["group_id"]].append(row["repo_id"]) + except KeyError: + group_repo_ids[row["group_id"]] = [row["repo_id"]] - # remove data from table before modifiying it remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") session.execute_sql(remove_data_from_user_repos_query) - op.add_column('user_repos', sa.Column('group_id', sa.BigInteger(), nullable=False), schema='augur_operations') - op.drop_constraint('user_repos_repo_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') - op.drop_constraint('user_repos_user_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') - op.create_foreign_key('user_repo_user_id_fkey', 'user_repos', 'repo', ['repo_id'], ['repo_id'], source_schema='augur_operations', referent_schema='augur_data') - op.create_foreign_key('user_repo_group_id_fkey', 'user_repos', 'user_groups', ['group_id'], ['group_id'], source_schema='augur_operations', referent_schema='augur_operations') - op.drop_column('user_repos', 'user_id', schema='augur_operations') - op.create_primary_key('user_repos_pk', 'user_repos', ['repo_id', 'group_id']) + table_changes = """ + ALTER TABLE user_repos + ADD COLUMN user_id INT, + ADD CONSTRAINT user_repos_user_id_fkey FOREIGN KEY (user_id) REFERENCES users(user_id), + DROP COLUMN group_id, + ADD PRIMARY KEY (user_id, repo_id); + DROP TABLE user_groups; + """ + session.execute_sql(sa.sql.text(table_changes)) - session.insert_data(user_repo_data, UserRepo, ["group_id", "repo_id"]) - # ### end Alembic commands ### + print("user group ids") + print(user_group_ids) + + print("Group repo ids") + print(group_repo_ids) + + for user_id, group_ids in user_group_ids.items(): + + print(f"User id: {user_id}") + print(f"Group ids: {group_ids}") + + repos = [] + for group_id in group_ids: + try: + repos.extend(group_repo_ids[group_id]) + except KeyError: + continue + + print(f"User: {user_id} Repos: {repos}") + + query_text_array = ["""INSERT INTO "augur_operations"."user_repos" ("repo_id", "user_id") VALUES """] + for i, repo_id in enumerate(repos): + query_text_array.append(f"({repo_id}, {user_id})") + + delimiter = ";" if i == len(repos) -1 else "," + + query_text_array.append(delimiter) + + + query_text = "".join(query_text_array) + + print(query_text) + + session.execute_sql(sa.sql.text(query_text)) -def downgrade(): - # ### commands auto generated by Alembic - please adjust! ### - op.add_column('user_repos', sa.Column('user_id', sa.INTEGER(), autoincrement=False, nullable=False), schema='augur_operations') - op.drop_constraint('user_repo_group_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') - op.drop_constraint('user_repo_user_id_fkey', 'user_repos', schema='augur_operations', type_='foreignkey') - op.create_foreign_key('user_repos_user_id_fkey', 'user_repos', 'users', ['user_id'], ['user_id'], source_schema='augur_operations', referent_schema='augur_operations') - op.create_foreign_key('user_repos_repo_id_fkey', 'user_repos', 'repo', ['repo_id'], ['repo_id'], source_schema='augur_operations') - op.drop_column('user_repos', 'group_id', schema='augur_operations') - op.drop_table('user_groups', schema='augur_operations') # ### end Alembic commands ### From bc8e38e61218d409dcd35e8b3b54a2221a7be7bc Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 20 Dec 2022 14:30:10 -0600 Subject: [PATCH 007/150] Remove prints from script Signed-off-by: Andrew Brain --- .../versions/2_added_user_group_table.py | 22 ------------------- 1 file changed, 22 deletions(-) diff --git a/augur/application/schema/alembic/versions/2_added_user_group_table.py b/augur/application/schema/alembic/versions/2_added_user_group_table.py index 092f7c287f..460b41aa1c 100644 --- a/augur/application/schema/alembic/versions/2_added_user_group_table.py +++ b/augur/application/schema/alembic/versions/2_added_user_group_table.py @@ -26,7 +26,6 @@ def upgrade(): with DatabaseSession(logger) as session: - print("Creating user groups table") create_user_groups_table = """ CREATE TABLE "augur_operations"."user_groups" ( "group_id" BIGSERIAL NOT NULL, @@ -47,7 +46,6 @@ def upgrade(): user_repos = [] - print("Creating user groups") # create user group for all the users that have repos user_id_query = sa.sql.text("""SELECT DISTINCT(user_id) FROM user_repos;""") user_groups = session.fetchall_data_from_sql_text(user_id_query) @@ -66,7 +64,6 @@ def upgrade(): user_group_id_mapping[row["user_id"]] = row["group_id"] - print("Getting users repos") user_repo_query = sa.sql.text("""SELECT * FROM user_repos;""") user_repo_data = session.fetchall_data_from_sql_text(user_repo_query) for row in user_repo_data: @@ -74,7 +71,6 @@ def upgrade(): del row["user_id"] user_repos.extend(user_repo_data) - print("Removing data from user repos table") # remove data from table before modifiying it remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") session.execute_sql(remove_data_from_user_repos_query) @@ -90,9 +86,6 @@ def upgrade(): session.execute_sql(sa.sql.text(table_changes)) - print(user_repos) - - print("Inserting data into user repos table") for data in user_repos: group_id = data["group_id"] @@ -106,7 +99,6 @@ def upgrade(): def downgrade(): # ### commands auto generated by Alembic - please adjust! ### - print("Downgrade") user_group_ids = {} group_repo_ids = {} @@ -143,18 +135,8 @@ def downgrade(): session.execute_sql(sa.sql.text(table_changes)) - - print("user group ids") - print(user_group_ids) - - print("Group repo ids") - print(group_repo_ids) - for user_id, group_ids in user_group_ids.items(): - print(f"User id: {user_id}") - print(f"Group ids: {group_ids}") - repos = [] for group_id in group_ids: try: @@ -162,8 +144,6 @@ def downgrade(): except KeyError: continue - print(f"User: {user_id} Repos: {repos}") - query_text_array = ["""INSERT INTO "augur_operations"."user_repos" ("repo_id", "user_id") VALUES """] for i, repo_id in enumerate(repos): query_text_array.append(f"({repo_id}, {user_id})") @@ -175,8 +155,6 @@ def downgrade(): query_text = "".join(query_text_array) - print(query_text) - session.execute_sql(sa.sql.text(query_text)) # ### end Alembic commands ### From 9c6ad2c5d2857305ca2dd45b07812e392cc328bc Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 20 Dec 2022 14:35:53 -0600 Subject: [PATCH 008/150] Fixes to repo insertion methods Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index f7d46cb272..c2a87957a0 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -184,27 +184,22 @@ def add_repo_to_user_group(self, repo_id, group_id=CLI_GROUP_ID): repo_user_group_unique = ["group_id", "repo_id"] return_columns = ["group_id", "repo_id"] - data = self.session.insert_data(repo_user_group_data, UserGroup, repo_user_group_unique, return_columns) + data = self.session.insert_data(repo_user_group_data, UserRepo, repo_user_group_unique, return_columns) - if data[0]["group_id"] == group_id and data[0]["repo_id"] == repo_id: - return True - - return False + return data[0]["group_id"] == group_id and data[0]["repo_id"] == repo_id def add_user_group(self, user_id, group_name): user_group_data = { - "group_name": group_id, - "user_id": repo_id + "name": group_name, + "user_id": user_id } - # TODO Add exception for duplicate groups - group_obj = UserGroup(**user_group_data) - self.session.add(group_obj) - self.session.commit() - - return True + result = session.insert_data(user_group_data, UserGroup, ["name", "user_id"], return_columns=["group_id"]) + + return result is not None + def get_user_groups(self, user_id): return self.session.query(UserGroup).filter(UserGroup.user_id == user_id).all() From e63c27ede7dbd7ce6721ea2dd96787a0a3f91414 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 20 Dec 2022 16:21:23 -0600 Subject: [PATCH 009/150] First run of adding repos to groups Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 35 ++++++++++++++++++++++--- augur/application/db/models/__init__.py | 3 ++- augur/util/repo_load_controller.py | 14 +++++----- 3 files changed, 42 insertions(+), 10 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 62539be357..896166e6cf 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -16,7 +16,7 @@ from augur.util.repo_load_controller import RepoLoadController -from augur.application.db.models import User, UserRepo +from augur.application.db.models import User, UserRepo, UserGroup from augur.application.config import get_development_flag logger = logging.getLogger(__name__) development = get_development_flag() @@ -206,19 +206,48 @@ def add_user_repo(): username = request.args.get("username") repo = request.args.get("repo_url") + group_name = request.args.get("group_name") with GithubTaskSession(logger) as session: - if username is None: + if username is None or repo is None or group_name is None: return jsonify({"status": "Missing argument"}), 400 user = session.query(User).filter( User.login_name == username).first() if user is None: return jsonify({"status": "User does not exist"}) + user_group = session.query(UserGroup).filter(UserGroup.user_id == user.user_id, UserGroup.name == group_name).first() + if user_group is None: + return jsonify({"status": "User group does not exists"}) + + repo_load_controller = RepoLoadController(gh_session=session) + + result = repo_load_controller.add_frontend_repo(repo, user.user_id, user_group.group_id) + + return jsonify(result) + + + @server.app.route(f"/{AUGUR_API_VERSION}/user/add_group", methods=['GET', 'POST']) + def add_user_group(): + if not development and not request.is_secure: + return generate_upgrade_request() + + username = request.args.get("username") + group_name = request.args.get("group_name") + + with GithubTaskSession(logger) as session: + + if username is None or group_name is None: + return jsonify({"status": "Missing argument"}), 400 + + user = session.query(User).filter(User.login_name == username).first() + if user is None: + return jsonify({"status": "User does not exist"}) + repo_load_controller = RepoLoadController(gh_session=session) - result = repo_load_controller.add_frontend_repo(repo, user.user_id) + result = repo_load_controller.add_user_group(user.user_id, group_name) return jsonify(result) diff --git a/augur/application/db/models/__init__.py b/augur/application/db/models/__init__.py index ab9c17953b..f51e768ed9 100644 --- a/augur/application/db/models/__init__.py +++ b/augur/application/db/models/__init__.py @@ -99,5 +99,6 @@ WorkerSettingsFacade, Config, User, - UserRepo + UserRepo, + UserGroup ) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index c2a87957a0..efc619285f 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -10,7 +10,7 @@ from augur.tasks.github.util.github_paginator import GithubPaginator from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.application.db.session import DatabaseSession -from augur.application.db.models import Repo, UserRepo, RepoGroup +from augur.application.db.models import Repo, UserRepo, RepoGroup, UserGroup from augur.application.db.util import execute_session_query @@ -73,7 +73,7 @@ def is_valid_repo(self, url: str) -> bool: def is_valid_user_group(self, user_id, group_id) -> bool: try: - self.session.query(UserRepo).filter(UserRepo.user_id == user_id, UserRepo.group_id == group_id).one() + self.session.query(UserRepo).filter(UserGroup.user_id == user_id, UserGroup.group_id == group_id).one() return True except s.orm.exc.NoResultFound: return False @@ -195,10 +195,12 @@ def add_user_group(self, user_id, group_name): "user_id": user_id } + result = self.session.insert_data(user_group_data, UserGroup, ["name", "user_id"], return_columns=["group_id"]) - result = session.insert_data(user_group_data, UserGroup, ["name", "user_id"], return_columns=["group_id"]) - - return result is not None + if result: + return {"status": "Group created"} + else: + return {"status": "Group already exists"} def get_user_groups(self, user_id): @@ -229,7 +231,7 @@ def add_frontend_repo(self, url: List[str], user_id: int, group_id: int, valid_g if not valid_group and not self.is_valid_user_group(user_id, group_id): return {"status": "Invalid user group", "group_id": group_id} - repo_id = self.add_repo_row(url, DEFAULT_REPO_GROUP_ID, "Frontend") + repo_id = self.add_repo_row(url, DEFAULT_REPO_GROUP_IDS[0], "Frontend") if not repo_id: return {"status": "Repo insertion failed", "repo_url": url} From 84f766815aa58da72d59e77c6505794be1fb9b98 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 20 Dec 2022 16:29:22 -0600 Subject: [PATCH 010/150] Match the group id data types Signed-off-by: Andrew Brain --- .../schema/alembic/versions/2_added_user_group_table.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/augur/application/schema/alembic/versions/2_added_user_group_table.py b/augur/application/schema/alembic/versions/2_added_user_group_table.py index 460b41aa1c..4334d94a82 100644 --- a/augur/application/schema/alembic/versions/2_added_user_group_table.py +++ b/augur/application/schema/alembic/versions/2_added_user_group_table.py @@ -78,7 +78,7 @@ def upgrade(): table_changes = """ ALTER TABLE user_repos - ADD COLUMN group_id INT, + ADD COLUMN group_id BIGINT, ADD CONSTRAINT user_repos_group_id_fkey FOREIGN KEY (group_id) REFERENCES user_groups(group_id), DROP COLUMN user_id, ADD PRIMARY KEY (group_id, repo_id); From 43f3eb065262a2c7487394692e60e4a3b64c98be Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Wed, 21 Dec 2022 15:25:50 -0600 Subject: [PATCH 011/150] Major improvements to user group functionality Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 65 ++++++++-- augur/application/db/models/augur_data.py | 1 + .../application/db/models/augur_operations.py | 9 ++ .../versions/2_added_user_group_table.py | 20 ++- augur/util/repo_load_controller.py | 109 +++++++++++++---- .../test_repo_load_controller.py | 114 ++++++++++++++---- 6 files changed, 257 insertions(+), 61 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 896166e6cf..b228ccfdf3 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -217,13 +217,9 @@ def add_user_repo(): if user is None: return jsonify({"status": "User does not exist"}) - user_group = session.query(UserGroup).filter(UserGroup.user_id == user.user_id, UserGroup.name == group_name).first() - if user_group is None: - return jsonify({"status": "User group does not exists"}) - repo_load_controller = RepoLoadController(gh_session=session) - result = repo_load_controller.add_frontend_repo(repo, user.user_id, user_group.group_id) + result = repo_load_controller.add_frontend_repo(repo, user.user_id, group_name) return jsonify(result) @@ -236,6 +232,9 @@ def add_user_group(): username = request.args.get("username") group_name = request.args.get("group_name") + if group_name == "default": + return jsonify({"status": "Reserved Group Name"}) + with GithubTaskSession(logger) as session: if username is None or group_name is None: @@ -251,6 +250,31 @@ def add_user_group(): return jsonify(result) + @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_group", methods=['GET', 'POST']) + def remove_user_group(): + if not development and not request.is_secure: + return generate_upgrade_request() + + username = request.args.get("username") + group_name = request.args.get("group_name") + + with GithubTaskSession(logger) as session: + + if username is None or group_name is None + return jsonify({"status": "Missing argument"}), 400 + + user = session.query(User).filter(User.login_name == username).first() + if user is None: + return jsonify({"status": "User does not exist"}) + + repo_load_controller = RepoLoadController(gh_session=session) + + result = repo_load_controller.remove_user_group(user.user_id, group_name) + + return jsonify(result) + + + @server.app.route(f"/{AUGUR_API_VERSION}/user/add_org", methods=['GET', 'POST']) def add_user_org(): @@ -259,10 +283,37 @@ def add_user_org(): username = request.args.get("username") org = request.args.get("org_url") + group_name = request.args.get("group_name") with GithubTaskSession(logger) as session: - if username is None: + if username is None or org is None or group_name is None: + return jsonify({"status": "Missing argument"}), 400 + + user = session.query(User).filter( + User.login_name == username).first() + if user is None: + return jsonify({"status": "User does not exist"}) + + repo_load_controller = RepoLoadController(gh_session=session) + + result = repo_load_controller.add_frontend_org(org, user.user_id, group_name) + + return jsonify(result) + + + @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_repo", methods=['GET', 'POST']) + def remove_user_repo(): + if not development and not request.is_secure: + return generate_upgrade_request() + + username = request.args.get("username") + repo_id = request.args.get("repo_id") + group_name = request.args.get("group_name") + + with GithubTaskSession(logger) as session: + + if username is None or repo is None or group_name is None: return jsonify({"status": "Missing argument"}), 400 user = session.query(User).filter( User.login_name == username).first() @@ -271,7 +322,7 @@ def add_user_org(): repo_load_controller = RepoLoadController(gh_session=session) - result = repo_load_controller.add_frontend_org(org, user.user_id) + result = repo_load_controller.remove_frontend_repo(repo_id, user.user_id, group_name) return jsonify(result) diff --git a/augur/application/db/models/augur_data.py b/augur/application/db/models/augur_data.py index 63f105ef0b..5dd5618623 100644 --- a/augur/application/db/models/augur_data.py +++ b/augur/application/db/models/augur_data.py @@ -813,6 +813,7 @@ class Repo(Base): ) repo_group = relationship("RepoGroup") + user_repo = relationship("UserRepo") class RepoTestCoverage(Base): diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index 51002a84c9..782bdb11bc 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -4,6 +4,7 @@ from augur.application.db.models.base import Base +from sqlalchemy.orm import relationship metadata = Base.metadata @@ -191,6 +192,8 @@ class User(Base): {"schema": "augur_operations"} ) + groups = relationship("UserGroup") + class UserGroup(Base): group_id = Column(BigInteger, primary_key=True) @@ -204,6 +207,9 @@ class UserGroup(Base): {"schema": "augur_operations"} ) + user = relationship("User") + repos = relationship("UserRepo") + class UserRepo(Base): @@ -221,3 +227,6 @@ class UserRepo(Base): ForeignKey("augur_data.repo.repo_id", name="user_repo_user_id_fkey"), primary_key=True, nullable=False ) + repo = relationship("Repo") + group = relationship("UserGroup") + diff --git a/augur/application/schema/alembic/versions/2_added_user_group_table.py b/augur/application/schema/alembic/versions/2_added_user_group_table.py index 4334d94a82..6dbc7c8551 100644 --- a/augur/application/schema/alembic/versions/2_added_user_group_table.py +++ b/augur/application/schema/alembic/versions/2_added_user_group_table.py @@ -12,6 +12,7 @@ from augur.application.db.session import DatabaseSession from augur.application.db.models.augur_operations import UserGroup, UserRepo +CLI_USER_ID = 1 # revision identifiers, used by Alembic. @@ -37,9 +38,12 @@ def upgrade(): ); - ALTER TABLE "augur_operations"."user_groups" - OWNER TO "augur"; - """ + ALTER TABLE "augur_operations"."user_groups" + OWNER TO "augur"; + + INSERT INTO "augur_operations"."user_groups" ("group_id", "user_id", "name") VALUES (1, {}, 'default') ON CONFLICT ("user_id", "name") DO NOTHING; + ALTER SEQUENCE user_groups_group_id_seq RESTART WITH 2; + """.format(CLI_USER_ID) session.execute_sql(sa.sql.text(create_user_groups_table)) @@ -52,14 +56,18 @@ def upgrade(): if user_groups: result = [] - for row in user_groups: + for group in user_groups: - user_id = row["user_id"] + user_id = group["user_id"] + + if user_id == CLI_USER_ID: + continue user_group_insert = sa.sql.text(f"""INSERT INTO "augur_operations"."user_groups" ("user_id", "name") VALUES ({user_id}, 'default') RETURNING group_id, user_id;""") result.append(session.fetchall_data_from_sql_text(user_group_insert)[0]) - user_group_id_mapping = {} + # cli user mapping by default + user_group_id_mapping = {CLI_USER_ID: "1"} for row in result: user_group_id_mapping[row["user_id"]] = row["group_id"] diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index efc619285f..ec47bcca6e 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -10,19 +10,33 @@ from augur.tasks.github.util.github_paginator import GithubPaginator from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.application.db.session import DatabaseSession -from augur.application.db.models import Repo, UserRepo, RepoGroup, UserGroup +from augur.application.db.models import Repo, UserRepo, RepoGroup, UserGroup, User from augur.application.db.util import execute_session_query - logger = logging.getLogger(__name__) - REPO_ENDPOINT = "https://api.github.com/repos/{}/{}" ORG_REPOS_ENDPOINT = "https://api.github.com/orgs/{}/repos?per_page=100" DEFAULT_REPO_GROUP_IDS = [1, 10] CLI_USER_ID = 1 -CLI_GROUP_ID = 1 + + +# determine what that CLI Group ID is +with DatabaseSession(logger) as session: + + user = session.query(User).filter(User.user_id == CLI_USER_ID).one() + user_groups = user.groups + + if len(user_groups) == 0: + cli_user_group = UserGroup(user_id=CLI_USER_ID, name="CLI_Repo_Group") + session.add(cli_user_group) + session.commit() + + else: + cli_user_group = user_groups[0] + + CLI_GROUP_ID = cli_user_group.group_id class RepoLoadController: @@ -176,6 +190,8 @@ def add_repo_to_user_group(self, repo_id, group_id=CLI_GROUP_ID): user_id: id of user_id from users table """ + print(f"Group id: {group_id}") + repo_user_group_data = { "group_id": group_id, "repo_id": repo_id @@ -201,19 +217,46 @@ def add_user_group(self, user_id, group_name): return {"status": "Group created"} else: return {"status": "Group already exists"} + + def remove_user_group(self, user_id, group_name): + + # convert group_name to group_id + group_id = self.convert_group_name_to_id(user_id, group_name) + if group_id is None: + return {"status": "WARNING: Trying to delete group that does not exist"} + + # delete rows from user repos with group_id + self.session.query(UserRepo).filter(UserRepo.group_id == group_id).delete() + + # delete group from user groups table + self.session.query(UserGroup).filter(UserGroup.group_id == group_id).delete() + + self.session.commit() + + return {"status": "Group deleted"} + + + def convert_group_name_to_id(self, user_id, group_name): + + try: + user_group = self.session.query(UserGroup).filter(UserGroup.user_id == user_id, UserGroup.name == group_name).one() + except s.orm.exc.NoResultFound: + return None + + return user_group.group_id def get_user_groups(self, user_id): return self.session.query(UserGroup).filter(UserGroup.user_id == user_id).all() - def get_user_group_repos(self, user_id, group_id): + def get_user_group_repos(self, group_id): - repos = self.session.query(UserRepo).filter(UserGroup.user_id == user_id, UserGroup.group_id == group_id).all() + user_repos = self.session.query(UserRepo).filter(UserRepo.user_id == user_id, UserRepo.group_id == group_id).all() - return [repo["repo_id"] for repo in repos] + return [user_repo.repo.repo_id for user_repo in user_repos] - def add_frontend_repo(self, url: List[str], user_id: int, group_id: int, valid_group=False): + def add_frontend_repo(self, url: List[str], user_id: int, group_name: str, group_id=None, valid_repo=False): """Add list of repos to a users repos. Args: @@ -225,11 +268,14 @@ def add_frontend_repo(self, url: List[str], user_id: int, group_id: int, valid_g If no repo_group_id is passed the repo will be added to a default repo_group """ - if not self.is_valid_repo(url): - return {"status": "Invalid repo", "repo_url": url} + if group_id is None: - if not valid_group and not self.is_valid_user_group(user_id, group_id): - return {"status": "Invalid user group", "group_id": group_id} + group_id = self.convert_group_name_to_id(user_id, group_name) + if group_id is None: + return {"status": "Invalid group name"} + + if not valid_repo and not self.is_valid_repo(url): + return {"status": "Invalid repo", "repo_url": url} repo_id = self.add_repo_row(url, DEFAULT_REPO_GROUP_IDS[0], "Frontend") if not repo_id: @@ -242,23 +288,36 @@ def add_frontend_repo(self, url: List[str], user_id: int, group_id: int, valid_g return {"status": "Repo Added", "repo_url": url} - + def remove_frontend_repo(self, repo_id, user_id, group_name): + + group_id = self.convert_group_name_to_id(user_id, group_name) + if group_id is None: + return {"status": "Invalid group name"} + + # delete rows from user repos with group_id + self.session.query(UserRepo).filter(UserRepo.group_id == group_id, UserRepo.repo_id == repo_id).delete() + self.session.commit() - def add_frontend_org(self, url: List[str], user_id: int, group_id: int): + return {"status": "Repo Removed"} + + + def add_frontend_org(self, url: List[str], user_id: int, group_name: int): """Add list of orgs and their repos to a users repos. Args: urls: list of org urls user_id: id of user_id from users table """ + group_id = self.convert_group_name_to_id(user_id, group_name) + print(group_id) + if group_id is None: + return {"status": "Invalid group name"} repos = self.retrieve_org_repos(url) if not repos: return {"status": "Invalid org", "org_url": url} - if not self.is_valid_user_group(user_id, group_id): - return {"status": "Invalid user group", "group_id": group_id} org_name = self.parse_org_url(url) if not org_name: @@ -269,7 +328,7 @@ def add_frontend_org(self, url: List[str], user_id: int, group_id: int): failed_repos = [] for repo in repos: - result = self.add_frontend_repo(repo, user_id, group_id, valid_group=True) + result = self.add_frontend_repo(repo, user_id, group_name, group_id, valid_repo=True) # keep track of all the repos that failed if result["status"] != "Repo Added": @@ -351,23 +410,21 @@ def get_user_repo_ids(self, user_id: int) -> List[int]: list of repo ids """ - user_repo_id_query = s.sql.text(f"""SELECT * FROM augur_operations.user_repos WHERE user_id={user_id};""") - - - result = self.session.execute_sql(user_repo_id_query).fetchall() + user_groups = session.query(UserGroup).filter(UserGroup.user_id).all() - if len(result) == 0: - return [] + all_repo_ids = set() + for group in user_groups: - repo_ids = [dict(row)["repo_id"] for row in result] + repo_ids = [user_repo.repo.repo_id for user_repo in group.repos] + all_repo_ids.update(repo_ids) - return repo_ids + return list(all_repo_ids) def parse_repo_url(self, url): - if url.endswith(".github") or url.endswith(".github.io"): + if url.endswith(".github") or url.endswith(".github.io") or url.endswith(".js"): result = re.search(r"https?:\/\/github\.com\/([A-Za-z0-9 \- _]+)\/([A-Za-z0-9 \- _ \.]+)(.git)?\/?$", url) else: diff --git a/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py b/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py index 449d26dba3..bbdece1655 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py +++ b/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py @@ -16,7 +16,7 @@ logger = logging.getLogger(__name__) -VALID_ORG = {"org": "CDCgov", "repo_count": 235} +VALID_ORG = {"org": "CDCgov", "repo_count": 241} ######## Helper Functions to Get Delete statements ################# @@ -41,6 +41,10 @@ def get_user_repo_delete_statement(): return get_delete_statement("augur_operations", "user_repos") +def get_user_group_delete_statement(): + + return get_delete_statement("augur_operations", "user_groups") + def get_config_delete_statement(): return get_delete_statement("augur_operations", "config") @@ -58,6 +62,9 @@ def get_repo_related_delete_statements(table_list): if "user_repos" in table_list or "user_repo" in table_list: query_list.append(get_user_repo_delete_statement()) + if "user_groups" in table_list or "user_group" in table_list: + query_list.append(get_user_group_delete_statement()) + if "repos" in table_list or "repo" in table_list: query_list.append(get_repo_delete_statement()) @@ -102,6 +109,13 @@ def get_user_insert_statement(user_id): return """INSERT INTO "augur_operations"."users" ("user_id", "login_name", "login_hashword", "email", "first_name", "last_name", "admin") VALUES ({}, 'bil', 'pass', 'b@gmil.com', 'bill', 'bob', false);""".format(user_id) +def get_user_group_insert_statement(user_id, group_name, group_id=None): + + if group_id: + return """INSERT INTO "augur_operations"."user_groups" ("group_id", "user_id", "name") VALUES ({}, {}, '{}');""".format(group_id, user_id, group_name) + + return """INSERT INTO "augur_operations"."user_groups" (user_id", "name") VALUES (1, 'default');""".format(user_id, group_name) + ######## Helper Functions to get retrieve data from tables ################# @@ -243,32 +257,33 @@ def test_add_repo_row_with_updates(test_db_engine): connection.execute(clear_tables_statement) -def test_add_repo_to_user(test_db_engine): +def test_add_repo_to_user_group(test_db_engine): - clear_tables = ["user_repos", "repo", "repo_groups", "users"] + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: with test_db_engine.connect() as connection: - data = {"repo_id": 1, "user_id": 2, "user_repo_group_id": 1} + data = {"repo_id": 1, "user_id": 2, "user_repo_group_id": 1, "user_group_id": 1, "user_group_name": "test_group"} query_statements = [] query_statements.append(clear_tables_statement) query_statements.append(get_repo_group_insert_statement(data["user_repo_group_id"])) query_statements.append(get_repo_insert_statement(data["repo_id"], data["user_repo_group_id"])) query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) query = s.text("".join(query_statements)) connection.execute(query) with DatabaseSession(logger, test_db_engine) as session: - RepoLoadController(session).add_repo_to_user(data["repo_id"], data["user_id"]) + RepoLoadController(session).add_repo_to_user_group(data["repo_id"], data["user_group_id"]) with test_db_engine.connect() as connection: - query = s.text("""SELECT * FROM "augur_operations"."user_repos" WHERE "user_id"=:user_id AND "repo_id"=:repo_id""") + query = s.text("""SELECT * FROM "augur_operations"."user_repos" WHERE "group_id"=:user_group_id AND "repo_id"=:repo_id""") result = connection.execute(query, **data).fetchall() assert result is not None @@ -281,7 +296,7 @@ def test_add_repo_to_user(test_db_engine): def test_add_frontend_repos_with_duplicates(test_db_engine): - clear_tables = ["user_repos", "repo", "repo_groups", "users", "config"] + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: @@ -289,12 +304,13 @@ def test_add_frontend_repos_with_duplicates(test_db_engine): url = "https://github.com/operate-first/operate-first-twitter" - data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0]} + data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "user_group_name": "test_group", "user_group_id": 1} query_statements = [] query_statements.append(clear_tables_statement) query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) connection.execute("".join(query_statements)) @@ -303,8 +319,11 @@ def test_add_frontend_repos_with_duplicates(test_db_engine): with GithubTaskSession(logger, test_db_engine) as session: controller = RepoLoadController(session) - controller.add_frontend_repo(url, data["user_id"]) - controller.add_frontend_repo(url, data["user_id"]) + result = controller.add_frontend_repo(url, data["user_id"], data["user_group_name"]) + result2 = controller.add_frontend_repo(url, data["user_id"], data["user_group_name"]) + + assert result["status"] == "Repo Added" + assert result2["status"] == "Repo Added" with test_db_engine.connect() as connection: @@ -320,7 +339,7 @@ def test_add_frontend_repos_with_duplicates(test_db_engine): def test_add_frontend_repos_with_invalid_repo(test_db_engine): - clear_tables = ["user_repos", "repo", "repo_groups", "users", "config"] + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: @@ -328,12 +347,13 @@ def test_add_frontend_repos_with_invalid_repo(test_db_engine): url = "https://github.com/chaoss/whitepaper" - data = {"user_id": 2, "repo_group_id": 5} + data = {"user_id": 2, "repo_group_id": 5, "user_group_name": "test_group", "user_group_id": 1} query_statements = [] query_statements.append(clear_tables_statement) query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) connection.execute("".join(query_statements)) @@ -341,7 +361,9 @@ def test_add_frontend_repos_with_invalid_repo(test_db_engine): with GithubTaskSession(logger, test_db_engine) as session: - RepoLoadController(session).add_frontend_repo(url, data["user_id"]) + result = RepoLoadController(session).add_frontend_repo(url, data["user_id"], data["user_group_name"]) + + assert result["status"] == "Invalid repo" with test_db_engine.connect() as connection: @@ -356,12 +378,12 @@ def test_add_frontend_repos_with_invalid_repo(test_db_engine): def test_add_frontend_org_with_invalid_org(test_db_engine): - clear_tables = ["user_repos", "repo", "repo_groups", "users", "config"] + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: - data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "org_name": "chaosssss"} + data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "org_name": "chaosssss", "user_group_name": "test_group", "user_group_id": 1} with test_db_engine.connect() as connection: @@ -369,6 +391,7 @@ def test_add_frontend_org_with_invalid_org(test_db_engine): query_statements.append(clear_tables_statement) query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) connection.execute("".join(query_statements)) @@ -376,7 +399,8 @@ def test_add_frontend_org_with_invalid_org(test_db_engine): with GithubTaskSession(logger, test_db_engine) as session: url = f"https://github.com/{data['org_name']}/" - controller = RepoLoadController(session).add_frontend_org(url, data["user_id"]) + result = RepoLoadController(session).add_frontend_org(url, data["user_id"], data["user_group_name"]) + assert result["status"] == "Invalid org" with test_db_engine.connect() as connection: @@ -391,18 +415,20 @@ def test_add_frontend_org_with_invalid_org(test_db_engine): def test_add_frontend_org_with_valid_org(test_db_engine): - clear_tables = ["user_repos", "repo", "repo_groups", "users", "config"] + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: with test_db_engine.connect() as connection: - data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "org_name": VALID_ORG["org"]} + data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "org_name": VALID_ORG["org"], "user_group_name": "test_group", "user_group_id": 1} query_statements = [] query_statements.append(clear_tables_statement) query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + connection.execute("".join(query_statements)) add_keys_to_test_db(test_db_engine) @@ -410,7 +436,9 @@ def test_add_frontend_org_with_valid_org(test_db_engine): with GithubTaskSession(logger, test_db_engine) as session: url = "https://github.com/{}/".format(data["org_name"]) - RepoLoadController(session).add_frontend_org(url, data["user_id"]) + result = RepoLoadController(session).add_frontend_org(url, data["user_id"], data["user_group_name"]) + print(result) + assert result["status"] == "Org repos added" with test_db_engine.connect() as connection: @@ -429,7 +457,7 @@ def test_add_frontend_org_with_valid_org(test_db_engine): def test_add_cli_org_with_valid_org(test_db_engine): - clear_tables = ["user_repos", "repo", "repo_groups", "users", "config"] + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: @@ -442,6 +470,7 @@ def test_add_cli_org_with_valid_org(test_db_engine): query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) query_statements.append(get_user_insert_statement(data["user_id"])) + connection.execute("".join(query_statements)) repo_count = None @@ -450,7 +479,8 @@ def test_add_cli_org_with_valid_org(test_db_engine): with GithubTaskSession(logger, test_db_engine) as session: - RepoLoadController(session).add_cli_org(data["org_name"]) + result = RepoLoadController(session).add_cli_org(data["org_name"]) + print(result) with test_db_engine.connect() as connection: @@ -464,7 +494,8 @@ def test_add_cli_org_with_valid_org(test_db_engine): finally: with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) + pass + # connection.execute(clear_tables_statement) def test_add_cli_repos_with_duplicates(test_db_engine): @@ -507,3 +538,42 @@ def test_add_cli_repos_with_duplicates(test_db_engine): with test_db_engine.connect() as connection: connection.execute(clear_tables_statement) + + +def test_convert_group_name_to_id(test_db_engine): + + clear_tables = ["user_repos", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + data = {"user_id": 1, "group_name": "test_group_name", "group_id": 1} + url = f"https://github.com/{data['org_name']}/{data['repo_name']}" + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_user_insert_statement(data["user-id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["group_name"], data["group_id"])) + + connection.execute("".join(query_statements)) + + with GithubTaskSession(logger, test_db_engine) as session: + + repo_data = {"url": url, "repo_group_id": data["repo_group_id"]} + + controller = RepoLoadController(session) + group_id = controller.convert_group_name_to_id(data["user_id"], data["group_name"]) + + assert group_id is not None + assert group_id == data["group_id"] + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + + + + + From 9cfafbf32fa1e25b4132accedc75ebcde4aa2327 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Wed, 21 Dec 2022 16:04:16 -0600 Subject: [PATCH 012/150] Pass more repo load controller tests Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 11 +++++------ .../test_repo_load_controller.py | 14 +++++++------- 2 files changed, 12 insertions(+), 13 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index ec47bcca6e..3b055d2acc 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -55,6 +55,8 @@ def is_valid_repo(self, url: str) -> bool: True if repo url is valid and False if not """ + print("Is repo valid?") + owner, repo = self.parse_repo_url(url) if not owner or not repo: return False @@ -190,8 +192,6 @@ def add_repo_to_user_group(self, repo_id, group_id=CLI_GROUP_ID): user_id: id of user_id from users table """ - print(f"Group id: {group_id}") - repo_user_group_data = { "group_id": group_id, "repo_id": repo_id @@ -309,7 +309,6 @@ def add_frontend_org(self, url: List[str], user_id: int, group_name: int): user_id: id of user_id from users table """ group_id = self.convert_group_name_to_id(user_id, group_name) - print(group_id) if group_id is None: return {"status": "Invalid group name"} @@ -341,7 +340,7 @@ def add_frontend_org(self, url: List[str], user_id: int, group_name: int): return {"status": "Org repos added", "org_url": url} - def add_cli_repo(self, repo_data: Dict[str, Any]): + def add_cli_repo(self, repo_data: Dict[str, Any], valid_repo=False): """Add list of repos to specified repo_groups Args: @@ -351,7 +350,7 @@ def add_cli_repo(self, repo_data: Dict[str, Any]): url = repo_data["url"] repo_group_id = repo_data["repo_group_id"] - if self.is_valid_repo(url): + if valid_repo or self.is_valid_repo(url): # if the repo doesn't exist it adds it # if the repo does exist it updates the repo_group_id @@ -397,7 +396,7 @@ def add_cli_org(self, org_name): for repo_url in repos: logger.info( f"Adding {repo_url}") - self.add_cli_repo({"url": repo_url, "repo_group_id": repo_group_id}) + self.add_cli_repo({"url": repo_url, "repo_group_id": repo_group_id}, valid_repo=True) def get_user_repo_ids(self, user_id: int) -> List[int]: diff --git a/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py b/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py index bbdece1655..5440e100b2 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py +++ b/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py @@ -219,7 +219,7 @@ def test_add_repo_row(test_db_engine): def test_add_repo_row_with_updates(test_db_engine): - clear_tables = ["user_repos", "repo", "repo_groups", "users"] + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: @@ -437,7 +437,6 @@ def test_add_frontend_org_with_valid_org(test_db_engine): url = "https://github.com/{}/".format(data["org_name"]) result = RepoLoadController(session).add_frontend_org(url, data["user_id"], data["user_group_name"]) - print(result) assert result["status"] == "Org repos added" with test_db_engine.connect() as connection: @@ -463,13 +462,13 @@ def test_add_cli_org_with_valid_org(test_db_engine): try: with test_db_engine.connect() as connection: - data = {"user_id": CLI_USER_ID, "repo_group_id": 5, "org_name": VALID_ORG["org"]} + data = {"user_id": CLI_USER_ID, "repo_group_id": 5, "org_name": VALID_ORG["org"], "user_group_name": "test_group", "user_group_id": 1} query_statements = [] query_statements.append(clear_tables_statement) query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) query_statements.append(get_user_insert_statement(data["user_id"])) - + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) connection.execute("".join(query_statements)) @@ -500,19 +499,20 @@ def test_add_cli_org_with_valid_org(test_db_engine): def test_add_cli_repos_with_duplicates(test_db_engine): - clear_tables = ["user_repos", "repo", "repo_groups", "users", "config"] + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: with test_db_engine.connect() as connection: - data = {"user_id": CLI_USER_ID, "repo_group_id": 5, "org_name": "operate-first", "repo_name": "operate-first-twitter"} + data = {"user_id": CLI_USER_ID, "repo_group_id": 5, "org_name": "operate-first", "repo_name": "operate-first-twitter", "user_group_name": "test_group", "user_group_id": 1} url = f"https://github.com/{data['org_name']}/{data['repo_name']}" query_statements = [] query_statements.append(clear_tables_statement) query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) connection.execute("".join(query_statements)) @@ -542,7 +542,7 @@ def test_add_cli_repos_with_duplicates(test_db_engine): def test_convert_group_name_to_id(test_db_engine): - clear_tables = ["user_repos", "repo", "repo_groups", "users"] + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: From 035ea8d532da5cfa3af813bcbae61f8f65571b0e Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 22 Dec 2022 09:42:30 -0600 Subject: [PATCH 013/150] Move around tests for readability Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 28 +- .../test_repo_load_controller/helper.py | 159 +++++ .../test_adding_orgs.py | 134 ++++ .../test_adding_repos.py | 140 +++++ .../test_helper_functions.py | 177 ++++++ .../test_repo_load_controller.py | 579 ------------------ .../test_repo_load_controller/util.py | 146 +++++ 7 files changed, 757 insertions(+), 606 deletions(-) create mode 100644 tests/test_applicaton/test_repo_load_controller/helper.py create mode 100644 tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py create mode 100644 tests/test_applicaton/test_repo_load_controller/test_adding_repos.py create mode 100644 tests/test_applicaton/test_repo_load_controller/test_helper_functions.py delete mode 100644 tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py create mode 100644 tests/test_applicaton/test_repo_load_controller/util.py diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index 3b055d2acc..ec644d6232 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -21,24 +21,6 @@ DEFAULT_REPO_GROUP_IDS = [1, 10] CLI_USER_ID = 1 - -# determine what that CLI Group ID is -with DatabaseSession(logger) as session: - - user = session.query(User).filter(User.user_id == CLI_USER_ID).one() - user_groups = user.groups - - if len(user_groups) == 0: - cli_user_group = UserGroup(user_id=CLI_USER_ID, name="CLI_Repo_Group") - session.add(cli_user_group) - session.commit() - - else: - cli_user_group = user_groups[0] - - CLI_GROUP_ID = cli_user_group.group_id - - class RepoLoadController: def __init__(self, gh_session): @@ -86,14 +68,6 @@ def is_valid_repo(self, url: str) -> bool: return True - def is_valid_user_group(self, user_id, group_id) -> bool: - - try: - self.session.query(UserRepo).filter(UserGroup.user_id == user_id, UserGroup.group_id == group_id).one() - return True - except s.orm.exc.NoResultFound: - return False - def retrieve_org_repos(self, url: str) -> List[str]: """Get the repos for an org. @@ -184,7 +158,7 @@ def add_repo_row(self, url: str, repo_group_id: int, tool_source): return result[0]["repo_id"] - def add_repo_to_user_group(self, repo_id, group_id=CLI_GROUP_ID): + def add_repo_to_user_group(self, repo_id, group_id=1): """Add a repo to a user in the user_repos table. Args: diff --git a/tests/test_applicaton/test_repo_load_controller/helper.py b/tests/test_applicaton/test_repo_load_controller/helper.py new file mode 100644 index 0000000000..9223f3b071 --- /dev/null +++ b/tests/test_applicaton/test_repo_load_controller/helper.py @@ -0,0 +1,159 @@ +import sqlalchemy as s +import logging + +from augur.util.repo_load_controller import ORG_REPOS_ENDPOINT + +from augur.application.db.session import DatabaseSession +from augur.application.db.models import Config +from augur.tasks.github.util.github_paginator import hit_api +from augur.application.db.util import execute_session_query + +logger = logging.getLogger(__name__) + + +######## Helper Functions to Get Delete statements ################# + +def get_delete_statement(schema, table): + + return """DELETE FROM "{}"."{}";""".format(schema, table) + +def get_repo_delete_statement(): + + return get_delete_statement("augur_data", "repo") + +def get_repo_group_delete_statement(): + + return get_delete_statement("augur_data", "repo_groups") + +def get_user_delete_statement(): + + return get_delete_statement("augur_operations", "users") + +def get_user_repo_delete_statement(): + + return get_delete_statement("augur_operations", "user_repos") + +def get_user_group_delete_statement(): + + return get_delete_statement("augur_operations", "user_groups") + +def get_config_delete_statement(): + + return get_delete_statement("augur_operations", "config") + +def get_repo_related_delete_statements(table_list): + """Takes a list of tables related to the RepoLoadController class and generates a delete statement. + + Args: + table_list: list of table names. Valid table names are + "user_repos" or "user_repo", "repo" or "repos", "repo_groups" or "repo_group:, "user" or "users", and "config" + + """ + + query_list = [] + if "user_repos" in table_list or "user_repo" in table_list: + query_list.append(get_user_repo_delete_statement()) + + if "user_groups" in table_list or "user_group" in table_list: + query_list.append(get_user_group_delete_statement()) + + if "repos" in table_list or "repo" in table_list: + query_list.append(get_repo_delete_statement()) + + if "repo_groups" in table_list or "repo_group" in table_list: + query_list.append(get_repo_group_delete_statement()) + + if "users" in table_list or "user" in table_list: + query_list.append(get_user_delete_statement()) + + if "config" in table_list: + query_list.append(get_config_delete_statement()) + + return " ".join(query_list) + +######## Helper Functions to add github api keys from prod db to test db ################# +def add_keys_to_test_db(test_db_engine): + + row = None + section_name = "Keys" + setting_name = "github_api_key" + with DatabaseSession(logger) as session: + query = session.query(Config).filter(Config.section_name==section_name, Config.setting_name==setting_name) + row = execute_session_query(query, 'one') + + with DatabaseSession(logger, test_db_engine) as test_session: + new_row = Config(section_name=section_name, setting_name=setting_name, value=row.value, type="str") + test_session.add(new_row) + test_session.commit() + + +######## Helper Functions to get insert statements ################# + +def get_repo_insert_statement(repo_id, rg_id, repo_url="place holder url", repo_status="New"): + + return """INSERT INTO "augur_data"."repo" ("repo_id", "repo_group_id", "repo_git", "repo_path", "repo_name", "repo_added", "repo_status", "repo_type", "url", "owner_id", "description", "primary_language", "created_at", "forked_from", "updated_at", "repo_archived_date_collected", "repo_archived", "tool_source", "tool_version", "data_source", "data_collection_date") VALUES ({}, {}, '{}', NULL, NULL, '2022-08-15 21:08:07', '{}', '', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'CLI', '1.0', 'Git', '2022-08-15 21:08:07');""".format(repo_id, rg_id, repo_url, repo_status) + +def get_repo_group_insert_statement(rg_id): + + return """INSERT INTO "augur_data"."repo_groups" ("repo_group_id", "rg_name", "rg_description", "rg_website", "rg_recache", "rg_last_modified", "rg_type", "tool_source", "tool_version", "data_source", "data_collection_date") VALUES ({}, 'Default Repo Group', 'The default repo group created by the schema generation script', '', 0, '2019-06-03 15:55:20', 'GitHub Organization', 'load', 'one', 'git', '2019-06-05 13:36:25');""".format(rg_id) + +def get_user_insert_statement(user_id): + + return """INSERT INTO "augur_operations"."users" ("user_id", "login_name", "login_hashword", "email", "first_name", "last_name", "admin") VALUES ({}, 'bil', 'pass', 'b@gmil.com', 'bill', 'bob', false);""".format(user_id) + +def get_user_group_insert_statement(user_id, group_name, group_id=None): + + if group_id: + return """INSERT INTO "augur_operations"."user_groups" ("group_id", "user_id", "name") VALUES ({}, {}, '{}');""".format(group_id, user_id, group_name) + + return """INSERT INTO "augur_operations"."user_groups" (user_id", "name") VALUES (1, 'default');""".format(user_id, group_name) + + +######## Helper Functions to get retrieve data from tables ################# + +def get_repos(connection, where_string=None): + + query_list = [] + query_list.append('SELECT * FROM "augur_data"."repo"') + + if where_string: + if where_string.endswith(";"): + query_list.append(where_string[:-1]) + + query_list.append(where_string) + + query_list.append(";") + + query = s.text(" ".join(query_list)) + + return connection.execute(query).fetchall() + +def get_user_repos(connection): + + return connection.execute(s.text("""SELECT * FROM "augur_operations"."user_repos";""")).fetchall() + + +######## Helper Functions to get repos in an org ################# + +def get_org_repos(org_name, session): + + attempts = 0 + while attempts < 10: + result = hit_api(session.oauths, ORG_REPOS_ENDPOINT.format(org_name), logger) + + # if result is None try again + if not result: + attempts += 1 + continue + + response = result.json() + + if response: + return response + + return None + +def get_org_repo_count(org_name, session): + + repos = get_org_repos(org_name, session) + return len(repos) diff --git a/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py b/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py new file mode 100644 index 0000000000..985b663016 --- /dev/null +++ b/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py @@ -0,0 +1,134 @@ +import pytest +import logging + +from tests.test_applicaton.test_repo_load_controller.helper import * +from augur.tasks.github.util.github_task_session import GithubTaskSession + +from augur.util.repo_load_controller import RepoLoadController, DEFAULT_REPO_GROUP_IDS, CLI_USER_ID + + +logger = logging.getLogger(__name__) + + +VALID_ORG = {"org": "CDCgov", "repo_count": 241} + + +def test_add_frontend_org_with_invalid_org(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + + data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "org_name": "chaosssss", "user_group_name": "test_group", "user_group_id": 1} + + with test_db_engine.connect() as connection: + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) + query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + + connection.execute("".join(query_statements)) + + add_keys_to_test_db(test_db_engine) + with GithubTaskSession(logger, test_db_engine) as session: + + url = f"https://github.com/{data['org_name']}/" + result = RepoLoadController(session).add_frontend_org(url, data["user_id"], data["user_group_name"]) + assert result["status"] == "Invalid org" + + with test_db_engine.connect() as connection: + + result = get_repos(connection) + assert result is not None + assert len(result) == 0 + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + +def test_add_frontend_org_with_valid_org(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "org_name": VALID_ORG["org"], "user_group_name": "test_group", "user_group_id": 1} + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) + query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + + connection.execute("".join(query_statements)) + + add_keys_to_test_db(test_db_engine) + + with GithubTaskSession(logger, test_db_engine) as session: + + url = "https://github.com/{}/".format(data["org_name"]) + result = RepoLoadController(session).add_frontend_org(url, data["user_id"], data["user_group_name"]) + assert result["status"] == "Org repos added" + + with test_db_engine.connect() as connection: + + result = get_repos(connection) + assert result is not None + assert len(result) == VALID_ORG["repo_count"] + + user_repo_result = get_user_repos(connection) + assert user_repo_result is not None + assert len(user_repo_result) == VALID_ORG["repo_count"] + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + +def test_add_cli_org_with_valid_org(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + data = {"user_id": CLI_USER_ID, "repo_group_id": 5, "org_name": VALID_ORG["org"], "user_group_name": "test_group", "user_group_id": 1} + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) + query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + + connection.execute("".join(query_statements)) + + repo_count = None + + add_keys_to_test_db(test_db_engine) + + with GithubTaskSession(logger, test_db_engine) as session: + + result = RepoLoadController(session).add_cli_org(data["org_name"]) + print(result) + + with test_db_engine.connect() as connection: + + result = get_repos(connection) + assert result is not None + assert len(result) == VALID_ORG["repo_count"] + + user_repo_result = get_user_repos(connection) + assert user_repo_result is not None + assert len(user_repo_result) == VALID_ORG["repo_count"] + + finally: + with test_db_engine.connect() as connection: + pass + # connection.execute(clear_tables_statement) diff --git a/tests/test_applicaton/test_repo_load_controller/test_adding_repos.py b/tests/test_applicaton/test_repo_load_controller/test_adding_repos.py new file mode 100644 index 0000000000..ebef2280e4 --- /dev/null +++ b/tests/test_applicaton/test_repo_load_controller/test_adding_repos.py @@ -0,0 +1,140 @@ +import pytest +import logging + +from tests.test_applicaton.test_repo_load_controller.helper import * +from augur.tasks.github.util.github_task_session import GithubTaskSession + +from augur.util.repo_load_controller import RepoLoadController, DEFAULT_REPO_GROUP_IDS, CLI_USER_ID + + + +logger = logging.getLogger(__name__) + + +def test_add_frontend_repos_with_invalid_repo(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + url = "https://github.com/chaoss/whitepaper" + + data = {"user_id": 2, "repo_group_id": 5, "user_group_name": "test_group", "user_group_id": 1} + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) + query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + + connection.execute("".join(query_statements)) + + add_keys_to_test_db(test_db_engine) + + with GithubTaskSession(logger, test_db_engine) as session: + + result = RepoLoadController(session).add_frontend_repo(url, data["user_id"], data["user_group_name"]) + + assert result["status"] == "Invalid repo" + + with test_db_engine.connect() as connection: + + result = get_repos(connection) + assert result is not None + assert len(result) == 0 + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + + + + +def test_add_cli_repos_with_duplicates(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + data = {"user_id": CLI_USER_ID, "repo_group_id": 5, "org_name": "operate-first", "repo_name": "operate-first-twitter", "user_group_name": "test_group", "user_group_id": 1} + url = f"https://github.com/{data['org_name']}/{data['repo_name']}" + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) + query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + + connection.execute("".join(query_statements)) + + add_keys_to_test_db(test_db_engine) + + with GithubTaskSession(logger, test_db_engine) as session: + + repo_data = {"url": url, "repo_group_id": data["repo_group_id"]} + + controller = RepoLoadController(session) + controller.add_cli_repo(repo_data) + controller.add_cli_repo(repo_data) + + with test_db_engine.connect() as connection: + + result = get_repos(connection) + + assert result is not None + assert len(result) == 1 + assert dict(result[0])["repo_git"] == url + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + + + +def test_add_frontend_repos_with_duplicates(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + url = "https://github.com/operate-first/operate-first-twitter" + + data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "user_group_name": "test_group", "user_group_id": 1} + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) + query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + + connection.execute("".join(query_statements)) + + add_keys_to_test_db(test_db_engine) + + with GithubTaskSession(logger, test_db_engine) as session: + + controller = RepoLoadController(session) + result = controller.add_frontend_repo(url, data["user_id"], data["user_group_name"]) + result2 = controller.add_frontend_repo(url, data["user_id"], data["user_group_name"]) + + assert result["status"] == "Repo Added" + assert result2["status"] == "Repo Added" + + with test_db_engine.connect() as connection: + + result = get_repos(connection) + assert result is not None + assert len(result) == 1 + assert dict(result[0])["repo_git"] == url + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py new file mode 100644 index 0000000000..c7c3807d44 --- /dev/null +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -0,0 +1,177 @@ +import logging +import pytest +import sqlalchemy as s + + +from augur.util.repo_load_controller import RepoLoadController, DEFAULT_REPO_GROUP_IDS, CLI_USER_ID + +from augur.application.db.session import DatabaseSession +from augur.tasks.github.util.github_task_session import GithubTaskSession +from tests.test_applicaton.test_repo_load_controller.helper import * + +logger = logging.getLogger(__name__) + + + +def test_is_valid_repo(): + + with GithubTaskSession(logger) as session: + + controller = RepoLoadController(session) + + assert controller.is_valid_repo("hello world") is False + assert controller.is_valid_repo("https://github.com/chaoss/hello") is False + assert controller.is_valid_repo("https://github.com/hello124/augur") is False + assert controller.is_valid_repo("https://github.com//augur") is False + assert controller.is_valid_repo("https://github.com/chaoss/") is False + assert controller.is_valid_repo("https://github.com//") is False + assert controller.is_valid_repo("https://github.com/chaoss/augur") is True + assert controller.is_valid_repo("https://github.com/chaoss/augur/") is True + assert controller.is_valid_repo("https://github.com/chaoss/augur.git") is True + + +def test_add_repo_row(test_db_engine): + + clear_tables = ["repo", "repo_groups"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + data = {"rg_id": 1, "repo_id": 1, "tool_source": "Frontend", + "repo_url": "https://github.com/chaoss/augur"} + + with test_db_engine.connect() as connection: + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["rg_id"])) + query = s.text("".join(query_statements)) + + connection.execute(query) + + with DatabaseSession(logger, test_db_engine) as session: + + assert RepoLoadController(session).add_repo_row(data["repo_url"], data["rg_id"], data["tool_source"]) is not None + + with test_db_engine.connect() as connection: + + result = get_repos(connection, where_string=f"WHERE repo_git='{data['repo_url']}'") + assert result is not None + assert len(result) > 0 + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + +def test_add_repo_row_with_updates(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + data = {"old_rg_id": 1, "new_rg_id": 2, "repo_id": 1, "repo_id_2": 2, "tool_source": "Test", + "repo_url": "https://github.com/chaoss/augur", "repo_url_2": "https://github.com/chaoss/grimoirelab-perceval-opnfv", "repo_status": "Complete"} + + with test_db_engine.connect() as connection: + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["old_rg_id"])) + query_statements.append(get_repo_group_insert_statement(data["new_rg_id"])) + query_statements.append(get_repo_insert_statement(data["repo_id"], data["old_rg_id"], repo_url=data["repo_url"], repo_status=data["repo_status"])) + query = s.text("".join(query_statements)) + + connection.execute(query) + + with DatabaseSession(logger, test_db_engine) as session: + + result = RepoLoadController(session).add_repo_row(data["repo_url"], data["new_rg_id"], data["tool_source"]) is not None + assert result == data["repo_id"] + + with test_db_engine.connect() as connection: + + result = get_repos(connection, where_string=f"WHERE repo_git='{data['repo_url']}'") + assert result is not None + assert len(result) == 1 + + value = dict(result[0]) + assert value["repo_status"] == data["repo_status"] + assert value["repo_group_id"] == data["new_rg_id"] + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + +def test_add_repo_to_user_group(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + data = {"repo_id": 1, "user_id": 2, "user_repo_group_id": 1, "user_group_id": 1, "user_group_name": "test_group"} + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["user_repo_group_id"])) + query_statements.append(get_repo_insert_statement(data["repo_id"], data["user_repo_group_id"])) + query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + query = s.text("".join(query_statements)) + + connection.execute(query) + + with DatabaseSession(logger, test_db_engine) as session: + + RepoLoadController(session).add_repo_to_user_group(data["repo_id"], data["user_group_id"]) + + with test_db_engine.connect() as connection: + + query = s.text("""SELECT * FROM "augur_operations"."user_repos" WHERE "group_id"=:user_group_id AND "repo_id"=:repo_id""") + + result = connection.execute(query, **data).fetchall() + assert result is not None + assert len(result) > 0 + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + + +def test_convert_group_name_to_id(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + data = {"user_id": 1, "group_name": "test_group_name", "group_id": 1} + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["group_name"], data["group_id"])) + + connection.execute("".join(query_statements)) + + with GithubTaskSession(logger, test_db_engine) as session: + + controller = RepoLoadController(session) + group_id = controller.convert_group_name_to_id(data["user_id"], data["group_name"]) + + assert group_id is not None + assert group_id == data["group_id"] + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + + + + + diff --git a/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py b/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py deleted file mode 100644 index 5440e100b2..0000000000 --- a/tests/test_applicaton/test_repo_load_controller/test_repo_load_controller.py +++ /dev/null @@ -1,579 +0,0 @@ -import logging -import pytest -import uuid -import sqlalchemy as s - - -from augur.util.repo_load_controller import RepoLoadController, ORG_REPOS_ENDPOINT, DEFAULT_REPO_GROUP_IDS, CLI_USER_ID - -from augur.tasks.github.util.github_task_session import GithubTaskSession -from augur.application.db.session import DatabaseSession -from augur.tasks.github.util.github_paginator import GithubPaginator -from augur.application.db.models import Contributor, Issue, Config -from augur.tasks.github.util.github_paginator import hit_api -from augur.application.db.util import execute_session_query - - -logger = logging.getLogger(__name__) - -VALID_ORG = {"org": "CDCgov", "repo_count": 241} - - -######## Helper Functions to Get Delete statements ################# - -def get_delete_statement(schema, table): - - return """DELETE FROM "{}"."{}";""".format(schema, table) - -def get_repo_delete_statement(): - - return get_delete_statement("augur_data", "repo") - -def get_repo_group_delete_statement(): - - return get_delete_statement("augur_data", "repo_groups") - -def get_user_delete_statement(): - - return get_delete_statement("augur_operations", "users") - -def get_user_repo_delete_statement(): - - return get_delete_statement("augur_operations", "user_repos") - -def get_user_group_delete_statement(): - - return get_delete_statement("augur_operations", "user_groups") - -def get_config_delete_statement(): - - return get_delete_statement("augur_operations", "config") - -def get_repo_related_delete_statements(table_list): - """Takes a list of tables related to the RepoLoadController class and generates a delete statement. - - Args: - table_list: list of table names. Valid table names are - "user_repos" or "user_repo", "repo" or "repos", "repo_groups" or "repo_group:, "user" or "users", and "config" - - """ - - query_list = [] - if "user_repos" in table_list or "user_repo" in table_list: - query_list.append(get_user_repo_delete_statement()) - - if "user_groups" in table_list or "user_group" in table_list: - query_list.append(get_user_group_delete_statement()) - - if "repos" in table_list or "repo" in table_list: - query_list.append(get_repo_delete_statement()) - - if "repo_groups" in table_list or "repo_group" in table_list: - query_list.append(get_repo_group_delete_statement()) - - if "users" in table_list or "user" in table_list: - query_list.append(get_user_delete_statement()) - - if "config" in table_list: - query_list.append(get_config_delete_statement()) - - return " ".join(query_list) - -######## Helper Functions to add github api keys from prod db to test db ################# -def add_keys_to_test_db(test_db_engine): - - row = None - section_name = "Keys" - setting_name = "github_api_key" - with DatabaseSession(logger) as session: - query = session.query(Config).filter(Config.section_name==section_name, Config.setting_name==setting_name) - row = execute_session_query(query, 'one') - - with DatabaseSession(logger, test_db_engine) as test_session: - new_row = Config(section_name=section_name, setting_name=setting_name, value=row.value, type="str") - test_session.add(new_row) - test_session.commit() - - -######## Helper Functions to get insert statements ################# - -def get_repo_insert_statement(repo_id, rg_id, repo_url="place holder url", repo_status="New"): - - return """INSERT INTO "augur_data"."repo" ("repo_id", "repo_group_id", "repo_git", "repo_path", "repo_name", "repo_added", "repo_status", "repo_type", "url", "owner_id", "description", "primary_language", "created_at", "forked_from", "updated_at", "repo_archived_date_collected", "repo_archived", "tool_source", "tool_version", "data_source", "data_collection_date") VALUES ({}, {}, '{}', NULL, NULL, '2022-08-15 21:08:07', '{}', '', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'CLI', '1.0', 'Git', '2022-08-15 21:08:07');""".format(repo_id, rg_id, repo_url, repo_status) - -def get_repo_group_insert_statement(rg_id): - - return """INSERT INTO "augur_data"."repo_groups" ("repo_group_id", "rg_name", "rg_description", "rg_website", "rg_recache", "rg_last_modified", "rg_type", "tool_source", "tool_version", "data_source", "data_collection_date") VALUES ({}, 'Default Repo Group', 'The default repo group created by the schema generation script', '', 0, '2019-06-03 15:55:20', 'GitHub Organization', 'load', 'one', 'git', '2019-06-05 13:36:25');""".format(rg_id) - -def get_user_insert_statement(user_id): - - return """INSERT INTO "augur_operations"."users" ("user_id", "login_name", "login_hashword", "email", "first_name", "last_name", "admin") VALUES ({}, 'bil', 'pass', 'b@gmil.com', 'bill', 'bob', false);""".format(user_id) - -def get_user_group_insert_statement(user_id, group_name, group_id=None): - - if group_id: - return """INSERT INTO "augur_operations"."user_groups" ("group_id", "user_id", "name") VALUES ({}, {}, '{}');""".format(group_id, user_id, group_name) - - return """INSERT INTO "augur_operations"."user_groups" (user_id", "name") VALUES (1, 'default');""".format(user_id, group_name) - - -######## Helper Functions to get retrieve data from tables ################# - -def get_repos(connection, where_string=None): - - query_list = [] - query_list.append('SELECT * FROM "augur_data"."repo"') - - if where_string: - if where_string.endswith(";"): - query_list.append(where_string[:-1]) - - query_list.append(where_string) - - query_list.append(";") - - query = s.text(" ".join(query_list)) - - return connection.execute(query).fetchall() - -def get_user_repos(connection): - - return connection.execute(s.text("""SELECT * FROM "augur_operations"."user_repos";""")).fetchall() - - -######## Helper Functions to get repos in an org ################# - -def get_org_repos(org_name, session): - - attempts = 0 - while attempts < 10: - result = hit_api(session.oauths, ORG_REPOS_ENDPOINT.format(org_name), logger) - - # if result is None try again - if not result: - attempts += 1 - continue - - response = result.json() - - if response: - return response - - return None - -def get_org_repo_count(org_name, session): - - repos = get_org_repos(org_name, session) - return len(repos) - - -def test_is_valid_repo(): - - with GithubTaskSession(logger) as session: - - controller = RepoLoadController(session) - - assert controller.is_valid_repo("hello world") is False - assert controller.is_valid_repo("https://github.com/chaoss/hello") is False - assert controller.is_valid_repo("https://github.com/hello124/augur") is False - assert controller.is_valid_repo("https://github.com//augur") is False - assert controller.is_valid_repo("https://github.com/chaoss/") is False - assert controller.is_valid_repo("https://github.com//") is False - assert controller.is_valid_repo("https://github.com/chaoss/augur") is True - assert controller.is_valid_repo("https://github.com/chaoss/augur/") is True - assert controller.is_valid_repo("https://github.com/chaoss/augur.git") is True - - -def test_add_repo_row(test_db_engine): - - clear_tables = ["repo", "repo_groups"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - data = {"rg_id": 1, "repo_id": 1, "tool_source": "Frontend", - "repo_url": "https://github.com/chaoss/augur"} - - with test_db_engine.connect() as connection: - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["rg_id"])) - query = s.text("".join(query_statements)) - - connection.execute(query) - - with DatabaseSession(logger, test_db_engine) as session: - - assert RepoLoadController(session).add_repo_row(data["repo_url"], data["rg_id"], data["tool_source"]) is not None - - with test_db_engine.connect() as connection: - - result = get_repos(connection, where_string=f"WHERE repo_git='{data['repo_url']}'") - assert result is not None - assert len(result) > 0 - - finally: - with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) - - -def test_add_repo_row_with_updates(test_db_engine): - - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - data = {"old_rg_id": 1, "new_rg_id": 2, "repo_id": 1, "repo_id_2": 2, "tool_source": "Test", - "repo_url": "https://github.com/chaoss/augur", "repo_url_2": "https://github.com/chaoss/grimoirelab-perceval-opnfv", "repo_status": "Complete"} - - with test_db_engine.connect() as connection: - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["old_rg_id"])) - query_statements.append(get_repo_group_insert_statement(data["new_rg_id"])) - query_statements.append(get_repo_insert_statement(data["repo_id"], data["old_rg_id"], repo_url=data["repo_url"], repo_status=data["repo_status"])) - query = s.text("".join(query_statements)) - - connection.execute(query) - - with DatabaseSession(logger, test_db_engine) as session: - - result = RepoLoadController(session).add_repo_row(data["repo_url"], data["new_rg_id"], data["tool_source"]) is not None - assert result == data["repo_id"] - - with test_db_engine.connect() as connection: - - result = get_repos(connection, where_string=f"WHERE repo_git='{data['repo_url']}'") - assert result is not None - assert len(result) == 1 - - value = dict(result[0]) - assert value["repo_status"] == data["repo_status"] - assert value["repo_group_id"] == data["new_rg_id"] - - finally: - with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) - - -def test_add_repo_to_user_group(test_db_engine): - - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - with test_db_engine.connect() as connection: - - data = {"repo_id": 1, "user_id": 2, "user_repo_group_id": 1, "user_group_id": 1, "user_group_name": "test_group"} - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["user_repo_group_id"])) - query_statements.append(get_repo_insert_statement(data["repo_id"], data["user_repo_group_id"])) - query_statements.append(get_user_insert_statement(data["user_id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) - query = s.text("".join(query_statements)) - - connection.execute(query) - - with DatabaseSession(logger, test_db_engine) as session: - - RepoLoadController(session).add_repo_to_user_group(data["repo_id"], data["user_group_id"]) - - with test_db_engine.connect() as connection: - - query = s.text("""SELECT * FROM "augur_operations"."user_repos" WHERE "group_id"=:user_group_id AND "repo_id"=:repo_id""") - - result = connection.execute(query, **data).fetchall() - assert result is not None - assert len(result) > 0 - - finally: - with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) - - -def test_add_frontend_repos_with_duplicates(test_db_engine): - - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - with test_db_engine.connect() as connection: - - url = "https://github.com/operate-first/operate-first-twitter" - - data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "user_group_name": "test_group", "user_group_id": 1} - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) - query_statements.append(get_user_insert_statement(data["user_id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) - - connection.execute("".join(query_statements)) - - add_keys_to_test_db(test_db_engine) - - with GithubTaskSession(logger, test_db_engine) as session: - - controller = RepoLoadController(session) - result = controller.add_frontend_repo(url, data["user_id"], data["user_group_name"]) - result2 = controller.add_frontend_repo(url, data["user_id"], data["user_group_name"]) - - assert result["status"] == "Repo Added" - assert result2["status"] == "Repo Added" - - with test_db_engine.connect() as connection: - - result = get_repos(connection) - assert result is not None - assert len(result) == 1 - assert dict(result[0])["repo_git"] == url - - finally: - with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) - - -def test_add_frontend_repos_with_invalid_repo(test_db_engine): - - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - with test_db_engine.connect() as connection: - - url = "https://github.com/chaoss/whitepaper" - - data = {"user_id": 2, "repo_group_id": 5, "user_group_name": "test_group", "user_group_id": 1} - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) - query_statements.append(get_user_insert_statement(data["user_id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) - - connection.execute("".join(query_statements)) - - add_keys_to_test_db(test_db_engine) - - with GithubTaskSession(logger, test_db_engine) as session: - - result = RepoLoadController(session).add_frontend_repo(url, data["user_id"], data["user_group_name"]) - - assert result["status"] == "Invalid repo" - - with test_db_engine.connect() as connection: - - result = get_repos(connection) - assert result is not None - assert len(result) == 0 - - finally: - with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) - - -def test_add_frontend_org_with_invalid_org(test_db_engine): - - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - - data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "org_name": "chaosssss", "user_group_name": "test_group", "user_group_id": 1} - - with test_db_engine.connect() as connection: - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) - query_statements.append(get_user_insert_statement(data["user_id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) - - connection.execute("".join(query_statements)) - - add_keys_to_test_db(test_db_engine) - with GithubTaskSession(logger, test_db_engine) as session: - - url = f"https://github.com/{data['org_name']}/" - result = RepoLoadController(session).add_frontend_org(url, data["user_id"], data["user_group_name"]) - assert result["status"] == "Invalid org" - - with test_db_engine.connect() as connection: - - result = get_repos(connection) - assert result is not None - assert len(result) == 0 - - finally: - with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) - - -def test_add_frontend_org_with_valid_org(test_db_engine): - - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - with test_db_engine.connect() as connection: - - data = {"user_id": 2, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "org_name": VALID_ORG["org"], "user_group_name": "test_group", "user_group_id": 1} - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) - query_statements.append(get_user_insert_statement(data["user_id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) - - connection.execute("".join(query_statements)) - - add_keys_to_test_db(test_db_engine) - - with GithubTaskSession(logger, test_db_engine) as session: - - url = "https://github.com/{}/".format(data["org_name"]) - result = RepoLoadController(session).add_frontend_org(url, data["user_id"], data["user_group_name"]) - assert result["status"] == "Org repos added" - - with test_db_engine.connect() as connection: - - result = get_repos(connection) - assert result is not None - assert len(result) == VALID_ORG["repo_count"] - - user_repo_result = get_user_repos(connection) - assert user_repo_result is not None - assert len(user_repo_result) == VALID_ORG["repo_count"] - - finally: - with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) - - -def test_add_cli_org_with_valid_org(test_db_engine): - - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - with test_db_engine.connect() as connection: - - data = {"user_id": CLI_USER_ID, "repo_group_id": 5, "org_name": VALID_ORG["org"], "user_group_name": "test_group", "user_group_id": 1} - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) - query_statements.append(get_user_insert_statement(data["user_id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) - - connection.execute("".join(query_statements)) - - repo_count = None - - add_keys_to_test_db(test_db_engine) - - with GithubTaskSession(logger, test_db_engine) as session: - - result = RepoLoadController(session).add_cli_org(data["org_name"]) - print(result) - - with test_db_engine.connect() as connection: - - result = get_repos(connection) - assert result is not None - assert len(result) == VALID_ORG["repo_count"] - - user_repo_result = get_user_repos(connection) - assert user_repo_result is not None - assert len(user_repo_result) == VALID_ORG["repo_count"] - - finally: - with test_db_engine.connect() as connection: - pass - # connection.execute(clear_tables_statement) - - -def test_add_cli_repos_with_duplicates(test_db_engine): - - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - with test_db_engine.connect() as connection: - - data = {"user_id": CLI_USER_ID, "repo_group_id": 5, "org_name": "operate-first", "repo_name": "operate-first-twitter", "user_group_name": "test_group", "user_group_id": 1} - url = f"https://github.com/{data['org_name']}/{data['repo_name']}" - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) - query_statements.append(get_user_insert_statement(data["user_id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) - - connection.execute("".join(query_statements)) - - add_keys_to_test_db(test_db_engine) - - with GithubTaskSession(logger, test_db_engine) as session: - - repo_data = {"url": url, "repo_group_id": data["repo_group_id"]} - - controller = RepoLoadController(session) - controller.add_cli_repo(repo_data) - controller.add_cli_repo(repo_data) - - with test_db_engine.connect() as connection: - - result = get_repos(connection) - - assert result is not None - assert len(result) == 1 - assert dict(result[0])["repo_git"] == url - - finally: - with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) - - - -def test_convert_group_name_to_id(test_db_engine): - - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] - clear_tables_statement = get_repo_related_delete_statements(clear_tables) - - try: - with test_db_engine.connect() as connection: - - data = {"user_id": 1, "group_name": "test_group_name", "group_id": 1} - url = f"https://github.com/{data['org_name']}/{data['repo_name']}" - - query_statements = [] - query_statements.append(clear_tables_statement) - query_statements.append(get_user_insert_statement(data["user-id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["group_name"], data["group_id"])) - - connection.execute("".join(query_statements)) - - with GithubTaskSession(logger, test_db_engine) as session: - - repo_data = {"url": url, "repo_group_id": data["repo_group_id"]} - - controller = RepoLoadController(session) - group_id = controller.convert_group_name_to_id(data["user_id"], data["group_name"]) - - assert group_id is not None - assert group_id == data["group_id"] - - finally: - with test_db_engine.connect() as connection: - connection.execute(clear_tables_statement) - - - - - - diff --git a/tests/test_applicaton/test_repo_load_controller/util.py b/tests/test_applicaton/test_repo_load_controller/util.py new file mode 100644 index 0000000000..b77cdb8bfe --- /dev/null +++ b/tests/test_applicaton/test_repo_load_controller/util.py @@ -0,0 +1,146 @@ +######## Helper Functions to Get Delete statements ################# + +def get_delete_statement(schema, table): + + return """DELETE FROM "{}"."{}";""".format(schema, table) + +def get_repo_delete_statement(): + + return get_delete_statement("augur_data", "repo") + +def get_repo_group_delete_statement(): + + return get_delete_statement("augur_data", "repo_groups") + +def get_user_delete_statement(): + + return get_delete_statement("augur_operations", "users") + +def get_user_repo_delete_statement(): + + return get_delete_statement("augur_operations", "user_repos") + +def get_user_group_delete_statement(): + + return get_delete_statement("augur_operations", "user_groups") + +def get_config_delete_statement(): + + return get_delete_statement("augur_operations", "config") + +def get_repo_related_delete_statements(table_list): + """Takes a list of tables related to the RepoLoadController class and generates a delete statement. + + Args: + table_list: list of table names. Valid table names are + "user_repos" or "user_repo", "repo" or "repos", "repo_groups" or "repo_group:, "user" or "users", and "config" + + """ + + query_list = [] + if "user_repos" in table_list or "user_repo" in table_list: + query_list.append(get_user_repo_delete_statement()) + + if "user_groups" in table_list or "user_group" in table_list: + query_list.append(get_user_group_delete_statement()) + + if "repos" in table_list or "repo" in table_list: + query_list.append(get_repo_delete_statement()) + + if "repo_groups" in table_list or "repo_group" in table_list: + query_list.append(get_repo_group_delete_statement()) + + if "users" in table_list or "user" in table_list: + query_list.append(get_user_delete_statement()) + + if "config" in table_list: + query_list.append(get_config_delete_statement()) + + return " ".join(query_list) + +######## Helper Functions to add github api keys from prod db to test db ################# +def add_keys_to_test_db(test_db_engine): + + row = None + section_name = "Keys" + setting_name = "github_api_key" + with DatabaseSession(logger) as session: + query = session.query(Config).filter(Config.section_name==section_name, Config.setting_name==setting_name) + row = execute_session_query(query, 'one') + + with DatabaseSession(logger, test_db_engine) as test_session: + new_row = Config(section_name=section_name, setting_name=setting_name, value=row.value, type="str") + test_session.add(new_row) + test_session.commit() + + +######## Helper Functions to get insert statements ################# + +def get_repo_insert_statement(repo_id, rg_id, repo_url="place holder url", repo_status="New"): + + return """INSERT INTO "augur_data"."repo" ("repo_id", "repo_group_id", "repo_git", "repo_path", "repo_name", "repo_added", "repo_status", "repo_type", "url", "owner_id", "description", "primary_language", "created_at", "forked_from", "updated_at", "repo_archived_date_collected", "repo_archived", "tool_source", "tool_version", "data_source", "data_collection_date") VALUES ({}, {}, '{}', NULL, NULL, '2022-08-15 21:08:07', '{}', '', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'CLI', '1.0', 'Git', '2022-08-15 21:08:07');""".format(repo_id, rg_id, repo_url, repo_status) + +def get_repo_group_insert_statement(rg_id): + + return """INSERT INTO "augur_data"."repo_groups" ("repo_group_id", "rg_name", "rg_description", "rg_website", "rg_recache", "rg_last_modified", "rg_type", "tool_source", "tool_version", "data_source", "data_collection_date") VALUES ({}, 'Default Repo Group', 'The default repo group created by the schema generation script', '', 0, '2019-06-03 15:55:20', 'GitHub Organization', 'load', 'one', 'git', '2019-06-05 13:36:25');""".format(rg_id) + +def get_user_insert_statement(user_id): + + return """INSERT INTO "augur_operations"."users" ("user_id", "login_name", "login_hashword", "email", "first_name", "last_name", "admin") VALUES ({}, 'bil', 'pass', 'b@gmil.com', 'bill', 'bob', false);""".format(user_id) + +def get_user_group_insert_statement(user_id, group_name, group_id=None): + + if group_id: + return """INSERT INTO "augur_operations"."user_groups" ("group_id", "user_id", "name") VALUES ({}, {}, '{}');""".format(group_id, user_id, group_name) + + return """INSERT INTO "augur_operations"."user_groups" (user_id", "name") VALUES (1, 'default');""".format(user_id, group_name) + + +######## Helper Functions to get retrieve data from tables ################# + +def get_repos(connection, where_string=None): + + query_list = [] + query_list.append('SELECT * FROM "augur_data"."repo"') + + if where_string: + if where_string.endswith(";"): + query_list.append(where_string[:-1]) + + query_list.append(where_string) + + query_list.append(";") + + query = s.text(" ".join(query_list)) + + return connection.execute(query).fetchall() + +def get_user_repos(connection): + + return connection.execute(s.text("""SELECT * FROM "augur_operations"."user_repos";""")).fetchall() + + +######## Helper Functions to get repos in an org ################# + +def get_org_repos(org_name, session): + + attempts = 0 + while attempts < 10: + result = hit_api(session.oauths, ORG_REPOS_ENDPOINT.format(org_name), logger) + + # if result is None try again + if not result: + attempts += 1 + continue + + response = result.json() + + if response: + return response + + return None + +def get_org_repo_count(org_name, session): + + repos = get_org_repos(org_name, session) + return len(repos) From ef508edc929cbc1ae01502e5d83dc9f99afa44e4 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 22 Dec 2022 10:32:11 -0600 Subject: [PATCH 014/150] Add more tests Signed-off-by: Andrew Brain --- augur/application/db/session.py | 2 +- augur/util/repo_load_controller.py | 13 +- .../test_helper_functions.py | 138 ++++++++++++++---- 3 files changed, 123 insertions(+), 30 deletions(-) diff --git a/augur/application/db/session.py b/augur/application/db/session.py index 65b913a713..d4745fab5b 100644 --- a/augur/application/db/session.py +++ b/augur/application/db/session.py @@ -202,7 +202,7 @@ def insert_data(self, data: Union[List[dict], dict], table, natural_keys: List[s if deadlock_detected is True: self.logger.error("Made it through even though Deadlock was detected") - return None + return "success" # othewise it gets the requested return columns and returns them as a list of dicts diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index ec644d6232..f211242b2d 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -37,8 +37,6 @@ def is_valid_repo(self, url: str) -> bool: True if repo url is valid and False if not """ - print("Is repo valid?") - owner, repo = self.parse_repo_url(url) if not owner or not repo: return False @@ -109,7 +107,11 @@ def retrieve_org_repos(self, url: str) -> List[str]: def is_valid_repo_group_id(self, repo_group_id): query = self.session.query(RepoGroup).filter(RepoGroup.repo_group_id == repo_group_id) - result = execute_session_query(query, 'one') + + try: + result = execute_session_query(query, 'one') + except (s.orm.exc.NoResultFound, s.orm.exc.MultipleResultsFound): + return False if result and result.repo_group_id == repo_group_id: return True @@ -127,6 +129,9 @@ def add_repo_row(self, url: str, repo_group_id: int, tool_source): If repo row exists then it will update the repo_group_id if param repo_group_id is not a default. If it does not exist is will simply insert the repo. """ + if not isinstance(url, str) or not isinstance(repo_group_id, int) or not isinstance(tool_source, str): + return None + if not self.is_valid_repo_group_id(repo_group_id): return None @@ -153,7 +158,7 @@ def add_repo_row(self, url: str, repo_group_id: int, tool_source): if not repo.repo_group_id == repo_group_id: repo.repo_group_id = repo_group_id - self.session.commit() + self.session.commit() return result[0]["repo_id"] diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py index c7c3807d44..2a303ba8c1 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -12,6 +12,37 @@ logger = logging.getLogger(__name__) +def test_parse_repo_url(): + + with DatabaseSession(logger) as session: + + controller = RepoLoadController(session) + + assert controller.parse_repo_url("hello world") == (None, None) + assert controller.parse_repo_url("https://github.com/chaoss/hello") == ("chaoss", "hello") + assert controller.parse_repo_url("https://github.com/hello124/augur") == ("hello124", "augur") + assert controller.parse_repo_url("https://github.com//augur") == (None, None) + assert controller.parse_repo_url("https://github.com/chaoss/") == (None, None) + assert controller.parse_repo_url("https://github.com//") == (None, None) + assert controller.parse_repo_url("https://github.com/chaoss/augur") == ("chaoss", "augur") + assert controller.parse_repo_url("https://github.com/chaoss/augur/") == ("chaoss", "augur") + assert controller.parse_repo_url("https://github.com/chaoss/augur.git") == ("chaoss", "augur") + + +def test_parse_org_url(): + + with DatabaseSession(logger) as session: + + controller = RepoLoadController(session) + + assert controller.parse_org_url("hello world") == None, None + assert controller.parse_org_url("https://github.com/chaoss/") == "chaoss" + assert controller.parse_org_url("https://github.com/chaoss") == "chaoss" + assert controller.parse_org_url("https://github.com/hello124/augur") == None + assert controller.parse_org_url("https://github.com//augur") == None, None + assert controller.parse_org_url("https://github.com//") == None + assert controller.parse_org_url("https://github.com/chaoss/augur") == None + def test_is_valid_repo(): @@ -29,80 +60,137 @@ def test_is_valid_repo(): assert controller.is_valid_repo("https://github.com/chaoss/augur/") is True assert controller.is_valid_repo("https://github.com/chaoss/augur.git") is True +def test_is_valid_repo_group_id(test_db_engine): -def test_add_repo_row(test_db_engine): - - clear_tables = ["repo", "repo_groups"] + clear_tables = ["repo_groups"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: - data = {"rg_id": 1, "repo_id": 1, "tool_source": "Frontend", + + + data = {"rg_ids": [1, 2, 3], "repo_id": 1, "tool_source": "Frontend", "repo_url": "https://github.com/chaoss/augur"} with test_db_engine.connect() as connection: query_statements = [] query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["rg_id"])) + query_statements.append(get_repo_group_insert_statement(data["rg_ids"][0])) + query_statements.append(get_repo_group_insert_statement(data["rg_ids"][1])) + query_statements.append(get_repo_group_insert_statement(data["rg_ids"][2])) query = s.text("".join(query_statements)) connection.execute(query) with DatabaseSession(logger, test_db_engine) as session: - assert RepoLoadController(session).add_repo_row(data["repo_url"], data["rg_id"], data["tool_source"]) is not None + controller = RepoLoadController(session) - with test_db_engine.connect() as connection: + # valid + assert controller.is_valid_repo_group_id(data["rg_ids"][0]) is True + assert controller.is_valid_repo_group_id(data["rg_ids"][1]) is True + assert controller.is_valid_repo_group_id(data["rg_ids"][2]) is True + + + # invalid + assert controller.is_valid_repo_group_id(-1) is False + assert controller.is_valid_repo_group_id(12) is False + assert controller.is_valid_repo_group_id(11111) is False - result = get_repos(connection, where_string=f"WHERE repo_git='{data['repo_url']}'") - assert result is not None - assert len(result) > 0 finally: with test_db_engine.connect() as connection: connection.execute(clear_tables_statement) -def test_add_repo_row_with_updates(test_db_engine): +def test_add_repo_row(test_db_engine): - clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables = ["repo", "repo_groups"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) try: - data = {"old_rg_id": 1, "new_rg_id": 2, "repo_id": 1, "repo_id_2": 2, "tool_source": "Test", - "repo_url": "https://github.com/chaoss/augur", "repo_url_2": "https://github.com/chaoss/grimoirelab-perceval-opnfv", "repo_status": "Complete"} + data = {"rg_id": 1, + "tool_source": "Frontend", + "repo_urls": ["https://github.com/chaoss/augur", "https://github.com/chaoss/grimoirelab-sortinghat"] + } with test_db_engine.connect() as connection: query_statements = [] query_statements.append(clear_tables_statement) - query_statements.append(get_repo_group_insert_statement(data["old_rg_id"])) - query_statements.append(get_repo_group_insert_statement(data["new_rg_id"])) - query_statements.append(get_repo_insert_statement(data["repo_id"], data["old_rg_id"], repo_url=data["repo_url"], repo_status=data["repo_status"])) + query_statements.append(get_repo_group_insert_statement(data["rg_id"])) query = s.text("".join(query_statements)) connection.execute(query) with DatabaseSession(logger, test_db_engine) as session: - result = RepoLoadController(session).add_repo_row(data["repo_url"], data["new_rg_id"], data["tool_source"]) is not None - assert result == data["repo_id"] + assert RepoLoadController(session).add_repo_row(data["repo_urls"][0], data["rg_id"], data["tool_source"]) is not None + assert RepoLoadController(session).add_repo_row(data["repo_urls"][1], data["rg_id"], data["tool_source"]) is not None + + # invalid rg_id + assert RepoLoadController(session).add_repo_row(data["repo_urls"][0], 12, data["tool_source"]) is None + + # invalid type for repo url + assert RepoLoadController(session).add_repo_row(1, data["rg_id"], data["tool_source"]) is None + + # invalid type for rg_id + assert RepoLoadController(session).add_repo_row(data["repo_urls"][1], "1", data["tool_source"]) is None + + # invalid type for tool_source + assert RepoLoadController(session).add_repo_row(data["repo_urls"][1], data["rg_id"], 52) is None with test_db_engine.connect() as connection: - result = get_repos(connection, where_string=f"WHERE repo_git='{data['repo_url']}'") + result = get_repos(connection) assert result is not None - assert len(result) == 1 - - value = dict(result[0]) - assert value["repo_status"] == data["repo_status"] - assert value["repo_group_id"] == data["new_rg_id"] + assert len(result) == len(data["repo_urls"]) finally: with test_db_engine.connect() as connection: connection.execute(clear_tables_statement) +# def test_add_repo_row_with_updates(test_db_engine): + +# clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] +# clear_tables_statement = get_repo_related_delete_statements(clear_tables) + +# try: +# data = {"old_rg_id": 1, "new_rg_id": 2, "repo_id": 1, "repo_id_2": 2, "tool_source": "Test", +# "repo_url": "https://github.com/chaoss/augur", "repo_url_2": "https://github.com/chaoss/grimoirelab-perceval-opnfv", "repo_status": "Complete"} + +# with test_db_engine.connect() as connection: + +# query_statements = [] +# query_statements.append(clear_tables_statement) +# query_statements.append(get_repo_group_insert_statement(data["old_rg_id"])) +# query_statements.append(get_repo_group_insert_statement(data["new_rg_id"])) +# query_statements.append(get_repo_insert_statement(data["repo_id"], data["old_rg_id"], repo_url=data["repo_url"], repo_status=data["repo_status"])) +# query = s.text("".join(query_statements)) + +# connection.execute(query) + +# with DatabaseSession(logger, test_db_engine) as session: + +# result = RepoLoadController(session).add_repo_row(data["repo_url"], data["new_rg_id"], data["tool_source"]) is not None +# assert result == data["repo_id"] + +# with test_db_engine.connect() as connection: + +# result = get_repos(connection, where_string=f"WHERE repo_git='{data['repo_url']}'") +# assert result is not None +# assert len(result) == 1 + +# value = dict(result[0]) +# assert value["repo_status"] == data["repo_status"] +# assert value["repo_group_id"] == data["new_rg_id"] + +# finally: +# with test_db_engine.connect() as connection: +# connection.execute(clear_tables_statement) + + def test_add_repo_to_user_group(test_db_engine): clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] From b42648fd01e5a06f210e6b356ba77666445e2d48 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 22 Dec 2022 10:58:12 -0600 Subject: [PATCH 015/150] Add more tests Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 9 +- .../test_helper_functions.py | 125 +++++++++++++----- 2 files changed, 99 insertions(+), 35 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index f211242b2d..e5ee26a08a 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -171,6 +171,9 @@ def add_repo_to_user_group(self, repo_id, group_id=1): user_id: id of user_id from users table """ + if not isinstance(repo_id, int) or not isinstance(group_id, int): + return False + repo_user_group_data = { "group_id": group_id, "repo_id": repo_id @@ -179,7 +182,11 @@ def add_repo_to_user_group(self, repo_id, group_id=1): repo_user_group_unique = ["group_id", "repo_id"] return_columns = ["group_id", "repo_id"] - data = self.session.insert_data(repo_user_group_data, UserRepo, repo_user_group_unique, return_columns) + + try: + data = self.session.insert_data(repo_user_group_data, UserRepo, repo_user_group_unique, return_columns) + except s.exc.IntegrityError: + return False return data[0]["group_id"] == group_id and data[0]["repo_id"] == repo_id diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py index 2a303ba8c1..8d3d779178 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -151,44 +151,44 @@ def test_add_repo_row(test_db_engine): connection.execute(clear_tables_statement) -# def test_add_repo_row_with_updates(test_db_engine): +def test_add_repo_row_with_updates(test_db_engine): -# clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] -# clear_tables_statement = get_repo_related_delete_statements(clear_tables) + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) -# try: -# data = {"old_rg_id": 1, "new_rg_id": 2, "repo_id": 1, "repo_id_2": 2, "tool_source": "Test", -# "repo_url": "https://github.com/chaoss/augur", "repo_url_2": "https://github.com/chaoss/grimoirelab-perceval-opnfv", "repo_status": "Complete"} + try: + data = {"old_rg_id": 1, "new_rg_id": 2, "repo_id": 1, "repo_id_2": 2, "tool_source": "Test", + "repo_url": "https://github.com/chaoss/augur", "repo_url_2": "https://github.com/chaoss/grimoirelab-perceval-opnfv", "repo_status": "Complete"} -# with test_db_engine.connect() as connection: + with test_db_engine.connect() as connection: -# query_statements = [] -# query_statements.append(clear_tables_statement) -# query_statements.append(get_repo_group_insert_statement(data["old_rg_id"])) -# query_statements.append(get_repo_group_insert_statement(data["new_rg_id"])) -# query_statements.append(get_repo_insert_statement(data["repo_id"], data["old_rg_id"], repo_url=data["repo_url"], repo_status=data["repo_status"])) -# query = s.text("".join(query_statements)) + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["old_rg_id"])) + query_statements.append(get_repo_group_insert_statement(data["new_rg_id"])) + query_statements.append(get_repo_insert_statement(data["repo_id"], data["old_rg_id"], repo_url=data["repo_url"], repo_status=data["repo_status"])) + query = s.text("".join(query_statements)) -# connection.execute(query) + connection.execute(query) -# with DatabaseSession(logger, test_db_engine) as session: + with DatabaseSession(logger, test_db_engine) as session: -# result = RepoLoadController(session).add_repo_row(data["repo_url"], data["new_rg_id"], data["tool_source"]) is not None -# assert result == data["repo_id"] + result = RepoLoadController(session).add_repo_row(data["repo_url"], data["new_rg_id"], data["tool_source"]) is not None + assert result == data["repo_id"] -# with test_db_engine.connect() as connection: + with test_db_engine.connect() as connection: -# result = get_repos(connection, where_string=f"WHERE repo_git='{data['repo_url']}'") -# assert result is not None -# assert len(result) == 1 + result = get_repos(connection, where_string=f"WHERE repo_git='{data['repo_url']}'") + assert result is not None + assert len(result) == 1 -# value = dict(result[0]) -# assert value["repo_status"] == data["repo_status"] -# assert value["repo_group_id"] == data["new_rg_id"] + value = dict(result[0]) + assert value["repo_status"] == data["repo_status"] + assert value["repo_group_id"] == data["new_rg_id"] -# finally: -# with test_db_engine.connect() as connection: -# connection.execute(clear_tables_statement) + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) def test_add_repo_to_user_group(test_db_engine): @@ -199,35 +199,92 @@ def test_add_repo_to_user_group(test_db_engine): try: with test_db_engine.connect() as connection: - data = {"repo_id": 1, "user_id": 2, "user_repo_group_id": 1, "user_group_id": 1, "user_group_name": "test_group"} + data = {"repo_ids": [1, 2, 3], "repo_urls":["url 1", "url2", "url3"], "user_id": 2, "user_repo_group_id": 1, "user_group_ids": [1, 2], "user_group_names": ["test_group", "test_group_2"]} query_statements = [] query_statements.append(clear_tables_statement) query_statements.append(get_repo_group_insert_statement(data["user_repo_group_id"])) - query_statements.append(get_repo_insert_statement(data["repo_id"], data["user_repo_group_id"])) + + for i in range(0, len(data["repo_ids"])): + query_statements.append(get_repo_insert_statement(data["repo_ids"][i], data["user_repo_group_id"], data["repo_urls"][i])) + query_statements.append(get_user_insert_statement(data["user_id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + + for i in range(0, len(data["user_group_ids"])): + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_names"][i], data["user_group_ids"][i])) + query = s.text("".join(query_statements)) connection.execute(query) with DatabaseSession(logger, test_db_engine) as session: - RepoLoadController(session).add_repo_to_user_group(data["repo_id"], data["user_group_id"]) + controller = RepoLoadController(session) + + # add valid repo to group 0 + assert controller.add_repo_to_user_group(data["repo_ids"][0], data["user_group_ids"][0]) is True + + # add repo again to group 0 ... should be 1 repo row still + assert controller.add_repo_to_user_group(data["repo_ids"][0], data["user_group_ids"][0]) is True + + # add another valid repo to group 0 + assert controller.add_repo_to_user_group(data["repo_ids"][1], data["user_group_ids"][0]) is True + + # add same repo to group 1 + assert controller.add_repo_to_user_group(data["repo_ids"][0], data["user_group_ids"][1]) is True + + # add different repo to group 1 + assert controller.add_repo_to_user_group(data["repo_ids"][2], data["user_group_ids"][1]) is True + + # add with invalid repo id + assert controller.add_repo_to_user_group(130000, data["user_group_ids"][1]) is False + + # add with invalid group_id + assert controller.add_repo_to_user_group(data["repo_ids"][0], 133333) is False + + # pass invalid tpyes + assert controller.add_repo_to_user_group("130000", data["user_group_ids"][1]) is False + assert controller.add_repo_to_user_group(data["repo_ids"][0], "133333") is False + + + # end result + # 4 rows in table + # 2 rows in each group + with test_db_engine.connect() as connection: - query = s.text("""SELECT * FROM "augur_operations"."user_repos" WHERE "group_id"=:user_group_id AND "repo_id"=:repo_id""") + query = s.text("""SELECT * FROM "augur_operations"."user_repos";""") + # WHERE "group_id"=:user_group_id AND "repo_id"=:repo_id + + result = connection.execute(query).fetchall() + assert result is not None + assert len(result) == 4 + + + query = s.text("""SELECT * FROM "augur_operations"."user_repos" WHERE "group_id"={};""".format(data["user_group_ids"][0])) + + result = connection.execute(query).fetchall() + assert result is not None + assert len(result) == 2 - result = connection.execute(query, **data).fetchall() + + query = s.text("""SELECT * FROM "augur_operations"."user_repos" WHERE "group_id"={};""".format(data["user_group_ids"][0])) + + result = connection.execute(query).fetchall() assert result is not None - assert len(result) > 0 + assert len(result) == 2 finally: with test_db_engine.connect() as connection: connection.execute(clear_tables_statement) +def test_add_user_group(): + + pass + + def test_convert_group_name_to_id(test_db_engine): From 3920591a2e2fd77d8adb59b1253bc2f91b04d1ba Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 22 Dec 2022 11:44:46 -0600 Subject: [PATCH 016/150] Add more tests Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 14 +- .../test_repo_load_controller/helper.py | 4 +- .../test_helper_functions.py | 127 ++++++++++++++++-- 3 files changed, 133 insertions(+), 12 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index e5ee26a08a..ccecb93d2b 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -192,17 +192,24 @@ def add_repo_to_user_group(self, repo_id, group_id=1): def add_user_group(self, user_id, group_name): + if not isinstance(user_id, int) or not isinstance(group_name, str): + return {"status": "Invalid input"} + user_group_data = { "name": group_name, "user_id": user_id } - result = self.session.insert_data(user_group_data, UserGroup, ["name", "user_id"], return_columns=["group_id"]) + try: + result = self.session.insert_data(user_group_data, UserGroup, ["name", "user_id"], return_columns=["group_id"]) + except s.exc.IntegrityError: + return {"status": "Error: User id does not exist"} + if result: return {"status": "Group created"} else: - return {"status": "Group already exists"} + return {"status": "Error while creating group"} def remove_user_group(self, user_id, group_name): @@ -224,6 +231,9 @@ def remove_user_group(self, user_id, group_name): def convert_group_name_to_id(self, user_id, group_name): + if not isinstance(user_id, int) or not isinstance(group_name, str): + return None + try: user_group = self.session.query(UserGroup).filter(UserGroup.user_id == user_id, UserGroup.name == group_name).one() except s.orm.exc.NoResultFound: diff --git a/tests/test_applicaton/test_repo_load_controller/helper.py b/tests/test_applicaton/test_repo_load_controller/helper.py index 9223f3b071..cea59fccf1 100644 --- a/tests/test_applicaton/test_repo_load_controller/helper.py +++ b/tests/test_applicaton/test_repo_load_controller/helper.py @@ -97,9 +97,9 @@ def get_repo_group_insert_statement(rg_id): return """INSERT INTO "augur_data"."repo_groups" ("repo_group_id", "rg_name", "rg_description", "rg_website", "rg_recache", "rg_last_modified", "rg_type", "tool_source", "tool_version", "data_source", "data_collection_date") VALUES ({}, 'Default Repo Group', 'The default repo group created by the schema generation script', '', 0, '2019-06-03 15:55:20', 'GitHub Organization', 'load', 'one', 'git', '2019-06-05 13:36:25');""".format(rg_id) -def get_user_insert_statement(user_id): +def get_user_insert_statement(user_id, username="bil", email="default@gmail.com"): - return """INSERT INTO "augur_operations"."users" ("user_id", "login_name", "login_hashword", "email", "first_name", "last_name", "admin") VALUES ({}, 'bil', 'pass', 'b@gmil.com', 'bill', 'bob', false);""".format(user_id) + return """INSERT INTO "augur_operations"."users" ("user_id", "login_name", "login_hashword", "email", "first_name", "last_name", "admin") VALUES ({}, '{}', 'pass', '{}', 'bill', 'bob', false);""".format(user_id, username, email) def get_user_group_insert_statement(user_id, group_name, group_id=None): diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py index 8d3d779178..90e983ae6e 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -280,9 +280,94 @@ def test_add_repo_to_user_group(test_db_engine): connection.execute(clear_tables_statement) -def test_add_user_group(): +def test_add_user_group(test_db_engine): - pass + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + data = { + "users": [ + { + "id": 0, + "username": "user 1", + "email": "email 1" + }, + { + "id": 1, + "username": "user 2", + "email": "email 2" + } + ], + "group_names": ["test_group", "test_group_2"]} + + query_statements = [] + query_statements.append(clear_tables_statement) + + for user in data["users"]: + query_statements.append(get_user_insert_statement(user["id"], user["username"], user["email"])) + + query = s.text("".join(query_statements)) + + connection.execute(query) + + with DatabaseSession(logger, test_db_engine) as session: + + controller = RepoLoadController(session) + + # add valid group to user 0 + assert controller.add_user_group(data["users"][0]["id"], data["group_names"][0])["status"] == "Group created" + + # add group again to user 0 ... should be 1 group row still + assert controller.add_user_group(data["users"][0]["id"], data["group_names"][0])["status"] == "Group created" + + # add another valid group to user 0 + assert controller.add_user_group(data["users"][0]["id"], data["group_names"][1])["status"] == "Group created" + + # add same group to user 1 + assert controller.add_user_group(data["users"][1]["id"], data["group_names"][0])["status"] == "Group created" + + + # add with invalid user id + assert controller.add_user_group(130000, data["group_names"][0])["status"] == "Error: User id does not exist" + + # pass invalid tpyes + assert controller.add_user_group("130000", data["group_names"][0])["status"] == "Invalid input" + assert controller.add_user_group(data["users"][0]["id"], 133333)["status"] == "Invalid input" + + + # end result + # 3 groups in table + # 1 row for user 1 + # 2 rows for user 0 + + + with test_db_engine.connect() as connection: + + query = s.text("""SELECT * FROM "augur_operations"."user_groups";""") + + result = connection.execute(query).fetchall() + assert result is not None + assert len(result) == 3 + + query = s.text("""SELECT * FROM "augur_operations"."user_groups" WHERE "user_id"={};""".format(data["users"][0]["id"])) + + result = connection.execute(query).fetchall() + assert result is not None + assert len(result) == 2 + + query = s.text("""SELECT * FROM "augur_operations"."user_groups" WHERE "user_id"={};""".format(data["users"][1]["id"])) + + result = connection.execute(query).fetchall() + assert result is not None + assert len(result) == 1 + + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) @@ -294,22 +379,48 @@ def test_convert_group_name_to_id(test_db_engine): try: with test_db_engine.connect() as connection: - data = {"user_id": 1, "group_name": "test_group_name", "group_id": 1} + user_id =1 + + groups = [ + { + "group_name": "test group 1", + "group_id": 1 + }, + { + "group_name": "test group 2", + "group_id": 2 + }, + { + "group_name": "test group 3", + "group_id": 3 + }, + ] query_statements = [] query_statements.append(clear_tables_statement) - query_statements.append(get_user_insert_statement(data["user_id"])) - query_statements.append(get_user_group_insert_statement(data["user_id"], data["group_name"], data["group_id"])) + query_statements.append(get_user_insert_statement(user_id)) + + for group in groups: + query_statements.append(get_user_group_insert_statement(user_id, group["group_name"], group["group_id"])) connection.execute("".join(query_statements)) with GithubTaskSession(logger, test_db_engine) as session: controller = RepoLoadController(session) - group_id = controller.convert_group_name_to_id(data["user_id"], data["group_name"]) - assert group_id is not None - assert group_id == data["group_id"] + for group in groups: + assert controller.convert_group_name_to_id(user_id, group["group_name"]) == group["group_id"] + + # test invalid group name + assert controller.convert_group_name_to_id(user_id, "hello") is None + + # test invalid user id + assert controller.convert_group_name_to_id(user_id*2, groups[0]["group_name"]) is None + + # test invalid types + assert controller.convert_group_name_to_id(user_id, 5) is None + assert controller.convert_group_name_to_id("5", groups[0]["group_name"]) is None finally: with test_db_engine.connect() as connection: From f75e217b455e425fb74a1938d4e0d411763b9a58 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 22 Dec 2022 12:04:17 -0600 Subject: [PATCH 017/150] Add more tests Signed-off-by: Andrew Brain --- .../test_helper_functions.py | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py index 90e983ae6e..a75a323b10 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -427,6 +427,85 @@ def test_convert_group_name_to_id(test_db_engine): connection.execute(clear_tables_statement) +def test_remove_user_group(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + user_id =1 + + groups = [ + { + "group_name": "test group 1", + "group_id": 1 + }, + { + "group_name": "test group 2", + "group_id": 2 + }, + { + "group_name": "test group 3", + "group_id": 3 + }, + { + "group_name": "test group 4", + "group_id": 4 + }, + { + "group_name": "test group 5", + "group_id": 5 + } + ] + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_user_insert_statement(user_id)) + + for group in groups: + query_statements.append(get_user_group_insert_statement(user_id, group["group_name"], group["group_id"])) + + connection.execute("".join(query_statements)) + + with GithubTaskSession(logger, test_db_engine) as session: + + controller = RepoLoadController(session) + + assert controller.remove_user_group(user_id, "hello")["status"] == "WARNING: Trying to delete group that does not exist" + + i = 0 + while(i < len(groups)-2): + assert controller.remove_user_group(user_id, groups[i]["group_name"])["status"] == "Group deleted" + i += 1 + + + with test_db_engine.connect() as connection: + + query = s.text("""SELECT * FROM "augur_operations"."user_groups";""") + + result = connection.execute(query).fetchall() + assert result is not None + assert len(result) == len(groups)-i + + + while(i < len(groups)): + + assert controller.remove_user_group(user_id, groups[i]["group_name"])["status"] == "Group deleted" + i += 1 + + with test_db_engine.connect() as connection: + + query = s.text("""SELECT * FROM "augur_operations"."user_groups";""") + + result = connection.execute(query).fetchall() + assert result is not None + assert len(result) == 0 + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) From 3d24577ff18d33a36fcb60e42cd1f61dc887db1a Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 22 Dec 2022 12:16:01 -0600 Subject: [PATCH 018/150] Add more tests Signed-off-by: Andrew Brain --- .../test_helper_functions.py | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py index a75a323b10..c294ed791d 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -510,3 +510,68 @@ def test_remove_user_group(test_db_engine): +def test_get_user_groups(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + user_id =1 + + groups = [ + { + "group_name": "test group 1", + "group_id": 1 + }, + { + "group_name": "test group 2", + "group_id": 2 + }, + { + "group_name": "test group 3", + "group_id": 3 + }, + { + "group_name": "test group 4", + "group_id": 4 + }, + { + "group_name": "test group 5", + "group_id": 5 + } + ] + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_user_insert_statement(user_id)) + + for group in groups: + query_statements.append(get_user_group_insert_statement(user_id, group["group_name"], group["group_id"])) + + connection.execute("".join(query_statements)) + + with GithubTaskSession(logger, test_db_engine) as session: + + controller = RepoLoadController(session) + + assert len(controller.get_user_groups(user_id)) == len(groups) + + + with test_db_engine.connect() as connection: + + user_group_delete_statement = get_user_group_delete_statement() + query = s.text(user_group_delete_statement) + + result = connection.execute(query) + + assert len(controller.get_user_groups(user_id)) == 0 + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + + + From 8e01729ca747c58deb3a4b4ddab4fd2afeab2b87 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 22 Dec 2022 12:34:01 -0600 Subject: [PATCH 019/150] Add more tests Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 5 +- .../test_repo_load_controller/helper.py | 4 ++ .../test_helper_functions.py | 49 +++++++++++++++++++ 3 files changed, 55 insertions(+), 3 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index ccecb93d2b..b58f9f20b6 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -246,10 +246,9 @@ def get_user_groups(self, user_id): return self.session.query(UserGroup).filter(UserGroup.user_id == user_id).all() def get_user_group_repos(self, group_id): + user_repos = self.session.query(UserRepo).filter(UserRepo.group_id == group_id).all() - user_repos = self.session.query(UserRepo).filter(UserRepo.user_id == user_id, UserRepo.group_id == group_id).all() - - return [user_repo.repo.repo_id for user_repo in user_repos] + return [user_repo.repo for user_repo in user_repos] def add_frontend_repo(self, url: List[str], user_id: int, group_name: str, group_id=None, valid_repo=False): diff --git a/tests/test_applicaton/test_repo_load_controller/helper.py b/tests/test_applicaton/test_repo_load_controller/helper.py index cea59fccf1..b05be747a7 100644 --- a/tests/test_applicaton/test_repo_load_controller/helper.py +++ b/tests/test_applicaton/test_repo_load_controller/helper.py @@ -93,6 +93,10 @@ def get_repo_insert_statement(repo_id, rg_id, repo_url="place holder url", repo_ return """INSERT INTO "augur_data"."repo" ("repo_id", "repo_group_id", "repo_git", "repo_path", "repo_name", "repo_added", "repo_status", "repo_type", "url", "owner_id", "description", "primary_language", "created_at", "forked_from", "updated_at", "repo_archived_date_collected", "repo_archived", "tool_source", "tool_version", "data_source", "data_collection_date") VALUES ({}, {}, '{}', NULL, NULL, '2022-08-15 21:08:07', '{}', '', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'CLI', '1.0', 'Git', '2022-08-15 21:08:07');""".format(repo_id, rg_id, repo_url, repo_status) +def get_user_repo_insert_statement(repo_id, group_id): + + return """INSERT INTO "augur_operations"."user_repos" ("repo_id", "group_id") VALUES ({}, {});""".format(repo_id, group_id) + def get_repo_group_insert_statement(rg_id): return """INSERT INTO "augur_data"."repo_groups" ("repo_group_id", "rg_name", "rg_description", "rg_website", "rg_recache", "rg_last_modified", "rg_type", "tool_source", "tool_version", "data_source", "data_collection_date") VALUES ({}, 'Default Repo Group', 'The default repo group created by the schema generation script', '', 0, '2019-06-03 15:55:20', 'GitHub Organization', 'load', 'one', 'git', '2019-06-05 13:36:25');""".format(rg_id) diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py index c294ed791d..2492cc3cca 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -573,5 +573,54 @@ def test_get_user_groups(test_db_engine): connection.execute(clear_tables_statement) +def test_get_user_group_repos(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + user_id =1 + group_id = 1 + rg_id = 1 + group_name = "test_group 1" + repo_ids = [1, 2, 3, 4, 5] + repo_urls = ["url1", "url2", "url3", "url4", "url5"] + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_user_insert_statement(user_id)) + query_statements.append(get_repo_group_insert_statement(rg_id)) + query_statements.append(get_user_group_insert_statement(user_id, group_name, group_id)) + for i in range(0, len(repo_ids)): + query_statements.append(get_repo_insert_statement(repo_ids[i], rg_id, repo_urls[i])) + query_statements.append(get_user_repo_insert_statement(repo_ids[i], group_id)) + + connection.execute("".join(query_statements)) + + with GithubTaskSession(logger, test_db_engine) as session: + + controller = RepoLoadController(session) + + result = controller.get_user_group_repos(group_id) + + assert len(result) == len(repo_ids) + assert set([repo.repo_id for repo in result]) == set(repo_ids) + + with test_db_engine.connect() as connection: + + user_repo_delete_statement = get_user_repo_delete_statement() + query = s.text(user_repo_delete_statement) + + result = connection.execute(query) + + assert len(controller.get_user_group_repos(group_id)) == 0 + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + From 30ea9ce83d4cfbd3cef0feb2d498fb2f47a23837 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 2 Jan 2023 12:46:16 -0600 Subject: [PATCH 020/150] Add more tests to repo load controller Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 2 +- .../test_adding_orgs.py | 2 +- .../test_helper_functions.py | 48 +++++++++++++++++++ 3 files changed, 50 insertions(+), 2 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index b58f9f20b6..b2fe271da9 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -404,7 +404,7 @@ def get_user_repo_ids(self, user_id: int) -> List[int]: list of repo ids """ - user_groups = session.query(UserGroup).filter(UserGroup.user_id).all() + user_groups = self.session.query(UserGroup).filter(UserGroup.user_id == user_id).all() all_repo_ids = set() for group in user_groups: diff --git a/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py b/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py index 985b663016..d1fda916e0 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py +++ b/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py @@ -10,7 +10,7 @@ logger = logging.getLogger(__name__) -VALID_ORG = {"org": "CDCgov", "repo_count": 241} +VALID_ORG = {"org": "CDCgov", "repo_count": 246} def test_add_frontend_org_with_invalid_org(test_db_engine): diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py index 2492cc3cca..c52a9ad839 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -621,6 +621,54 @@ def test_get_user_group_repos(test_db_engine): with test_db_engine.connect() as connection: connection.execute(clear_tables_statement) +def test_get_user_repo_ids(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + user_id =1 + group_id = 1 + rg_id = 1 + group_name = "test_group 1" + repo_ids = [1, 2, 3, 4, 5] + repo_urls = ["url1", "url2", "url3", "url4", "url5"] + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_user_insert_statement(user_id)) + query_statements.append(get_repo_group_insert_statement(rg_id)) + query_statements.append(get_user_group_insert_statement(user_id, group_name, group_id)) + for i in range(0, len(repo_ids)): + query_statements.append(get_repo_insert_statement(repo_ids[i], rg_id, repo_urls[i])) + query_statements.append(get_user_repo_insert_statement(repo_ids[i], group_id)) + + connection.execute("".join(query_statements)) + + with GithubTaskSession(logger, test_db_engine) as session: + + controller = RepoLoadController(session) + + result = controller.get_user_repo_ids(user_id) + + assert len(result) == len(repo_ids) + assert set(result) == set(repo_ids) + + with test_db_engine.connect() as connection: + + user_repo_delete_statement = get_user_repo_delete_statement() + query = s.text(user_repo_delete_statement) + + result = connection.execute(query) + + assert len(controller.get_user_group_repos(group_id)) == 0 + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + From 6ee51c182fab757f352786d88484036cf0ff3d8a Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 2 Jan 2023 12:59:27 -0600 Subject: [PATCH 021/150] Add more tests to repo load controller Signed-off-by: Andrew Brain --- .../test_helper_functions.py | 63 ++++++++++++++++--- 1 file changed, 54 insertions(+), 9 deletions(-) diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py index c52a9ad839..cfd69521d4 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -518,7 +518,9 @@ def test_get_user_groups(test_db_engine): try: with test_db_engine.connect() as connection: - user_id =1 + user_id_1 = 1 + user_id_2 = 2 + groups = [ { @@ -545,10 +547,13 @@ def test_get_user_groups(test_db_engine): query_statements = [] query_statements.append(clear_tables_statement) - query_statements.append(get_user_insert_statement(user_id)) + query_statements.append(get_user_insert_statement(user_id_1)) + + # add user with no user groups + query_statements.append(get_user_insert_statement(user_id_2, username="hello", email="hello@gmail.com")) for group in groups: - query_statements.append(get_user_group_insert_statement(user_id, group["group_name"], group["group_id"])) + query_statements.append(get_user_group_insert_statement(user_id_1, group["group_name"], group["group_id"])) connection.execute("".join(query_statements)) @@ -556,7 +561,9 @@ def test_get_user_groups(test_db_engine): controller = RepoLoadController(session) - assert len(controller.get_user_groups(user_id)) == len(groups) + assert len(controller.get_user_groups(user_id_1)) == len(groups) + + assert len(controller.get_user_groups(user_id_2)) == 0 with test_db_engine.connect() as connection: @@ -565,8 +572,6 @@ def test_get_user_groups(test_db_engine): query = s.text(user_group_delete_statement) result = connection.execute(query) - - assert len(controller.get_user_groups(user_id)) == 0 finally: with test_db_engine.connect() as connection: @@ -582,7 +587,9 @@ def test_get_user_group_repos(test_db_engine): with test_db_engine.connect() as connection: user_id =1 + user_id_2 = 2 group_id = 1 + group_id_2 = 2 rg_id = 1 group_name = "test_group 1" repo_ids = [1, 2, 3, 4, 5] @@ -590,9 +597,17 @@ def test_get_user_group_repos(test_db_engine): query_statements = [] query_statements.append(clear_tables_statement) + + # add user with a group that has multiple repos query_statements.append(get_user_insert_statement(user_id)) - query_statements.append(get_repo_group_insert_statement(rg_id)) query_statements.append(get_user_group_insert_statement(user_id, group_name, group_id)) + + # add user with a group that has no repos + query_statements.append(get_user_insert_statement(user_id_2, username="hello", email="hello@gmail.com")) + query_statements.append(get_user_group_insert_statement(user_id_2, group_name, group_id_2)) + + query_statements.append(get_repo_group_insert_statement(rg_id)) + for i in range(0, len(repo_ids)): query_statements.append(get_repo_insert_statement(repo_ids[i], rg_id, repo_urls[i])) query_statements.append(get_user_repo_insert_statement(repo_ids[i], group_id)) @@ -608,6 +623,11 @@ def test_get_user_group_repos(test_db_engine): assert len(result) == len(repo_ids) assert set([repo.repo_id for repo in result]) == set(repo_ids) + result = controller.get_user_group_repos(group_id_2) + + assert len(result) == 0 + + with test_db_engine.connect() as connection: user_repo_delete_statement = get_user_repo_delete_statement() @@ -621,7 +641,8 @@ def test_get_user_group_repos(test_db_engine): with test_db_engine.connect() as connection: connection.execute(clear_tables_statement) -def test_get_user_repo_ids(test_db_engine): + +def test_get_user_group_repos(test_db_engine): clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users"] clear_tables_statement = get_repo_related_delete_statements(clear_tables) @@ -630,7 +651,9 @@ def test_get_user_repo_ids(test_db_engine): with test_db_engine.connect() as connection: user_id =1 + user_id_2 = 2 group_id = 1 + group_id_2 = 2 rg_id = 1 group_name = "test_group 1" repo_ids = [1, 2, 3, 4, 5] @@ -638,9 +661,16 @@ def test_get_user_repo_ids(test_db_engine): query_statements = [] query_statements.append(clear_tables_statement) + + # add user with a group that has multiple repos query_statements.append(get_user_insert_statement(user_id)) - query_statements.append(get_repo_group_insert_statement(rg_id)) query_statements.append(get_user_group_insert_statement(user_id, group_name, group_id)) + + # add user with a group that has no repos + query_statements.append(get_user_insert_statement(user_id_2, username="hello", email="hello@gmail.com")) + + query_statements.append(get_repo_group_insert_statement(rg_id)) + for i in range(0, len(repo_ids)): query_statements.append(get_repo_insert_statement(repo_ids[i], rg_id, repo_urls[i])) query_statements.append(get_user_repo_insert_statement(repo_ids[i], group_id)) @@ -651,11 +681,26 @@ def test_get_user_repo_ids(test_db_engine): controller = RepoLoadController(session) + # test user with a group that has multiple repos result = controller.get_user_repo_ids(user_id) assert len(result) == len(repo_ids) assert set(result) == set(repo_ids) + + # test user without any groups or repos + result = controller.get_user_repo_ids(user_id_2) + + assert len(result) == 0 + + query_statements.append(get_user_group_insert_statement(user_id_2, group_name, group_id_2)) + + + # test user with a group that doesn't have any repos + result = controller.get_user_repo_ids(user_id_2) + + assert len(result) == 0 + with test_db_engine.connect() as connection: user_repo_delete_statement = get_user_repo_delete_statement() From 17de8ebdf1cc4583bac0c3ac2156e55f8d719f01 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 3 Jan 2023 10:50:14 -0600 Subject: [PATCH 022/150] Fix deleting user errors Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 12 ++++++++---- augur/util/repo_load_controller.py | 4 ---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index b228ccfdf3..3640cc817f 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -122,9 +122,13 @@ def delete_user(): if user is None: return jsonify({"status": "User does not exist"}) - user_repos = session.query(UserRepo).filter(UserRepo.user_id == user.user_id).all() - for repo in user_repos: - session.delete(repo) + for group in user.groups: + user_repos_list = group.repos + + for user_repo_entry in user_repos_list: + session.delete(user_repo_entry) + + session.delete(group) session.delete(user) session.commit() @@ -260,7 +264,7 @@ def remove_user_group(): with GithubTaskSession(logger) as session: - if username is None or group_name is None + if username is None or group_name is None: return jsonify({"status": "Missing argument"}), 400 user = session.query(User).filter(User.login_name == username).first() diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index b2fe271da9..de8c4baa21 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -452,7 +452,3 @@ def parse_org_url(self, url): return owner except IndexError: return None - - - - From 965f41551a4c3714f97269b40c708dce307063c9 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 3 Jan 2023 11:10:05 -0600 Subject: [PATCH 023/150] Small fixes to user endpoints Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 2 +- augur/util/repo_load_controller.py | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 3640cc817f..af1b862a3f 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -317,7 +317,7 @@ def remove_user_repo(): with GithubTaskSession(logger) as session: - if username is None or repo is None or group_name is None: + if username is None or repo_id is None or group_name is None: return jsonify({"status": "Missing argument"}), 400 user = session.query(User).filter( User.login_name == username).first() diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index de8c4baa21..6958cb2fa9 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -218,11 +218,14 @@ def remove_user_group(self, user_id, group_name): if group_id is None: return {"status": "WARNING: Trying to delete group that does not exist"} + group = self.session.query(UserGroup).filter(UserGroup.group_id == group_id).one() + # delete rows from user repos with group_id - self.session.query(UserRepo).filter(UserRepo.group_id == group_id).delete() - + for repo in group.repos: + self.session.delete(repo) + # delete group from user groups table - self.session.query(UserGroup).filter(UserGroup.group_id == group_id).delete() + self.session.delete(group) self.session.commit() From 215449341bb5c1075ea7b16bf836055f846a719e Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Tue, 3 Jan 2023 12:26:43 -0600 Subject: [PATCH 024/150] scaling fix for repo_move Signed-off-by: Isaac Milarsky --- augur/tasks/github/detect_move/tasks.py | 11 +++++++---- augur/tasks/start_tasks.py | 14 +++++++------- 2 files changed, 14 insertions(+), 11 deletions(-) diff --git a/augur/tasks/github/detect_move/tasks.py b/augur/tasks/github/detect_move/tasks.py index 475ebbc523..9277a90f02 100644 --- a/augur/tasks/github/detect_move/tasks.py +++ b/augur/tasks/github/detect_move/tasks.py @@ -6,10 +6,13 @@ @celery.task -def detect_github_repo_move(repo_git: str) -> None: +def detect_github_repo_move(repo_git_identifiers : str) -> None: logger = logging.getLogger(detect_github_repo_move.__name__) with GithubTaskSession(logger) as session: - query = session.query(Repo).filter(Repo.repo_git == repo_git) - repo = execute_session_query(query, 'one') - ping_github_for_repo_move(session, repo) \ No newline at end of file + #Ping each repo with the given repo_git to make sure + #that they are still in place. + for repo_git in repo_git_identifiers: + query = session.query(Repo).filter(Repo.repo_git == repo_git) + repo = execute_session_query(query, 'one') + ping_github_for_repo_move(session, repo) \ No newline at end of file diff --git a/augur/tasks/start_tasks.py b/augur/tasks/start_tasks.py index f5a48e3112..b65290c77c 100644 --- a/augur/tasks/start_tasks.py +++ b/augur/tasks/start_tasks.py @@ -39,19 +39,19 @@ def prelim_phase(): logger = logging.getLogger(prelim_phase.__name__) - tasks_with_repo_domain = [] + tasks_with_repo_domain = None + + with DatabaseSession(logger) as session: query = session.query(Repo) repos = execute_session_query(query, 'all') + repo_git_list = [repo.repo_git for repo in repos] + + tasks_with_repo_domain = create_grouped_task_load(dataList=repo_git_list,task=detect_github_repo_move) - for repo in repos: - tasks_with_repo_domain.append(detect_github_repo_move.si(repo.repo_git)) - #preliminary_task_list = [detect_github_repo_move.si()] - preliminary_tasks = group(*tasks_with_repo_domain) - #preliminary_tasks.apply_async() - return preliminary_tasks + return tasks_with_repo_domain def repo_collect_phase(): logger = logging.getLogger(repo_collect_phase.__name__) From 427b0da7893f460f22df1e94c7d553f2ca9be00b Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Tue, 3 Jan 2023 14:27:50 -0600 Subject: [PATCH 025/150] syntax Signed-off-by: Isaac Milarsky --- augur/tasks/start_tasks.py | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/augur/tasks/start_tasks.py b/augur/tasks/start_tasks.py index b65290c77c..c3d29c4535 100644 --- a/augur/tasks/start_tasks.py +++ b/augur/tasks/start_tasks.py @@ -38,20 +38,13 @@ def prelim_phase(): logger = logging.getLogger(prelim_phase.__name__) - - tasks_with_repo_domain = None - - with DatabaseSession(logger) as session: query = session.query(Repo) repos = execute_session_query(query, 'all') repo_git_list = [repo.repo_git for repo in repos] - tasks_with_repo_domain = create_grouped_task_load(dataList=repo_git_list,task=detect_github_repo_move) - - - return tasks_with_repo_domain + return create_grouped_task_load(dataList=repo_git_list,task=detect_github_repo_move) def repo_collect_phase(): logger = logging.getLogger(repo_collect_phase.__name__) From 3db3aadf758a757c6214663285964aa58d01fc95 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 3 Jan 2023 14:38:29 -0600 Subject: [PATCH 026/150] Add more tests for coverage Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 53 ++++------- .../test_adding_orgs.py | 24 ++++- .../test_adding_repos.py | 93 +++++++++++++++++++ .../test_helper_functions.py | 7 ++ 4 files changed, 135 insertions(+), 42 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index 6958cb2fa9..4628c40a0f 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -41,14 +41,6 @@ def is_valid_repo(self, url: str) -> bool: if not owner or not repo: return False - if repo.endswith(".git"): - # removes .git - repo = repo[:-4] - - if repo.endswith("/"): - # reomves / - repo = repo[:-1] - url = REPO_ENDPOINT.format(owner, repo) attempts = 0 @@ -84,10 +76,6 @@ def retrieve_org_repos(self, url: str) -> List[str]: if not owner: return False - if owner.endswith("/"): - # reomves / - owner = owner[:-1] - url = ORG_REPOS_ENDPOINT.format(owner) repos = [] @@ -113,10 +101,7 @@ def is_valid_repo_group_id(self, repo_group_id): except (s.orm.exc.NoResultFound, s.orm.exc.MultipleResultsFound): return False - if result and result.repo_group_id == repo_group_id: - return True - - return False + return True def add_repo_row(self, url: str, repo_group_id: int, tool_source): """Add a repo to the repo table. @@ -288,6 +273,9 @@ def add_frontend_repo(self, url: List[str], user_id: int, group_name: str, group def remove_frontend_repo(self, repo_id, user_id, group_name): + if not isinstance(repo_id, int) or not isinstance(user_id, int) or not isinstance(group_name, str): + return {"status": "Invalid input params"} + group_id = self.convert_group_name_to_id(user_id, group_name) if group_id is None: return {"status": "Invalid group name"} @@ -315,11 +303,6 @@ def add_frontend_org(self, url: List[str], user_id: int, group_name: int): if not repos: return {"status": "Invalid org", "org_url": url} - - org_name = self.parse_org_url(url) - if not org_name: - return {"status": "Invalid org", "org_url": url} - # try to get the repo group with this org name # if it does not exist create one failed_repos = [] @@ -356,7 +339,7 @@ def add_cli_repo(self, repo_data: Dict[str, Any], valid_repo=False): if not repo_id: logger.warning(f"Invalid repo group id specified for {url}, skipping.") - return + return {"status": f"Invalid repo group id specified for {url}, skipping."} self.add_repo_to_user_group(repo_id) @@ -373,14 +356,15 @@ def add_cli_org(self, org_name): if not repos: print( f"No organization with name {org_name} could be found") - return + return {"status": "No organization found"} # check if the repo group already exists query = self.session.query(RepoGroup).filter(RepoGroup.rg_name == org_name) rg = execute_session_query(query, 'first') if rg: print(f"{rg.rg_name} is already a repo group") - return + + return {"status": "Already a repo group"} print(f'Organization "{org_name}" found') @@ -395,6 +379,8 @@ def add_cli_org(self, org_name): logger.info( f"Adding {repo_url}") self.add_cli_repo({"url": repo_url, "repo_group_id": repo_group_id}, valid_repo=True) + + return {"status": "Org added"} def get_user_repo_ids(self, user_id: int) -> List[int]: @@ -433,13 +419,11 @@ def parse_repo_url(self, url): capturing_groups = result.groups() - try: - owner = capturing_groups[0] - repo = capturing_groups[1] + + owner = capturing_groups[0] + repo = capturing_groups[1] - return owner, repo - except IndexError: - return None, None + return owner, repo def parse_org_url(self, url): @@ -448,10 +432,5 @@ def parse_org_url(self, url): if not result: return None - capturing_groups = result.groups() - - try: - owner = capturing_groups[0] - return owner - except IndexError: - return None + # if the result is not None then the groups should be valid so we don't worry about index errors here + return result.groups()[0] diff --git a/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py b/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py index d1fda916e0..8e9b104b38 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py +++ b/tests/test_applicaton/test_repo_load_controller/test_adding_orgs.py @@ -35,10 +35,16 @@ def test_add_frontend_org_with_invalid_org(test_db_engine): add_keys_to_test_db(test_db_engine) with GithubTaskSession(logger, test_db_engine) as session: + controller = RepoLoadController(session) + url = f"https://github.com/{data['org_name']}/" - result = RepoLoadController(session).add_frontend_org(url, data["user_id"], data["user_group_name"]) + result = controller.add_frontend_org(url, data["user_id"], data["user_group_name"]) assert result["status"] == "Invalid org" + # test with invalid group name + result = controller.add_frontend_org(url, data["user_id"], "Invalid group name") + assert result["status"] == "Invalid group name" + with test_db_engine.connect() as connection: result = get_repos(connection) @@ -115,8 +121,15 @@ def test_add_cli_org_with_valid_org(test_db_engine): with GithubTaskSession(logger, test_db_engine) as session: - result = RepoLoadController(session).add_cli_org(data["org_name"]) - print(result) + controller = RepoLoadController(session) + + result = controller.add_cli_org(data["org_name"]) + + assert result["status"] == "Org added" + + result2 = controller.add_cli_org("Invalid org") + assert result2["status"] == "No organization found" + with test_db_engine.connect() as connection: @@ -130,5 +143,6 @@ def test_add_cli_org_with_valid_org(test_db_engine): finally: with test_db_engine.connect() as connection: - pass - # connection.execute(clear_tables_statement) + connection.execute(clear_tables_statement) + + diff --git a/tests/test_applicaton/test_repo_load_controller/test_adding_repos.py b/tests/test_applicaton/test_repo_load_controller/test_adding_repos.py index ebef2280e4..7f65b1e017 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_adding_repos.py +++ b/tests/test_applicaton/test_repo_load_controller/test_adding_repos.py @@ -50,6 +50,37 @@ def test_add_frontend_repos_with_invalid_repo(test_db_engine): connection.execute(clear_tables_statement) +def test_add_cli_repos_with_invalid_repo_group_id(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + data = {"user_id": CLI_USER_ID, "repo_group_id": 5, "org_name": "operate-first", "repo_name": "operate-first-twitter", "user_group_name": "test_group", "user_group_id": 1} + url = f"https://github.com/{data['org_name']}/{data['repo_name']}" + + query_statements = [] + query_statements.append(clear_tables_statement) + + connection.execute("".join(query_statements)) + + add_keys_to_test_db(test_db_engine) + + with GithubTaskSession(logger, test_db_engine) as session: + + repo_data = {"url": url, "repo_group_id": 5} + + controller = RepoLoadController(session) + result = controller.add_cli_repo(repo_data) + assert result["status"] == f"Invalid repo group id specified for {repo_data['url']}, skipping." + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) + + @@ -125,8 +156,12 @@ def test_add_frontend_repos_with_duplicates(test_db_engine): result = controller.add_frontend_repo(url, data["user_id"], data["user_group_name"]) result2 = controller.add_frontend_repo(url, data["user_id"], data["user_group_name"]) + # add repo with invalid group name + result3 = controller.add_frontend_repo(url, data["user_id"], "Invalid group name") + assert result["status"] == "Repo Added" assert result2["status"] == "Repo Added" + assert result3["status"] == "Invalid group name" with test_db_engine.connect() as connection: @@ -138,3 +173,61 @@ def test_add_frontend_repos_with_duplicates(test_db_engine): finally: with test_db_engine.connect() as connection: connection.execute(clear_tables_statement) + + + + +def test_remove_frontend_repo(test_db_engine): + + clear_tables = ["user_repos", "user_groups", "repo", "repo_groups", "users", "config"] + clear_tables_statement = get_repo_related_delete_statements(clear_tables) + + try: + with test_db_engine.connect() as connection: + + url = "https://github.com/operate-first/operate-first-twitter" + + data = {"user_id": 2, "repo_id": 5, "repo_group_id": DEFAULT_REPO_GROUP_IDS[0], "user_group_name": "test_group", "user_group_id": 1} + + query_statements = [] + query_statements.append(clear_tables_statement) + query_statements.append(get_repo_group_insert_statement(data["repo_group_id"])) + query_statements.append(get_user_insert_statement(data["user_id"])) + query_statements.append(get_user_group_insert_statement(data["user_id"], data["user_group_name"], data["user_group_id"])) + query_statements.append(get_repo_insert_statement(data["repo_id"], data["repo_group_id"], repo_url="url")) + query_statements.append(get_user_repo_insert_statement(data["repo_id"], data["user_group_id"])) + + connection.execute("".join(query_statements)) + + add_keys_to_test_db(test_db_engine) + + with GithubTaskSession(logger, test_db_engine) as session: + + controller = RepoLoadController(session) + + # remove valid user repo + result = controller.remove_frontend_repo(data["repo_id"], data["user_id"], data["user_group_name"]) + assert result["status"] == "Repo Removed" + + with test_db_engine.connect() as connection: + + repos = get_user_repos(connection) + assert len(repos) == 0 + + # remove invalid group + result = controller.remove_frontend_repo(data["repo_id"], data["user_id"], "invalid group") + assert result["status"] == "Invalid group name" + + # pass invalid data types + result = controller.remove_frontend_repo("5", data["user_id"], data["user_group_name"]) + assert result["status"] == "Invalid input params" + + result = controller.remove_frontend_repo(data["repo_id"], "1", data["user_group_name"]) + assert result["status"] == "Invalid input params" + + result = controller.remove_frontend_repo(data["repo_id"], data["user_id"], 5) + assert result["status"] == "Invalid input params" + + finally: + with test_db_engine.connect() as connection: + connection.execute(clear_tables_statement) \ No newline at end of file diff --git a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py index cfd69521d4..9034b42a84 100644 --- a/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py +++ b/tests/test_applicaton/test_repo_load_controller/test_helper_functions.py @@ -59,6 +59,7 @@ def test_is_valid_repo(): assert controller.is_valid_repo("https://github.com/chaoss/augur") is True assert controller.is_valid_repo("https://github.com/chaoss/augur/") is True assert controller.is_valid_repo("https://github.com/chaoss/augur.git") is True + assert controller.is_valid_repo("https://github.com/chaoss/augur/") is True def test_is_valid_repo_group_id(test_db_engine): @@ -436,6 +437,8 @@ def test_remove_user_group(test_db_engine): with test_db_engine.connect() as connection: user_id =1 + repo_id = 1 + rg_id = 1 groups = [ { @@ -467,6 +470,10 @@ def test_remove_user_group(test_db_engine): for group in groups: query_statements.append(get_user_group_insert_statement(user_id, group["group_name"], group["group_id"])) + query_statements.append(get_repo_group_insert_statement(rg_id)) + query_statements.append(get_repo_insert_statement(repo_id, rg_id)) + query_statements.append(get_user_repo_insert_statement(repo_id, groups[0]["group_id"])) + connection.execute("".join(query_statements)) with GithubTaskSession(logger, test_db_engine) as session: From 167ca50809240938769d86e7f47047ee492d9fa2 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 3 Jan 2023 18:52:54 -0600 Subject: [PATCH 027/150] Add more endpoints to get the group and repo data for the frontend Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 164 ++++++++++++++++++++++++++++++++++----- 1 file changed, 143 insertions(+), 21 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index af1b862a3f..a8bf8bde11 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -7,6 +7,8 @@ import requests import json import os +import base64 +import pandas as pd from flask import request, Response, jsonify from werkzeug.security import generate_password_hash, check_password_hash from sqlalchemy.sql import text @@ -182,26 +184,6 @@ def update_user(): return jsonify({"status": "Missing argument"}), 400 - @server.app.route(f"/{AUGUR_API_VERSION}/user/repos", methods=['GET', 'POST']) - def user_repos(): - if not development and not request.is_secure: - return generate_upgrade_request() - - username = request.args.get("username") - - with DatabaseSession(logger) as session: - - if username is None: - return jsonify({"status": "Missing argument"}), 400 - user = session.query(User).filter(User.login_name == username).first() - if user is None: - return jsonify({"status": "User does not exist"}) - - repo_load_controller = RepoLoadController(gh_session=session) - - repo_ids = repo_load_controller.get_user_repo_ids(user.user_id) - - return jsonify({"status": "success", "repo_ids": repo_ids}) @server.app.route(f"/{AUGUR_API_VERSION}/user/add_repo", methods=['GET', 'POST']) def add_user_repo(): @@ -331,4 +313,144 @@ def remove_user_repo(): return jsonify(result) - + + @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repos", methods=['GET', 'POST']) + def group_repos(): + if not development and not request.is_secure: + return generate_upgrade_request() + + username = request.args.get("username") + group_name = request.args.get("group_name") + page = request.args.get("page") + page_size = request.args.get("page_size") + sort = request.args.get("sort") + direction = request.args.get("direction") + + if (not username) or (not group_name) or (not page) or (not page_size) or (sort and not direction) or (not sort and direction): + return jsonify({"status": "Missing argument"}), 400 + + if direction and direction != "ASC" and direction != "DESC": + return {"status": "Invalid direction"} + + try: + page = int(page) + page_size = int(page_size) + except ValueError: + return jsonify({"status": "Page size and page should be integers"}), 400 + + if page < 0 or page_size < 0: + return jsonify({"status": "Page size and page should be postive"}), 400 + + + with DatabaseSession(logger) as session: + + controller = RepoLoadController(session) + + user = session.query(User).filter(User.login_name == username).first() + + group_id = controller.convert_group_name_to_id(user.user_id, group_name) + if group_id is None: + return jsonify({"status": "Group does not exist"}), 400 + + + order_by = sort if sort else "repo_id" + order_direction = direction if direction else "ASC" + + get_page_of_repos_sql = text(f""" + SELECT + augur_data.repo.repo_id, + augur_data.repo.repo_name, + augur_data.repo.description, + augur_data.repo.repo_git AS url, + augur_data.repo.repo_status, + a.commits_all_time, + b.issues_all_time, + rg_name, + augur_data.repo.repo_group_id + FROM + augur_data.repo + LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id + LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id + JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id + JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id + WHERE augur_operations.user_repos.group_id = {group_id} + ORDER BY {order_by} {order_direction} + LIMIT {page_size} + OFFSET {page*page_size}; + """) + + results = pd.read_sql(get_page_of_repos_sql, create_database_engine()) + results['url'] = results['url'].apply(lambda datum: datum.split('//')[1]) + + b64_urls = [] + for i in results.index: + b64_urls.append(base64.b64encode((results.at[i, 'url']).encode())) + results['base64_url'] = b64_urls + + data = results.to_json(orient="records", date_format='iso', date_unit='ms') + return Response(response=data, + status=200, + mimetype="application/json") + + + + @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repo_count", methods=['GET', 'POST']) + def group_repo_count(): + if not development and not request.is_secure: + return generate_upgrade_request() + + username = request.args.get("username") + group_name = request.args.get("group_name") + + if (not username) or (not group_name): + return jsonify({"status": "Missing argument"}), 400 + + with DatabaseSession(logger) as session: + + controller = RepoLoadController(session) + + user = session.query(User).filter(User.login_name == username).first() + + group_id = controller.convert_group_name_to_id(user.user_id, group_name) + if group_id is None: + return jsonify({"status": "Group does not exist"}), 400 + + get_page_of_repos_sql = text(f""" + SELECT + count(*) + FROM + augur_data.repo + LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id + LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id + JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id + JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id + WHERE augur_operations.user_repos.group_id = {group_id} + """) + + result = session.fetchall_data_from_sql_text(get_page_of_repos_sql) + + return jsonify({"repos": result[0]["count"]}), 200 + + + @server.app.route(f"/{AUGUR_API_VERSION}/user/groups", methods=['GET', 'POST']) + def get_user_groups(): + if not development and not request.is_secure: + return generate_upgrade_request() + + username = request.args.get("username") + + if not username: + return jsonify({"status": "Missing argument"}), 400 + + with DatabaseSession(logger) as session: + + controller = RepoLoadController(session) + + user = session.query(User).filter(User.login_name == username).first() + + user_groups = controller.get_user_groups(user.user_id) + + group_names = [group.name for group in user_groups] + + return jsonify({"group_names": group_names}), 200 + From f65a88b4e49bd493f529f67f291d4cee0e5ac43a Mon Sep 17 00:00:00 2001 From: Ulincsys <28362836a@gmail.com> Date: Wed, 4 Jan 2023 05:49:29 -0600 Subject: [PATCH 028/150] Add documentation and update User endpoints: - Make ancillary arguments optional for group_repos - Add documentation clarifying new repo group endpoints --- augur/api/routes/user.py | 65 ++++++++++++++++++++++++++++++++++++---- 1 file changed, 60 insertions(+), 5 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index a8bf8bde11..77987168e5 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -316,21 +316,48 @@ def remove_user_repo(): @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repos", methods=['GET', 'POST']) def group_repos(): + """Select repos from a user group by name + + Arguments + ---------- + username : str + The username of the user making the request + group_name : str + The name of the group to select + page : int = 0 -> [>= 0] + The page offset to use for pagination (optional) + page_size : int = 25 -> [> 0] + The number of result per page (optional) + sort : str + The name of the column to sort the data by (optional) + direction : str = "ASC" -> ["ASC" | "DESC"] + The direction to be used for sorting (optional) + + Returns + ------- + list + A list of dictionaries containing repos which match the given arguments + """ + if not development and not request.is_secure: return generate_upgrade_request() username = request.args.get("username") group_name = request.args.get("group_name") - page = request.args.get("page") - page_size = request.args.get("page_size") + + # Set default values for ancillary arguments + page = request.args.get("page") or 0 + page_size = request.args.get("page_size") or 25 sort = request.args.get("sort") - direction = request.args.get("direction") + direction = request.args.get("direction") or ("ASC" if sort else None) + - if (not username) or (not group_name) or (not page) or (not page_size) or (sort and not direction) or (not sort and direction): + + if (not username) or (not group_name): return jsonify({"status": "Missing argument"}), 400 if direction and direction != "ASC" and direction != "DESC": - return {"status": "Invalid direction"} + return jsonify({"status": "Invalid direction"}), 400 try: page = int(page) @@ -396,6 +423,21 @@ def group_repos(): @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repo_count", methods=['GET', 'POST']) def group_repo_count(): + """Count repos from a user group by name + + Arguments + ---------- + username : str + The username of the user making the request + group_name : str + The name of the group to select + + Returns + ------- + int + A count of the repos in the given user group + """ + if not development and not request.is_secure: return generate_upgrade_request() @@ -434,6 +476,19 @@ def group_repo_count(): @server.app.route(f"/{AUGUR_API_VERSION}/user/groups", methods=['GET', 'POST']) def get_user_groups(): + """Get a list of user groups by username + + Arguments + ---------- + username : str + The username of the user making the request + + Returns + ------- + list + A list of group names associated with the given username + """ + if not development and not request.is_secure: return generate_upgrade_request() From 87da819e1d99779b2024c7a66cd936e9b2b5b092 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Wed, 4 Jan 2023 14:17:19 -0600 Subject: [PATCH 029/150] Change to rabbitmq broker Signed-off-by: Isaac Milarsky --- augur/application/cli/config.py | 6 +++++- augur/application/config.py | 3 +++ augur/tasks/init/__init__.py | 10 ++++++++++ augur/tasks/init/celery_app.py | 2 +- scripts/install/config.sh | 23 +++++++++++++++++++++-- 5 files changed, 40 insertions(+), 4 deletions(-) diff --git a/augur/application/cli/config.py b/augur/application/cli/config.py index dca75ad115..3d93d363d7 100644 --- a/augur/application/cli/config.py +++ b/augur/application/cli/config.py @@ -27,9 +27,10 @@ def cli(): @click.option('--facade-repo-directory', help="Directory on the database server where Facade should clone repos", envvar=ENVVAR_PREFIX + 'FACADE_REPO_DIRECTORY') @click.option('--gitlab-api-key', help="GitLab API key for data collection from the GitLab API", envvar=ENVVAR_PREFIX + 'GITLAB_API_KEY') @click.option('--redis-conn-string', help="String to connect to redis cache", envvar=ENVVAR_PREFIX + 'REDIS_CONN_STRING') +@click.option('--rabbitmq-conn-string', help="String to connect to rabbitmq broker", envvar=ENVVAR_PREFIX + 'RABBITMQ_CONN_STRING') @test_connection @test_db_connection -def init_config(github_api_key, facade_repo_directory, gitlab_api_key, redis_conn_string): +def init_config(github_api_key, facade_repo_directory, gitlab_api_key, redis_conn_string, rabbitmq_conn_string): if not github_api_key: @@ -89,6 +90,9 @@ def init_config(github_api_key, facade_repo_directory, gitlab_api_key, redis_con default_config["Redis"]["connection_string"] = redis_conn_string + if rabbitmq_conn_string: + default_config["RabbitMQ"]["connection_string"] = rabbitmq_conn_string + default_config["Keys"] = keys default_config["Facade"]["repo_directory"] = facade_repo_directory diff --git a/augur/application/config.py b/augur/application/config.py index 58c2fa3eea..ee1cdff367 100644 --- a/augur/application/config.py +++ b/augur/application/config.py @@ -71,6 +71,9 @@ def get_development_flag(): "cache_group": 0, "connection_string": "redis://127.0.0.1:6379/" }, + "RabbitMQ": { + "connection_string": "amqp://augur:password123@localhost:5672/augur_vhost" + }, "Tasks": { "collection_interval": 2592000 }, diff --git a/augur/tasks/init/__init__.py b/augur/tasks/init/__init__.py index 36486d08bb..eb590a99ab 100644 --- a/augur/tasks/init/__init__.py +++ b/augur/tasks/init/__init__.py @@ -18,3 +18,13 @@ def get_redis_conn_values(): redis_conn_string += "/" return redis_db_number, redis_conn_string + +def get_rabbitmq_conn_string(): + logger = logging.getLogger(__name__) + + with DatabaseSession(logger) as session: + config = AugurConfig(logger, session) + + rabbbitmq_conn_string = config.get_value("RabbitMQ", "connection_string") + + return rabbbitmq_conn_string diff --git a/augur/tasks/init/celery_app.py b/augur/tasks/init/celery_app.py index b4dacc9c66..ef34344ab4 100644 --- a/augur/tasks/init/celery_app.py +++ b/augur/tasks/init/celery_app.py @@ -48,7 +48,7 @@ redis_db_number, redis_conn_string = get_redis_conn_values() # initialize the celery app -BROKER_URL = f'{redis_conn_string}{redis_db_number}' +BROKER_URL = get_rabbitmq_conn_string()#f'{redis_conn_string}{redis_db_number}' BACKEND_URL = f'{redis_conn_string}{redis_db_number+1}' celery_app = Celery('tasks', broker=BROKER_URL, backend=BACKEND_URL, include=tasks) diff --git a/scripts/install/config.sh b/scripts/install/config.sh index 962c865707..10a1645cf3 100755 --- a/scripts/install/config.sh +++ b/scripts/install/config.sh @@ -87,6 +87,14 @@ function get_facade_repo_path() { [[ "${facade_repo_directory}" != */ ]] && facade_repo_directory="${facade_repo_directory}/" } +function get_rabbitmq_broker_url(){ + echo + echo "Please provide your rabbitmq broker url." + echo "** This is required for Augur to run all collection tasks. ***" + read -p "broker_url: " rabbitmq_conn_string + echo +} + function create_config(){ @@ -146,13 +154,24 @@ function create_config(){ echo "Please unset AUGUR_FACADE_REPO_DIRECTORY if you would like to be prompted for the facade repo directory" facade_repo_directory=$AUGUR_FACADE_REPO_DIRECTORY fi + + if [[ -z "${RABBITMQ_CONN_STRING}" ]] + then + get_rabbitmq_broker_url + else + echo + echo "Found RABBITMQ_CONN_STRING environment variable with value $RABBITMQ_CONN_STRING" + echo "Using it in the config" + echo "Please unset RABBITMQ_CONN_STRING if you would like to be prompted for the facade repo directory" + rabbitmq_conn_string=$RABBITMQ_CONN_STRING + fi #special case for docker entrypoint if [ $target = "docker" ]; then - cmd=( augur config init --github-api-key $github_api_key --gitlab-api-key $gitlab_api_key --facade-repo-directory $facade_repo_directory --redis-conn-string $redis_conn_string ) + cmd=( augur config init --github-api-key $github_api_key --gitlab-api-key $gitlab_api_key --facade-repo-directory $facade_repo_directory --redis-conn-string $redis_conn_string --rabbitmq-conn-string $rabbitmq_conn_string ) echo "init with redis $redis_conn_string" else - cmd=( augur config init --github-api-key $github_api_key --gitlab-api-key $gitlab_api_key --facade-repo-directory $facade_repo_directory ) + cmd=( augur config init --github-api-key $github_api_key --gitlab-api-key $gitlab_api_key --facade-repo-directory $facade_repo_directory --rabbitmq-conn-string $rabbitmq_conn_string ) fi From ff116a6b66b56b2a01fade528cfa94983e62cb67 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Wed, 4 Jan 2023 14:29:23 -0600 Subject: [PATCH 030/150] syntax Signed-off-by: Isaac Milarsky --- augur/tasks/init/celery_app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/augur/tasks/init/celery_app.py b/augur/tasks/init/celery_app.py index ef34344ab4..ff58da60ce 100644 --- a/augur/tasks/init/celery_app.py +++ b/augur/tasks/init/celery_app.py @@ -12,7 +12,7 @@ from augur.application.logs import TaskLogConfig from augur.application.db.session import DatabaseSession from augur.application.db.engine import get_database_string -from augur.tasks.init import get_redis_conn_values +from augur.tasks.init import get_redis_conn_values, get_rabbitmq_conn_string logger = logging.getLogger(__name__) From 5412ae47fa0f024a4afdc556e6abb5beea34998b Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Wed, 4 Jan 2023 15:24:10 -0600 Subject: [PATCH 031/150] Add docs and a few fixes Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 139 ++++++++++++++++++++++------- 1 file changed, 108 insertions(+), 31 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index 4628c40a0f..25042d465b 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -29,7 +29,7 @@ def __init__(self, gh_session): def is_valid_repo(self, url: str) -> bool: """Determine whether repo url is valid. - + Args: url: repo_url @@ -55,7 +55,7 @@ def is_valid_repo(self, url: str) -> bool: # if there was an error return False if "message" in result.json().keys(): return False - + return True @@ -64,7 +64,7 @@ def retrieve_org_repos(self, url: str) -> List[str]: Note: If the org url is not valid it will return [] - + Args: url: org url @@ -74,13 +74,14 @@ def retrieve_org_repos(self, url: str) -> List[str]: owner = self.parse_org_url(url) if not owner: + # TODO: Change to return empty list so it matches the docs return False url = ORG_REPOS_ENDPOINT.format(owner) - + repos = [] with GithubTaskSession(logger) as session: - + for page_data, page in GithubPaginator(url, session.oauths, logger).iter_pages(): if page_data is None: @@ -93,7 +94,16 @@ def retrieve_org_repos(self, url: str) -> List[str]: return repo_urls - def is_valid_repo_group_id(self, repo_group_id): + def is_valid_repo_group_id(self, repo_group_id: int) -> bool: + """Deterime is repo_group_id exists. + + Args: + repo_group_id: id from the repo groups table + + Returns: + True if it exists, False if it does not + """ + query = self.session.query(RepoGroup).filter(RepoGroup.repo_group_id == repo_group_id) try: @@ -137,18 +147,18 @@ def add_repo_row(self, url: str, repo_group_id: int, tool_source): return None if repo_group_id not in DEFAULT_REPO_GROUP_IDS: - # update the repo group id + # update the repo group id query = self.session.query(Repo).filter(Repo.repo_git == url) repo = execute_session_query(query, 'one') if not repo.repo_group_id == repo_group_id: repo.repo_group_id = repo_group_id - self.session.commit() - + self.session.commit() + return result[0]["repo_id"] - def add_repo_to_user_group(self, repo_id, group_id=1): + def add_repo_to_user_group(self, repo_id: int, group_id:int = 1) -> bool: """Add a repo to a user in the user_repos table. Args: @@ -163,8 +173,8 @@ def add_repo_to_user_group(self, repo_id, group_id=1): "group_id": group_id, "repo_id": repo_id } - - + + repo_user_group_unique = ["group_id", "repo_id"] return_columns = ["group_id", "repo_id"] @@ -175,7 +185,20 @@ def add_repo_to_user_group(self, repo_id, group_id=1): return data[0]["group_id"] == group_id and data[0]["repo_id"] == repo_id - def add_user_group(self, user_id, group_name): + def add_user_group(self, user_id:int, group_name:str) -> dict: + """Add a group to the user. + + Args + user_id: id of the user + group_name: name of the group being added + + Returns: + Dict with status key that indicates the success of the operation + + Note: + If group already exists the function will return that it has been added, but a duplicate group isn't added. + It simply detects that it already exists and doesn't add it. + """ if not isinstance(user_id, int) or not isinstance(group_name, str): return {"status": "Invalid input"} @@ -189,14 +212,24 @@ def add_user_group(self, user_id, group_name): result = self.session.insert_data(user_group_data, UserGroup, ["name", "user_id"], return_columns=["group_id"]) except s.exc.IntegrityError: return {"status": "Error: User id does not exist"} - + if result: return {"status": "Group created"} else: return {"status": "Error while creating group"} - def remove_user_group(self, user_id, group_name): + def remove_user_group(self, user_id: int, group_name: str) -> dict: + """ Delete a users group of repos. + + Args: + user_id: id of the user + group_name: name of the users group + + Returns: + Dict with a status key that indicates the result of the operation + + """ # convert group_name to group_id group_id = self.convert_group_name_to_id(user_id, group_name) @@ -217,7 +250,17 @@ def remove_user_group(self, user_id, group_name): return {"status": "Group deleted"} - def convert_group_name_to_id(self, user_id, group_name): + def convert_group_name_to_id(self, user_id: int, group_name: str) -> int: + """Convert a users group name to the database group id. + + Args: + user_id: id of the user + group_name: name of the users group + + Returns: + None on failure. The group id on success. + + """ if not isinstance(user_id, int) or not isinstance(group_name, str): return None @@ -228,29 +271,37 @@ def convert_group_name_to_id(self, user_id, group_name): return None return user_group.group_id - - def get_user_groups(self, user_id): - return self.session.query(UserGroup).filter(UserGroup.user_id == user_id).all() + def get_user_groups(self, user_id: int) -> List: + + return self.session.query(UserGroup).filter(UserGroup.user_id == user_id).all() - def get_user_group_repos(self, group_id): + def get_user_group_repos(self, group_id: int) -> List: user_repos = self.session.query(UserRepo).filter(UserRepo.group_id == group_id).all() return [user_repo.repo for user_repo in user_repos] - def add_frontend_repo(self, url: List[str], user_id: int, group_name: str, group_id=None, valid_repo=False): + def add_frontend_repo(self, url: List[str], user_id: int, group_name=None, group_id=None, valid_repo=False) -> dict: """Add list of repos to a users repos. Args: urls: list of repo urls user_id: id of user_id from users table - repo_group_id: repo_group_id to add the repo to + group_name: name of group to add repo to. + group_id: id of the group + valid_repo: boolean that indicates whether the repo has already been validated Note: - If no repo_group_id is passed the repo will be added to a default repo_group + Either the group_name or group_id can be passed not both + + Returns: + Dict that contains the key "status" and additional useful data """ + if group_name and group_id: + return {"status": "Pass only the group name or group id not both"} + if group_id is None: group_id = self.convert_group_name_to_id(user_id, group_name) @@ -271,7 +322,17 @@ def add_frontend_repo(self, url: List[str], user_id: int, group_name: str, group return {"status": "Repo Added", "repo_url": url} - def remove_frontend_repo(self, repo_id, user_id, group_name): + def remove_frontend_repo(self, repo_id:int, user_id:int, group_name:str) -> dict: + """ Remove repo from a users group. + + Args: + repo_id: id of the repo to remove + user_id: id of the user + group_name: name of group the repo is being removed from + + Returns: + Dict with a key of status that indicates the result of the operation + """ if not isinstance(repo_id, int) or not isinstance(user_id, int) or not isinstance(group_name, str): return {"status": "Invalid input params"} @@ -299,7 +360,7 @@ def add_frontend_org(self, url: List[str], user_id: int, group_name: int): return {"status": "Invalid group name"} repos = self.retrieve_org_repos(url) - + if not repos: return {"status": "Invalid org", "org_url": url} @@ -308,7 +369,7 @@ def add_frontend_org(self, url: List[str], user_id: int, group_name: int): failed_repos = [] for repo in repos: - result = self.add_frontend_repo(repo, user_id, group_name, group_id, valid_repo=True) + result = self.add_frontend_repo(repo, user_id, group_id=group_id, valid_repo=True) # keep track of all the repos that failed if result["status"] != "Repo Added": @@ -352,7 +413,7 @@ def add_cli_org(self, org_name): url = f"https://github.com/{org_name}" repos = self.retrieve_org_repos(url) - + if not repos: print( f"No organization with name {org_name} could be found") @@ -379,7 +440,7 @@ def add_cli_org(self, org_name): logger.info( f"Adding {repo_url}") self.add_cli_repo({"url": repo_url, "repo_group_id": repo_group_id}, valid_repo=True) - + return {"status": "Org added"} @@ -405,10 +466,18 @@ def get_user_repo_ids(self, user_id: int) -> List[int]: return list(all_repo_ids) - def parse_repo_url(self, url): + def parse_repo_url(self, url: str) -> tuple: + """ Gets the owner and repo from a url. + + Args: + url: Github url + + Returns: + Tuple of owner and repo. Or a tuple of None and None if the url is invalid. + """ if url.endswith(".github") or url.endswith(".github.io") or url.endswith(".js"): - + result = re.search(r"https?:\/\/github\.com\/([A-Za-z0-9 \- _]+)\/([A-Za-z0-9 \- _ \.]+)(.git)?\/?$", url) else: @@ -419,13 +488,21 @@ def parse_repo_url(self, url): capturing_groups = result.groups() - + owner = capturing_groups[0] repo = capturing_groups[1] return owner, repo def parse_org_url(self, url): + """ Gets the owner from a org url. + + Args: + url: Github org url + + Returns: + Org name. Or None if the url is invalid. + """ result = re.search(r"https?:\/\/github\.com\/([A-Za-z0-9 \- _]+)\/?$", url) From c5db0cf02d8585d9ec5a033a2928ab898fdc5128 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Wed, 4 Jan 2023 15:30:39 -0600 Subject: [PATCH 032/150] don't ignore result Signed-off-by: Isaac Milarsky --- augur/tasks/init/celery_app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/augur/tasks/init/celery_app.py b/augur/tasks/init/celery_app.py index ff58da60ce..457c913184 100644 --- a/augur/tasks/init/celery_app.py +++ b/augur/tasks/init/celery_app.py @@ -62,7 +62,7 @@ celery_app.conf.task_track_started = True #ignore task results by default -celery_app.conf.task_ignore_result = True +##celery_app.conf.task_ignore_result = True # store task erros even if the task result is ignored celery_app.conf.task_store_errors_even_if_ignored = True From af250fa2302a1f804822e1d4fd8aa31712a88b27 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Wed, 4 Jan 2023 15:45:44 -0600 Subject: [PATCH 033/150] More logging in detect_github_repo_move Signed-off-by: Isaac Milarsky --- augur/tasks/github/detect_move/tasks.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/augur/tasks/github/detect_move/tasks.py b/augur/tasks/github/detect_move/tasks.py index 9277a90f02..2acc440747 100644 --- a/augur/tasks/github/detect_move/tasks.py +++ b/augur/tasks/github/detect_move/tasks.py @@ -9,10 +9,12 @@ def detect_github_repo_move(repo_git_identifiers : str) -> None: logger = logging.getLogger(detect_github_repo_move.__name__) + logger.info(f"Starting repo_move operation with {repo_git_identifiers}") with GithubTaskSession(logger) as session: #Ping each repo with the given repo_git to make sure #that they are still in place. for repo_git in repo_git_identifiers: query = session.query(Repo).filter(Repo.repo_git == repo_git) repo = execute_session_query(query, 'one') + logger.info(f"Pinging repo: {repo_git}") ping_github_for_repo_move(session, repo) \ No newline at end of file From 7efce307b0afbd2e73efb53658db4e1f8f73282e Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Wed, 4 Jan 2023 16:03:03 -0600 Subject: [PATCH 034/150] debug Signed-off-by: Isaac Milarsky --- augur/tasks/util/worker_util.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/augur/tasks/util/worker_util.py b/augur/tasks/util/worker_util.py index 960ff9cc47..d6b3af6920 100644 --- a/augur/tasks/util/worker_util.py +++ b/augur/tasks/util/worker_util.py @@ -16,8 +16,10 @@ def create_grouped_task_load(*args,processes=8,dataList=[],task=None): if not dataList or not task: raise AssertionError + print(f"Splitting {len(dataList)} items") numpyData = np.array(list(dataList)) listsSplitForProcesses = np.array_split(numpyData, processes) + print("Done splitting items.") #print("args") #print(args) From a92df41f040e804a12ed47a00a5036b4ac7b6de6 Mon Sep 17 00:00:00 2001 From: Ulincsys <28362836a@gmail.com> Date: Thu, 5 Jan 2023 03:03:34 -0600 Subject: [PATCH 035/150] More oauth work --- augur/api/routes/user.py | 95 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 94 insertions(+), 1 deletion(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 77987168e5..973a09cbdf 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -27,6 +27,57 @@ AUGUR_API_VERSION = 'api/unstable' +""" + Extract Bearer token from request header, + using the standard oauth2 format +""" +def get_bearer_token(request): + token = request.headers.get("Authorization") + + if token and " " in token: + token = token.split(" ") + if len(token) == 2: + return token[1] + + for substr in token: + if substr and "Bearer" not in substr: + return substr + + return token + +def user_login_required(fun): + def wrapper(*args, **kwargs): + # TODO check that user session token is valid + + # We still need to decide on the format for this + + # If valid: + return fun(*args, **kwargs) + + # else: return error JSON + + return wrapper + +def api_key_required(fun): + def wrapper(*args, **kwargs): + # TODO check that API key is valid + + # If valid: + return fun(*args, **kwargs) + + # else: return error JSON + + return wrapper + +# usage: +""" +@app.route("/path") +@api_key_required +@user_login_required +def priviledged_function(): + stuff +""" + # TODO This should probably be available to all endpoints def generate_upgrade_request(): # https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/426 @@ -60,7 +111,49 @@ def validate_user(): return jsonify({"status": "Invalid username"}) if checkPassword == False: return jsonify({"status": "Invalid password"}) - return jsonify({"status": "Validated"}) + + # TODO Generate user session token to be stored in client browser + + token = "USER SESSION TOKEN" + + return jsonify({"status": "Validated", "session": token}) + + @server.app.route(f"/{AUGUR_API_VERSION}/user/oauth", methods=['POST']) + def oauth_validate(): + # Check if user has an active session + current_session = request.args.get("session") + + if current_session: + # TODO validate session token + # If invalid, set current_session to None to force validation + pass + + if not current_session: + return jsonify({"status": "Invalid session"}) + + # TODO generate oauth token and store in temporary table + # Ideally should be valid for ~1 minute + # oauth entry: (token: str, generated: date) + + token = "TEMPORARY VALUE" + + return jsonify({"status": "Validated", "oauth_token": token}) + + @server.app.route(f"/{AUGUR_API_VERSION}/user/generate_session", methods=['POST']) + def generate_session(): + # TODO Validate oauth token + oauth = request.args.get("oauth_token") + + # If invalid, return error JSON: + # return jsonify({"status": "Invalid oauth token"}) + + # If valid, pop oauth token from temporary table + # Generate user session token to be stored in client browser + + token = "USER SESSION TOKEN" + user = "USERNAME" + + return jsonify({"status": "Validated", "username": user, "session": token}) @server.app.route(f"/{AUGUR_API_VERSION}/user/query", methods=['POST']) def query_user(): From d55e8b261ad2af163564da4c4d3d46c711bb9443 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Thu, 5 Jan 2023 12:20:21 -0600 Subject: [PATCH 036/150] print Signed-off-by: Isaac Milarsky --- augur/tasks/util/worker_util.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/augur/tasks/util/worker_util.py b/augur/tasks/util/worker_util.py index d6b3af6920..8efac1db7b 100644 --- a/augur/tasks/util/worker_util.py +++ b/augur/tasks/util/worker_util.py @@ -17,8 +17,8 @@ def create_grouped_task_load(*args,processes=8,dataList=[],task=None): raise AssertionError print(f"Splitting {len(dataList)} items") - numpyData = np.array(list(dataList)) - listsSplitForProcesses = np.array_split(numpyData, processes) + #numpyData = np.array(list(dataList)) + listsSplitForProcesses = np.array_split(list(dataList), processes) print("Done splitting items.") #print("args") From 4cbc2108eba9b31814aeaeb6e50ebe8cae36ef83 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 5 Jan 2023 12:21:54 -0600 Subject: [PATCH 037/150] Add auth to endpoints Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 159 +++++++-------- augur/application/db/models/__init__.py | 4 +- .../application/db/models/augur_operations.py | 30 +++ .../versions/2_added_user_groups_and_login.py | 188 ++++++++++++++++++ augur/util/repo_load_controller.py | 2 +- 5 files changed, 296 insertions(+), 87 deletions(-) create mode 100644 augur/application/schema/alembic/versions/2_added_user_groups_and_login.py diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 973a09cbdf..e14cd8780d 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -13,12 +13,13 @@ from werkzeug.security import generate_password_hash, check_password_hash from sqlalchemy.sql import text from sqlalchemy.orm import sessionmaker +from sqlalchemy.orm.exc import NoResultFound from augur.application.db.session import DatabaseSession from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController -from augur.application.db.models import User, UserRepo, UserGroup +from augur.application.db.models import User, UserRepo, UserGroup, UserSessionToken, ClientToken from augur.application.config import get_development_flag logger = logging.getLogger(__name__) development = get_development_flag() @@ -51,22 +52,46 @@ def wrapper(*args, **kwargs): # We still need to decide on the format for this + user_token = request.args.get("user_token") + print(user_token) + # If valid: - return fun(*args, **kwargs) + if user_token: + + session = Session() + try: + user = session.query(UserSessionToken).filter(UserSessionToken.token == user_token).one().user + + return fun(user=user, *args, **kwargs) + except NoResultFound: + print("Not found") # else: return error JSON - + return {"status": "Invalid user session"} + + wrapper.__name__ = fun.__name__ return wrapper def api_key_required(fun): def wrapper(*args, **kwargs): # TODO check that API key is valid + client_token = request.args.get("client_api_key") + # If valid: - return fun(*args, **kwargs) + if client_token: + + session = Session() + try: + session.query(ClientToken).filter(ClientToken.token == client_token).one() + return fun(*args, **kwargs) + except NoResultFound: + pass # else: return error JSON + return {"status": "Unauthorized client"} + wrapper.__name__ = fun.__name__ return wrapper # usage: @@ -156,7 +181,9 @@ def generate_session(): return jsonify({"status": "Validated", "username": user, "session": token}) @server.app.route(f"/{AUGUR_API_VERSION}/user/query", methods=['POST']) - def query_user(): + @api_key_required + @user_login_required + def query_user(user): if not development and not request.is_secure: return generate_upgrade_request() @@ -203,19 +230,13 @@ def create_user(): return jsonify(msg='Error: {}. '.format(exception_message)), 400 @server.app.route(f"/{AUGUR_API_VERSION}/user/remove", methods=['POST', 'DELETE']) - def delete_user(): + @api_key_required + @user_login_required + def delete_user(user): if not development and not request.is_secure: return generate_upgrade_request() session = Session() - username = request.args.get("username") - if username is None: - return jsonify({"status": "Missing argument"}), 400 - - user = session.query(User).filter(User.login_name == username).first() - - if user is None: - return jsonify({"status": "User does not exist"}) for group in user.groups: user_repos_list = group.repos @@ -230,28 +251,17 @@ def delete_user(): return jsonify({"status": "User deleted"}), 200 @server.app.route(f"/{AUGUR_API_VERSION}/user/update", methods=['POST']) - def update_user(): + @api_key_required + @user_login_required + def update_user(user): if not development and not request.is_secure: return generate_upgrade_request() session = Session() - username = request.args.get("username") - password = request.args.get("password") email = request.args.get("email") new_login_name = request.args.get("new_username") new_password = request.args.get("new_password") - if username is None or password is None: - return jsonify({"status": "Missing argument"}), 400 - - user = session.query(User).filter(User.login_name == username).first() - if user is None: - return jsonify({"status": "User does not exist"}) - - checkPassword = check_password_hash(user.login_hashword, password) - if checkPassword == False: - return jsonify({"status": "Invalid password"}) - if email is not None: existing_user = session.query(User).filter(User.email == email).one() if existing_user is not None: @@ -279,22 +289,19 @@ def update_user(): @server.app.route(f"/{AUGUR_API_VERSION}/user/add_repo", methods=['GET', 'POST']) - def add_user_repo(): + @api_key_required + @user_login_required + def add_user_repo(user): if not development and not request.is_secure: return generate_upgrade_request() - username = request.args.get("username") repo = request.args.get("repo_url") group_name = request.args.get("group_name") with GithubTaskSession(logger) as session: - if username is None or repo is None or group_name is None: + if repo is None or group_name is None: return jsonify({"status": "Missing argument"}), 400 - user = session.query(User).filter( - User.login_name == username).first() - if user is None: - return jsonify({"status": "User does not exist"}) repo_load_controller = RepoLoadController(gh_session=session) @@ -304,11 +311,12 @@ def add_user_repo(): @server.app.route(f"/{AUGUR_API_VERSION}/user/add_group", methods=['GET', 'POST']) - def add_user_group(): + @api_key_required + @user_login_required + def add_user_group(user): if not development and not request.is_secure: return generate_upgrade_request() - username = request.args.get("username") group_name = request.args.get("group_name") if group_name == "default": @@ -316,13 +324,9 @@ def add_user_group(): with GithubTaskSession(logger) as session: - if username is None or group_name is None: + if group_name is None: return jsonify({"status": "Missing argument"}), 400 - user = session.query(User).filter(User.login_name == username).first() - if user is None: - return jsonify({"status": "User does not exist"}) - repo_load_controller = RepoLoadController(gh_session=session) result = repo_load_controller.add_user_group(user.user_id, group_name) @@ -330,22 +334,19 @@ def add_user_group(): return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_group", methods=['GET', 'POST']) - def remove_user_group(): + @api_key_required + @user_login_required + def remove_user_group(user): if not development and not request.is_secure: return generate_upgrade_request() - username = request.args.get("username") group_name = request.args.get("group_name") with GithubTaskSession(logger) as session: - if username is None or group_name is None: + if group_name is None: return jsonify({"status": "Missing argument"}), 400 - user = session.query(User).filter(User.login_name == username).first() - if user is None: - return jsonify({"status": "User does not exist"}) - repo_load_controller = RepoLoadController(gh_session=session) result = repo_load_controller.remove_user_group(user.user_id, group_name) @@ -356,24 +357,20 @@ def remove_user_group(): @server.app.route(f"/{AUGUR_API_VERSION}/user/add_org", methods=['GET', 'POST']) - def add_user_org(): + @api_key_required + @user_login_required + def add_user_org(user): if not development and not request.is_secure: return generate_upgrade_request() - username = request.args.get("username") org = request.args.get("org_url") group_name = request.args.get("group_name") with GithubTaskSession(logger) as session: - if username is None or org is None or group_name is None: + if org is None or group_name is None: return jsonify({"status": "Missing argument"}), 400 - user = session.query(User).filter( - User.login_name == username).first() - if user is None: - return jsonify({"status": "User does not exist"}) - repo_load_controller = RepoLoadController(gh_session=session) result = repo_load_controller.add_frontend_org(org, user.user_id, group_name) @@ -382,22 +379,23 @@ def add_user_org(): @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_repo", methods=['GET', 'POST']) - def remove_user_repo(): + @api_key_required + @user_login_required + def remove_user_repo(user): if not development and not request.is_secure: return generate_upgrade_request() + try: + repo_id = int(request.args.get("repo_id")) + except ValueError: + return {"status": "repo_id must be an integer"} - username = request.args.get("username") - repo_id = request.args.get("repo_id") group_name = request.args.get("group_name") + with GithubTaskSession(logger) as session: - if username is None or repo_id is None or group_name is None: + if repo_id is None or group_name is None: return jsonify({"status": "Missing argument"}), 400 - user = session.query(User).filter( - User.login_name == username).first() - if user is None: - return jsonify({"status": "User does not exist"}) repo_load_controller = RepoLoadController(gh_session=session) @@ -408,7 +406,9 @@ def remove_user_repo(): @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repos", methods=['GET', 'POST']) - def group_repos(): + @api_key_required + @user_login_required + def group_repos(user): """Select repos from a user group by name Arguments @@ -435,7 +435,6 @@ def group_repos(): if not development and not request.is_secure: return generate_upgrade_request() - username = request.args.get("username") group_name = request.args.get("group_name") # Set default values for ancillary arguments @@ -444,9 +443,7 @@ def group_repos(): sort = request.args.get("sort") direction = request.args.get("direction") or ("ASC" if sort else None) - - - if (not username) or (not group_name): + if not group_name: return jsonify({"status": "Missing argument"}), 400 if direction and direction != "ASC" and direction != "DESC": @@ -465,8 +462,6 @@ def group_repos(): with DatabaseSession(logger) as session: controller = RepoLoadController(session) - - user = session.query(User).filter(User.login_name == username).first() group_id = controller.convert_group_name_to_id(user.user_id, group_name) if group_id is None: @@ -515,7 +510,9 @@ def group_repos(): @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repo_count", methods=['GET', 'POST']) - def group_repo_count(): + @api_key_required + @user_login_required + def group_repo_count(user): """Count repos from a user group by name Arguments @@ -534,17 +531,14 @@ def group_repo_count(): if not development and not request.is_secure: return generate_upgrade_request() - username = request.args.get("username") group_name = request.args.get("group_name") - if (not username) or (not group_name): + if not group_name: return jsonify({"status": "Missing argument"}), 400 with DatabaseSession(logger) as session: controller = RepoLoadController(session) - - user = session.query(User).filter(User.login_name == username).first() group_id = controller.convert_group_name_to_id(user.user_id, group_name) if group_id is None: @@ -568,7 +562,9 @@ def group_repo_count(): @server.app.route(f"/{AUGUR_API_VERSION}/user/groups", methods=['GET', 'POST']) - def get_user_groups(): + @api_key_required + @user_login_required + def get_user_groups(user): """Get a list of user groups by username Arguments @@ -585,16 +581,9 @@ def get_user_groups(): if not development and not request.is_secure: return generate_upgrade_request() - username = request.args.get("username") - - if not username: - return jsonify({"status": "Missing argument"}), 400 - with DatabaseSession(logger) as session: controller = RepoLoadController(session) - - user = session.query(User).filter(User.login_name == username).first() user_groups = controller.get_user_groups(user.user_id) diff --git a/augur/application/db/models/__init__.py b/augur/application/db/models/__init__.py index f51e768ed9..5606168f64 100644 --- a/augur/application/db/models/__init__.py +++ b/augur/application/db/models/__init__.py @@ -100,5 +100,7 @@ Config, User, UserRepo, - UserGroup + UserGroup, + UserSessionToken, + ClientToken ) diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index 782bdb11bc..4ddb30b5fb 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -193,6 +193,7 @@ class User(Base): ) groups = relationship("UserGroup") + tokens = relationship("UserSessionToken") class UserGroup(Base): @@ -230,3 +231,32 @@ class UserRepo(Base): repo = relationship("Repo") group = relationship("UserGroup") +class UserSessionToken(Base): + __tablename__ = "user_session_tokens" + __table_args__ = ( + { + "schema": "augur_operations" + } + ) + + token = Column(String, primary_key=True, nullable=False) + user_id = Column(ForeignKey("augur_operations.users.user_id", name="user_session_token_user_id_fkey")) + expiration = Column(BigInteger) + + user = relationship("User") + + +class ClientToken(Base): + __tablename__ = "client_tokens" + __table_args__ = ( + { + "schema": "augur_operations" + } + ) + + token = Column(String, primary_key=True, nullable=False) + name = Column(String, nullable=False) + expiration = Column(BigInteger) + + + diff --git a/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py b/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py new file mode 100644 index 0000000000..94abb429cc --- /dev/null +++ b/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py @@ -0,0 +1,188 @@ +"""Added user groups and login keys + +Revision ID: 2 +Revises: 1 +Create Date: 2022-12-19 11:00:37.509132 + +""" +import logging + +from alembic import op +import sqlalchemy as sa +from augur.application.db.session import DatabaseSession +from augur.application.db.models.augur_operations import UserGroup, UserRepo + +CLI_USER_ID = 1 + + +# revision identifiers, used by Alembic. +revision = '2' +down_revision = '1' +branch_labels = None +depends_on = None + +logger = logging.getLogger(__name__) + +def upgrade(): + + with DatabaseSession(logger) as session: + + create_user_groups_table = """ + CREATE TABLE "augur_operations"."user_groups" ( + "group_id" BIGSERIAL NOT NULL, + "user_id" int4 NOT NULL, + "name" varchar COLLATE "pg_catalog"."default" NOT NULL, + PRIMARY KEY ("group_id"), + FOREIGN KEY ("user_id") REFERENCES "augur_operations"."users" ("user_id") ON DELETE NO ACTION ON UPDATE NO ACTION, + UNIQUE ("user_id", "name") + ); + + + ALTER TABLE "augur_operations"."user_groups" + OWNER TO "augur"; + + INSERT INTO "augur_operations"."user_groups" ("group_id", "user_id", "name") VALUES (1, {}, 'default') ON CONFLICT ("user_id", "name") DO NOTHING; + ALTER SEQUENCE user_groups_group_id_seq RESTART WITH 2; + """.format(CLI_USER_ID) + + session.execute_sql(sa.sql.text(create_user_groups_table)) + + + user_repos = [] + + # create user group for all the users that have repos + user_id_query = sa.sql.text("""SELECT DISTINCT(user_id) FROM user_repos;""") + user_groups = session.fetchall_data_from_sql_text(user_id_query) + if user_groups: + + result = [] + for group in user_groups: + + user_id = group["user_id"] + + if user_id == CLI_USER_ID: + continue + + user_group_insert = sa.sql.text(f"""INSERT INTO "augur_operations"."user_groups" ("user_id", "name") VALUES ({user_id}, 'default') RETURNING group_id, user_id;""") + result.append(session.fetchall_data_from_sql_text(user_group_insert)[0]) + + # cli user mapping by default + user_group_id_mapping = {CLI_USER_ID: "1"} + for row in result: + user_group_id_mapping[row["user_id"]] = row["group_id"] + + + user_repo_query = sa.sql.text("""SELECT * FROM user_repos;""") + user_repo_data = session.fetchall_data_from_sql_text(user_repo_query) + for row in user_repo_data: + row.update({"group_id": user_group_id_mapping[row["user_id"]]}) + del row["user_id"] + user_repos.extend(user_repo_data) + + # remove data from table before modifiying it + remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") + session.execute_sql(remove_data_from_user_repos_query) + + + table_changes = """ + ALTER TABLE user_repos + ADD COLUMN group_id BIGINT, + ADD CONSTRAINT user_repos_group_id_fkey FOREIGN KEY (group_id) REFERENCES user_groups(group_id), + DROP COLUMN user_id, + ADD PRIMARY KEY (group_id, repo_id); + """ + + session.execute_sql(sa.sql.text(table_changes)) + + for data in user_repos: + + group_id = data["group_id"] + repo_id = data["repo_id"] + + user_repo_insert = sa.sql.text(f"""INSERT INTO "augur_operations"."user_repos" ("group_id", "repo_id") VALUES ({group_id}, {repo_id});""") + result = session.execute_sql(user_repo_insert) + + op.create_table('client_tokens', + sa.Column('name', sa.String(), nullable=False), + sa.Column('token', sa.String(), nullable=False), + sa.Column('expiration', sa.BigInteger(), nullable=True), + sa.PrimaryKeyConstraint('token'), + schema='augur_operations' + ) + op.create_table('user_session_tokens', + sa.Column('token', sa.String(), nullable=False), + sa.Column('user_id', sa.Integer(), nullable=False), + sa.Column('expiration', sa.BigInteger(), nullable=True), + sa.ForeignKeyConstraint(['user_id'], ['augur_operations.users.user_id'], name='user_session_token_user_fk'), + sa.PrimaryKeyConstraint('token'), + schema='augur_operations' + ) + + # ### end Alembic commands ### + + +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### + + + user_group_ids = {} + group_repo_ids = {} + with DatabaseSession(logger) as session: + user_id_query = sa.sql.text("""SELECT * FROM user_groups;""") + user_groups = session.fetchall_data_from_sql_text(user_id_query) + for row in user_groups: + try: + user_group_ids[row["user_id"]].append(row["group_id"]) + except KeyError: + user_group_ids[row["user_id"]] = [row["group_id"]] + + + group_id_query = sa.sql.text("""SELECT * FROM user_repos;""") + group_repo_id_result = session.fetchall_data_from_sql_text(group_id_query) + for row in group_repo_id_result: + try: + group_repo_ids[row["group_id"]].append(row["repo_id"]) + except KeyError: + group_repo_ids[row["group_id"]] = [row["repo_id"]] + + remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") + session.execute_sql(remove_data_from_user_repos_query) + + + table_changes = """ + ALTER TABLE user_repos + ADD COLUMN user_id INT, + ADD CONSTRAINT user_repos_user_id_fkey FOREIGN KEY (user_id) REFERENCES users(user_id), + DROP COLUMN group_id, + ADD PRIMARY KEY (user_id, repo_id); + DROP TABLE user_groups; + """ + + session.execute_sql(sa.sql.text(table_changes)) + + for user_id, group_ids in user_group_ids.items(): + + repos = [] + for group_id in group_ids: + try: + repos.extend(group_repo_ids[group_id]) + except KeyError: + continue + + query_text_array = ["""INSERT INTO "augur_operations"."user_repos" ("repo_id", "user_id") VALUES """] + for i, repo_id in enumerate(repos): + query_text_array.append(f"({repo_id}, {user_id})") + + delimiter = ";" if i == len(repos) -1 else "," + + query_text_array.append(delimiter) + + + query_text = "".join(query_text_array) + + session.execute_sql(sa.sql.text(query_text)) + + op.drop_table('user_session_tokens', schema='augur_operations') + op.drop_table('client_tokens', schema='augur_operations') + + # ### end Alembic commands ### diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index 25042d465b..e96ec0676e 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -335,7 +335,7 @@ def remove_frontend_repo(self, repo_id:int, user_id:int, group_name:str) -> dict """ if not isinstance(repo_id, int) or not isinstance(user_id, int) or not isinstance(group_name, str): - return {"status": "Invalid input params"} + return {"status": "Invalid types"} group_id = self.convert_group_name_to_id(user_id, group_name) if group_id is None: From 4d72ffc7d5897d028054b87e261b4f016411c34e Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Thu, 5 Jan 2023 13:02:34 -0600 Subject: [PATCH 038/150] re-add facade contributors to task queue Signed-off-by: Isaac Milarsky --- augur/tasks/git/facade_tasks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/augur/tasks/git/facade_tasks.py b/augur/tasks/git/facade_tasks.py index 16d111f12b..fbe4783b01 100644 --- a/augur/tasks/git/facade_tasks.py +++ b/augur/tasks/git/facade_tasks.py @@ -377,7 +377,7 @@ def generate_facade_chain(logger): facade_sequence.extend(generate_analysis_sequence(logger)) #Generate contributor analysis task group. - #facade_sequence.append(generate_contributor_sequence(logger)) + facade_sequence.append(generate_contributor_sequence(logger)) if nuke_stored_affiliations: facade_sequence.append(nuke_affiliations_facade_task.si().on_error(facade_error_handler.s()))#nuke_affiliations(session.cfg) From cf8b2466ba1c3b263fc75f626110a52ae3358f8b Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Thu, 5 Jan 2023 14:02:46 -0600 Subject: [PATCH 039/150] better handling and logging files model Signed-off-by: Isaac Milarsky --- augur/tasks/github/util/gh_graphql_entities.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/augur/tasks/github/util/gh_graphql_entities.py b/augur/tasks/github/util/gh_graphql_entities.py index 3323bcf3be..137bac06d3 100644 --- a/augur/tasks/github/util/gh_graphql_entities.py +++ b/augur/tasks/github/util/gh_graphql_entities.py @@ -341,8 +341,8 @@ def __iter__(self): self.logger.error( ''.join(traceback.format_exception(None, e, e.__traceback__))) - data = self.request_graphql_dict(variables=params) - coreData = self.extract_paginate_result(data) + self.logger.info(f"Graphql paramters: {params}") + return if int(coreData['totalCount']) == 0: From 22d10bd1942a0b3a8e6be978d98d4bef445c0b4c Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 5 Jan 2023 14:58:40 -0600 Subject: [PATCH 040/150] Remove unneeded file Signed-off-by: Andrew Brain --- .../versions/2_added_user_group_table.py | 168 ------------------ 1 file changed, 168 deletions(-) delete mode 100644 augur/application/schema/alembic/versions/2_added_user_group_table.py diff --git a/augur/application/schema/alembic/versions/2_added_user_group_table.py b/augur/application/schema/alembic/versions/2_added_user_group_table.py deleted file mode 100644 index 6dbc7c8551..0000000000 --- a/augur/application/schema/alembic/versions/2_added_user_group_table.py +++ /dev/null @@ -1,168 +0,0 @@ -"""Added user group table - -Revision ID: 2 -Revises: 1 -Create Date: 2022-12-19 11:00:37.509132 - -""" -import logging - -from alembic import op -import sqlalchemy as sa -from augur.application.db.session import DatabaseSession -from augur.application.db.models.augur_operations import UserGroup, UserRepo - -CLI_USER_ID = 1 - - -# revision identifiers, used by Alembic. -revision = '2' -down_revision = '1' -branch_labels = None -depends_on = None - -logger = logging.getLogger(__name__) - -def upgrade(): - - with DatabaseSession(logger) as session: - - create_user_groups_table = """ - CREATE TABLE "augur_operations"."user_groups" ( - "group_id" BIGSERIAL NOT NULL, - "user_id" int4 NOT NULL, - "name" varchar COLLATE "pg_catalog"."default" NOT NULL, - PRIMARY KEY ("group_id"), - FOREIGN KEY ("user_id") REFERENCES "augur_operations"."users" ("user_id") ON DELETE NO ACTION ON UPDATE NO ACTION, - UNIQUE ("user_id", "name") - ); - - - ALTER TABLE "augur_operations"."user_groups" - OWNER TO "augur"; - - INSERT INTO "augur_operations"."user_groups" ("group_id", "user_id", "name") VALUES (1, {}, 'default') ON CONFLICT ("user_id", "name") DO NOTHING; - ALTER SEQUENCE user_groups_group_id_seq RESTART WITH 2; - """.format(CLI_USER_ID) - - session.execute_sql(sa.sql.text(create_user_groups_table)) - - - user_repos = [] - - # create user group for all the users that have repos - user_id_query = sa.sql.text("""SELECT DISTINCT(user_id) FROM user_repos;""") - user_groups = session.fetchall_data_from_sql_text(user_id_query) - if user_groups: - - result = [] - for group in user_groups: - - user_id = group["user_id"] - - if user_id == CLI_USER_ID: - continue - - user_group_insert = sa.sql.text(f"""INSERT INTO "augur_operations"."user_groups" ("user_id", "name") VALUES ({user_id}, 'default') RETURNING group_id, user_id;""") - result.append(session.fetchall_data_from_sql_text(user_group_insert)[0]) - - # cli user mapping by default - user_group_id_mapping = {CLI_USER_ID: "1"} - for row in result: - user_group_id_mapping[row["user_id"]] = row["group_id"] - - - user_repo_query = sa.sql.text("""SELECT * FROM user_repos;""") - user_repo_data = session.fetchall_data_from_sql_text(user_repo_query) - for row in user_repo_data: - row.update({"group_id": user_group_id_mapping[row["user_id"]]}) - del row["user_id"] - user_repos.extend(user_repo_data) - - # remove data from table before modifiying it - remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") - session.execute_sql(remove_data_from_user_repos_query) - - - table_changes = """ - ALTER TABLE user_repos - ADD COLUMN group_id BIGINT, - ADD CONSTRAINT user_repos_group_id_fkey FOREIGN KEY (group_id) REFERENCES user_groups(group_id), - DROP COLUMN user_id, - ADD PRIMARY KEY (group_id, repo_id); - """ - - session.execute_sql(sa.sql.text(table_changes)) - - for data in user_repos: - - group_id = data["group_id"] - repo_id = data["repo_id"] - - user_repo_insert = sa.sql.text(f"""INSERT INTO "augur_operations"."user_repos" ("group_id", "repo_id") VALUES ({group_id}, {repo_id});""") - result = session.execute_sql(user_repo_insert) - # ### end Alembic commands ### - - -def downgrade(): - # ### commands auto generated by Alembic - please adjust! ### - - - user_group_ids = {} - group_repo_ids = {} - with DatabaseSession(logger) as session: - user_id_query = sa.sql.text("""SELECT * FROM user_groups;""") - user_groups = session.fetchall_data_from_sql_text(user_id_query) - for row in user_groups: - try: - user_group_ids[row["user_id"]].append(row["group_id"]) - except KeyError: - user_group_ids[row["user_id"]] = [row["group_id"]] - - - group_id_query = sa.sql.text("""SELECT * FROM user_repos;""") - group_repo_id_result = session.fetchall_data_from_sql_text(group_id_query) - for row in group_repo_id_result: - try: - group_repo_ids[row["group_id"]].append(row["repo_id"]) - except KeyError: - group_repo_ids[row["group_id"]] = [row["repo_id"]] - - remove_data_from_user_repos_query = sa.sql.text("""DELETE FROM user_repos;""") - session.execute_sql(remove_data_from_user_repos_query) - - - table_changes = """ - ALTER TABLE user_repos - ADD COLUMN user_id INT, - ADD CONSTRAINT user_repos_user_id_fkey FOREIGN KEY (user_id) REFERENCES users(user_id), - DROP COLUMN group_id, - ADD PRIMARY KEY (user_id, repo_id); - DROP TABLE user_groups; - """ - - session.execute_sql(sa.sql.text(table_changes)) - - for user_id, group_ids in user_group_ids.items(): - - repos = [] - for group_id in group_ids: - try: - repos.extend(group_repo_ids[group_id]) - except KeyError: - continue - - query_text_array = ["""INSERT INTO "augur_operations"."user_repos" ("repo_id", "user_id") VALUES """] - for i, repo_id in enumerate(repos): - query_text_array.append(f"({repo_id}, {user_id})") - - delimiter = ";" if i == len(repos) -1 else "," - - query_text_array.append(delimiter) - - - query_text = "".join(query_text_array) - - session.execute_sql(sa.sql.text(query_text)) - - # ### end Alembic commands ### From 9c15799dcebd2c891a5064707b4a05f7fcf7e8ca Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Thu, 5 Jan 2023 15:18:29 -0600 Subject: [PATCH 041/150] take advantage of rabbitmq allowing us to use celery result Signed-off-by: Isaac Milarsky --- augur/tasks/data_analysis/__init__.py | 7 +++++-- augur/tasks/start_tasks.py | 14 +++++++++++--- 2 files changed, 16 insertions(+), 5 deletions(-) diff --git a/augur/tasks/data_analysis/__init__.py b/augur/tasks/data_analysis/__init__.py index 1d0877cdaf..69c2e690d8 100644 --- a/augur/tasks/data_analysis/__init__.py +++ b/augur/tasks/data_analysis/__init__.py @@ -11,6 +11,7 @@ from augur.tasks.init.celery_app import celery_app as celery import logging +@celery.task def machine_learning_phase(): logger = logging.getLogger(machine_learning_phase.__name__) @@ -40,5 +41,7 @@ def machine_learning_phase(): task_chain = chain(*ml_tasks) - #task_chain.apply_async() - return task_chain \ No newline at end of file + result = task_chain.apply_async() + with allow_join_result(): + return result.get() + #return task_chain \ No newline at end of file diff --git a/augur/tasks/start_tasks.py b/augur/tasks/start_tasks.py index c3d29c4535..54974c2bdd 100644 --- a/augur/tasks/start_tasks.py +++ b/augur/tasks/start_tasks.py @@ -35,6 +35,7 @@ #Predefine phases. For new phases edit this and the config to reflect. #The domain of tasks ran should be very explicit. +@celery.task def prelim_phase(): logger = logging.getLogger(prelim_phase.__name__) @@ -44,8 +45,12 @@ def prelim_phase(): repos = execute_session_query(query, 'all') repo_git_list = [repo.repo_git for repo in repos] - return create_grouped_task_load(dataList=repo_git_list,task=detect_github_repo_move) + result = create_grouped_task_load(dataList=repo_git_list,task=detect_github_repo_move).apply_async() + + with allow_join_result(): + return result.get() +@celery.task def repo_collect_phase(): logger = logging.getLogger(repo_collect_phase.__name__) @@ -75,7 +80,10 @@ def repo_collect_phase(): collect_releases.si() ) - return chain(repo_task_group, refresh_materialized_views.si()) + result = chain(repo_task_group, refresh_materialized_views.si()).get() + + with allow_join_result(): + return result.get() DEFINED_COLLECTION_PHASES = [prelim_phase, repo_collect_phase] @@ -130,7 +138,7 @@ def start_data_collection(self): #Add the phase to the sequence in order as a celery task. #The preliminary task creates the larger task chain - augur_collection_sequence.append(job()) + augur_collection_sequence.append(job.si()) #Link all phases in a chain and send to celery augur_collection_chain = chain(*augur_collection_sequence) From b0829d0295601cb146d865359ed86a18d9951924 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Thu, 5 Jan 2023 15:28:16 -0600 Subject: [PATCH 042/150] syntax Signed-off-by: Isaac Milarsky --- augur/tasks/start_tasks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/augur/tasks/start_tasks.py b/augur/tasks/start_tasks.py index 54974c2bdd..f8c02cc95d 100644 --- a/augur/tasks/start_tasks.py +++ b/augur/tasks/start_tasks.py @@ -80,7 +80,7 @@ def repo_collect_phase(): collect_releases.si() ) - result = chain(repo_task_group, refresh_materialized_views.si()).get() + result = chain(repo_task_group, refresh_materialized_views.si()).apply_async() with allow_join_result(): return result.get() From b12908721f5a06fc8f864429c6535df2c5c935f4 Mon Sep 17 00:00:00 2001 From: Ulincsys Date: Thu, 5 Jan 2023 16:10:48 -0600 Subject: [PATCH 043/150] Initial integration and testing --- .gitignore | 2 + augur/api/server.py | 12 +- augur/api/view/.gitignore | 1 + augur/api/view/api.py | 71 +++ augur/api/view/augur_view.py | 46 ++ augur/api/view/init.py | 93 ++++ augur/api/view/routes.py | 276 +++++++++++ augur/api/view/run.sh | 11 + augur/api/view/server/Environment.py | 52 +++ augur/api/view/server/LoginException.py | 3 + augur/api/view/server/ServerThread.py | 35 ++ augur/api/view/server/User.py | 276 +++++++++++ augur/api/view/server/__init__.py | 4 + augur/api/view/url_converters.py | 27 ++ augur/api/view/utils.py | 435 ++++++++++++++++++ augur/static/css/dashboard.css | 45 ++ augur/static/css/first_time.css | 148 ++++++ augur/static/css/stylesheet.css | 424 +++++++++++++++++ .../static/favicon/android-chrome-192x192.png | Bin 0 -> 5679 bytes .../static/favicon/android-chrome-512x512.png | Bin 0 -> 12926 bytes augur/static/favicon/apple-touch-icon.png | Bin 0 -> 5236 bytes augur/static/favicon/favicon-16x16.png | Bin 0 -> 389 bytes augur/static/favicon/favicon-32x32.png | Bin 0 -> 649 bytes augur/static/favicon/favicon.ico | Bin 0 -> 15406 bytes augur/static/favicon/favicon.png | Bin 0 -> 14195 bytes augur/static/favicon/favicon_source.svg | 78 ++++ augur/static/favicon/site.webmanifest | 1 + augur/static/img/Chaoss_Logo.png | Bin 0 -> 19432 bytes augur/static/img/Chaoss_Logo_white.png | Bin 0 -> 21153 bytes augur/static/img/auggie_shrug.png | Bin 0 -> 29646 bytes augur/static/img/augur_logo.png | Bin 0 -> 35590 bytes augur/static/img/augur_logo_black.png | Bin 0 -> 42763 bytes augur/static/img/notification-icon.svg | 80 ++++ augur/static/js/range.js | 3 + augur/static/js/sleep.js | 4 + augur/static/js/textarea_resize.js | 12 + augur/templates/admin-dashboard.html | 178 +++++++ augur/templates/first-time.html | 211 +++++++++ augur/templates/groups-table.html | 33 ++ augur/templates/index.html | 67 +++ augur/templates/loading.html | 14 + augur/templates/login.html | 157 +++++++ augur/templates/navbar.html | 67 +++ augur/templates/notice.html | 6 + augur/templates/notifications.html | 79 ++++ augur/templates/repo-commits.html | 0 augur/templates/repo-info.html | 128 ++++++ augur/templates/repos-card.html | 27 ++ augur/templates/repos-table.html | 92 ++++ augur/templates/settings.html | 139 ++++++ augur/templates/status.html | 233 ++++++++++ augur/templates/toasts.html | 60 +++ setup.py | 3 +- 53 files changed, 3631 insertions(+), 2 deletions(-) create mode 100644 augur/api/view/.gitignore create mode 100644 augur/api/view/api.py create mode 100644 augur/api/view/augur_view.py create mode 100644 augur/api/view/init.py create mode 100644 augur/api/view/routes.py create mode 100755 augur/api/view/run.sh create mode 100644 augur/api/view/server/Environment.py create mode 100644 augur/api/view/server/LoginException.py create mode 100644 augur/api/view/server/ServerThread.py create mode 100644 augur/api/view/server/User.py create mode 100644 augur/api/view/server/__init__.py create mode 100644 augur/api/view/url_converters.py create mode 100644 augur/api/view/utils.py create mode 100644 augur/static/css/dashboard.css create mode 100644 augur/static/css/first_time.css create mode 100644 augur/static/css/stylesheet.css create mode 100644 augur/static/favicon/android-chrome-192x192.png create mode 100644 augur/static/favicon/android-chrome-512x512.png create mode 100644 augur/static/favicon/apple-touch-icon.png create mode 100644 augur/static/favicon/favicon-16x16.png create mode 100644 augur/static/favicon/favicon-32x32.png create mode 100644 augur/static/favicon/favicon.ico create mode 100644 augur/static/favicon/favicon.png create mode 100644 augur/static/favicon/favicon_source.svg create mode 100644 augur/static/favicon/site.webmanifest create mode 100644 augur/static/img/Chaoss_Logo.png create mode 100644 augur/static/img/Chaoss_Logo_white.png create mode 100644 augur/static/img/auggie_shrug.png create mode 100644 augur/static/img/augur_logo.png create mode 100644 augur/static/img/augur_logo_black.png create mode 100644 augur/static/img/notification-icon.svg create mode 100644 augur/static/js/range.js create mode 100644 augur/static/js/sleep.js create mode 100644 augur/static/js/textarea_resize.js create mode 100644 augur/templates/admin-dashboard.html create mode 100644 augur/templates/first-time.html create mode 100644 augur/templates/groups-table.html create mode 100644 augur/templates/index.html create mode 100644 augur/templates/loading.html create mode 100644 augur/templates/login.html create mode 100644 augur/templates/navbar.html create mode 100644 augur/templates/notice.html create mode 100644 augur/templates/notifications.html create mode 100644 augur/templates/repo-commits.html create mode 100644 augur/templates/repo-info.html create mode 100644 augur/templates/repos-card.html create mode 100644 augur/templates/repos-table.html create mode 100644 augur/templates/settings.html create mode 100644 augur/templates/status.html create mode 100644 augur/templates/toasts.html diff --git a/.gitignore b/.gitignore index 887b67269c..7ebccb6a15 100644 --- a/.gitignore +++ b/.gitignore @@ -7,6 +7,8 @@ augur_export_env.sh .DS_Store *.config.json !docker.config.json +config.yml +reports.yml node_modules/ diff --git a/augur/api/server.py b/augur/api/server.py index b2e069e6a1..0d41dedb4f 100644 --- a/augur/api/server.py +++ b/augur/api/server.py @@ -13,6 +13,8 @@ from typing import Optional, List, Any, Tuple +from pathlib import Path + from flask import Flask, request, Response, redirect from flask_cors import CORS import pandas as pd @@ -58,7 +60,10 @@ def __init__(self): def create_app(self): """Define the flask app and configure the routes.""" - self.app = Flask(__name__) + template_dir = str(Path(__file__).parent.parent / "templates") + static_dir = str(Path(__file__).parent.parent / "static") + + self.app = Flask(__name__, template_folder=template_dir, static_folder=static_dir) self.logger.debug("Created Flask app") # defines the api version on the flask app, @@ -126,6 +131,11 @@ def create_all_routes(self): # and this line is calling that function and passing the flask app, # so that the routes in the files can be added to the flask app module.create_routes(self) + + for route_file in ["augur_view", "routes", "api"]: + module = importlib.import_module('.' + route_file, 'augur.api.view') + + module.create_routes(self) def get_route_files(self) -> List[str]: diff --git a/augur/api/view/.gitignore b/augur/api/view/.gitignore new file mode 100644 index 0000000000..ad30bfec28 --- /dev/null +++ b/augur/api/view/.gitignore @@ -0,0 +1 @@ +*.yml \ No newline at end of file diff --git a/augur/api/view/api.py b/augur/api/view/api.py new file mode 100644 index 0000000000..ba53557d9b --- /dev/null +++ b/augur/api/view/api.py @@ -0,0 +1,71 @@ +from flask import Flask, render_template, render_template_string, request, abort, jsonify, redirect, url_for, session, flash +from flask_login import current_user, login_required +from .utils import * + +def create_routes(server): + @server.app.route('/cache/file/') + @server.app.route('/cache/file/') + def cache(file=None): + if file is None: + return redirect(url_for('root', path=getSetting('caching'))) + return redirect(url_for('root', path=toCacheFilepath(file))) + + # API endpoint to clear server cache + # TODO: Add verification + @server.app.route('/cache/clear') + def clear_cache(): + try: + for f in os.listdir(getSetting('caching')): + os.remove(os.path.join(getSetting('caching'), f)) + return renderMessage("Cache Cleared", "Server cache was successfully cleared", redirect="/") + except Exception as err: + print(err) + return renderMessage("Error", "An error occurred while clearing server cache.", redirect="/", pause=5) + + # API endpoint to reload settings from disk + @server.app.route('/settings/reload') + def reload_settings(): + loadSettings() + return renderMessage("Settings Reloaded", "Server settings were successfully reloaded.", redirect="/", pause=5) + + # Request the frontend version as a JSON string + @server.app.route('/version') + def get_version(): + return jsonify(version) + + @server.app.route('/account/repos/add/') + @server.app.route('/account/repos/add') + @login_required + def av_add_user_repo(repo_url = None): + if not repo_url: + flash("Repo or org URL must not be empty") + elif current_user.try_add_url(repo_url): + flash("Successfully added repo or org") + else: + flash("Could not add repo or org") + + return redirect(url_for("user_settings")) + + """ ---------------------------------------------------------------- + """ + @server.app.route('/requests/make/') + def make_api_request(request_endpoint): + do_cache = True + if request.headers.get("nocache") or request.args.get("nocache"): + do_cache = False + + data = requestJson(request_endpoint, do_cache) + if type(data) == tuple: + return jsonify({"request_error": data[1]}), 400 + return jsonify(data) + + """ ---------------------------------------------------------------- + Locking request loop: + This route will lock the current request until the + report request completes. A json response is guaranteed. + Assumes that the requested repo exists. + """ + @server.app.route('/requests/report/wait/') + def wait_for_report_request(id): + requestReports(id) + return jsonify(report_requests[id]) diff --git a/augur/api/view/augur_view.py b/augur/api/view/augur_view.py new file mode 100644 index 0000000000..5eb5cf55df --- /dev/null +++ b/augur/api/view/augur_view.py @@ -0,0 +1,46 @@ +from flask import Flask, render_template, redirect, url_for, session, request +from flask_login import LoginManager +from .utils import * +from .url_converters import * +from .server import User + +login_manager = LoginManager() + +def create_routes(server): + login_manager.init_app(server.app) + + server.app.secret_key = getSetting("session_key") + + server.app.url_map.converters['list'] = ListConverter + server.app.url_map.converters['bool'] = BoolConverter + server.app.url_map.converters['json'] = JSONConverter + + # Code 404 response page, for pages not found + @server.app.errorhandler(404) + def page_not_found(error): + return render_template('index.html', title='404', api_url=getSetting('serving')), 404 + + @server.app.errorhandler(405) + def unsupported_method(error): + return renderMessage("405 - Method not supported", "The resource you are trying to access does not support the request method used"), 405 + + @login_manager.unauthorized_handler + def unauthorized(): + session["login_next"] = url_for(request.endpoint, **request.args) + return redirect(url_for('user_login')) + + @login_manager.user_loader + def load_user(user_id): + user = User(user_id) + + if not user.exists: + return None + + # The flask_login library sets a unique session["_id"] + # when login_user() is called successfully + if session.get("_id") is not None: + user._is_authenticated = True + user._is_active = True + + return user + diff --git a/augur/api/view/init.py b/augur/api/view/init.py new file mode 100644 index 0000000000..556bcc93e5 --- /dev/null +++ b/augur/api/view/init.py @@ -0,0 +1,93 @@ +from pathlib import Path +from .server import Environment +import logging, sqlite3, secrets, hashlib, yaml + +env = Environment() + +# load configuration files and initialize globals +configFile = Path(env.setdefault("CONFIG_LOCATION", "config.yml")) + +version = {"major": 0, "minor": 0.1, "series": "Alpha"} + +report_requests = {} +settings = {} + +def init_settings(): + global settings + settings["approot"] = "/" + settings["caching"] = "static/cache/" + settings["cache_expiry"] = 604800 + settings["serving"] = "http://augur.chaoss.io/api/unstable" + settings["pagination_offset"] = 25 + settings["reports"] = "reports.yml" + settings["session_key"] = secrets.token_hex() + settings["version"] = version + +def write_settings(current_settings): + current_settings["caching"] = str(current_settings["caching"]) + + if "valid" in current_settings: + current_settings.pop("valid") + + with open(configFile, 'w') as file: + yaml.dump(current_settings, file) + +""" ---------------------------------------------------------------- +""" +def version_check(current_settings): + def to_version_string(version_object): + if version_object is None: + return "Undefined_version" + return f'{version_object["major"]}-{version_object["minor"]}-{version_object["series"]}' + + def update_from(old): + if old == None: + if "pagination_offset" not in current_settings: + current_settings["pagination_offset"] = current_settings.pop("paginationOffset") + if "session_key" not in current_settings: + current_settings["session_key"] = secrets.token_hex() + + else: + raise ValueError(f"Updating from {to_version_string(old)} to {to_version_string(version)} is unsupported") + + current_settings["version"] = version + write_settings(current_settings) + logging.info(f"Configuration updated from {to_version_string(old)} to {to_version_string(version)}") + + def compare_versions(old, new): + if old["major"] < new["major"]: + return -1, old["series"] == new["series"] + elif old["major"] > new["major"]: + return 1, old["series"] == new["series"] + elif old["minor"] < new["minor"]: + return -1, old["series"] == new["series"] + elif old["minor"] > new["minor"]: + return 1, old["series"] == new["series"] + return 0, old["series"] == new["series"] + + if "version" not in current_settings: + update_from(None) + + version_diff = compare_versions(current_settings["version"], version) + + if current_settings["version"] == version: + return + elif version_diff[0] == -1: + update_from(current_settings["version"]) + elif version_diff[0] == 1: + raise ValueError("Downgrading configuration versions is unsupported: " + + f"from {to_version_string(current_settings['version'])} to {to_version_string(version)}") + + global settings + settings = current_settings + +# default reports definition +reports = {'pull_request_reports': [{'url': 'pull_request_reports/average_commits_per_PR/', 'description': 'Average commits per pull request'}, {'url': 'pull_request_reports/average_comments_per_PR/', 'description': 'Average comments per pull request'}, {'url': 'pull_request_reports/PR_counts_by_merged_status/', 'description': 'Pull request counts by merged status'}, {'url': 'pull_request_reports/mean_response_times_for_PR/', 'description': 'Mean response times for pull requests'}, {'url': 'pull_request_reports/mean_days_between_PR_comments/', 'description': 'Mean days between pull request comments'}, {'url': 'pull_request_reports/PR_time_to_first_response/', 'description': 'Pull request time until first response'}, {'url': 'pull_request_reports/average_PR_events_for_closed_PRs/', 'description': 'Average pull request events for closed pull requests'}, {'url': 'pull_request_reports/Average_PR_duration/', 'description': 'Average pull request duration'}], 'contributor_reports': [{'url': 'contributor_reports/new_contributors_bar/', 'description': 'New contributors bar graph'}, {'url': 'contributor_reports/returning_contributors_pie_chart/', 'description': 'Returning contributors pie chart'}], 'contributor_reports_stacked': [{'url': 'contributor_reports/new_contributors_stacked_bar/', 'description': 'New contributors stacked bar chart'}, {'url': 'contributor_reports/returning_contributors_stacked_bar/', 'description': 'Returning contributors stacked bar chart'}]} + +# Initialize logging +def init_logging(): + format = "%(asctime)s: %(message)s" + global logger + logger = logging.getLogger("augur view") + logger.setLevel("DEBUG") + logging.basicConfig(filename="augur_view.log", filemode='a', format=format, level=logging.INFO, datefmt="%H:%M:%S") diff --git a/augur/api/view/routes.py b/augur/api/view/routes.py new file mode 100644 index 0000000000..5fe14b94e3 --- /dev/null +++ b/augur/api/view/routes.py @@ -0,0 +1,276 @@ +from flask import Flask, render_template, render_template_string, request, abort, jsonify, redirect, url_for, session, flash +from .utils import * +from flask_login import login_user, logout_user, current_user, login_required +from .server import User +from .server import LoginException + +# ROUTES ----------------------------------------------------------------------- + +def create_routes(server): + """ ---------------------------------------------------------------- + root: + This route returns a redirect to the application root, appended + by the provided path, if any. + """ + @server.app.route('/root/') + @server.app.route('/root/') + def root(path=""): + return redirect(getSetting("approot") + path) + + """ ---------------------------------------------------------------- + logo: + this route returns a redirect to the application logo associated + with the provided brand, otherwise the inverted Augur logo if no + brand is provided. + """ + @server.app.route('/logo/') + @server.app.route('/logo/') + def logo(brand=None): + if brand is None: + return redirect(url_for('static', filename='img/augur_logo.png')) + elif "augur" in brand: + return logo(None) + elif "chaoss" in brand: + return redirect(url_for('static', filename='img/Chaoss_Logo_white.png')) + return "" + + """ ---------------------------------------------------------------- + default: + table: + This route returns the default view of the application, which + is currently defined as the repository table view + """ + @server.app.route('/') + @server.app.route('/repos/views/table') + def repo_table_view(): + query = request.args.get('q') + page = request.args.get('p') + sorting = request.args.get('s') + rev = request.args.get('r') + if rev is not None: + if rev == "False": + rev = False + elif rev == "True": + rev = True + else: + rev = False + + if current_user.is_authenticated: + data = requestJson("repos", cached = False) + user_repo_ids = current_user.query_repos() + user_repos = [] + for repo in data: + if repo["repo_id"] in user_repo_ids: + user_repos.append(repo) + + data = user_repos or None + else: + data = requestJson("repos") + + #if not cacheFileExists("repos.json"): + # return renderLoading("repos/views/table", query, "repos.json") + + return renderRepos("table", query, data, sorting, rev, page, True) + + """ ---------------------------------------------------------------- + card: + This route returns the repository card view + """ + @server.app.route('/repos/views/card') + def repo_card_view(): + query = request.args.get('q') + return renderRepos("card", query, requestJson("repos"), filter = True) + + """ ---------------------------------------------------------------- + groups: + This route returns the groups table view, listing all the current + groups in the backend + """ + @server.app.route('/groups') + @server.app.route('/groups/') + def repo_groups_view(group=None): + query = request.args.get('q') + page = request.args.get('p') + + if(group is not None): + query = group + + if(query is not None): + buffer = [] + data = requestJson("repos") + for repo in data: + if query == str(repo["repo_group_id"]) or query in repo["rg_name"]: + buffer.append(repo) + return renderRepos("table", query, buffer, page = page, pageSource = "repo_groups_view") + else: + groups = requestJson("repo-groups") + return render_template('index.html', body="groups-table", title="Groups", groups=groups, query_key=query, api_url=getSetting('serving')) + + """ ---------------------------------------------------------------- + status: + This route returns the status view, which displays information + about the current status of collection in the backend + """ + @server.app.route('/status') + def status_view(): + return render_module("status", title="Status") + + """ ---------------------------------------------------------------- + login: + Under development + """ + @server.app.route('/account/login', methods=['GET', 'POST']) + def user_login(): + if request.method == 'POST': + try: + user_id = request.form.get('username') + remember = request.form.get('remember') is not None + if user_id is None: + raise LoginException("A login issue occurred") + + user = User(user_id) + + if request.form.get('register') is not None: + if user.exists: + raise LoginException("User already exists") + if not user.register(request): + raise LoginException("An error occurred registering your account") + else: + flash("Account successfully created") + + if user.validate(request) and login_user(user, remember = remember): + flash(f"Welcome, {user_id}!") + if "login_next" in session: + return redirect(session.pop("login_next")) + return redirect(url_for('root')) + else: + raise LoginException("Invalid login credentials") + except LoginException as e: + flash(str(e)) + return render_module('login', title="Login") + + """ ---------------------------------------------------------------- + logout: + Under development + """ + @server.app.route('/account/logout') + @login_required + def user_logout(): + logout_user() + flash("You have been logged out") + return redirect(url_for('root')) + + @server.app.route('/account/delete') + @login_required + def user_delete(): + if current_user.delete(): + flash(f"Account {current_user.id} successfully removed") + logout_user() + else: + flash("An error occurred removing the account") + + return redirect(url_for("root")) + + @server.app.route('/account/update') + @login_required + def user_update_password(): + if current_user.update_password(request): + flash(f"Account {current_user.id} successfully updated") + else: + flash("An error occurred updating the account") + + return redirect(url_for("user_settings")) + + """ ---------------------------------------------------------------- + settings: + Under development + """ + @server.app.route('/account/settings') + @login_required + def user_settings(): + return render_module("settings", title="Settings") + + """ ---------------------------------------------------------------- + report page: + This route returns a report view of the requested repo (by ID). + """ + @server.app.route('/repos/views/repo/') + def repo_repo_view(id): + # For some reason, there is no reports definition (shouldn't be possible) + if reports is None: + return renderMessage("Report Definitions Missing", "You requested a report for a repo on this instance, but a definition for the report layout was not found.") + data = requestJson("repos") + repo = {} + # Need to convert the repo id parameter to int so it's comparable + try: + id = int(id) + except: + pass + # Finding the report object in the data so the name is accessible on the page + for item in data: + if item['repo_id'] == id: + repo = item + break + + return render_module("repo-info", reports=reports.keys(), images=reports, title="Repo", repo=repo, repo_id=id) + + """ ---------------------------------------------------------------- + default: + table: + This route returns the default view of the application, which + is currently defined as the repository table view + """ + @server.app.route('/user/group/') + def user_group_view(group): + params = {} + + # NOT IMPLEMENTED + # query = request.args.get('q') + + try: + params["page"] = int(request.args.get('p')) + except: + pass + + if sort := request.args.get('s'): + params["sort"] = sort + + rev = request.args.get('r') + if rev is not None: + if rev == "False": + params["direction"] = "ASC" + elif rev == "True": + params["direction"] = "DESC" + + if current_user.is_authenticated: + data = current_user.select_group(group, **params) + + if not data: + return renderMessage("Error Loading Group", "Either the group you requestion does not exist, or an unspecified error occurred.") + else: + return renderMessage("Authentication Required", "You must be logged in to view this page.") + + #if not cacheFileExists("repos.json"): + # return renderLoading("repos/views/table", query, "repos.json") + + return renderRepos("table", None, data, sort, rev, params.get("page"), True) + + """ ---------------------------------------------------------------- + Admin dashboard: + View the admin dashboard. + """ + @server.app.route('/dashboard') + def dashboard_view(): + empty = [ + { "title": "Placeholder", "settings": [ + { "id": "empty", + "display_name": "Empty Entry", + "value": "NULL", + "description": "There's nothing here 👻" + } + ]} + ] + + backend_config = requestJson("config/get", False) + + return render_template('admin-dashboard.html', sections = empty, config = backend_config) diff --git a/augur/api/view/run.sh b/augur/api/view/run.sh new file mode 100755 index 0000000000..12070743db --- /dev/null +++ b/augur/api/view/run.sh @@ -0,0 +1,11 @@ +export CONFIG_LOCATION="config.yml" +export SERVER_ADDRESS="0.0.0.0" +export SERVER_PORT="8000" + +# Notify the bootstrapper not to generate a Gunicorn config +# Also launch with the development server +export DEVELOPMENT=1 + +export TEMPLATES_AUTO_RELOAD=True + +python3 bootstrap.py diff --git a/augur/api/view/server/Environment.py b/augur/api/view/server/Environment.py new file mode 100644 index 0000000000..409a5975e5 --- /dev/null +++ b/augur/api/view/server/Environment.py @@ -0,0 +1,52 @@ +import os + +class Environment: + """ + This class is used to make dealing with environment variables easier. It + allows you to set multiple environment variables at once, and to get items + with subscript notation without needing to deal with the particularities of + non-existent values. + """ + def __init__(self, **kwargs): + for (key, value) in kwargs.items(): + self[key] = value + + def setdefault(self, key, value): + if not self[key]: + self[key] = value + return value + return self[key] + + def setall(self, **kwargs): + result = {} + for (key, value) in kwargs.items(): + if self[key]: + result[key] = self[key] + self[key] = value + + def getany(self, *args): + result = {} + for arg in args: + if self[arg]: + result[arg] = self[arg] + return result + + def as_type(self, type, key): + if self[key]: + return type(self[key]) + return None + + def __getitem__(self, key): + return os.getenv(key) + + def __setitem__(self, key, value): + os.environ[key] = str(value) + + def __len__(self)-> int: + return len(os.environ) + + def __str__(self)-> str: + return str(os.environ) + + def __iter__(self): + return (item for item in os.environ.items) \ No newline at end of file diff --git a/augur/api/view/server/LoginException.py b/augur/api/view/server/LoginException.py new file mode 100644 index 0000000000..f13a31fc06 --- /dev/null +++ b/augur/api/view/server/LoginException.py @@ -0,0 +1,3 @@ + +class LoginException(Exception): + pass diff --git a/augur/api/view/server/ServerThread.py b/augur/api/view/server/ServerThread.py new file mode 100644 index 0000000000..af3651a8f1 --- /dev/null +++ b/augur/api/view/server/ServerThread.py @@ -0,0 +1,35 @@ +from werkzeug.debug import DebuggedApplication +from werkzeug.serving import make_server +import threading + +class ServerThread(threading.Thread): + """ + Create a runnable Flask server app that automatically launches on a separate + thread. + """ + def __init__(self, app, port = 5000, address = "0.0.0.0", reraise = False): + threading.Thread.__init__(self) + + # Required to enable debugging with make_server + if reraise: + app.config['PROPAGATE_EXCEPTIONS'] = True + app.config['TESTING'] = True + app.config['DEBUG'] = True + app.config['TRAP_HTTP_EXCEPTIONS'] = True + app.config['TEMPLATES_AUTO_RELOAD'] = True + + debug_app = DebuggedApplication(app, True) + + self.server = make_server(address, port, debug_app, threaded = True) + self.ctx = app.app_context() + self.ctx.push() + + # For compatibility with subprocesses + self.terminate = self.shutdown + self.wait = self.join + + def run(self): + self.server.serve_forever() + + def shutdown(self): + self.server.shutdown() \ No newline at end of file diff --git a/augur/api/view/server/User.py b/augur/api/view/server/User.py new file mode 100644 index 0000000000..4889922ce1 --- /dev/null +++ b/augur/api/view/server/User.py @@ -0,0 +1,276 @@ +from flask_login import UserMixin +# I'm using requests here to avoid circular integration with utils +import requests, time, re + +""" ---------------------------------------------------------------- +""" +class User(UserMixin): + # User.api is set in utils.py + # User.logger is set in utils.py + + @property + def is_authenticated(self): + return self._is_authenticated + + @is_authenticated.setter + def is_authenticated(self, val): + self._is_authenticated = val + + @property + def is_active(self): + return self._is_active + + @is_active.setter + def is_active(self, val): + self._is_active = val + + @property + def is_anoymous(self): + return self._is_anoymous + + @is_anoymous.setter + def is_anoymous(self, val): + self._is_anoymous = val + + @property + def exists(self): + return self._exists + + @property + def default_group(self): + if not self.is_authenticated: + return None + elif self._default_group: + return self._default_group + + group_name = self.id + "_default" + groups = self.get_groups() + + if group_name not in groups: + if not self.add_repo_group(group_name): + User.logger.warning("Default user group does not exist, and could not be created") + return None + + self._default_group = group_name + return group_name + + def __init__(self, id): + # flask_login requires that the id be of type string + self.id = str(id) + self._exists = False + self._is_anonymous = False + self._is_authenticated = False + self._is_active = False + self._default_group = None + + # Query the server for the existence of this user + self.query_user() + + def query_user(self): + if self._exists: + # User has already been queried and verified to exist + return True + + endpoint = User.api + "/user/query" + + response = requests.post(endpoint, params = {"username": self.id}) + + if response.status_code == 200 and response.json().get("status") == True: + self._exists = True + return True + + return False + + def get_id(self): + return self.id + + def query_repos(self, group = None): + endpoint = User.api + "/user/repos" + + if not group: + group = self.default_group + + response = requests.post(endpoint, params = {"username": self.id}) + + if response.status_code == 200: + data = response.json() + if data.get("status") == "success": + return data.get("repo_ids") + else: + User.logger.warning(f"Could not get user repos: {data.get('status')}") + else: + User.logger.warning(f"Could not get user repos: {response.status_code}") + + def try_add_url(self, url, group = None): + repo = re.search("https?:\/\/github\.com\/([A-Za-z0-9 \- _]+)\/([A-Za-z0-9 \- _]+)(.git)?\/?$", url) + org = re.search("https?:\/\/github\.com\/([A-Za-z0-9 \- _]+)\/?$", url) + + if repo: + return self.add_repo(url, group) + elif org: + return self.add_org(url, group) + + return False + + def add_repo(self, url, group = None): + endpoint = User.api + "/user/add_repo" + + if not group: + group = self.default_group + + response = requests.post(endpoint, params = {"username": self.id, "repo_url": url}) + + if response.status_code == 200: + data = response.json() + if data.get("status") == "Repo Added": + return True + else: + User.logger.warning(f"Could not add user repo {url}: {data.get('status')}") + else: + User.logger.warning(f"Could not add user repo {url}: {response.status_code}") + + return False + + def add_org(self, url, group = None): + endpoint = User.api + "/user/add_org" + + response = requests.post(endpoint, params = {"username": self.id, "org_url": url}) + + if response.status_code == 200: + data = response.json() + if data.get("status") == "Org repos added": + return True + else: + User.logger.warning(f"Could not add user org {url}: {data.get('status')}") + else: + User.logger.warning(f"Could not add user org {url}: {response.status_code}") + + return False + + def get_groups(self): + endpoint = User.api + "/user/groups" + + response = requests.post(endpoint, params = {"username": self.id}) + + if response.status_code == 200: + return response.json() + else: + data = response.json() + User.logger.warning(f"Could not get user groups: {data.get('status')}") + + def add_repo_group(self, group_name): + endpoint = User.api + "/user/add_group" + + response = requests.post(endpoint, params = {"username": self.id, "group_name": group_name}) + + if response.status_code == 200: + data = response.json() + if data.get("status") == "Group created": + return True + else: + User.logger.warning(f"Could not add user group: {data.get('status')}") + else: + User.logger.warning(f"Could not add user group: {response.status_code}") + + def remove_repo_group(self, group_name): + endpoint = User.api + "/user/remove_group" + + response = requests.post(endpoint, params = {"username": self.id, "group_name": group_name}) + + if response.status_code == 200: + data = response.json() + if data.get("status") == "Group deleted": + return True + else: + User.logger.warning(f"Could not remove user group: {data.get('status')}") + else: + User.logger.warning(f"Could not remove user group: {response.status_code}") + + def select_group(self, group_name, **kwargs): + endpoint = User.api + "/user/group_repos" + + kwargs["username"] = self.id + kwargs["group_name"] = group_name + + response = requests.post(endpoint, params = kwargs) + + if response.status_code == 200: + return response.json() + elif response.status_code == 400: + data = response.json() + User.logger.warning(f"Could not select user group {group_name}: {data.get('status')}") + else: + User.logger.warning(f"Could not select user group {group_name}: {response.status_code}") + + def register(self, request): + endpoint = User.api + "/user/create" + + data = request.form.to_dict() + + # admin creation is CLI only for now + if "create_admin" in data: + data.pop("create_admin") + + response = requests.post(endpoint, params = request.form.to_dict()) + + if response.status_code == 200: + return True + elif response.status_code != 200: + User.logger.debug(f"Could not register user: {response.status_code}") + else: # :/ + User.logger.debug(f"Could not register user: {response.json()['status']}") + + return False + + def validate(self, request): + endpoint = User.api + "/user/validate" + + response = requests.post(endpoint, params = request.form.to_dict()) + + if response.status_code == 200 and response.json()["status"] == "Validated": + self._is_authenticated = True + self._is_active = True + return True + elif response.status_code != 200: + User.logger.debug(f"Could not validate user: {response.status_code}") + else: + User.logger.debug(f"Could not validate user: {response.json()['status']}") + + + # Avoid abuse by malicious actors + time.sleep(2) + return False + + def update_password(self, request): + endpoint = User.api + "/user/update" + + data = request.form.to_dict() + data["username"] = self.id + + response = requests.post(endpoint, params = data) + + if response.status_code == 200 and "Updated" in response.json()["status"]: + return True + elif response.status_code != 200: + User.logger.debug(f"Could not update user password: {response.status_code}") + else: + User.logger.debug(f"Could not update user password: {response.json()['status']}") + + return False + + def delete(self): + endpoint = User.api + "/user/remove" + + response = requests.delete(endpoint, params = {"username": self.id}) + + if response.status_code == 200: + return True + elif response.status_code != 200: + User.logger.debug(f"Could not remove user: {response.status_code}") + else: + User.logger.debug(f"Could not remove user: {response.json()['status']}") + + return False + + def __str__(self) -> str: + return f"" diff --git a/augur/api/view/server/__init__.py b/augur/api/view/server/__init__.py new file mode 100644 index 0000000000..287457c4fd --- /dev/null +++ b/augur/api/view/server/__init__.py @@ -0,0 +1,4 @@ +from .Environment import Environment +from .User import User +from .ServerThread import ServerThread +from .LoginException import LoginException diff --git a/augur/api/view/url_converters.py b/augur/api/view/url_converters.py new file mode 100644 index 0000000000..4d43a411f6 --- /dev/null +++ b/augur/api/view/url_converters.py @@ -0,0 +1,27 @@ +from werkzeug.routing import BaseConverter +import json + +class ListConverter(BaseConverter): + def to_python(self, value): + return value.split('+') + + def to_url(self, values): + return '+'.join(BaseConverter.to_url(value) + for value in values) + +class BoolConverter(BaseConverter): + def to_python(self, value): + if value == "False": + return False + elif value == "True": + return True + + def to_url(self, value): + return str(value) + +class JSONConverter(BaseConverter): + def to_python(self, value): + return json.loads(value) + + def to_url(self, value): + return json.dumps(value) diff --git a/augur/api/view/utils.py b/augur/api/view/utils.py new file mode 100644 index 0000000000..9ae6137ad3 --- /dev/null +++ b/augur/api/view/utils.py @@ -0,0 +1,435 @@ +from pathlib import Path +from concurrent.futures import ThreadPoolExecutor +from flask import render_template, flash +from .init import * +from .server import User +import urllib.request, urllib.error, json, os, math, yaml, urllib3, time, logging, re + +def parse_url(url): + from urllib.parse import urlparse + + # localhost is not a valid host + if "localhost" in url: + url = url.replace("localhost", "127.0.0.1") + + if not url.startswith("http"): + url = f"http://{url}" + + parts = urlparse(url) + directories = parts.path.strip('/').split('/') + queries = parts.query.strip('&').split('&') + + elements = { + 'scheme': parts.scheme, + 'netloc': parts.netloc, + 'path': parts.path, + 'params': parts.params, + 'query': parts.query, + 'fragment': parts.fragment + } + + return elements, directories, queries + +def validate_api_url(url): + from urllib.parse import urlunparse + + parts = parse_url(url)[0] + + if not parts["scheme"]: + parts["scheme"] = "http" + + staged_url = urlunparse(parts.values()) + + def is_status_ok(): + try: + with urllib.request.urlopen(staged_url) as request: + response = json.loads(request.read().decode()) + if "status" in response: + return request.url + except Exception as e: + logging.error(f"Error during serving URL verification: {str(e)}") + + return False + + status = is_status_ok() + if not status: + if "/api/unstable" not in parts["path"]: + # The URL does not point directly to the API + # try once more with a new suffix + parts["path"] = str(Path(parts["path"]).joinpath("api/unstable")) + staged_url = urlunparse(parts.values()) + + status = is_status_ok() + if not status: + # The URL does not point to a valid augur instance + return "" + else: + return status + else: + return "" + + return status + + +""" ---------------------------------------------------------------- +loadSettings: + This function attempts to load the application settings from the config file + (defined in init.py). It is assumed that the filename or file path defined + during initialization is sufficient to locate the config file, and that the + current process has read access to that file. + + If loading the config file fails, default settings are loaded via + init_settings() and an attempt is made to write default settings to the + provided config file. +""" +def loadSettings(): + global settings + configFilePath = Path(configFile) + if not configFilePath.is_file(): + init_settings() + with open(configFile, 'w') as file: + logging.info(f"Generating default configuration file: {configFile}") + yaml.dump(settings, file) + logging.info("Default configuration file successfully generated.") + else: + with open(configFilePath) as file: + settings = yaml.load(file, Loader=yaml.FullLoader) + + # Ensure that the cache directory exists and is valid + cachePath = Path(settings["caching"]) + if not cachePath.is_dir(): + if cachePath.is_file(): + raise Exception(f"Cannot initialize caching: cache path [{cachePath}] is a file") + else: + try: + cachePath.mkdir(parents=True) + logging.info("cache directory initialized") + except Exception as err: + raise Exception(f"Cannot initialize caching: could not create cache directory [{cachePath}]") + + # Use the resolved path for cache directory access + settings["caching"] = cachePath + + staged_url = validate_api_url(settings["serving"]) + if staged_url: + settings["serving"] = re.sub("/$", "", staged_url) + settings["valid"] = True + else: + settings["valid"] = False + raise ValueError(f"The provided serving URL is not valid: {settings['serving']}") + +""" ---------------------------------------------------------------- +""" +def getSetting(key): + if key == "serving": + return "http://127.0.0.1:5000/api/unstable" + return settings[key] + +init_logging() + +loadSettings() + +from .init import logger + +User.api = getSetting("serving") +User.logger = logger + +version_check(settings) + +""" ---------------------------------------------------------------- +""" +def loadReports(): + global reports + try: + with open(getSetting("reports")) as file: + reports = yaml.load(file, Loader=yaml.FullLoader) + id = -1 + for report in reports: + for image in reports[report]: + image['id'] = id = id + 1 + return True + except Exception as err: + logging.error(f"An exception occurred reading reports endpoints from [{getSetting('reports')}]:") + logging.error(err) + try: + with open(getSetting("reports"), 'w') as file: + logging.info("Attempting to generate default reports.yml") + yaml.dump(reports, file) + logging.info("Default reports file successfully generated.") + except Exception as ioErr: + logging.error("Error creating default report configuration:") + logging.error(ioErr) + return False + +loadReports() +cache_files_requested = [] + +""" ---------------------------------------------------------------- +""" +def cacheFileExists(filename): + cache_file = Path(filename) + if cache_file.is_file(): + if(getSetting('cache_expiry') > 0): + cache_file_age = time.time() - cache_file.stat().st_mtime + if(cache_file_age > getSetting('cache_expiry')): + try: + cache_file.unlink() + logging.info(f"Cache file {filename} removed due to expiry") + return False + except Exception as e: + logging.error("Error: cache file age exceeds expiry limit, but an exception occurred while attempting to remove") + logging.error(e) + return True + else: + return False + +def stripStatic(url): + return url.replace("static/", "") + +""" ---------------------------------------------------------------- +""" +def toCacheFilename(endpoint): + return endpoint.replace("/", ".").replace("?", "_").replace("=", "_") + '.agcache' + +def toCacheFilepath(endpoint): + return getSetting('caching').joinpath(toCacheFilename(endpoint)) + +def toCacheURL(endpoint): + return getSetting('approot') + str(toCacheFilepath(endpoint)) + +""" ---------------------------------------------------------------- +requestJson: + Attempts to load JSON data from cache for the given endpoint. + If no cache file is found, a request is made to the URL for + the given endpoint and, if successful, the resulting JSON is + cached for future use. Cached files will be stored with all + '/' characters replaced with '.' for filesystem compatibility. + +@PARAM: endpoint: String + A String representation of the requested + json endpoint (relative to the api root). + +@RETURN: data: JSON + An object representing the JSON data read + from either the cache file or the enpoint + URL. Will return None if an error isreturn None + encountered. +""" +def requestJson(endpoint, cached = True): + filename = toCacheFilepath(endpoint) + requestURL = getSetting('serving') + "/" + endpoint + logging.info(f'requesting json from: {endpoint}') + try: + if cached and cacheFileExists(filename): + with open(filename) as f: + data = json.load(f) + else: + with urllib.request.urlopen(requestURL) as url: + if url.getcode() != 200: + raise urllib.error.HTTPError(code = url.getcode()) + + data = json.loads(url.read().decode()) + + if cached: + with open(filename, 'w') as f: + json.dump(data, f) + if filename in cache_files_requested: + cache_files_requested.remove(filename) + return data + except Exception as err: + logging.error("An exception occurred while fulfilling a json request") + logging.error(err) + return False, str(err) + +""" ---------------------------------------------------------------- +""" +def requestPNG(endpoint): + filename = toCacheFilepath(endpoint) + requestURL = getSetting('serving') + "/" + endpoint + try: + if cacheFileExists(filename): + return toCacheURL(endpoint) + else: + urllib.request.urlretrieve(requestURL, filename) + if filename in cache_files_requested: + cache_files_requested.remove(filename) + return toCacheURL(endpoint) + except Exception as err: + logging.error("An exception occurred while fulfilling a png request") + logging.error(err) + +""" ---------------------------------------------------------------- +""" +def download(url, cmanager, filename, image_cache, image_id, repo_id = None): + image_cache[image_id] = {} + image_cache[image_id]['filename'] = filename + filename = toCacheFilepath(filename) + if cacheFileExists(filename): + image_cache[image_id]['exists'] = True + return + response = cmanager.request('GET', url) + if "json" in response.headers['Content-Type']: + logging.warn(f"repo {repo_id}: unexpected json response in image request") + logging.warn(f" response: {response.data.decode('utf-8')}") + image_cache[image_id]['exists'] = False + return + if response and response.status == 200: + image_cache[image_id]['exists'] = True + try: + with open(filename, 'wb') as f: + f.write(response.data) + except Exception as err: + logging.error("An exception occurred writing a cache file to disk") + logging.error(err) + +""" ---------------------------------------------------------------- +""" +def requestReports(repo_id): + # If this request has already been fulfilled, no need to process it again + if(repo_id in report_requests.keys()): + return + + # initialize a new request entry to hold the resulting data + report_requests[repo_id] = {} + report_requests[repo_id]['complete'] = False + + """ ---------- + If the report definition could not be loaded, we cannot determine what + files to request from the backend to compose the report. Returning here + causes the completion status of the request to be False, which will + display an error message when sent to the frontend. + """ + if reports is None: + return + + threadPools = [] + reportImages = {} + for report in reports: + # Reports is a dictionary of lists, so we get the size of each list + size = len(reports[report]) + + # Set up various threading components to manage image downloading + connection_mgr = urllib3.PoolManager(maxsize=size) + thread_pool = ThreadPoolExecutor(size) + threadPools.append(thread_pool) + + for image in reports[report]: + # Where should the downloaded image be stored (in cache) + filename = toCacheFilename(f"{image['url']}?repo_id={repo_id}") + # Where are we downloading the image from + image_url = f"{getSetting('serving')}/{image['url']}?repo_id={repo_id}" + # Add a request for this image to the thread pool using the download function + thread_pool.submit(download, image_url, connection_mgr, filename, reportImages, image['id'], repo_id) + + # Wait for all connections to resolve, then clean up + for thread_pool in threadPools: + thread_pool.shutdown() + + report_requests[repo_id]['images'] = reportImages + + # Remove the request from the queue when completed + report_requests[repo_id]['complete'] = True + +""" ---------------------------------------------------------------- +renderRepos: + This function renders a list of repos using a given view, while passing query + data along. This function also processes pagination automatically for the + range of data provided. If a query is provided and filtering is enabled, the + data will be filtered using the 'repo_name', 'repo_group_id' or 'rg_name'. +@PARAM: view: String + A string representing the template to use for displaying the repos. +@PARAM: query: String + The query argument from the previous page. +@PARAM: data: Dictionary + The repo data to display on the page +@PARAM: sorting: String = None + The key in the data to sort by +@PARAM: rev: Boolean = False + Determines if the sorted data should be displayed in descending order +@PARAM: page: String = None + The current page to use within pagination +@PARAM: filter: Boolean = False + Filter data using query +@PARAM: pageSource: String = "repos/views/table" + The base url to use for the page links +""" +def renderRepos(view, query, data, sorting = None, rev = False, page = None, filter = False, pageSource = "repo_table_view", sortBasis = None): + pagination_offset = getSetting('pagination_offset') + + """ ---------- + If the data does not exist, we cannot construct the table to display on + site. Rendering the table module without data displays an error message + """ + if(data is None): + return render_template('index.html', body="repos-" + view, title="Repos") + + # If a query exists and filtering is set to true, attempt to filter the data + if((query is not None) and filter): + results = [] + for repo in data: + if (query in repo["repo_name"]) or (query == str(repo["repo_group_id"])) or (query in repo["rg_name"]): + results.append(repo) + data = results + + # Determine the maximum number of pages which can be displayed from the data + pages = math.ceil(len(data) / pagination_offset) + + if page is not None: + page = int(page) + else: + page = 1 + + """ ---------- + Caller requested sorting of the data. The data is a list of dictionaries + with numerous sortable elements, and the "sorting" parameter is assumed + to be the key of the desired element in the dictionary by which to sort. + + We need the "or 0" here to ensure the comparison is valid for rows which + do not have data for the requested column (we're making the assumption + that the data type is comparable to integer 0). + """ + if sorting is not None: + try: + data = sorted(data, key = lambda i: i[sorting] or 0, reverse = rev) + except Exception as e: + flash("An error occurred during sorting") + logger.error(str(e)) + + """ ---------- + Here we extract a subset of the data for display on the site. First we + calculate the start index within the data of our current "page" (x), + then we index to that position plus the pagination offset (or page size) + defined above. The result is a list which contains *at most* a number of + entries equal to the pagination offset + """ + x = pagination_offset * (page - 1) + data = data[x: x + pagination_offset] + + return render_module("repos-" + view, title="Repos", repos=data, query_key=query, activePage=page, pages=pages, offset=pagination_offset, PS=pageSource, reverse = rev, sorting = sorting) + +""" ---------------------------------------------------------------- + Renders a simple page with the given message information, and optional page + title and redirect +""" +def renderMessage(messageTitle, messageBody, title = None, redirect = None, pause = None): + return render_module("notice", messageTitle=messageTitle, messageBody=messageBody, title=title, redirect=redirect, pause=pause) + +""" ---------------------------------------------------------------- +""" +def render_module(module, **args): + # args.setdefault("title", "Augur View") + args.setdefault("api_url", getSetting("serving")) + args.setdefault("body", module) + + if not getSetting("valid"): + args.setdefault("invalid", True) + + return render_template('index.html', **args) + +""" ---------------------------------------------------------------- + No longer used +""" +# My attempt at a loading page +def renderLoading(dest, query, request): + cache_files_requested.append(request) + return render_template('index.html', body="loading", title="Loading", d=dest, query_key=query, api_url=getSetting('serving')) diff --git a/augur/static/css/dashboard.css b/augur/static/css/dashboard.css new file mode 100644 index 0000000000..6be0de9643 --- /dev/null +++ b/augur/static/css/dashboard.css @@ -0,0 +1,45 @@ +:root { + --color-bg: #1A233A; + --color-bg-light: #272E48; + --color-fg: white; + --color-fg-contrast: black; + --color-accent: #6f42c1; + --color-accent-dark: #6134b3; + --color-notice: #00ddff; + --color-notice-contrast: #006979; +} + +body { + background-color: var(--color-bg); + color: var(--color-fg); + overflow: hidden; +} + +.content-column { + overflow-y: scroll; +} + +.dashboard-content { + background-color: var(--color-bg-light); + margin-top: 10px; + margin-bottom: 10px; +} + +.nav-pills .nav-link.active, .nav-pills .show > .nav-link { + background-color: var(--color-accent); +} + +.dashboard-sidebar { + width: 280px; + background-color: var(--color-bg-light) !important; +} + +.form-control { + border: 1px solid #596280; + -webkit-border-radius: 2px; + -moz-border-radius: 2px; + border-radius: 2px; + font-size: .825rem; + background: #1A233A; + color: #bcd0f7; +} diff --git a/augur/static/css/first_time.css b/augur/static/css/first_time.css new file mode 100644 index 0000000000..12f8ae9f54 --- /dev/null +++ b/augur/static/css/first_time.css @@ -0,0 +1,148 @@ +body{ + margin-top:20px; + color: #bcd0f7; + background: #1A233A; +} +h1 { + font-size: 2rem; +} +.sidebar .sidebar-top { + margin: 0 0 1rem 0; + padding-bottom: 1rem; + text-align: center; +} +.sidebar .sidebar-top .brand-logo { + margin: 0 0 1rem 0; +} +.sidebar .sidebar-top .brand-logo img { + height: 90px; + -webkit-border-radius: 100px; + -moz-border-radius: 100px; + border-radius: 100px; +} +.sidebar .about { + margin: 1rem 0 0 0; + font-size: 0.8rem; + text-align: center; +} +.card { + background: #272E48; + -webkit-border-radius: 5px; + -moz-border-radius: 5px; + border-radius: 5px; + border: 0; + margin-bottom: 1rem; +} +.form-control { + border: 1px solid #596280; + -webkit-border-radius: 2px; + -moz-border-radius: 2px; + border-radius: 2px; + font-size: .825rem; + background: #1A233A; + color: #bcd0f7; +} +.modal-content { + color: black; +} +.editor-container { + height: 300px !important; +} + +.spinner { + -webkit-animation: rotator 1.4s linear infinite; + animation: rotator 1.4s linear infinite; +} + +.spinner-container { + display: flex; + align-items: center; + justify-content: center; +} + +@-webkit-keyframes rotator { + 0% { + transform: rotate(0deg); + } + 100% { + transform: rotate(270deg); + } +} + +@keyframes rotator { + 0% { + transform: rotate(0deg); + } + 100% { + transform: rotate(270deg); + } +} +.path { + stroke-dasharray: 187; + stroke-dashoffset: 0; + transform-origin: center; + -webkit-animation: dash 1.4s ease-in-out infinite, colors 5.6s ease-in-out infinite; + animation: dash 1.4s ease-in-out infinite, colors 5.6s ease-in-out infinite; +} + +@-webkit-keyframes colors { + 0% { + stroke: #4285F4; + } + 25% { + stroke: #DE3E35; + } + 50% { + stroke: #F7C223; + } + 75% { + stroke: #1B9A59; + } + 100% { + stroke: #4285F4; + } +} + +@keyframes colors { + 0% { + stroke: #4285F4; + } + 25% { + stroke: #DE3E35; + } + 50% { + stroke: #F7C223; + } + 75% { + stroke: #1B9A59; + } + 100% { + stroke: #4285F4; + } +} +@-webkit-keyframes dash { + 0% { + stroke-dashoffset: 187; + } + 50% { + stroke-dashoffset: 46.75; + transform: rotate(135deg); + } + 100% { + stroke-dashoffset: 187; + transform: rotate(450deg); + } +} +@keyframes dash { + 0% { + stroke-dashoffset: 187; + } + 50% { + stroke-dashoffset: 46.75; + transform: rotate(135deg); + } + 100% { + stroke-dashoffset: 187; + transform: rotate(450deg); + } +} diff --git a/augur/static/css/stylesheet.css b/augur/static/css/stylesheet.css new file mode 100644 index 0000000000..171d86b884 --- /dev/null +++ b/augur/static/css/stylesheet.css @@ -0,0 +1,424 @@ +:root { + --color-bg: #252525; + --color-bg-light: #4a4651; + --color-fg: white; + --color-fg-contrast: black; + --color-accent: #6f42c1; + --color-accent-dark: #6134b3; + --color-notice: #00ddff; + --color-notice-contrast: #006979; + --color-link: #5de4ff +} + +html, +body { + /* IE 10-11 didn't like using min-height */ + height: 100%; +} + +body { + display: flex; + flex-direction: column; + background-color: var(--color-bg); +} + +.hidden { + display: none; +} + +.content { + flex: 1 0 auto; + /* Prevent Chrome, Opera, and Safari from letting these items shrink to smaller than their content's default minimum size. */ + padding: 20px; + padding-top: 100px; + color: var(--color-fg); + text-align: center; +} + +.footer { + flex-shrink: 0; + /* Prevent Chrome, Opera, and Safari from letting these items shrink to smaller than their content's default minimum size. */ + padding: 5px; + background-color: var(--color-bg-light); + width: 100%; +} + +.nav-image { + width: 100px; +} + +.nav-separator { + background-color: var(--color-accent-dark); + max-width: 5px; + min-width: 5px; + height: 35px; +} + +.notification-icon { + height: 30px; + -webkit-filter: invert(100%); + /* safari 6.0 - 9.0 */ + filter: invert(100%); +} + +.submitContainer { + background-color: var(--color-accent); +} + +.toast-container { + top: 80px !important; + right: 16px !important; +} + +.toast { + background-color: var(--color-notice); + color: var(--color-fg); +} + +#toast-placeholder { + display: none; +} + +.dashboard-sidebar { + height: 100%; +} + +.display-table { + background-color: white !important; + overflow: auto; +} + +.paginationActive { + background-color: var(--color-accent-dark); + border-color: var(--color-accent-dark); + color: var(--color-fg); +} + +.sorting-link { + color: var(--color-fg-contrast); + text-decoration: none; +} + +/* User settings page */ + +.user-settings-form { + width: 30%; + min-width: 300px; + margin: auto; +} + +.user-settings-form label { + margin-top: 10px; +} + +.user-card { + background-color: var(--color-bg-light); + margin-bottom: 40px; +} + +.user-card a { + color: var(--color-link); +} + +/* Login Page */ + +#registration-div { + -webkit-transition: opacity 0.5s ease; + -moz-transition: opacity 0.5s ease; + -ms-transition: opacity 0.5s ease; + -o-transition: opacity 0.5s ease; + transition: opacity 0.5s ease; +} + +form i { + pointer-events: none; +} + +.password-toggle { + background-color: var(--color-fg); + border: 1px solid #ced4da; + border-top-left-radius: 0; + border-bottom-left-radius: 0; +} + +/* Image Zoom */ + +img[id^="report_image_"] { + border-radius: 5px; + cursor: pointer; + transition: 0.3s; +} + +img[id^="report_image_"]:hover { + filter: brightness(50%); +} + +/* The Modal (background) */ +.modal { + display: none; + /* Hidden by default */ + position: fixed; + /* Stay in place */ + z-index: 1; + /* Sit on top */ + padding-top: 100px; + /* Location of the box */ + left: 0; + top: 0; + width: 100%; + /* Full width */ + height: 100%; + /* Full height */ + overflow: auto; + /* Enable scroll if needed */ + background-color: rgb(0, 0, 0); + /* Fallback color */ + background-color: rgba(0, 0, 0, 0.9); + /* Black w/ opacity */ +} + +/* Modal Content (image) */ +.modal-content { + margin: auto; + display: block; + width: 70%; +} + +/* Caption of Modal Image */ +#caption { + margin: auto; + display: block; + width: 80%; + max-width: 700px; + text-align: center; + color: #ccc; + padding: 10px 0; + height: 80px; +} + +#close-caption { + margin: auto; + display: block; + width: 80%; + max-width: 700px; + text-align: center; + color: #ccc; + padding: 10px 0; + height: 50px; +} + +/* Add Animation */ +.modal-content, +#caption { + -webkit-animation-name: zoom; + -webkit-animation-duration: 0.6s; + animation-name: zoom; + animation-duration: 0.6s; +} + +@-webkit-keyframes zoom { + from { + -webkit-transform: scale(0) + } + + to { + -webkit-transform: scale(1) + } +} + +@keyframes zoom { + from { + transform: scale(0) + } + + to { + transform: scale(1) + } +} + +/* The Close Button */ +.close { + position: absolute; + top: 45px; + right: 35px; + color: #f1f1f1; + font-size: 40px; + font-weight: bold; + transition: 0.3s; +} + +.close:hover, +.close:focus { + color: #bbb; + text-decoration: none; + cursor: pointer; +} + +/* 100% Image Width on Smaller Screens */ +@media only screen and (max-width: 700px) { + .modal-content { + width: 100%; + } +} + +.img_placeholder { + width: 256px; + height: 256px; +} + +.card-footer-wrap { + width: 256px; + +} + +/* Loading Animation */ + +.dot-flashing { + position: relative; + width: 10px; + height: 10px; + border-radius: 5px; + background-color: #9880ff; + color: #9880ff; + animation: dotFlashing 1s infinite linear alternate; + animation-delay: .5s; +} + +.dot-flashing::before, +.dot-flashing::after { + content: ''; + display: inline-block; + position: absolute; + top: 0; +} + +.dot-flashing::before { + left: -15px; + width: 10px; + height: 10px; + border-radius: 5px; + background-color: #9880ff; + color: #9880ff; + animation: dotFlashing 1s infinite alternate; + animation-delay: 0s; +} + +.dot-flashing::after { + left: 15px; + width: 10px; + height: 10px; + border-radius: 5px; + background-color: #9880ff; + color: #9880ff; + animation: dotFlashing 1s infinite alternate; + animation-delay: 1s; +} + +@keyframes dotFlashing { + 0% { + background-color: #9880ff; + } + + 50%, + 100% { + background-color: #ebe6ff; + } +} + +.spinner { + -webkit-animation: rotator 1.4s linear infinite; + animation: rotator 1.4s linear infinite; +} + +.spinner-container { + display: flex; + align-items: center; + justify-content: center; +} + +@-webkit-keyframes rotator { + 0% { + transform: rotate(0deg); + } + 100% { + transform: rotate(270deg); + } +} + +@keyframes rotator { + 0% { + transform: rotate(0deg); + } + 100% { + transform: rotate(270deg); + } +} +.path { + stroke-dasharray: 187; + stroke-dashoffset: 0; + transform-origin: center; + -webkit-animation: dash 1.4s ease-in-out infinite, colors 5.6s ease-in-out infinite; + animation: dash 1.4s ease-in-out infinite, colors 5.6s ease-in-out infinite; +} + +@-webkit-keyframes colors { + 0% { + stroke: #4285F4; + } + 25% { + stroke: #DE3E35; + } + 50% { + stroke: #F7C223; + } + 75% { + stroke: #1B9A59; + } + 100% { + stroke: #4285F4; + } +} + +@keyframes colors { + 0% { + stroke: #4285F4; + } + 25% { + stroke: #DE3E35; + } + 50% { + stroke: #F7C223; + } + 75% { + stroke: #1B9A59; + } + 100% { + stroke: #4285F4; + } +} +@-webkit-keyframes dash { + 0% { + stroke-dashoffset: 187; + } + 50% { + stroke-dashoffset: 46.75; + transform: 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+
+
+
+ Dashboard +
+
+ +
+
+ + Augur logo + + {# Reserved for future use + + #} +
+
+ {# Start dashboard content #} +
+

Stats

+ {# Start content card #} +
+
+ {# Start form body #} +
+ {% for section in sections %} +
+
+
{{ section.title }}
+
+ {% for setting in section.settings %} +
+
+ + +
{{ setting.description or "No description available" }}
+
+
+ {% endfor %} +
+ {% endfor %} + {#
+
+ +
+
#} +
+
+
+

User Accounts

+ {# Start content card #} +
+
+
+ {% for section in sections %} +
+
+
{{ section.title }}
+
+ {% for setting in section.settings %} +
+
+ + +
{{ setting.description or "No description available" }}
+
+
+ {% endfor %} +
+ {% endfor %} + {#
+
+ +
+
#} +
+
+
+

Configuration

+ {# Start content card #} +
+
+
+ {% for section in config.items() %} +
+
+
{{ section[0] }}
+
+ {% for setting in section[1].items() %} +
+
+ + +
No description available
+
+
+ {% endfor %} +
+ {% endfor %} +
+
+ +
+
+
+
+
+
+
+
+ + + + diff --git a/augur/templates/first-time.html b/augur/templates/first-time.html new file mode 100644 index 0000000000..c8eb284da8 --- /dev/null +++ b/augur/templates/first-time.html @@ -0,0 +1,211 @@ +{# https://www.bootdey.com/snippets/view/dark-profile-settings #} + + + + + + + + + + + + + + +
+
+ {# Start sidebar #} +
+
+
+
+
+ +
+
+

First Time Setup

+

Take a moment to create or update the configuration for your instance.

+
+

Default values are shown. When you are done updating, click the restart button to save the settings and bring the primary server up.

+
+ +
+
+
+ {% if version %} + Version: {{ version.major }}-{{ version.minor }}-{{ version.series }} + {% else %} + Version: Unspecified + {% endif %} +
+
+
+ {# Start form body #} +
+
+
+
+ {% for section in sections %} +
+
+
{{ section.title }}
+
+ {% for setting in section.settings %} +
+
+ + +
{{ setting.description }}
+
+
+ {% endfor %} +
+ {% endfor %} +
+
+
Gunicorn Settings
+
+
+
+
{{ gunicorn_placeholder }}
+
+
+
+
+
+ +
+
+
+
+
+
+
+
+ + + + + + + diff --git a/augur/templates/groups-table.html b/augur/templates/groups-table.html new file mode 100644 index 0000000000..abe57a5774 --- /dev/null +++ b/augur/templates/groups-table.html @@ -0,0 +1,33 @@ +{% if groups %} +
+ + + + + + + + + + + + + {% for group in groups %} + + + + + + + + + + {% endfor %} + +
#Group NameGroup IDDescriptionLast ModifiedData Collection Date
{{loop.index}}{{ group.rg_name }}{{ group.repo_group_id }}{{ group.rg_description }}{{ group.rg_last_modified }}{{ group.data_collection_date }}TODO
+
+{% elif query_key %} +

Your search did not match any results

+{% else %} +

Unable to load group information

+{% endif %} diff --git a/augur/templates/index.html b/augur/templates/index.html new file mode 100644 index 0000000000..1049e4b777 --- /dev/null +++ b/augur/templates/index.html @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + {% if title %} + {{title}} - Augur View + {% else %} + Augur View + {% endif %} + + {% if redirect %} + + {% endif %} + + + + + + + {% include 'notifications.html' %} + + {% include 'navbar.html' %} + +
+ {% if invalid %} +

Invalid API URL

+

The API URL [{{ api_url or 'unspecified'}}] is invalid

+ {% elif body %} + {% include '%s.html' % body ignore missing %} + {% else %} +

404 - Page Not Found

+

The page you were looking for isn't here, try clicking one of the navigation links above

+ {% endif %} +
+ +
+
+
+

This is a beta build of Augur-View. Experimental frontend features may not be fully functional.

+

Currently serving: {{api_url or 'api_url unspecified'}}

+
+
+ + Chaos Logo + +
+
+
+ + diff --git a/augur/templates/loading.html b/augur/templates/loading.html new file mode 100644 index 0000000000..052af79eab --- /dev/null +++ b/augur/templates/loading.html @@ -0,0 +1,14 @@ +{% if not d %} +

Uh oh, Something went wrong!

+

You were sent to this page because we were loading something for you, but we didn't catch your destination.

+

Go back to the previous page and try again. If that doesn't help, submit an issue to https://github.com/chaoss/augur .

+{% else %} + +

Give us a moment!

+

We are retreiving some data for you, and it may take up to a few seconds to load.

+

If you aren't redirected in a few seconds, go back to the previous page and try again.

+ +

Redirecting to: {{url_for('root', path=d)}}

+{% endif %} diff --git a/augur/templates/login.html b/augur/templates/login.html new file mode 100644 index 0000000000..72744d780a --- /dev/null +++ b/augur/templates/login.html @@ -0,0 +1,157 @@ +
+
+ +
+
+ + + + \ No newline at end of file diff --git a/augur/templates/navbar.html b/augur/templates/navbar.html new file mode 100644 index 0000000000..e84c639a9b --- /dev/null +++ b/augur/templates/navbar.html @@ -0,0 +1,67 @@ + diff --git a/augur/templates/notice.html b/augur/templates/notice.html new file mode 100644 index 0000000000..46ed7ead66 --- /dev/null +++ b/augur/templates/notice.html @@ -0,0 +1,6 @@ +{% if messageTitle %} +

{{messageTitle}}

+{% endif %} +{% if messageBody %} +

{{messageBody}}

+{% endif %} diff --git a/augur/templates/notifications.html b/augur/templates/notifications.html new file mode 100644 index 0000000000..b59c673391 --- /dev/null +++ b/augur/templates/notifications.html @@ -0,0 +1,79 @@ +{% with messages = get_flashed_messages() %} + +
+ {% if messages %} + {% for message in messages %} + + {% endfor %} + {% endif %} +
+ + + + +{% endwith %} + diff --git a/augur/templates/repo-commits.html b/augur/templates/repo-commits.html new file mode 100644 index 0000000000..e69de29bb2 diff --git a/augur/templates/repo-info.html b/augur/templates/repo-info.html new file mode 100644 index 0000000000..e5aa225ec9 --- /dev/null +++ b/augur/templates/repo-info.html @@ -0,0 +1,128 @@ + + +
+
+ {% if repo.repo_id %} +

Report for: {{ repo.repo_name|title }}

+

https://{{ repo.url }}

+ {% for report in reports %} +

{{ report|replace("_", " ")|title }}

+ {% for image in images[report] %} +
+
+
+
+
+
+ {{ image['description'] }} +
+
+
+ {% endfor %} + {% endfor %} + {% else %} +

Repository {{ repo_id }} not found

+ {% endif %} +

+
+{% if repo.repo_id %} +{# Wait for cache response: + This method queries the server from the client, asking for confirmation + of which images are available on the server. The server will asynchronously + download the requested images as the page is loading, then once the page + loads, the client will query a locking endpoint on the server and wait + for a response. +#} + +{% endif %} + + + + + + diff --git a/augur/templates/repos-card.html b/augur/templates/repos-card.html new file mode 100644 index 0000000000..9bd6cc4f38 --- /dev/null +++ b/augur/templates/repos-card.html @@ -0,0 +1,27 @@ +{% if repos %} +
+
+ {% for repo in repos %} +
+
+
+
+
{{ repo.repo_name }}
 +

Repository Status: {{ repo.repo_status }}

+

All Time Commits: {{ repo.commits_all_time|int }}

+

All Time Issues: {{ repo.issues_all_time|int }}

+
+
+ Repository ID: {{ repo.repo_id }} +
+
+
+
+ {% endfor %} +
+
+{% elif query_key %} +

Your search did not match any repositories

+{% else %} +

Unable to load repository information

+{% endif %} diff --git a/augur/templates/repos-table.html b/augur/templates/repos-table.html new file mode 100644 index 0000000000..96e6563b25 --- /dev/null +++ b/augur/templates/repos-table.html @@ -0,0 +1,92 @@ +{% if repos %} + + + +{# Create the header row for the repo table: + Here we dynamically generate the header row by defining a dictionary list + which contains the titles of each column, accompanied by an optional "key" + item. If a column definition contains a "key" item, that column is assumed + to be sortable, sorting links for that data are generated using the given + key. It is done this way because the client does not receive the full data + each time they load the page, and instead the server sorts the full data. +#} +{%- set tableHeaders = + [{"title" : "#"}, + {"title" : "Repo Name", "key" : "repo_name"}, + {"title" : "Group", "key" : "rg_name"}, + {"title" : "Reports"}, + {"title" : "Commits", "key" : "commits_all_time"}, + {"title" : "Issues", "key" : "issues_all_time"}, + {"title" : "Change Requests"}] -%} +
+ + + + + {%- for header in tableHeaders -%} + {% if header.key %} + {%- if sorting == header.key -%} + {%- set sorting_link = url_for(PS, q=query_key, p=activePage, s=header.key, r= not reverse) -%} + {%- else -%} + {%- set sorting_link = url_for(PS, q=query_key, p=activePage, s=header.key) -%} + {%- endif -%} + + {% else -%} + + {% endif %} {%- endfor -%} + + + + + {% for repo in repos %} + + + + + + + + + + {% endfor %} + +
{{ header.title }} + {%- if sorting == header.key and reverse %} ▲ {% elif sorting == header.key %} ▼ {% endif %}{{ header.title }}
{{loop.index + (activePage - 1) * offset}}{{ repo.repo_name }}{{ repo.rg_name }}TODO{{ repo.commits_all_time|int }}{{ repo.issues_all_time|int }}TODO
+
+ +
+ +{% elif query_key %} +

Your search did not match any repositories

+{% elif current_user.is_authenticated %} +

No Repos Tracked

+

Add repos to your personal tracker in your profile page

+{% else %} +

Unable to load repository information

+{% endif %} diff --git a/augur/templates/settings.html b/augur/templates/settings.html new file mode 100644 index 0000000000..9a6052fe02 --- /dev/null +++ b/augur/templates/settings.html @@ -0,0 +1,139 @@ +
+
+
+
+
+

{{ current_user.id }}

+ Delete Account +
+
+ User Profile +
+
+
+
+

Update Password

+ +
+
+
+
+
+

Your Repo Groups

+ {%- set groups = current_user.get_groups() -%} + {% if groups %} + {% for group in groups %} + {%- set tableHeaders = + [{"title" : "Group ID"}, + {"title" : "Group Name"}] + -%} +
+ + + + + {%- for header in tableHeaders -%} + + {%- endfor -%} + + + + + {% for repo in repos %} + + + + + {% endfor %} + +
{{ header.title }}
{{ group.group_id }}{{ group.name }}
+
+ {% else %} +

No repos selected

+ {% endif %} +
+
+
+

Add Repos

+ +
+
+
+ + + \ No newline at end of file diff --git a/augur/templates/status.html b/augur/templates/status.html new file mode 100644 index 0000000000..80a9ff05c9 --- /dev/null +++ b/augur/templates/status.html @@ -0,0 +1,233 @@ + + + +

Collection Status

+
+
+
+

Pull Requests

+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

Issues

+
+
+
+
+
+
+
+

Time between most recently collected issue and last collection run

+
+
+
+
+
+
+
+

Commits

+
+
+
+
+
+
+
+ +
+
+ + diff --git a/augur/templates/toasts.html b/augur/templates/toasts.html new file mode 100644 index 0000000000..cf707754f2 --- /dev/null +++ b/augur/templates/toasts.html @@ -0,0 +1,60 @@ +{% with messages = get_flashed_messages() %} +
+ {% if messages %} + {% for message in messages %} + + {% endfor %} + {% endif %} +
+ +{% endwith %} + + + + diff --git a/setup.py b/setup.py index 80891ead96..75f424036d 100644 --- a/setup.py +++ b/setup.py @@ -39,7 +39,7 @@ "Beaker==1.11.0", # 1.11.0 "SQLAlchemy==1.3.23", # 1.4.40 "itsdangerous==2.0.1", # 2.1.2 - "Jinja2==3.0.2", # 3.1.2 + 'Jinja2~=3.0.3', "Flask==2.0.2", # 2.2.2 "Flask-Cors==3.0.10", "Flask-Login==0.5.0", @@ -77,6 +77,7 @@ "eventlet==0.33.1", "flower==1.2.0", "tornado==6.1", # added because it sometimes errors when tornado is not 6.1 even though nothing we install depends on it + 'Werkzeug~=2.0.0', "pylint==2.15.5" ], extras_require={ From 95702ed5325c47793881bf3978861d6cf4c65206 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 5 Jan 2023 19:56:05 -0600 Subject: [PATCH 044/150] Convert augur view login logic to the user orm model Signed-off-by: Andrew Brain --- augur/api/view/augur_view.py | 11 +- augur/api/view/routes.py | 39 ++++-- .../application/db/models/augur_operations.py | 118 ++++++++++++++++++ 3 files changed, 156 insertions(+), 12 deletions(-) diff --git a/augur/api/view/augur_view.py b/augur/api/view/augur_view.py index 5eb5cf55df..ff25847906 100644 --- a/augur/api/view/augur_view.py +++ b/augur/api/view/augur_view.py @@ -2,7 +2,9 @@ from flask_login import LoginManager from .utils import * from .url_converters import * -from .server import User +# from .server import User +from augur.application.db.models import User +from augur.application.db.session import DatabaseSession login_manager = LoginManager() @@ -31,14 +33,17 @@ def unauthorized(): @login_manager.user_loader def load_user(user_id): - user = User(user_id) - if not user.exists: + user = User.get_user(user_id) + + if not user: return None # The flask_login library sets a unique session["_id"] # when login_user() is called successfully if session.get("_id") is not None: + + # TODO: Add these as properties user._is_authenticated = True user._is_active = True diff --git a/augur/api/view/routes.py b/augur/api/view/routes.py index 5fe14b94e3..3c7281114a 100644 --- a/augur/api/view/routes.py +++ b/augur/api/view/routes.py @@ -1,8 +1,15 @@ +import logging from flask import Flask, render_template, render_template_string, request, abort, jsonify, redirect, url_for, session, flash +from sqlalchemy.orm.exc import NoResultFound from .utils import * from flask_login import login_user, logout_user, current_user, login_required -from .server import User +# from .server import User +from augur.application.db.models import User from .server import LoginException +from augur.application.db.session import DatabaseSession + +logger = logging.getLogger(__name__) + # ROUTES ----------------------------------------------------------------------- @@ -123,23 +130,37 @@ def status_view(): def user_login(): if request.method == 'POST': try: - user_id = request.form.get('username') + username = request.form.get('username') remember = request.form.get('remember') is not None - if user_id is None: + password = request.form.get('password') + + if username is None: raise LoginException("A login issue occurred") - user = User(user_id) + # test if the user does not exist then the login is invalid + user = User.get_user(username) + if not user and not request.form.get('register'): + raise LoginException("Invalid login credentials") + # register a user if request.form.get('register') is not None: - if user.exists: + if user: raise LoginException("User already exists") - if not user.register(request): + + email = request.form.get('email') + first_name = request.form.get('first_name') + last_name = request.form.get('last_name') + admin = request.form.get('admin') + + result = User.create_user(username, password, email, first_name, last_name, admin) + if "Error" in result.keys(): raise LoginException("An error occurred registering your account") else: - flash("Account successfully created") + flash(result["status"]) - if user.validate(request) and login_user(user, remember = remember): - flash(f"Welcome, {user_id}!") + # Log the user in if the password is valid + if User.validate(password) and login_user(user, remember = remember): + flash(f"Welcome, {username}!") if "login_next" in session: return redirect(session.pop("login_next")) return redirect(url_for('root')) diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index 4ddb30b5fb..e08b961607 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -1,6 +1,12 @@ # coding: utf-8 from sqlalchemy import BigInteger, SmallInteger, Column, Index, Integer, String, Table, text, UniqueConstraint, Boolean, ForeignKey from sqlalchemy.dialects.postgresql import TIMESTAMP, UUID +from sqlalchemy.orm.exc import NoResultFound +from werkzeug.security import generate_password_hash, check_password_hash +import logging + +logger = logging.getLogger(__name__) + from augur.application.db.models.base import Base @@ -171,6 +177,7 @@ class Config(Base): # add admit column to database class User(Base): + user_id = Column(Integer, primary_key=True) login_name = Column(String, nullable=False) login_hashword = Column(String, nullable=False) @@ -195,6 +202,117 @@ class User(Base): groups = relationship("UserGroup") tokens = relationship("UserSessionToken") + _is_authenticated = False + _is_active = False + _is_anoymous = True + + @property + def is_authenticated(self): + return self._is_authenticated + + @is_authenticated.setter + def is_authenticated(self, val): + self._is_authenticated = val + + @property + def is_active(self): + return self._is_active + + @is_active.setter + def is_active(self, val): + self._is_active = val + + @property + def is_anoymous(self): + return self._is_anoymous + + @is_anoymous.setter + def is_anoymous(self, val): + self._is_anoymous = val + + @staticmethod + def exists(username): + return User.get_user(username) is not None + + def validate(self, password) -> bool: + + from augur.application.db.session import DatabaseSession + + if not password: + return False + + return check_password_hash(self.login_hashword, password) + + @staticmethod + def get_user(username: str): + + from augur.application.db.session import DatabaseSession + + with DatabaseSession(logger) as session: + try: + return session.query(User).filter(User.login_name == username).one() + except NoResultFound: + return None + + @staticmethod + def create_user(username: str, password: str, email: str, first_name:str, last_name:str, admin=False): + + from augur.application.db.session import DatabaseSession + + if username is None or password is None or email is None or first_name is None or last_name is None: + return {"status": "Missing field"} + + with DatabaseSession(logger) as session: + + user = session.query(User).filter(User.login_name == username).first() + if user is not None: + return {"status": "A User already exists with that username"} + + emailCheck = session.query(User).filter(User.email == email).first() + if emailCheck is not None: + return {"status": "A User already exists with that email"} + + try: + user = User(login_name = username, login_hashword = generate_password_hash(password), email = email, first_name = first_name, last_name = last_name, tool_source="User API", tool_version=None, data_source="API", admin=admin) + session.add(user) + session.commit() + return {"status": "Account successfully created"} + except AssertionError as exception_message: + return {"Error": f"{exception_message}."} + + @staticmethod + def delete_user(): + + from augur.application.db.session import DatabaseSession + + def update_user(): + pass + + def add_group(): + + pass + + def remove_group(): + pass + + def add_repo(): + pass + + def remove_repo(): + pass + + def add_org(): + pass + + def get_groups(): + pass + + def get_group_repos(): + pass + + def get_group_repo_count(): + pass + class UserGroup(Base): group_id = Column(BigInteger, primary_key=True) From 626c15f930317546b9864dd6da9106642082f7d1 Mon Sep 17 00:00:00 2001 From: Andrew Brain <61482022+ABrain7710@users.noreply.github.com> Date: Fri, 6 Jan 2023 09:31:19 -0600 Subject: [PATCH 045/150] Outline user methods on the user orm class Signed-off-by: Andrew Brain <61482022+ABrain7710@users.noreply.github.com> --- .../application/db/models/augur_operations.py | 199 ++++++++++++++++-- 1 file changed, 182 insertions(+), 17 deletions(-) diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index e08b961607..cef0cceccd 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -285,33 +285,198 @@ def delete_user(): from augur.application.db.session import DatabaseSession - def update_user(): + def update_user(self): + + from augur.application.db.session import DatabaseSession pass - def add_group(): + def add_group(self, group_name): - pass + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController - def remove_group(): - pass + if group_name == "default": + return {"status": "Reserved Group Name"} + + with GithubTaskSession(logger) as session: - def add_repo(): - pass + repo_load_controller = RepoLoadController(gh_session=session) - def remove_repo(): - pass + result = repo_load_controller.add_user_group(self.user_id, group_name) - def add_org(): - pass + return result - def get_groups(): - pass + def remove_group(self, group_name): - def get_group_repos(): - pass + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + with GithubTaskSession(logger) as session: - def get_group_repo_count(): - pass + repo_load_controller = RepoLoadController(gh_session=session) + + result = repo_load_controller.remove_user_group(self.user_id, group_name) + + return result + + def add_repo(self, group_name, repo_url): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + with GithubTaskSession(logger) as session: + + repo_load_controller = RepoLoadController(gh_session=session) + + result = repo_load_controller.add_frontend_repo(repo_url, self.user_id, group_name) + + return result + + def remove_repo(self, group_name, repo_id): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + with GithubTaskSession(logger) as session: + + repo_load_controller = RepoLoadController(gh_session=session) + + result = repo_load_controller.remove_frontend_repo(repo_id, self.user_id, group_name) + + return result + + def add_org(self, group_name, org_url): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + with GithubTaskSession(logger) as session: + + repo_load_controller = RepoLoadController(gh_session=session) + + result = repo_load_controller.add_frontend_org(org, user.user_id, group_name) + + return result + + def get_groups(self): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + with GithubTaskSession(logger) as session: + + controller = RepoLoadController(session) + + user_groups = controller.get_user_groups(user.user_id) + + return {"groups": user_groups} + + def get_group_names(self): + + user_groups = self.get_groups()["groups"] + + group_names = [group.name for group in user_groups] + + return {"group_names": group_names} + + + + def get_group_repos(self, group_name, page=0, page_size=25, sort="repo_id", direction="ASC"): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + if not group_name: + return {"status": "Missing argument"} + + if direction and direction != "ASC" and direction != "DESC": + return {"status": "Invalid direction"} + + try: + page = int(page) + page_size = int(page_size) + except ValueError: + return {"status": "Page size and page should be integers"} + + if page < 0 or page_size < 0: + return {"status": "Page size and page should be postive"} + + + with GithubTaskSession(logger) as session: + + controller = RepoLoadController(session) + + group_id = controller.convert_group_name_to_id(user.user_id, group_name) + if group_id is None: + return {"status": "Group does not exist"} + + + order_by = sort if sort else "repo_id" + order_direction = direction if direction else "ASC" + + get_page_of_repos_sql = text(f""" + SELECT + augur_data.repo.repo_id, + augur_data.repo.repo_name, + augur_data.repo.description, + augur_data.repo.repo_git AS url, + augur_data.repo.repo_status, + a.commits_all_time, + b.issues_all_time, + rg_name, + augur_data.repo.repo_group_id + FROM + augur_data.repo + LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id + LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id + JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id + JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id + WHERE augur_operations.user_repos.group_id = {group_id} + ORDER BY {order_by} {order_direction} + LIMIT {page_size} + OFFSET {page*page_size}; + """) + + results = pd.read_sql(get_page_of_repos_sql, create_database_engine()) + results['url'] = results['url'].apply(lambda datum: datum.split('//')[1]) + + b64_urls = [] + for i in results.index: + b64_urls.append(base64.b64encode((results.at[i, 'url']).encode())) + results['base64_url'] = b64_urls + + data = results.to_json(orient="records", date_format='iso', date_unit='ms') + + return {"status": "success", "data": data} + + def get_group_repo_count(self, group_name): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + with GithubTaskSession(logger) as session: + + controller = RepoLoadController(session) + + group_id = controller.convert_group_name_to_id(user.user_id, group_name) + if group_id is None: + return {"status": "Group does not exist"} + + get_page_of_repos_sql = text(f""" + SELECT + count(*) + FROM + augur_data.repo + LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id + LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id + JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id + JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id + WHERE augur_operations.user_repos.group_id = {group_id} + """) + + result = session.fetchall_data_from_sql_text(get_page_of_repos_sql) + + return {"repos": result[0]["count"]} class UserGroup(Base): From dd9eed0c84282a40b5f00d25aacc96113e2d1980 Mon Sep 17 00:00:00 2001 From: Andrew Brain <61482022+ABrain7710@users.noreply.github.com> Date: Fri, 6 Jan 2023 09:49:29 -0600 Subject: [PATCH 046/150] Update routes to use orm functions Signed-off-by: Andrew Brain <61482022+ABrain7710@users.noreply.github.com> --- augur/api/routes/user.py | 228 ++++++++------------------------------- 1 file changed, 42 insertions(+), 186 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index e14cd8780d..afe3919139 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -10,6 +10,7 @@ import base64 import pandas as pd from flask import request, Response, jsonify +from flask_login import login_user, logout_user, current_user, login_required from werkzeug.security import generate_password_hash, check_password_hash from sqlalchemy.sql import text from sqlalchemy.orm import sessionmaker @@ -199,12 +200,20 @@ def query_user(user): return jsonify({"status": True}) + @server.app.route(f"/{AUGUR_API_VERSION}/user/test", methods=['POST']) + def test(): + if not development and not request.is_secure: + return generate_upgrade_request() + + test = request.args.get("test") + + return jsonify({"result": test}) + @server.app.route(f"/{AUGUR_API_VERSION}/user/create", methods=['POST']) def create_user(): if not development and not request.is_secure: return generate_upgrade_request() - session = Session() username = request.args.get("username") password = request.args.get("password") email = request.args.get("email") @@ -212,26 +221,13 @@ def create_user(): last_name = request.args.get("last_name") admin = request.args.get("create_admin") or False - if username is None or password is None or email is None: - # https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/400 - return jsonify({"status": "Missing argument"}), 400 - user = session.query(User).filter(User.login_name == username).first() - if user is not None: - return jsonify({"status": "User already exists"}) - emailCheck = session.query(User).filter(User.email == email).first() - if emailCheck is not None: - return jsonify({"status": "Email already exists"}) - try: - user = User(login_name = username, login_hashword = generate_password_hash(password), email = email, first_name = first_name, last_name = last_name, tool_source="User API", tool_version=None, data_source="API", admin=False) - session.add(user) - session.commit() - return jsonify({"status": "User created"}) - except AssertionError as exception_message: - return jsonify(msg='Error: {}. '.format(exception_message)), 400 + result = User.create_user(username, password, email, first_name, last_name, admin) + + return jsonify(result) + @server.app.route(f"/{AUGUR_API_VERSION}/user/remove", methods=['POST', 'DELETE']) - @api_key_required - @user_login_required + @login_required def delete_user(user): if not development and not request.is_secure: return generate_upgrade_request() @@ -251,8 +247,7 @@ def delete_user(user): return jsonify({"status": "User deleted"}), 200 @server.app.route(f"/{AUGUR_API_VERSION}/user/update", methods=['POST']) - @api_key_required - @user_login_required + @login_required def update_user(user): if not development and not request.is_secure: return generate_upgrade_request() @@ -289,8 +284,7 @@ def update_user(user): @server.app.route(f"/{AUGUR_API_VERSION}/user/add_repo", methods=['GET', 'POST']) - @api_key_required - @user_login_required + @login_required def add_user_repo(user): if not development and not request.is_secure: return generate_upgrade_request() @@ -298,40 +292,22 @@ def add_user_repo(user): repo = request.args.get("repo_url") group_name = request.args.get("group_name") - with GithubTaskSession(logger) as session: - - if repo is None or group_name is None: - return jsonify({"status": "Missing argument"}), 400 + result = user.add_repo(group_name, repo) - repo_load_controller = RepoLoadController(gh_session=session) - - result = repo_load_controller.add_frontend_repo(repo, user.user_id, group_name) - - return jsonify(result) + return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/add_group", methods=['GET', 'POST']) - @api_key_required - @user_login_required + @login_required def add_user_group(user): if not development and not request.is_secure: return generate_upgrade_request() group_name = request.args.get("group_name") - if group_name == "default": - return jsonify({"status": "Reserved Group Name"}) - - with GithubTaskSession(logger) as session: + result = user.add_group(group_name) - if group_name is None: - return jsonify({"status": "Missing argument"}), 400 - - repo_load_controller = RepoLoadController(gh_session=session) - - result = repo_load_controller.add_user_group(user.user_id, group_name) - - return jsonify(result) + return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_group", methods=['GET', 'POST']) @api_key_required @@ -341,24 +317,14 @@ def remove_user_group(user): return generate_upgrade_request() group_name = request.args.get("group_name") - - with GithubTaskSession(logger) as session: - - if group_name is None: - return jsonify({"status": "Missing argument"}), 400 - repo_load_controller = RepoLoadController(gh_session=session) + result = user.remove_group(group_name) - result = repo_load_controller.remove_user_group(user.user_id, group_name) - - return jsonify(result) - - + return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/add_org", methods=['GET', 'POST']) - @api_key_required - @user_login_required + @login_required def add_user_org(user): if not development and not request.is_secure: return generate_upgrade_request() @@ -366,48 +332,28 @@ def add_user_org(user): org = request.args.get("org_url") group_name = request.args.get("group_name") - with GithubTaskSession(logger) as session: - - if org is None or group_name is None: - return jsonify({"status": "Missing argument"}), 400 - - repo_load_controller = RepoLoadController(gh_session=session) + result = user.add_org(group_name, org_url) - result = repo_load_controller.add_frontend_org(org, user.user_id, group_name) - - return jsonify(result) + return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_repo", methods=['GET', 'POST']) - @api_key_required - @user_login_required + @login_required def remove_user_repo(user): if not development and not request.is_secure: return generate_upgrade_request() - try: - repo_id = int(request.args.get("repo_id")) - except ValueError: - return {"status": "repo_id must be an integer"} - group_name = request.args.get("group_name") + group_name = request.args.get("group_name") + repo_id = request.args.get("repo_id") - with GithubTaskSession(logger) as session: - - if repo_id is None or group_name is None: - return jsonify({"status": "Missing argument"}), 400 - - repo_load_controller = RepoLoadController(gh_session=session) - - result = repo_load_controller.remove_frontend_repo(repo_id, user.user_id, group_name) - - return jsonify(result) + result = user.remove_repo(group_name, repo_id) + return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repos", methods=['GET', 'POST']) - @api_key_required - @user_login_required + @login_required def group_repos(user): """Select repos from a user group by name @@ -436,76 +382,14 @@ def group_repos(user): return generate_upgrade_request() group_name = request.args.get("group_name") - - # Set default values for ancillary arguments page = request.args.get("page") or 0 page_size = request.args.get("page_size") or 25 - sort = request.args.get("sort") - direction = request.args.get("direction") or ("ASC" if sort else None) - - if not group_name: - return jsonify({"status": "Missing argument"}), 400 - - if direction and direction != "ASC" and direction != "DESC": - return jsonify({"status": "Invalid direction"}), 400 + sort = request.args.get("sort") or "repo_id" + direction = request.args.get("direction") or "ASC" - try: - page = int(page) - page_size = int(page_size) - except ValueError: - return jsonify({"status": "Page size and page should be integers"}), 400 + result = user.get_group_repos(group_name, page, page_size, sort, direction) - if page < 0 or page_size < 0: - return jsonify({"status": "Page size and page should be postive"}), 400 - - - with DatabaseSession(logger) as session: - - controller = RepoLoadController(session) - - group_id = controller.convert_group_name_to_id(user.user_id, group_name) - if group_id is None: - return jsonify({"status": "Group does not exist"}), 400 - - - order_by = sort if sort else "repo_id" - order_direction = direction if direction else "ASC" - - get_page_of_repos_sql = text(f""" - SELECT - augur_data.repo.repo_id, - augur_data.repo.repo_name, - augur_data.repo.description, - augur_data.repo.repo_git AS url, - augur_data.repo.repo_status, - a.commits_all_time, - b.issues_all_time, - rg_name, - augur_data.repo.repo_group_id - FROM - augur_data.repo - LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id - LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id - JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id - JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id - WHERE augur_operations.user_repos.group_id = {group_id} - ORDER BY {order_by} {order_direction} - LIMIT {page_size} - OFFSET {page*page_size}; - """) - - results = pd.read_sql(get_page_of_repos_sql, create_database_engine()) - results['url'] = results['url'].apply(lambda datum: datum.split('//')[1]) - - b64_urls = [] - for i in results.index: - b64_urls.append(base64.b64encode((results.at[i, 'url']).encode())) - results['base64_url'] = b64_urls - - data = results.to_json(orient="records", date_format='iso', date_unit='ms') - return Response(response=data, - status=200, - mimetype="application/json") + return jsonify(result) @@ -533,32 +417,9 @@ def group_repo_count(user): group_name = request.args.get("group_name") - if not group_name: - return jsonify({"status": "Missing argument"}), 400 - - with DatabaseSession(logger) as session: - - controller = RepoLoadController(session) - - group_id = controller.convert_group_name_to_id(user.user_id, group_name) - if group_id is None: - return jsonify({"status": "Group does not exist"}), 400 - - get_page_of_repos_sql = text(f""" - SELECT - count(*) - FROM - augur_data.repo - LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id - LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id - JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id - JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id - WHERE augur_operations.user_repos.group_id = {group_id} - """) - - result = session.fetchall_data_from_sql_text(get_page_of_repos_sql) - - return jsonify({"repos": result[0]["count"]}), 200 + result = user.group_repo_count(group_name) + + return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/groups", methods=['GET', 'POST']) @@ -581,13 +442,8 @@ def get_user_groups(user): if not development and not request.is_secure: return generate_upgrade_request() - with DatabaseSession(logger) as session: - - controller = RepoLoadController(session) - - user_groups = controller.get_user_groups(user.user_id) + result = user.get_groups() - group_names = [group.name for group in user_groups] + return jsonify(result) - return jsonify({"group_names": group_names}), 200 From 4e80daf968aba698836c45b9192d05fa6af062e2 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Fri, 6 Jan 2023 11:33:56 -0600 Subject: [PATCH 047/150] Fix some login bugs Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 28 ++++--------------- augur/api/view/augur_view.py | 6 +++- augur/api/view/routes.py | 13 +++++++-- .../application/db/models/augur_operations.py | 16 +++++++++-- 4 files changed, 34 insertions(+), 29 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index afe3919139..449f98b4ca 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -137,12 +137,10 @@ def validate_user(): return jsonify({"status": "Invalid username"}) if checkPassword == False: return jsonify({"status": "Invalid password"}) - - # TODO Generate user session token to be stored in client browser - token = "USER SESSION TOKEN" + login_user(user) - return jsonify({"status": "Validated", "session": token}) + return jsonify({"status": "Validated"}) @server.app.route(f"/{AUGUR_API_VERSION}/user/oauth", methods=['POST']) def oauth_validate(): @@ -182,8 +180,6 @@ def generate_session(): return jsonify({"status": "Validated", "username": user, "session": token}) @server.app.route(f"/{AUGUR_API_VERSION}/user/query", methods=['POST']) - @api_key_required - @user_login_required def query_user(user): if not development and not request.is_secure: return generate_upgrade_request() @@ -200,16 +196,7 @@ def query_user(user): return jsonify({"status": True}) - @server.app.route(f"/{AUGUR_API_VERSION}/user/test", methods=['POST']) - def test(): - if not development and not request.is_secure: - return generate_upgrade_request() - - test = request.args.get("test") - - return jsonify({"result": test}) - - @server.app.route(f"/{AUGUR_API_VERSION}/user/create", methods=['POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/create", methods=['GET', 'POST']) def create_user(): if not development and not request.is_secure: return generate_upgrade_request() @@ -310,8 +297,7 @@ def add_user_group(user): return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_group", methods=['GET', 'POST']) - @api_key_required - @user_login_required + @login_required def remove_user_group(user): if not development and not request.is_secure: return generate_upgrade_request() @@ -394,8 +380,7 @@ def group_repos(user): @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repo_count", methods=['GET', 'POST']) - @api_key_required - @user_login_required + @login_required def group_repo_count(user): """Count repos from a user group by name @@ -423,8 +408,7 @@ def group_repo_count(user): @server.app.route(f"/{AUGUR_API_VERSION}/user/groups", methods=['GET', 'POST']) - @api_key_required - @user_login_required + @login_required def get_user_groups(user): """Get a list of user groups by username diff --git a/augur/api/view/augur_view.py b/augur/api/view/augur_view.py index ff25847906..2347791d68 100644 --- a/augur/api/view/augur_view.py +++ b/augur/api/view/augur_view.py @@ -9,6 +9,7 @@ login_manager = LoginManager() def create_routes(server): + login_manager.init_app(server.app) server.app.secret_key = getSetting("session_key") @@ -34,15 +35,18 @@ def unauthorized(): @login_manager.user_loader def load_user(user_id): + print("Loading user") + user = User.get_user(user_id) if not user: + print("User not found") return None # The flask_login library sets a unique session["_id"] # when login_user() is called successfully if session.get("_id") is not None: - + # TODO: Add these as properties user._is_authenticated = True user._is_active = True diff --git a/augur/api/view/routes.py b/augur/api/view/routes.py index 3c7281114a..ef2e635ede 100644 --- a/augur/api/view/routes.py +++ b/augur/api/view/routes.py @@ -139,32 +139,39 @@ def user_login(): # test if the user does not exist then the login is invalid user = User.get_user(username) - if not user and not request.form.get('register'): + if not user and request.form.get('register'): raise LoginException("Invalid login credentials") # register a user if request.form.get('register') is not None: + print("Register user") if user: + print(f"User already exists: {user.__dict__}") raise LoginException("User already exists") email = request.form.get('email') first_name = request.form.get('first_name') last_name = request.form.get('last_name') - admin = request.form.get('admin') + admin = request.form.get('admin') or False result = User.create_user(username, password, email, first_name, last_name, admin) if "Error" in result.keys(): raise LoginException("An error occurred registering your account") else: + user = User.get_user(username) flash(result["status"]) # Log the user in if the password is valid - if User.validate(password) and login_user(user, remember = remember): + if user.validate(password): + + result = login_user(user, remember = remember) + print(result) flash(f"Welcome, {username}!") if "login_next" in session: return redirect(session.pop("login_next")) return redirect(url_for('root')) else: + print("Invalid login") raise LoginException("Invalid login credentials") except LoginException as e: flash(str(e)) diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index cef0cceccd..d9c7fcb15e 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -203,7 +203,7 @@ class User(Base): tokens = relationship("UserSessionToken") _is_authenticated = False - _is_active = False + _is_active = True _is_anoymous = True @property @@ -234,6 +234,9 @@ def is_anoymous(self, val): def exists(username): return User.get_user(username) is not None + def get_id(self): + return self.login_name + def validate(self, password) -> bool: from augur.application.db.session import DatabaseSession @@ -241,7 +244,10 @@ def validate(self, password) -> bool: if not password: return False - return check_password_hash(self.login_hashword, password) + result = check_password_hash(self.login_hashword, password) + print(f"Validating: {result}") + + return result @staticmethod def get_user(username: str): @@ -249,8 +255,11 @@ def get_user(username: str): from augur.application.db.session import DatabaseSession with DatabaseSession(logger) as session: + print("Get user") try: - return session.query(User).filter(User.login_name == username).one() + user = session.query(User).filter(User.login_name == username).one() + print(user.__dict__) + return user except NoResultFound: return None @@ -262,6 +271,7 @@ def create_user(username: str, password: str, email: str, first_name:str, last_n if username is None or password is None or email is None or first_name is None or last_name is None: return {"status": "Missing field"} + with DatabaseSession(logger) as session: user = session.query(User).filter(User.login_name == username).first() From 607d568cff0f190726f404de049d764539c8ff9b Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Fri, 6 Jan 2023 12:11:49 -0600 Subject: [PATCH 048/150] Add function to paginate all repos, user repos and group repos Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 83 ++++++++++++++++++++++++++++++ 1 file changed, 83 insertions(+) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index e96ec0676e..c399ced86e 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -511,3 +511,86 @@ def parse_org_url(self, url): # if the result is not None then the groups should be valid so we don't worry about index errors here return result.groups()[0] + + def paginate_repos(self, source, page=0, page_size=25, sort="repo_id", direction="ASC", **kwargs): + + + if not source: + return {"status": "Missing argument"} + + if source not in ["all", "user", "group"]: + return {"status": "Invalid source"} + + if direction and direction != "ASC" and direction != "DESC": + return {"status": "Invalid direction"} + + try: + page = int(page) + page_size = int(page_size) + except ValueError: + return {"status": "Page size and page should be integers"} + + if page < 0 or page_size < 0: + return {"status": "Page size and page should be postive"} + + order_by = sort if sort else "repo_id" + order_direction = direction if direction else "ASC" + + query = """ + SELECT + augur_data.repo.repo_id, + augur_data.repo.repo_name, + augur_data.repo.description, + augur_data.repo.repo_git AS url, + augur_data.repo.repo_status, + a.commits_all_time, + b.issues_all_time, + rg_name, + augur_data.repo.repo_group_id + FROM + augur_data.repo + LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id + LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id + JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id""" + + if source == "user": + + user = kwargs["user"] + group_ids = [group.group_id for group in user.groups] + + query.append("JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id") + query.append(f"WHERE augur_operations.user_repos.group_id in {str(group_ids)}") + + elif source == "group": + + with GithubTaskSession(logger) as session: + + controller = RepoLoadController(session) + user = kwargs["user"] + group_name = kwargs["group_name"] + + group_id = controller.convert_group_name_to_id(user, group_name) + if group_id is None: + return {"status": "Group does not exist"} + + query.append("JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id") + query.append(f"WHERE augur_operations.user_repos.group_id = {group_id}") + + query.append(f"ORDER BY {order_by} {order_direction}") + query.append(f"LIMIT {page_size}") + query.append(f"OFFSET {page*page_size};") + + get_page_of_repos_sql = text(base_query) + + results = pd.read_sql(get_page_of_repos_sql, create_database_engine()) + results['url'] = results['url'].apply(lambda datum: datum.split('//')[1]) + + b64_urls = [] + for i in results.index: + b64_urls.append(base64.b64encode((results.at[i, 'url']).encode())) + results['base64_url'] = b64_urls + + data = results.to_json(orient="records", date_format='iso', date_unit='ms') + + return {"status": "success", "data": data} + From 228bb7ac6a675455b408186ba5213a28c7917935 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Fri, 6 Jan 2023 15:20:11 -0600 Subject: [PATCH 049/150] A functions to paginate user, group and all repos Signed-off-by: Andrew Brain --- augur/api/routes/util.py | 29 ++++ .../application/db/models/augur_operations.py | 124 ++++++-------- augur/util/repo_load_controller.py | 156 +++++++++++++----- 3 files changed, 194 insertions(+), 115 deletions(-) diff --git a/augur/api/routes/util.py b/augur/api/routes/util.py index 8f9086b5ec..2c653d9594 100644 --- a/augur/api/routes/util.py +++ b/augur/api/routes/util.py @@ -13,6 +13,35 @@ AUGUR_API_VERSION = 'api/unstable' +def get_all_repos(self, page=0, page_size=25, sort="repo_id", direction="ASC"): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + with GithubTaskSession(logger) as session: + + with RepoLoadController(session) as controller: + + result = controller.paginate_repos("all", page, page_size, sort, direction) + + return result + +def get_all_repos_count(self): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + with GithubTaskSession(logger) as session: + + controller = RepoLoadController(session) + + result = controller.get_repo_count(source="all") + if result["status"] == "success": + return result["repos"] + + return result["status"] + + def create_routes(server): @server.app.route('/{}/repo-groups'.format(AUGUR_API_VERSION)) diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index d9c7fcb15e..fd7e0f7079 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -389,75 +389,58 @@ def get_group_names(self): return {"group_names": group_names} + def query_repos(self): + from augur.application.db.session import DatabaseSession + from augur.application.db.models.augur_data import Repo + + with DatabaseSession(logger) as session: + + return [repo.repo_id for repo in session.query(Repo).all()] + + + def get_repos(self, group_name, page=0, page_size=25, sort="repo_id", direction="ASC"): - def get_group_repos(self, group_name, page=0, page_size=25, sort="repo_id", direction="ASC"): - from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController - - if not group_name: - return {"status": "Missing argument"} - if direction and direction != "ASC" and direction != "DESC": - return {"status": "Invalid direction"} + with GithubTaskSession(logger) as session: - try: - page = int(page) - page_size = int(page_size) - except ValueError: - return {"status": "Page size and page should be integers"} + with RepoLoadController(session) as controller: - if page < 0 or page_size < 0: - return {"status": "Page size and page should be postive"} + result = controller.paginate_repos("user", page, page_size, sort, direction, user=self, group_name=group_name) + return result + + def get_repo_count(self): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController with GithubTaskSession(logger) as session: controller = RepoLoadController(session) - - group_id = controller.convert_group_name_to_id(user.user_id, group_name) - if group_id is None: - return {"status": "Group does not exist"} - - - order_by = sort if sort else "repo_id" - order_direction = direction if direction else "ASC" - - get_page_of_repos_sql = text(f""" - SELECT - augur_data.repo.repo_id, - augur_data.repo.repo_name, - augur_data.repo.description, - augur_data.repo.repo_git AS url, - augur_data.repo.repo_status, - a.commits_all_time, - b.issues_all_time, - rg_name, - augur_data.repo.repo_group_id - FROM - augur_data.repo - LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id - LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id - JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id - JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id - WHERE augur_operations.user_repos.group_id = {group_id} - ORDER BY {order_by} {order_direction} - LIMIT {page_size} - OFFSET {page*page_size}; - """) - - results = pd.read_sql(get_page_of_repos_sql, create_database_engine()) - results['url'] = results['url'].apply(lambda datum: datum.split('//')[1]) - - b64_urls = [] - for i in results.index: - b64_urls.append(base64.b64encode((results.at[i, 'url']).encode())) - results['base64_url'] = b64_urls - - data = results.to_json(orient="records", date_format='iso', date_unit='ms') - - return {"status": "success", "data": data} + + result = controller.get_repo_count(source="user", user=self) + if result["status"] == "success": + return result["repos"] + + return result["status"] + + + def get_group_repos(self, group_name, page=0, page_size=25, sort="repo_id", direction="ASC"): + + from augur.tasks.github.util.github_task_session import GithubTaskSession + from augur.util.repo_load_controller import RepoLoadController + + with GithubTaskSession(logger) as session: + + with RepoLoadController(session) as controller: + + result = controller.paginate_repos("group", page, page_size, sort, direction, user=self, group_name=group_name) + + return result + def get_group_repo_count(self, group_name): @@ -468,25 +451,14 @@ def get_group_repo_count(self, group_name): controller = RepoLoadController(session) - group_id = controller.convert_group_name_to_id(user.user_id, group_name) - if group_id is None: - return {"status": "Group does not exist"} - - get_page_of_repos_sql = text(f""" - SELECT - count(*) - FROM - augur_data.repo - LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id - LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id - JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id - JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id - WHERE augur_operations.user_repos.group_id = {group_id} - """) - - result = session.fetchall_data_from_sql_text(get_page_of_repos_sql) - - return {"repos": result[0]["count"]} + result = controller.get_repo_count(source="group", group_name=group_name, user=self) + if result["status"] == "success": + return result["repos"] + + return result["status"] + + + class UserGroup(Base): diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index c399ced86e..f916d046e7 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -512,9 +512,9 @@ def parse_org_url(self, url): # if the result is not None then the groups should be valid so we don't worry about index errors here return result.groups()[0] + def paginate_repos(self, source, page=0, page_size=25, sort="repo_id", direction="ASC", **kwargs): - if not source: return {"status": "Missing argument"} @@ -536,61 +536,139 @@ def paginate_repos(self, source, page=0, page_size=25, sort="repo_id", direction order_by = sort if sort else "repo_id" order_direction = direction if direction else "ASC" - query = """ - SELECT - augur_data.repo.repo_id, - augur_data.repo.repo_name, - augur_data.repo.description, - augur_data.repo.repo_git AS url, - augur_data.repo.repo_status, - a.commits_all_time, - b.issues_all_time, - rg_name, - augur_data.repo.repo_group_id - FROM - augur_data.repo - LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id - LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id - JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id""" + query = self.generate_repo_query(source, count=False, order_by=order_by, direction=order_direction, + page=page, page_size=page_size) + if isinstance(query, dict): + return query - if source == "user": + get_page_of_repos_sql = text(query) + results = pd.read_sql(get_page_of_repos_sql, create_database_engine()) + results['url'] = results['url'].apply(lambda datum: datum.split('//')[1]) + + b64_urls = [] + for i in results.index: + b64_urls.append(base64.b64encode((results.at[i, 'url']).encode())) + results['base64_url'] = b64_urls + + data = results.to_json(orient="records", date_format='iso', date_unit='ms') + + return {"status": "success", "data": data} + + def get_repo_count(self, source, **kwargs) + + if not source: + return {"status": "Missing argument"} + + if source not in ["all", "user", "group"]: + return {"status": "Invalid source"} + + try: user = kwargs["user"] - group_ids = [group.group_id for group in user.groups] + except ValueError: + user = None + + try: + group_name = kwargs["group_name"] + except ValueError: + group_name = None - query.append("JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id") - query.append(f"WHERE augur_operations.user_repos.group_id in {str(group_ids)}") + query = self.generate_repo_query(source, count=True, user=user, group_name=group_name) + if isinstance(query, dict): + return query + + get_page_of_repos_sql = text(query) + + result = self.session.fetchall_data_from_sql_text(get_page_of_repos_sql) + + return {"status": "success", "repos": result[0]["count"]} + + + def generate_repo_query(self, source, count, **kwargs): + + if count: + select = "count(*)" + else: + select = """ augur_data.repo.repo_id, + augur_data.repo.repo_name, + augur_data.repo.description, + augur_data.repo.repo_git AS url, + augur_data.repo.repo_status, + a.commits_all_time, + b.issues_all_time, + rg_name, + augur_data.repo.repo_group_id""" + + query = f""" + SELECT + {select} + FROM + augur_data.repo + LEFT OUTER JOIN augur_data.api_get_all_repos_commits a ON augur_data.repo.repo_id = a.repo_id + LEFT OUTER JOIN augur_data.api_get_all_repos_issues b ON augur_data.repo.repo_id = b.repo_id + JOIN augur_data.repo_groups ON augur_data.repo.repo_group_id = augur_data.repo_groups.repo_group_id\n""" + + if source == "user": + + try: + user = kwargs["user"] + except ValueError: + return {"status": "Missing argument"} + + group_ids = tuple([group.group_id for group in user.groups]) + + if len(group_ids) == 1: + group_ids_str = str(group_ids)[:-2] + ")" + else: + group_ids_str = str(group_ids) + + query += "\t\t JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id\n" + query += f"\t\t WHERE augur_operations.user_repos.group_id in {group_ids_str}\n" elif source == "group": with GithubTaskSession(logger) as session: controller = RepoLoadController(session) - user = kwargs["user"] - group_name = kwargs["group_name"] - - group_id = controller.convert_group_name_to_id(user, group_name) + + try: + user = kwargs["user"] + group_name = kwargs["group_name"] + except KeyError: + return {"status": "Missing argument"} + + group_id = controller.convert_group_name_to_id(user.user_id, group_name) if group_id is None: return {"status": "Group does not exist"} - query.append("JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id") - query.append(f"WHERE augur_operations.user_repos.group_id = {group_id}") + query += "\t\t JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id\n" + query += f"\t\t WHERE augur_operations.user_repos.group_id = {group_id}\n" - query.append(f"ORDER BY {order_by} {order_direction}") - query.append(f"LIMIT {page_size}") - query.append(f"OFFSET {page*page_size};") + if not count: - get_page_of_repos_sql = text(base_query) + try: + order_by = kwargs["order_by"] + except KeyError: + order_by = "repo_id" - results = pd.read_sql(get_page_of_repos_sql, create_database_engine()) - results['url'] = results['url'].apply(lambda datum: datum.split('//')[1]) + try: + direction = kwargs["direction"] + except KeyError: + direction = "ASC" - b64_urls = [] - for i in results.index: - b64_urls.append(base64.b64encode((results.at[i, 'url']).encode())) - results['base64_url'] = b64_urls + try: + page = kwargs["page"] + except KeyError: + page = 0 - data = results.to_json(orient="records", date_format='iso', date_unit='ms') + try: + page_size = kwargs["page_size"] + except KeyError: + page_size = 25 - return {"status": "success", "data": data} + query += f"\t ORDER BY {order_by} {direction}\n" + query += f"\t LIMIT {page_size}\n" + query += f"\t OFFSET {page*page_size};\n" + + return query From 653b40853d289bf6b1c45602269fee60736309cb Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Fri, 6 Jan 2023 15:22:08 -0600 Subject: [PATCH 050/150] Fix syntax error Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index f916d046e7..af4746065d 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -555,7 +555,7 @@ def paginate_repos(self, source, page=0, page_size=25, sort="repo_id", direction return {"status": "success", "data": data} - def get_repo_count(self, source, **kwargs) + def get_repo_count(self, source, **kwargs): if not source: return {"status": "Missing argument"} From 901452980558bb7dbbc13b01c9511b4302cb9b8c Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Fri, 6 Jan 2023 15:40:13 -0600 Subject: [PATCH 051/150] Fixes Signed-off-by: Andrew Brain --- augur/api/routes/util.py | 10 +++++----- augur/util/repo_load_controller.py | 8 +++++--- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/augur/api/routes/util.py b/augur/api/routes/util.py index 2c653d9594..519ad9980d 100644 --- a/augur/api/routes/util.py +++ b/augur/api/routes/util.py @@ -13,20 +13,20 @@ AUGUR_API_VERSION = 'api/unstable' -def get_all_repos(self, page=0, page_size=25, sort="repo_id", direction="ASC"): +def get_all_repos(page=0, page_size=25, sort="repo_id", direction="ASC"): from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController with GithubTaskSession(logger) as session: - with RepoLoadController(session) as controller: + controller = RepoLoadController(session) - result = controller.paginate_repos("all", page, page_size, sort, direction) + result = controller.paginate_repos("all", page, page_size, sort, direction) - return result + return result -def get_all_repos_count(self): +def get_all_repos_count(): from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index af4746065d..6f4ff75f98 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -2,10 +2,12 @@ import logging import sqlalchemy as s +import pandas as pd +import base64 from typing import List, Any, Dict - +from augur.application.db.engine import create_database_engine from augur.tasks.github.util.github_paginator import hit_api from augur.tasks.github.util.github_paginator import GithubPaginator from augur.tasks.github.util.github_task_session import GithubTaskSession @@ -541,7 +543,7 @@ def paginate_repos(self, source, page=0, page_size=25, sort="repo_id", direction if isinstance(query, dict): return query - get_page_of_repos_sql = text(query) + get_page_of_repos_sql = s.sql.text(query) results = pd.read_sql(get_page_of_repos_sql, create_database_engine()) results['url'] = results['url'].apply(lambda datum: datum.split('//')[1]) @@ -577,7 +579,7 @@ def get_repo_count(self, source, **kwargs): if isinstance(query, dict): return query - get_page_of_repos_sql = text(query) + get_page_of_repos_sql = s.sql.text(query) result = self.session.fetchall_data_from_sql_text(get_page_of_repos_sql) From bbe459364fa055c7e4df5d8f36246b01946d74b9 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Fri, 6 Jan 2023 16:50:56 -0600 Subject: [PATCH 052/150] Fix various bugs Signed-off-by: Andrew Brain --- augur/api/view/augur_view.py | 3 --- augur/api/view/routes.py | 15 +++++---------- 2 files changed, 5 insertions(+), 13 deletions(-) diff --git a/augur/api/view/augur_view.py b/augur/api/view/augur_view.py index 2347791d68..2da7f94f1d 100644 --- a/augur/api/view/augur_view.py +++ b/augur/api/view/augur_view.py @@ -35,12 +35,9 @@ def unauthorized(): @login_manager.user_loader def load_user(user_id): - print("Loading user") - user = User.get_user(user_id) if not user: - print("User not found") return None # The flask_login library sets a unique session["_id"] diff --git a/augur/api/view/routes.py b/augur/api/view/routes.py index ef2e635ede..48ad649d62 100644 --- a/augur/api/view/routes.py +++ b/augur/api/view/routes.py @@ -133,20 +133,18 @@ def user_login(): username = request.form.get('username') remember = request.form.get('remember') is not None password = request.form.get('password') + register = request.form.get('register') if username is None: raise LoginException("A login issue occurred") - # test if the user does not exist then the login is invalid user = User.get_user(username) - if not user and request.form.get('register'): + if not user and register is None: raise LoginException("Invalid login credentials") - + # register a user - if request.form.get('register') is not None: - print("Register user") + if register is not None: if user: - print(f"User already exists: {user.__dict__}") raise LoginException("User already exists") email = request.form.get('email') @@ -162,10 +160,7 @@ def user_login(): flash(result["status"]) # Log the user in if the password is valid - if user.validate(password): - - result = login_user(user, remember = remember) - print(result) + if user.validate(password) and login_user(user, remember = remember): flash(f"Welcome, {username}!") if "login_next" in session: return redirect(session.pop("login_next")) From 5c4ceb97ebf0a8877643e95adf15e31e5b9e14a0 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Sat, 7 Jan 2023 10:30:11 -0600 Subject: [PATCH 053/150] Remove prints Signed-off-by: Andrew Brain --- augur/application/db/models/augur_operations.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index fd7e0f7079..c6bcd1d2f2 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -245,8 +245,6 @@ def validate(self, password) -> bool: return False result = check_password_hash(self.login_hashword, password) - print(f"Validating: {result}") - return result @staticmethod @@ -255,10 +253,8 @@ def get_user(username: str): from augur.application.db.session import DatabaseSession with DatabaseSession(logger) as session: - print("Get user") try: user = session.query(User).filter(User.login_name == username).one() - print(user.__dict__) return user except NoResultFound: return None From e4b2a04a2b13e283de9139c135ff61e522beaa6f Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Sat, 7 Jan 2023 11:02:48 -0600 Subject: [PATCH 054/150] Make json endpoints only work when logged in Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 53 +++++++++++++++++++++++++--------------- 1 file changed, 33 insertions(+), 20 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 449f98b4ca..5677b0e844 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -132,15 +132,28 @@ def validate_user(): return jsonify({"status": "Missing argument"}), 400 user = session.query(User).filter(User.login_name == username).first() - checkPassword = check_password_hash(user.login_hashword, password) if user is None: return jsonify({"status": "Invalid username"}) + + checkPassword = check_password_hash(user.login_hashword, password) if checkPassword == False: return jsonify({"status": "Invalid password"}) login_user(user) return jsonify({"status": "Validated"}) + + @server.app.route(f"/{AUGUR_API_VERSION}/user/logout", methods=['POST']) + @login_required + def logout_user_func(): + if not development and not request.is_secure: + return generate_upgrade_request() + + if logout_user(): + return jsonify({"status": "Logged out"}) + + return jsonify({"status": "Error when logging out"}) + @server.app.route(f"/{AUGUR_API_VERSION}/user/oauth", methods=['POST']) def oauth_validate(): @@ -180,7 +193,7 @@ def generate_session(): return jsonify({"status": "Validated", "username": user, "session": token}) @server.app.route(f"/{AUGUR_API_VERSION}/user/query", methods=['POST']) - def query_user(user): + def query_user(): if not development and not request.is_secure: return generate_upgrade_request() @@ -215,7 +228,7 @@ def create_user(): @server.app.route(f"/{AUGUR_API_VERSION}/user/remove", methods=['POST', 'DELETE']) @login_required - def delete_user(user): + def delete_user(): if not development and not request.is_secure: return generate_upgrade_request() @@ -235,7 +248,7 @@ def delete_user(user): @server.app.route(f"/{AUGUR_API_VERSION}/user/update", methods=['POST']) @login_required - def update_user(user): + def update_user(): if not development and not request.is_secure: return generate_upgrade_request() @@ -272,60 +285,60 @@ def update_user(user): @server.app.route(f"/{AUGUR_API_VERSION}/user/add_repo", methods=['GET', 'POST']) @login_required - def add_user_repo(user): + def add_user_repo(): if not development and not request.is_secure: return generate_upgrade_request() repo = request.args.get("repo_url") group_name = request.args.get("group_name") - result = user.add_repo(group_name, repo) + result = current_user.add_repo(group_name, repo) return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/add_group", methods=['GET', 'POST']) @login_required - def add_user_group(user): + def add_user_group(): if not development and not request.is_secure: return generate_upgrade_request() group_name = request.args.get("group_name") - result = user.add_group(group_name) + result = current_user.add_group(group_name) return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_group", methods=['GET', 'POST']) @login_required - def remove_user_group(user): + def remove_user_group(): if not development and not request.is_secure: return generate_upgrade_request() group_name = request.args.get("group_name") - result = user.remove_group(group_name) + result = current_user.remove_group(group_name) return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/add_org", methods=['GET', 'POST']) @login_required - def add_user_org(user): + def add_user_org(): if not development and not request.is_secure: return generate_upgrade_request() org = request.args.get("org_url") group_name = request.args.get("group_name") - result = user.add_org(group_name, org_url) + result = current_user.add_org(group_name, org_url) return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_repo", methods=['GET', 'POST']) @login_required - def remove_user_repo(user): + def remove_user_repo(): if not development and not request.is_secure: return generate_upgrade_request() @@ -333,14 +346,14 @@ def remove_user_repo(user): group_name = request.args.get("group_name") repo_id = request.args.get("repo_id") - result = user.remove_repo(group_name, repo_id) + result = current_user.remove_repo(group_name, repo_id) return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repos", methods=['GET', 'POST']) @login_required - def group_repos(user): + def group_repos(): """Select repos from a user group by name Arguments @@ -373,7 +386,7 @@ def group_repos(user): sort = request.args.get("sort") or "repo_id" direction = request.args.get("direction") or "ASC" - result = user.get_group_repos(group_name, page, page_size, sort, direction) + result = current_user.get_group_repos(group_name, page, page_size, sort, direction) return jsonify(result) @@ -381,7 +394,7 @@ def group_repos(user): @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repo_count", methods=['GET', 'POST']) @login_required - def group_repo_count(user): + def group_repo_count(): """Count repos from a user group by name Arguments @@ -402,14 +415,14 @@ def group_repo_count(user): group_name = request.args.get("group_name") - result = user.group_repo_count(group_name) + result = current_user.group_repo_count(group_name) return jsonify(result) @server.app.route(f"/{AUGUR_API_VERSION}/user/groups", methods=['GET', 'POST']) @login_required - def get_user_groups(user): + def get_user_groups(): """Get a list of user groups by username Arguments @@ -426,7 +439,7 @@ def get_user_groups(user): if not development and not request.is_secure: return generate_upgrade_request() - result = user.get_groups() + result = current_user.get_groups() return jsonify(result) From 23928c15238323ceafcdeb068ac3ee908b37bfef Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Sat, 7 Jan 2023 11:18:59 -0600 Subject: [PATCH 055/150] Return error if user is not logged in when using the api Signed-off-by: Andrew Brain --- augur/api/view/augur_view.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/augur/api/view/augur_view.py b/augur/api/view/augur_view.py index 2da7f94f1d..a04b3a78f1 100644 --- a/augur/api/view/augur_view.py +++ b/augur/api/view/augur_view.py @@ -1,7 +1,8 @@ -from flask import Flask, render_template, redirect, url_for, session, request +from flask import Flask, render_template, redirect, url_for, session, request, jsonify from flask_login import LoginManager from .utils import * from .url_converters import * + # from .server import User from augur.application.db.models import User from augur.application.db.session import DatabaseSession @@ -29,6 +30,9 @@ def unsupported_method(error): @login_manager.unauthorized_handler def unauthorized(): + if "/api/unstable/" in str(request.url_rule): + return jsonify({"status": "Login required"}) + session["login_next"] = url_for(request.endpoint, **request.args) return redirect(url_for('user_login')) @@ -44,7 +48,6 @@ def load_user(user_id): # when login_user() is called successfully if session.get("_id") is not None: - # TODO: Add these as properties user._is_authenticated = True user._is_active = True From be82983f486a946eaea10011478fd4b3b8fd39a5 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Sat, 7 Jan 2023 12:48:46 -0600 Subject: [PATCH 056/150] Add more function to orm Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 22 ++----- .../application/db/models/augur_operations.py | 63 +++++++++++++++++-- 2 files changed, 63 insertions(+), 22 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 5677b0e844..eeb2669bd9 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -197,14 +197,11 @@ def query_user(): if not development and not request.is_secure: return generate_upgrade_request() - session = Session() username = request.args.get("username") if username is None: - # https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/400 return jsonify({"status": "Missing argument"}), 400 - user = session.query(User).filter(User.login_name == username).first() - - if user is None: + + if not User.exists(username): return jsonify({"status": "Invalid username"}) return jsonify({"status": True}) @@ -232,19 +229,9 @@ def delete_user(): if not development and not request.is_secure: return generate_upgrade_request() - session = Session() - - for group in user.groups: - user_repos_list = group.repos - - for user_repo_entry in user_repos_list: - session.delete(user_repo_entry) + status = current_user.delete() + return jsonify(status) - session.delete(group) - - session.delete(user) - session.commit() - return jsonify({"status": "User deleted"}), 200 @server.app.route(f"/{AUGUR_API_VERSION}/user/update", methods=['POST']) @login_required @@ -252,7 +239,6 @@ def update_user(): if not development and not request.is_secure: return generate_upgrade_request() - session = Session() email = request.args.get("email") new_login_name = request.args.get("new_username") new_password = request.args.get("new_password") diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index c6bcd1d2f2..ee8d67812a 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -250,6 +250,9 @@ def validate(self, password) -> bool: @staticmethod def get_user(username: str): + if not username: + return None + from augur.application.db.session import DatabaseSession with DatabaseSession(logger) as session: @@ -286,15 +289,67 @@ def create_user(username: str, password: str, email: str, first_name:str, last_n except AssertionError as exception_message: return {"Error": f"{exception_message}."} - @staticmethod - def delete_user(): + def delete_user(self): from augur.application.db.session import DatabaseSession - def update_user(self): + with DatabaseSession(logger) as session: + + for group in self.groups: + user_repos_list = group.repos + + for user_repo_entry in user_repos_list: + session.delete(user_repo_entry) + + session.delete(group) + + session.delete(self) + session.commit() + + return {"status": "User deleted"}) + + def update_user(self, **kwargs): from augur.application.db.session import DatabaseSession - pass + + with DatabaseSession(session) as session: + + valid_kwargs = ["email", "password", "username"] + + kwarg_present = False + for value in valid_kwargs: + + if value in kwargs: + if kwarg_present: + return {"status": "Please pass an email, password, or username, not multiple"} + + kwarg_present = True + + if "email" in kwargs: + + existing_user = session.query(User).filter(User.email == kwargs["email"]).one() + if existing_user is not None: + return jsonify({"status": "Already an account with this email"}) + + user.email = kwargs["email"] + session.commit() + return jsonify({"status": "Email Updated"}) + + if "password" in kwargs: + user.login_hashword = generate_password_hash(kwargs["password"]) + session.commit() + return jsonify({"status": "Password Updated"}) + + if "username" in kwargs: + existing_user = session.query(User).filter(User.login_name == kwargs["username"]).one() + if existing_user is not None: + return jsonify({"status": "Username already taken"}) + + user.login_name = kwargs["username"] + session.commit() + return jsonify({"status": "Username Updated"}) + + return jsonify({"status": "Missing argument"}), 400 def add_group(self, group_name): From a8541a980e81f75b163994d7d4058cb00ab617b0 Mon Sep 17 00:00:00 2001 From: Ulincsys <28362836a@gmail.com> Date: Sat, 7 Jan 2023 20:10:44 -0600 Subject: [PATCH 057/150] Integration work --- augur/api/routes/__init__.py | 1 + augur/api/routes/batch.py | 2 +- augur/api/routes/collection_status.py | 2 +- augur/api/routes/config.py | 2 +- augur/api/routes/contributor_reports.py | 2 +- augur/api/routes/manager.py | 2 +- augur/api/routes/metadata.py | 2 +- augur/api/routes/nonstandard_metrics.py | 2 +- augur/api/routes/pull_request_reports.py | 2 +- augur/api/routes/user.py | 110 ++++++------------ augur/api/routes/util.py | 2 +- augur/api/server.py | 2 +- augur/api/util.py | 32 ++++- augur/api/view/api.py | 23 ---- augur/api/view/augur_view.py | 18 ++- augur/api/view/init.py | 1 - augur/api/view/routes.py | 24 +++- .../application/db/models/augur_operations.py | 6 +- augur/templates/authorization.html | 41 +++++++ augur/templates/login.html | 6 +- 20 files changed, 164 insertions(+), 118 deletions(-) create mode 100644 augur/templates/authorization.html diff --git a/augur/api/routes/__init__.py b/augur/api/routes/__init__.py index e69de29bb2..f4cc69cb4e 100644 --- a/augur/api/routes/__init__.py +++ b/augur/api/routes/__init__.py @@ -0,0 +1 @@ +AUGUR_API_VERSION = 'api/unstable' diff --git a/augur/api/routes/batch.py b/augur/api/routes/batch.py index a967fb4f64..bb08bbc5a1 100644 --- a/augur/api/routes/batch.py +++ b/augur/api/routes/batch.py @@ -12,7 +12,7 @@ from augur.api.util import metric_metadata import json -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION logger = logging.getLogger(__name__) diff --git a/augur/api/routes/collection_status.py b/augur/api/routes/collection_status.py index fb8ea0f318..49c62e2d76 100644 --- a/augur/api/routes/collection_status.py +++ b/augur/api/routes/collection_status.py @@ -4,7 +4,7 @@ import json from flask import Response -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION def create_routes(server): diff --git a/augur/api/routes/config.py b/augur/api/routes/config.py index 7a3d7f7014..3dad0105d1 100644 --- a/augur/api/routes/config.py +++ b/augur/api/routes/config.py @@ -17,7 +17,7 @@ logger = logging.getLogger(__name__) development = get_development_flag() -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION def generate_upgrade_request(): # https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/426 diff --git a/augur/api/routes/contributor_reports.py b/augur/api/routes/contributor_reports.py index 7425695825..0d599e6acf 100644 --- a/augur/api/routes/contributor_reports.py +++ b/augur/api/routes/contributor_reports.py @@ -18,7 +18,7 @@ from bokeh.layouts import gridplot from bokeh.transform import cumsum -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION warnings.filterwarnings('ignore') diff --git a/augur/api/routes/manager.py b/augur/api/routes/manager.py index 7624322a02..fcb5524663 100755 --- a/augur/api/routes/manager.py +++ b/augur/api/routes/manager.py @@ -17,7 +17,7 @@ import os import traceback -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION logger = logging.getLogger(__name__) diff --git a/augur/api/routes/metadata.py b/augur/api/routes/metadata.py index 7a0f1ff20a..8d4cad3c5a 100644 --- a/augur/api/routes/metadata.py +++ b/augur/api/routes/metadata.py @@ -12,7 +12,7 @@ import os import requests -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION def create_routes(server): diff --git a/augur/api/routes/nonstandard_metrics.py b/augur/api/routes/nonstandard_metrics.py index d57ce50a10..71ac2ff13a 100644 --- a/augur/api/routes/nonstandard_metrics.py +++ b/augur/api/routes/nonstandard_metrics.py @@ -11,7 +11,7 @@ # from augur.api.server import transform from augur.api.server import server -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION def create_routes(server): diff --git a/augur/api/routes/pull_request_reports.py b/augur/api/routes/pull_request_reports.py index 1cfa33c9a2..b130e403a2 100644 --- a/augur/api/routes/pull_request_reports.py +++ b/augur/api/routes/pull_request_reports.py @@ -23,7 +23,7 @@ warnings.filterwarnings('ignore') -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION def create_routes(server): def pull_request_data_collection(repo_id, start_date, end_date): diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index eeb2669bd9..f88b6d47a3 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -1,6 +1,6 @@ #SPDX-License-Identifier: MIT """ -Creates routes for user login functionality +Creates routes for user functionality """ import logging @@ -9,7 +9,7 @@ import os import base64 import pandas as pd -from flask import request, Response, jsonify +from flask import request, Response, jsonify, session from flask_login import login_user, logout_user, current_user, login_required from werkzeug.security import generate_password_hash, check_password_hash from sqlalchemy.sql import text @@ -18,66 +18,25 @@ from augur.application.db.session import DatabaseSession from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController - +from augur.api.util import get_bearer_token +from augur.api.util import get_client_token from augur.application.db.models import User, UserRepo, UserGroup, UserSessionToken, ClientToken from augur.application.config import get_development_flag +from augur.tasks.init.redis_connection import redis_connection as redis + logger = logging.getLogger(__name__) development = get_development_flag() from augur.application.db.engine import create_database_engine Session = sessionmaker(bind=create_database_engine()) -AUGUR_API_VERSION = 'api/unstable' - -""" - Extract Bearer token from request header, - using the standard oauth2 format -""" -def get_bearer_token(request): - token = request.headers.get("Authorization") - - if token and " " in token: - token = token.split(" ") - if len(token) == 2: - return token[1] - - for substr in token: - if substr and "Bearer" not in substr: - return substr - - return token - -def user_login_required(fun): - def wrapper(*args, **kwargs): - # TODO check that user session token is valid - - # We still need to decide on the format for this - - user_token = request.args.get("user_token") - print(user_token) - - # If valid: - if user_token: - - session = Session() - try: - user = session.query(UserSessionToken).filter(UserSessionToken.token == user_token).one().user - - return fun(user=user, *args, **kwargs) - except NoResultFound: - print("Not found") - - # else: return error JSON - return {"status": "Invalid user session"} - - wrapper.__name__ = fun.__name__ - return wrapper +from augur.api.routes import AUGUR_API_VERSION def api_key_required(fun): def wrapper(*args, **kwargs): # TODO check that API key is valid - client_token = request.args.get("client_api_key") + client_token = get_client_token() # If valid: if client_token: @@ -155,42 +114,43 @@ def logout_user_func(): return jsonify({"status": "Error when logging out"}) - @server.app.route(f"/{AUGUR_API_VERSION}/user/oauth", methods=['POST']) - def oauth_validate(): - # Check if user has an active session - current_session = request.args.get("session") - - if current_session: - # TODO validate session token - # If invalid, set current_session to None to force validation - pass - - if not current_session: - return jsonify({"status": "Invalid session"}) - - # TODO generate oauth token and store in temporary table - # Ideally should be valid for ~1 minute - # oauth entry: (token: str, generated: date) + @server.app.route(f"/{AUGUR_API_VERSION}/user/authorize", methods=['POST', 'GET']) + @login_required + def user_authorize(): + code = secrets.token_hex() + username = current_user.login_name - token = "TEMPORARY VALUE" + redis.set(token, username, ex=30) - return jsonify({"status": "Validated", "oauth_token": token}) + return jsonify({"status": "Validated", "code": code}) @server.app.route(f"/{AUGUR_API_VERSION}/user/generate_session", methods=['POST']) + @api_key_required def generate_session(): # TODO Validate oauth token - oauth = request.args.get("oauth_token") + code = request.args.get("code") + + username = redis.get(code) + redis.delete(code) + if not username: + return jsonify({"status": "Invalid authorization code"}) - # If invalid, return error JSON: - # return jsonify({"status": "Invalid oauth token"}) + user = User.get_user(username) + if not user: + return jsonify({"status": "Invalid user"}) - # If valid, pop oauth token from temporary table - # Generate user session token to be stored in client browser + user_session_token = secrets.token_hex() + seconds_to_expire = 86400 + expiration = int(time.time()) + seconds_to_expire - token = "USER SESSION TOKEN" - user = "USERNAME" + session = Session() + user_session = UserSessionToken(token=user_session_token, user_id=user.user_id, expiration=expiration) - return jsonify({"status": "Validated", "username": user, "session": token}) + session.add(user_session) + session.commit() + session.close() + + return jsonify({"status": "Validated", "username": username, "access_token": user_session_token, "token_type": "Bearer", "expires": seconds_to_expire}) @server.app.route(f"/{AUGUR_API_VERSION}/user/query", methods=['POST']) def query_user(): diff --git a/augur/api/routes/util.py b/augur/api/routes/util.py index 519ad9980d..57df12c7aa 100644 --- a/augur/api/routes/util.py +++ b/augur/api/routes/util.py @@ -11,7 +11,7 @@ logger = AugurLogger("augur").get_logger() -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION def get_all_repos(page=0, page_size=25, sort="repo_id", direction="ASC"): diff --git a/augur/api/server.py b/augur/api/server.py index 0d41dedb4f..edc1c34051 100644 --- a/augur/api/server.py +++ b/augur/api/server.py @@ -26,7 +26,7 @@ from augur.application.logs import AugurLogger from metadata import __version__ as augur_code_version -AUGUR_API_VERSION = 'api/unstable' +from augur.api.routes import AUGUR_API_VERSION diff --git a/augur/api/util.py b/augur/api/util.py index 9beaf9e9cd..5a2eb7a703 100644 --- a/augur/api/util.py +++ b/augur/api/util.py @@ -9,6 +9,8 @@ import sys import beaker +from flask import request + __ROOT = os.path.abspath(os.path.dirname(__file__)) def get_data_path(path): """ @@ -73,4 +75,32 @@ def decorate(function): function.metadata.update(metadata) return function - return decorate \ No newline at end of file + return decorate + +""" + Extract authorization token by type from request header +""" +def get_token(token_type): + auth = request.headers.get("Authorization") + + tokens = auth.split(",") + + tokens = filter(lambda x: f"{token_type} " in x, tokens) + + if len(tokens) != 1: + return None + + return tokens[0].replace(f"{token_type} ", "") + +""" + Extract Bearer token from request header +""" +def get_bearer_token(): + return get_token("Bearer") + +""" + Extract Client token from request header +""" +def get_bearer_token(): + return get_token("Client") + \ No newline at end of file diff --git a/augur/api/view/api.py b/augur/api/view/api.py index ba53557d9b..3e4504ce3e 100644 --- a/augur/api/view/api.py +++ b/augur/api/view/api.py @@ -10,29 +10,6 @@ def cache(file=None): return redirect(url_for('root', path=getSetting('caching'))) return redirect(url_for('root', path=toCacheFilepath(file))) - # API endpoint to clear server cache - # TODO: Add verification - @server.app.route('/cache/clear') - def clear_cache(): - try: - for f in os.listdir(getSetting('caching')): - os.remove(os.path.join(getSetting('caching'), f)) - return renderMessage("Cache Cleared", "Server cache was successfully cleared", redirect="/") - except Exception as err: - print(err) - return renderMessage("Error", "An error occurred while clearing server cache.", redirect="/", pause=5) - - # API endpoint to reload settings from disk - @server.app.route('/settings/reload') - def reload_settings(): - loadSettings() - return renderMessage("Settings Reloaded", "Server settings were successfully reloaded.", redirect="/", pause=5) - - # Request the frontend version as a JSON string - @server.app.route('/version') - def get_version(): - return jsonify(version) - @server.app.route('/account/repos/add/') @server.app.route('/account/repos/add') @login_required diff --git a/augur/api/view/augur_view.py b/augur/api/view/augur_view.py index a04b3a78f1..a4db664a90 100644 --- a/augur/api/view/augur_view.py +++ b/augur/api/view/augur_view.py @@ -2,10 +2,13 @@ from flask_login import LoginManager from .utils import * from .url_converters import * +from .init import logger # from .server import User -from augur.application.db.models import User +from augur.application.db.models import User, UserSessionToken from augur.application.db.session import DatabaseSession +from augur.api.routes import AUGUR_API_VERSION +from augur.api.util import get_bearer_token login_manager = LoginManager() @@ -30,7 +33,7 @@ def unsupported_method(error): @login_manager.unauthorized_handler def unauthorized(): - if "/api/unstable/" in str(request.url_rule): + if AUGUR_API_VERSION in str(request.url_rule): return jsonify({"status": "Login required"}) session["login_next"] = url_for(request.endpoint, **request.args) @@ -53,3 +56,14 @@ def load_user(user_id): return user + @login_manager.request_loader + def load_user_request(request): + token = get_bearer_token(request) + + with DatabaseSession(logger) as session: + + token = session.query(UserSessionToken).filter(UserSessionToken.token == token).first() + if token: + return token.user + + return None \ No newline at end of file diff --git a/augur/api/view/init.py b/augur/api/view/init.py index 556bcc93e5..1026ae3641 100644 --- a/augur/api/view/init.py +++ b/augur/api/view/init.py @@ -90,4 +90,3 @@ def init_logging(): global logger logger = logging.getLogger("augur view") logger.setLevel("DEBUG") - logging.basicConfig(filename="augur_view.log", filemode='a', format=format, level=logging.INFO, datefmt="%H:%M:%S") diff --git a/augur/api/view/routes.py b/augur/api/view/routes.py index 48ad649d62..bc8996f121 100644 --- a/augur/api/view/routes.py +++ b/augur/api/view/routes.py @@ -3,10 +3,11 @@ from sqlalchemy.orm.exc import NoResultFound from .utils import * from flask_login import login_user, logout_user, current_user, login_required -# from .server import User + from augur.application.db.models import User from .server import LoginException from augur.application.db.session import DatabaseSession +from augur.tasks.init.redis_connection import redis_connection as redis logger = logging.getLogger(__name__) @@ -183,6 +184,27 @@ def user_logout(): flash("You have been logged out") return redirect(url_for('root')) + """ ---------------------------------------------------------------- + default: + table: + This route performs external authorization for a user + """ + @app.route('/user/authorize') + @login_required + def authorize_user(): + client_id = request.args.get("client_id") + state = request.args.get("state") + response_type = request.args.get("response_type") + + if not client_id or response_type != "Code": + return renderMessage("Invalid Request", "Something went wrong. You may need to return to the previous application and make the request again.") + + # TODO get application from client id + + client = "get client" + + return render_module("authorization", application = client, state = state) + @server.app.route('/account/delete') @login_required def user_delete(): diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index ee8d67812a..015f6ad88c 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -306,7 +306,7 @@ def delete_user(self): session.delete(self) session.commit() - return {"status": "User deleted"}) + return {"status": "User deleted"} def update_user(self, **kwargs): @@ -570,6 +570,10 @@ class ClientToken(Base): } ) + # TODO ClientApplication table (Application ID: str/int, User ID: FK, Name: str, Redirect URL: str) + + # It should probably be 1:1 client token to application, so we only need one table + token = Column(String, primary_key=True, nullable=False) name = Column(String, nullable=False) expiration = Column(BigInteger) diff --git a/augur/templates/authorization.html b/augur/templates/authorization.html new file mode 100644 index 0000000000..bdb7b65663 --- /dev/null +++ b/augur/templates/authorization.html @@ -0,0 +1,41 @@ +

Authorize App

+ +

{{ application.name }} Sample App is requesting access to your account.

+

Authorizing this application will grant it access to the following:

+
    +
  • Username
    • +
  • Your repo groups
    • +
  • Information collected by Augur, both public and private:
    • +
  • +
      +
    • Issues
      • +
    • Pull requests
      • +
    • Comments
      • +
    • Commit logs
      • +
    +
    • +
+ +

By continuing, you authorize this access, and will be redirected to the following link:

+

{{ application.response_url }}

+Make sure you trust the application and this link before proceeding. + +
+ + + + +
+ + \ No newline at end of file diff --git a/augur/templates/login.html b/augur/templates/login.html index 72744d780a..c71d02d50f 100644 --- a/augur/templates/login.html +++ b/augur/templates/login.html @@ -51,12 +51,10 @@

User Login

- +
- +
From 1e9cffc4e45ad20c0fe2a934ed99833e14195b75 Mon Sep 17 00:00:00 2001 From: Ulincsys <28362836a@gmail.com> Date: Sun, 8 Jan 2023 22:05:35 -0600 Subject: [PATCH 058/150] Further integration testing and stability improvements Signed-off-by: Ulincsys <28362836a@gmail.com> --- augur/api/routes/config.py | 6 - augur/api/routes/user.py | 36 +-- augur/api/routes/util.py | 29 --- augur/api/util.py | 15 +- augur/api/view/api.py | 28 +- augur/api/view/augur_view.py | 10 +- augur/api/view/init.py | 57 +++- augur/api/view/routes.py | 134 +++++----- augur/api/view/utils.py | 6 +- augur/application/__init__.py | 13 + augur/application/cli/backend.py | 2 - augur/application/config.py | 5 + augur/application/db/models/__init__.py | 2 +- augur/application/db/models/augur_data.py | 6 + .../application/db/models/augur_operations.py | 244 +++++++++--------- .../versions/2_added_user_groups_and_login.py | 16 +- augur/application/util.py | 29 +++ augur/templates/authorization.html | 4 +- augur/templates/groups-table.html | 4 +- augur/templates/navbar.html | 6 +- augur/templates/repos-table.html | 21 +- augur/templates/settings.html | 7 +- augur/templates/status.html | 6 +- augur/util/repo_load_controller.py | 214 +++++++-------- 24 files changed, 481 insertions(+), 419 deletions(-) create mode 100644 augur/application/util.py diff --git a/augur/api/routes/config.py b/augur/api/routes/config.py index 3dad0105d1..08bb92d06b 100644 --- a/augur/api/routes/config.py +++ b/augur/api/routes/config.py @@ -28,12 +28,6 @@ def generate_upgrade_request(): return response, 426 def create_routes(server): - - @server.app.errorhandler(405) - def unsupported_method(error): - return jsonify({"status": "Unsupported method"}), 405 - - @server.app.route(f"/{AUGUR_API_VERSION}/config/get", methods=['GET', 'POST']) def get_config(): if not development and not request.is_secure: diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index f88b6d47a3..40ba3c9417 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -21,7 +21,7 @@ from augur.api.util import get_bearer_token from augur.api.util import get_client_token -from augur.application.db.models import User, UserRepo, UserGroup, UserSessionToken, ClientToken +from augur.application.db.models import User, UserRepo, UserGroup, UserSessionToken, ClientApplication from augur.application.config import get_development_flag from augur.tasks.init.redis_connection import redis_connection as redis @@ -33,8 +33,8 @@ from augur.api.routes import AUGUR_API_VERSION def api_key_required(fun): + # TODO Optionally rate-limit non authenticated users instead of rejecting requests def wrapper(*args, **kwargs): - # TODO check that API key is valid client_token = get_client_token() @@ -43,12 +43,11 @@ def wrapper(*args, **kwargs): session = Session() try: - session.query(ClientToken).filter(ClientToken.token == client_token).one() + kwargs["application"] = session.query(ClientApplication).filter(ClientApplication.id == client_token).one() return fun(*args, **kwargs) except NoResultFound: pass - # else: return error JSON return {"status": "Unauthorized client"} wrapper.__name__ = fun.__name__ @@ -58,7 +57,6 @@ def wrapper(*args, **kwargs): """ @app.route("/path") @api_key_required -@user_login_required def priviledged_function(): stuff """ @@ -73,11 +71,6 @@ def generate_upgrade_request(): return response, 426 def create_routes(server): - # TODO This functionality isn't specific to the User endpoints, and should be moved - @server.app.errorhandler(405) - def unsupported_method(error): - return jsonify({"status": "Unsupported method"}), 405 - @server.app.route(f"/{AUGUR_API_VERSION}/user/validate", methods=['POST']) def validate_user(): if not development and not request.is_secure: @@ -124,10 +117,9 @@ def user_authorize(): return jsonify({"status": "Validated", "code": code}) - @server.app.route(f"/{AUGUR_API_VERSION}/user/generate_session", methods=['POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/session/generate", methods=['POST']) @api_key_required - def generate_session(): - # TODO Validate oauth token + def generate_session(application): code = request.args.get("code") username = redis.get(code) @@ -144,7 +136,7 @@ def generate_session(): expiration = int(time.time()) + seconds_to_expire session = Session() - user_session = UserSessionToken(token=user_session_token, user_id=user.user_id, expiration=expiration) + user_session = UserSessionToken(token=user_session_token, user_id=user.user_id, application_id = application.id, expiration=expiration) session.add(user_session) session.commit() @@ -229,7 +221,7 @@ def update_user(): return jsonify({"status": "Missing argument"}), 400 - @server.app.route(f"/{AUGUR_API_VERSION}/user/add_repo", methods=['GET', 'POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/repo/add", methods=['GET', 'POST']) @login_required def add_user_repo(): if not development and not request.is_secure: @@ -243,7 +235,7 @@ def add_user_repo(): return jsonify(result) - @server.app.route(f"/{AUGUR_API_VERSION}/user/add_group", methods=['GET', 'POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/group/add", methods=['GET', 'POST']) @login_required def add_user_group(): if not development and not request.is_secure: @@ -268,7 +260,7 @@ def remove_user_group(): return jsonify(result) - @server.app.route(f"/{AUGUR_API_VERSION}/user/add_org", methods=['GET', 'POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/org/add", methods=['GET', 'POST']) @login_required def add_user_org(): if not development and not request.is_secure: @@ -282,7 +274,7 @@ def add_user_org(): return jsonify(result) - @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_repo", methods=['GET', 'POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/repo/remove", methods=['GET', 'POST']) @login_required def remove_user_repo(): if not development and not request.is_secure: @@ -296,8 +288,7 @@ def remove_user_repo(): return jsonify(result) - - @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repos", methods=['GET', 'POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/group/repos", methods=['GET', 'POST']) @login_required def group_repos(): """Select repos from a user group by name @@ -336,9 +327,7 @@ def group_repos(): return jsonify(result) - - - @server.app.route(f"/{AUGUR_API_VERSION}/user/group_repo_count", methods=['GET', 'POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/group/repos/count", methods=['GET', 'POST']) @login_required def group_repo_count(): """Count repos from a user group by name @@ -365,7 +354,6 @@ def group_repo_count(): return jsonify(result) - @server.app.route(f"/{AUGUR_API_VERSION}/user/groups", methods=['GET', 'POST']) @login_required def get_user_groups(): diff --git a/augur/api/routes/util.py b/augur/api/routes/util.py index 57df12c7aa..e7e3102ff8 100644 --- a/augur/api/routes/util.py +++ b/augur/api/routes/util.py @@ -13,35 +13,6 @@ from augur.api.routes import AUGUR_API_VERSION -def get_all_repos(page=0, page_size=25, sort="repo_id", direction="ASC"): - - from augur.tasks.github.util.github_task_session import GithubTaskSession - from augur.util.repo_load_controller import RepoLoadController - - with GithubTaskSession(logger) as session: - - controller = RepoLoadController(session) - - result = controller.paginate_repos("all", page, page_size, sort, direction) - - return result - -def get_all_repos_count(): - - from augur.tasks.github.util.github_task_session import GithubTaskSession - from augur.util.repo_load_controller import RepoLoadController - - with GithubTaskSession(logger) as session: - - controller = RepoLoadController(session) - - result = controller.get_repo_count(source="all") - if result["status"] == "success": - return result["repos"] - - return result["status"] - - def create_routes(server): @server.app.route('/{}/repo-groups'.format(AUGUR_API_VERSION)) diff --git a/augur/api/util.py b/augur/api/util.py index 5a2eb7a703..b10c1f8c1c 100644 --- a/augur/api/util.py +++ b/augur/api/util.py @@ -83,14 +83,15 @@ def decorate(function): def get_token(token_type): auth = request.headers.get("Authorization") - tokens = auth.split(",") + if auth: + tokens = auth.split(",") - tokens = filter(lambda x: f"{token_type} " in x, tokens) + tokens = filter(lambda x: f"{token_type} " in x, tokens) - if len(tokens) != 1: - return None - - return tokens[0].replace(f"{token_type} ", "") + if len(tokens) != 1: + return None + + return tokens[0].replace(f"{token_type} ", "") """ Extract Bearer token from request header @@ -101,6 +102,6 @@ def get_bearer_token(): """ Extract Client token from request header """ -def get_bearer_token(): +def get_client_token(): return get_token("Client") \ No newline at end of file diff --git a/augur/api/view/api.py b/augur/api/view/api.py index 3e4504ce3e..c6f4c042e2 100644 --- a/augur/api/view/api.py +++ b/augur/api/view/api.py @@ -1,5 +1,6 @@ from flask import Flask, render_template, render_template_string, request, abort, jsonify, redirect, url_for, session, flash from flask_login import current_user, login_required +from augur.util.repo_load_controller import parse_org_url, parse_repo_url from .utils import * def create_routes(server): @@ -13,29 +14,20 @@ def cache(file=None): @server.app.route('/account/repos/add/') @server.app.route('/account/repos/add') @login_required - def av_add_user_repo(repo_url = None): - if not repo_url: + def av_add_user_repo(url = None): + # TODO finish UI and implement group adding + if not url: flash("Repo or org URL must not be empty") - elif current_user.try_add_url(repo_url): - flash("Successfully added repo or org") + elif result := parse_org_url(url): + current_user.add_org() + flash("Successfully added org") + elif result := parse_repo_url(url): + flash("Successfully added repo") else: flash("Could not add repo or org") return redirect(url_for("user_settings")) - - """ ---------------------------------------------------------------- - """ - @server.app.route('/requests/make/') - def make_api_request(request_endpoint): - do_cache = True - if request.headers.get("nocache") or request.args.get("nocache"): - do_cache = False - - data = requestJson(request_endpoint, do_cache) - if type(data) == tuple: - return jsonify({"request_error": data[1]}), 400 - return jsonify(data) - + """ ---------------------------------------------------------------- Locking request loop: This route will lock the current request until the diff --git a/augur/api/view/augur_view.py b/augur/api/view/augur_view.py index a4db664a90..0524b64ca2 100644 --- a/augur/api/view/augur_view.py +++ b/augur/api/view/augur_view.py @@ -25,11 +25,17 @@ def create_routes(server): # Code 404 response page, for pages not found @server.app.errorhandler(404) def page_not_found(error): + if AUGUR_API_VERSION in str(request.url_rule): + return jsonify({"status": "Not Found"}), 404 + return render_template('index.html', title='404', api_url=getSetting('serving')), 404 @server.app.errorhandler(405) def unsupported_method(error): - return renderMessage("405 - Method not supported", "The resource you are trying to access does not support the request method used"), 405 + if AUGUR_API_VERSION in str(request.url_rule): + return jsonify({"status": "Unsupported method"}), 405 + + return render_message("405 - Method not supported", "The resource you are trying to access does not support the request method used"), 405 @login_manager.unauthorized_handler def unauthorized(): @@ -58,7 +64,7 @@ def load_user(user_id): @login_manager.request_loader def load_user_request(request): - token = get_bearer_token(request) + token = get_bearer_token() with DatabaseSession(logger) as session: diff --git a/augur/api/view/init.py b/augur/api/view/init.py index 1026ae3641..fd98e12338 100644 --- a/augur/api/view/init.py +++ b/augur/api/view/init.py @@ -82,7 +82,62 @@ def compare_versions(old, new): settings = current_settings # default reports definition -reports = {'pull_request_reports': [{'url': 'pull_request_reports/average_commits_per_PR/', 'description': 'Average commits per pull request'}, {'url': 'pull_request_reports/average_comments_per_PR/', 'description': 'Average comments per pull request'}, {'url': 'pull_request_reports/PR_counts_by_merged_status/', 'description': 'Pull request counts by merged status'}, {'url': 'pull_request_reports/mean_response_times_for_PR/', 'description': 'Mean response times for pull requests'}, {'url': 'pull_request_reports/mean_days_between_PR_comments/', 'description': 'Mean days between pull request comments'}, {'url': 'pull_request_reports/PR_time_to_first_response/', 'description': 'Pull request time until first response'}, {'url': 'pull_request_reports/average_PR_events_for_closed_PRs/', 'description': 'Average pull request events for closed pull requests'}, {'url': 'pull_request_reports/Average_PR_duration/', 'description': 'Average pull request duration'}], 'contributor_reports': [{'url': 'contributor_reports/new_contributors_bar/', 'description': 'New contributors bar graph'}, {'url': 'contributor_reports/returning_contributors_pie_chart/', 'description': 'Returning contributors pie chart'}], 'contributor_reports_stacked': [{'url': 'contributor_reports/new_contributors_stacked_bar/', 'description': 'New contributors stacked bar chart'}, {'url': 'contributor_reports/returning_contributors_stacked_bar/', 'description': 'Returning contributors stacked bar chart'}]} +reports = { + "pull_request_reports":[ + { + "url":"average_commits_per_PR", + "description":"Average commits per pull request" + }, + { + "url":"average_comments_per_PR", + "description":"Average comments per pull request" + }, + { + "url":"PR_counts_by_merged_status", + "description":"Pull request counts by merged status" + }, + { + "url":"mean_response_times_for_PR", + "description":"Mean response times for pull requests" + }, + { + "url":"mean_days_between_PR_comments", + "description":"Mean days between pull request comments" + }, + { + "url":"PR_time_to_first_response", + "description":"Pull request time until first response" + }, + { + "url":"average_PR_events_for_closed_PRs", + "description":"Average pull request events for closed pull requests" + }, + { + "url":"Average_PR_duration", + "description":"Average pull request duration" + } + ], + "contributor_reports":[ + { + "url":"new_contributors_bar", + "description":"New contributors bar graph" + }, + { + "url":"returning_contributors_pie_chart", + "description":"Returning contributors pie chart" + } + ], + "contributor_reports_stacked":[ + { + "url":"new_contributors_stacked_bar", + "description":"New contributors stacked bar chart" + }, + { + "url":"returning_contributors_stacked_bar", + "description":"Returning contributors stacked bar chart" + } + ] +} # Initialize logging def init_logging(): diff --git a/augur/api/view/routes.py b/augur/api/view/routes.py index bc8996f121..d3c55ef289 100644 --- a/augur/api/view/routes.py +++ b/augur/api/view/routes.py @@ -4,13 +4,17 @@ from .utils import * from flask_login import login_user, logout_user, current_user, login_required -from augur.application.db.models import User +from augur.application.db.models import User, Repo from .server import LoginException from augur.application.db.session import DatabaseSession from augur.tasks.init.redis_connection import redis_connection as redis +from augur.application.util import * +from augur.application.config import AugurConfig logger = logging.getLogger(__name__) +with DatabaseSession(logger) as db_session: + config = AugurConfig(logger, db_session) # ROUTES ----------------------------------------------------------------------- @@ -52,33 +56,37 @@ def logo(brand=None): @server.app.route('/repos/views/table') def repo_table_view(): query = request.args.get('q') - page = request.args.get('p') + try: + page = int(request.args.get('p') or 0) + except: + page = 1 + sorting = request.args.get('s') rev = request.args.get('r') + if rev is not None: if rev == "False": rev = False elif rev == "True": rev = True - else: - rev = False + + direction = "DESC" if rev else "ASC" + + pagination_offset = config.get_value("frontend", "pagination_offset") if current_user.is_authenticated: - data = requestJson("repos", cached = False) - user_repo_ids = current_user.query_repos() - user_repos = [] - for repo in data: - if repo["repo_id"] in user_repo_ids: - user_repos.append(repo) + data = current_user.get_repos(page = page, sort = sorting, direction = direction) - data = user_repos or None + page_count = (current_user.get_repo_count() or 0) // pagination_offset else: - data = requestJson("repos") - + data = get_all_repos(page = page, sort = sorting, direction = direction) + page_count = (get_all_repos_count() or 0) // pagination_offset + #if not cacheFileExists("repos.json"): # return renderLoading("repos/views/table", query, "repos.json") - return renderRepos("table", query, data, sorting, rev, page, True) + # return renderRepos("table", query, data, sorting, rev, page, True) + return render_module("repos-table", title="Repos", repos=data, query_key=query, activePage=page, pages=page_count, offset=pagination_offset, PS="repo_table_view", reverse = rev, sorting = sorting) """ ---------------------------------------------------------------- card: @@ -87,32 +95,34 @@ def repo_table_view(): @server.app.route('/repos/views/card') def repo_card_view(): query = request.args.get('q') - return renderRepos("card", query, requestJson("repos"), filter = True) + count = get_all_repos_count() + data = get_all_repos(page_size=count) + return renderRepos("card", query, data, filter = True) """ ---------------------------------------------------------------- groups: This route returns the groups table view, listing all the current groups in the backend """ - @server.app.route('/groups') - @server.app.route('/groups/') - def repo_groups_view(group=None): - query = request.args.get('q') - page = request.args.get('p') - - if(group is not None): - query = group - - if(query is not None): - buffer = [] - data = requestJson("repos") - for repo in data: - if query == str(repo["repo_group_id"]) or query in repo["rg_name"]: - buffer.append(repo) - return renderRepos("table", query, buffer, page = page, pageSource = "repo_groups_view") - else: - groups = requestJson("repo-groups") - return render_template('index.html', body="groups-table", title="Groups", groups=groups, query_key=query, api_url=getSetting('serving')) + # @server.app.route('/groups') + # @server.app.route('/groups/') + # def repo_groups_view(group=None): + # query = request.args.get('q') + # page = request.args.get('p') + + # if(group is not None): + # query = group + + # if(query is not None): + # buffer = [] + # data = requestJson("repos") + # for repo in data: + # if query == str(repo["repo_group_id"]) or query in repo["rg_name"]: + # buffer.append(repo) + # return renderRepos("table", query, buffer, page = page, pageSource = "repo_groups_view") + # else: + # groups = requestJson("repo-groups") + # return render_template('index.html', body="groups-table", title="Groups", groups=groups, query_key=query, api_url=getSetting('serving')) """ ---------------------------------------------------------------- status: @@ -189,7 +199,7 @@ def user_logout(): table: This route performs external authorization for a user """ - @app.route('/user/authorize') + @server.app.route('/user/authorize') @login_required def authorize_user(): client_id = request.args.get("client_id") @@ -197,11 +207,10 @@ def authorize_user(): response_type = request.args.get("response_type") if not client_id or response_type != "Code": - return renderMessage("Invalid Request", "Something went wrong. You may need to return to the previous application and make the request again.") + return render_message("Invalid Request", "Something went wrong. You may need to return to the previous application and make the request again.") # TODO get application from client id - - client = "get client" + client = ClientApplication.get_by_id(client_id) return render_module("authorization", application = client, state = state) @@ -243,19 +252,9 @@ def user_settings(): def repo_repo_view(id): # For some reason, there is no reports definition (shouldn't be possible) if reports is None: - return renderMessage("Report Definitions Missing", "You requested a report for a repo on this instance, but a definition for the report layout was not found.") - data = requestJson("repos") - repo = {} - # Need to convert the repo id parameter to int so it's comparable - try: - id = int(id) - except: - pass - # Finding the report object in the data so the name is accessible on the page - for item in data: - if item['repo_id'] == id: - repo = item - break + return render_message("Report Definitions Missing", "You requested a report for a repo on this instance, but a definition for the report layout was not found.") + + repo = Repo.get_by_id(id) return render_module("repo-info", reports=reports.keys(), images=reports, title="Repo", repo=repo, repo_id=id) @@ -266,16 +265,17 @@ def repo_repo_view(id): is currently defined as the repository table view """ @server.app.route('/user/group/') - def user_group_view(group): - params = {} + @login_required + def user_group_view(): + group = request.args.get("group") - # NOT IMPLEMENTED - # query = request.args.get('q') + if not group: + return render_message("No Group Specified", "You must specify a group to view this page.") try: - params["page"] = int(request.args.get('p')) + params["page"] = int(request.args.get('p') or 0) except: - pass + params["page"] = 1 if sort := request.args.get('s'): params["sort"] = sort @@ -283,22 +283,26 @@ def user_group_view(group): rev = request.args.get('r') if rev is not None: if rev == "False": + rev = False params["direction"] = "ASC" elif rev == "True": + rev = True params["direction"] = "DESC" - - if current_user.is_authenticated: - data = current_user.select_group(group, **params) - if not data: - return renderMessage("Error Loading Group", "Either the group you requestion does not exist, or an unspecified error occurred.") - else: - return renderMessage("Authentication Required", "You must be logged in to view this page.") + pagination_offset = config.get_value("frontend", "pagination_offset") + + data = current_user.get_group_repos(group, **params) + page_count = current_user.get_group_repo_count(group) or 0 + page_count //= pagination_offset + + if not data: + return render_message("Error Loading Group", "Either the group you requested does not exist, or an unspecified error occurred.") #if not cacheFileExists("repos.json"): # return renderLoading("repos/views/table", query, "repos.json") - return renderRepos("table", None, data, sort, rev, params.get("page"), True) + # return renderRepos("table", None, data, sort, rev, params.get("page"), True) + return render_module("repos-table", title="Repos", repos=data, query_key=query, activePage=params["page"], pages=page_count, offset=pagination_offset, PS="user_group_view", reverse = rev, sorting = params["sort"]) """ ---------------------------------------------------------------- Admin dashboard: diff --git a/augur/api/view/utils.py b/augur/api/view/utils.py index 9ae6137ad3..4239f0625a 100644 --- a/augur/api/view/utils.py +++ b/augur/api/view/utils.py @@ -317,7 +317,9 @@ def requestReports(repo_id): # Where should the downloaded image be stored (in cache) filename = toCacheFilename(f"{image['url']}?repo_id={repo_id}") # Where are we downloading the image from - image_url = f"{getSetting('serving')}/{image['url']}?repo_id={repo_id}" + image_url = url_for(image['url'], repo_id = repo_id) + # f"{getSetting('serving')}/{image['url']}?repo_id={repo_id}" + # Add a request for this image to the thread pool using the download function thread_pool.submit(download, image_url, connection_mgr, filename, reportImages, image['id'], repo_id) @@ -411,7 +413,7 @@ def renderRepos(view, query, data, sorting = None, rev = False, page = None, fil Renders a simple page with the given message information, and optional page title and redirect """ -def renderMessage(messageTitle, messageBody, title = None, redirect = None, pause = None): +def render_message(messageTitle, messageBody = None, title = None, redirect = None, pause = None): return render_module("notice", messageTitle=messageTitle, messageBody=messageBody, title=title, redirect=redirect, pause=pause) """ ---------------------------------------------------------------- diff --git a/augur/application/__init__.py b/augur/application/__init__.py index e69de29bb2..9091d6232a 100644 --- a/augur/application/__init__.py +++ b/augur/application/__init__.py @@ -0,0 +1,13 @@ +def requires_db_session(logger): + def inner_decorator(fun): + def wrapper(*args, **kwargs): + + from augur.application.db.session import DatabaseSession + + # create DB session + with DatabaseSession(logger) as session: + + return fun(session, *args, **kwargs) + + return wrapper + return inner_decorator diff --git a/augur/application/cli/backend.py b/augur/application/cli/backend.py index b8b6559abf..5dc1dfb17a 100644 --- a/augur/application/cli/backend.py +++ b/augur/application/cli/backend.py @@ -35,7 +35,6 @@ def cli(): @cli.command("start") @click.option("--disable-collection", is_flag=True, default=False, help="Turns off data collection workers") @click.option("--development", is_flag=True, default=False, help="Enable development mode, implies --disable-collection") -@click.option("--development", is_flag=True, default=False, help="Enable development mode, implies --disable-collection") @click.option('--port') @test_connection @test_db_connection @@ -53,7 +52,6 @@ def start(disable_collection, development, port): raise e if development: - disable_collection = True os.environ["AUGUR_DEV"] = "1" logger.info("Starting in development mode") diff --git a/augur/application/config.py b/augur/application/config.py index 58c2fa3eea..b433c66240 100644 --- a/augur/application/config.py +++ b/augur/application/config.py @@ -176,6 +176,11 @@ def get_value(self, section_name: str, setting_name: str) -> Optional[Any]: Returns: The value from config if found, and None otherwise """ + + # TODO temporary until added to the DB schema + if section_name == "frontend" and setting_name == "pagination_offset": + return 25 + try: query = self.session.query(Config).filter(Config.section_name == section_name, Config.setting_name == setting_name) config_setting = execute_session_query(query, 'one') diff --git a/augur/application/db/models/__init__.py b/augur/application/db/models/__init__.py index 5606168f64..d76acf2157 100644 --- a/augur/application/db/models/__init__.py +++ b/augur/application/db/models/__init__.py @@ -102,5 +102,5 @@ UserRepo, UserGroup, UserSessionToken, - ClientToken + ClientApplication ) diff --git a/augur/application/db/models/augur_data.py b/augur/application/db/models/augur_data.py index 5dd5618623..178761ebdf 100644 --- a/augur/application/db/models/augur_data.py +++ b/augur/application/db/models/augur_data.py @@ -22,6 +22,7 @@ from sqlalchemy.orm import relationship from sqlalchemy.sql import text from augur.application.db.models.base import Base +from augur.application import requires_db_session metadata = Base.metadata @@ -815,7 +816,12 @@ class Repo(Base): repo_group = relationship("RepoGroup") user_repo = relationship("UserRepo") + @staticmethod + @requires_db_session + def get_by_id(session, repo_id): + return session.query(Repo).filter(Repo.repo_id == repo_id).first() + class RepoTestCoverage(Base): __tablename__ = "repo_test_coverage" __table_args__ = {"schema": "augur_data"} diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index 015f6ad88c..72402de202 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -2,19 +2,25 @@ from sqlalchemy import BigInteger, SmallInteger, Column, Index, Integer, String, Table, text, UniqueConstraint, Boolean, ForeignKey from sqlalchemy.dialects.postgresql import TIMESTAMP, UUID from sqlalchemy.orm.exc import NoResultFound +from sqlalchemy.orm import relationship from werkzeug.security import generate_password_hash, check_password_hash import logging -logger = logging.getLogger(__name__) +from augur.application.db.models.base import Base +logger = logging.getLogger(__name__) +def get_session(): + global session -from augur.application.db.models.base import Base -from sqlalchemy.orm import relationship + if "session" not in globals(): + from augur.application.db.session import DatabaseSession + session = DatabaseSession(logger) + return session + metadata = Base.metadata - t_all = Table( "all", metadata, @@ -201,6 +207,7 @@ class User(Base): groups = relationship("UserGroup") tokens = relationship("UserSessionToken") + applications = relationship("ClientApplication") _is_authenticated = False _is_active = True @@ -239,8 +246,6 @@ def get_id(self): def validate(self, password) -> bool: - from augur.application.db.session import DatabaseSession - if not password: return False @@ -253,132 +258,122 @@ def get_user(username: str): if not username: return None - from augur.application.db.session import DatabaseSession + local_session = get_session() - with DatabaseSession(logger) as session: - try: - user = session.query(User).filter(User.login_name == username).one() - return user - except NoResultFound: - return None + try: + user = local_session.query(User).filter(User.login_name == username).one() + return user + except NoResultFound: + return None @staticmethod def create_user(username: str, password: str, email: str, first_name:str, last_name:str, admin=False): - from augur.application.db.session import DatabaseSession - if username is None or password is None or email is None or first_name is None or last_name is None: return {"status": "Missing field"} + local_session = get_session() - with DatabaseSession(logger) as session: - - user = session.query(User).filter(User.login_name == username).first() - if user is not None: - return {"status": "A User already exists with that username"} + user = local_session.query(User).filter(User.login_name == username).first() + if user is not None: + return {"status": "A User already exists with that username"} - emailCheck = session.query(User).filter(User.email == email).first() - if emailCheck is not None: - return {"status": "A User already exists with that email"} + emailCheck = local_session.query(User).filter(User.email == email).first() + if emailCheck is not None: + return {"status": "A User already exists with that email"} - try: - user = User(login_name = username, login_hashword = generate_password_hash(password), email = email, first_name = first_name, last_name = last_name, tool_source="User API", tool_version=None, data_source="API", admin=admin) - session.add(user) - session.commit() - return {"status": "Account successfully created"} - except AssertionError as exception_message: - return {"Error": f"{exception_message}."} + try: + user = User(login_name = username, login_hashword = generate_password_hash(password), email = email, first_name = first_name, last_name = last_name, tool_source="User API", tool_version=None, data_source="API", admin=admin) + local_session.add(user) + local_session.commit() + return {"status": "Account successfully created"} + except AssertionError as exception_message: + return {"Error": f"{exception_message}."} def delete_user(self): - - from augur.application.db.session import DatabaseSession - with DatabaseSession(logger) as session: + local_session = get_session() - for group in self.groups: - user_repos_list = group.repos + for group in self.groups: + user_repos_list = group.repos - for user_repo_entry in user_repos_list: - session.delete(user_repo_entry) + for user_repo_entry in user_repos_list: + local_session.delete(user_repo_entry) - session.delete(group) + local_session.delete(group) - session.delete(self) - session.commit() + local_session.delete(self) + local_session.commit() - return {"status": "User deleted"} + return {"status": "User deleted"} def update_user(self, **kwargs): - from augur.application.db.session import DatabaseSession + local_session = get_session() - with DatabaseSession(session) as session: - - valid_kwargs = ["email", "password", "username"] + valid_kwargs = ["email", "password", "username"] - kwarg_present = False - for value in valid_kwargs: + kwarg_present = False + for value in valid_kwargs: - if value in kwargs: - if kwarg_present: - return {"status": "Please pass an email, password, or username, not multiple"} + if value in kwargs: + if kwarg_present: + return {"status": "Please pass an email, password, or username, not multiple"} - kwarg_present = True + kwarg_present = True - if "email" in kwargs: + if "email" in kwargs: - existing_user = session.query(User).filter(User.email == kwargs["email"]).one() - if existing_user is not None: - return jsonify({"status": "Already an account with this email"}) + existing_user = local_session.query(User).filter(User.email == kwargs["email"]).one() + if existing_user is not None: + return jsonify({"status": "Already an account with this email"}) - user.email = kwargs["email"] - session.commit() - return jsonify({"status": "Email Updated"}) + user.email = kwargs["email"] + local_session.commit() + return jsonify({"status": "Email Updated"}) - if "password" in kwargs: - user.login_hashword = generate_password_hash(kwargs["password"]) - session.commit() - return jsonify({"status": "Password Updated"}) + if "password" in kwargs: + user.login_hashword = generate_password_hash(kwargs["password"]) + local_session.commit() + return jsonify({"status": "Password Updated"}) - if "username" in kwargs: - existing_user = session.query(User).filter(User.login_name == kwargs["username"]).one() - if existing_user is not None: - return jsonify({"status": "Username already taken"}) + if "username" in kwargs: + existing_user = local_session.query(User).filter(User.login_name == kwargs["username"]).one() + if existing_user is not None: + return jsonify({"status": "Username already taken"}) - user.login_name = kwargs["username"] - session.commit() - return jsonify({"status": "Username Updated"}) + user.login_name = kwargs["username"] + local_session.commit() + return jsonify({"status": "Username Updated"}) - return jsonify({"status": "Missing argument"}), 400 + return jsonify({"status": "Missing argument"}), 400 def add_group(self, group_name): - from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController if group_name == "default": return {"status": "Reserved Group Name"} - with GithubTaskSession(logger) as session: + local_session = get_session() - repo_load_controller = RepoLoadController(gh_session=session) + repo_load_controller = RepoLoadController(gh_session=local_session) - result = repo_load_controller.add_user_group(self.user_id, group_name) + result = repo_load_controller.add_user_group(self.user_id, group_name) - return result + return result def remove_group(self, group_name): - from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController - with GithubTaskSession(logger) as session: + local_session = get_session() - repo_load_controller = RepoLoadController(gh_session=session) + repo_load_controller = RepoLoadController(gh_session=local_session) - result = repo_load_controller.remove_user_group(self.user_id, group_name) + result = repo_load_controller.remove_user_group(self.user_id, group_name) - return result + return result def add_repo(self, group_name, repo_url): @@ -395,16 +390,15 @@ def add_repo(self, group_name, repo_url): def remove_repo(self, group_name, repo_id): - from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController - with GithubTaskSession(logger) as session: + local_session = get_session() - repo_load_controller = RepoLoadController(gh_session=session) + repo_load_controller = RepoLoadController(gh_session=local_session) - result = repo_load_controller.remove_frontend_repo(repo_id, self.user_id, group_name) + result = repo_load_controller.remove_frontend_repo(repo_id, self.user_id, group_name) - return result + return result def add_org(self, group_name, org_url): @@ -421,16 +415,15 @@ def add_org(self, group_name, org_url): def get_groups(self): - from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController - with GithubTaskSession(logger) as session: + local_session = get_session() - controller = RepoLoadController(session) - - user_groups = controller.get_user_groups(user.user_id) + controller = RepoLoadController(local_session) + + user_groups = controller.get_user_groups(self.user_id) - return {"groups": user_groups} + return {"groups": user_groups} def get_group_names(self): @@ -442,72 +435,58 @@ def get_group_names(self): def query_repos(self): - from augur.application.db.session import DatabaseSession from augur.application.db.models.augur_data import Repo - with DatabaseSession(logger) as session: + local_session = get_session() - return [repo.repo_id for repo in session.query(Repo).all()] + return [repo.repo_id for repo in local_session.query(Repo).all()] - def get_repos(self, group_name, page=0, page_size=25, sort="repo_id", direction="ASC"): + def get_repos(self, page=0, page_size=25, sort="repo_id", direction="ASC"): - from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController - with GithubTaskSession(logger) as session: - - with RepoLoadController(session) as controller: + local_session = get_session() - result = controller.paginate_repos("user", page, page_size, sort, direction, user=self, group_name=group_name) + result = RepoLoadController(local_session).paginate_repos("user", page, page_size, sort, direction, user=self) - return result + return result def get_repo_count(self): - from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController - with GithubTaskSession(logger) as session: + local_session = get_session() - controller = RepoLoadController(session) + controller = RepoLoadController(local_session) - result = controller.get_repo_count(source="user", user=self) - if result["status"] == "success": - return result["repos"] + result = controller.get_repo_count(source="user", user=self) - return result["status"] + return result def get_group_repos(self, group_name, page=0, page_size=25, sort="repo_id", direction="ASC"): - from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController - with GithubTaskSession(logger) as session: - - with RepoLoadController(session) as controller: + local_session = get_session() - result = controller.paginate_repos("group", page, page_size, sort, direction, user=self, group_name=group_name) + result = RepoLoadController(local_session).paginate_repos("group", page, page_size, sort, direction, user=self, group_name=group_name) - return result + return result def get_group_repo_count(self, group_name): - from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.util.repo_load_controller import RepoLoadController - with GithubTaskSession(logger) as session: - - controller = RepoLoadController(session) + local_session = get_session() - result = controller.get_repo_count(source="group", group_name=group_name, user=self) - if result["status"] == "success": - return result["repos"] + controller = RepoLoadController(local_session) - return result["status"] + result = controller.get_repo_count(source="group", group_name=group_name, user=self) + return result @@ -558,25 +537,32 @@ class UserSessionToken(Base): token = Column(String, primary_key=True, nullable=False) user_id = Column(ForeignKey("augur_operations.users.user_id", name="user_session_token_user_id_fkey")) expiration = Column(BigInteger) + application_id = Column(ForeignKey("augur_operations.client_applications.id", name="user_session_token_application_id_fkey"), nullable=False) user = relationship("User") + application = relationship("ClientApplication") -class ClientToken(Base): - __tablename__ = "client_tokens" +class ClientApplication(Base): + __tablename__ = "client_applications" __table_args__ = ( { "schema": "augur_operations" } ) - # TODO ClientApplication table (Application ID: str/int, User ID: FK, Name: str, Redirect URL: str) + id = Column(String, primary_key=True, nullable=False) + user_id = Column(ForeignKey("augur_operations.users.user_id", name="client_application_user_id_fkey"), nullable=False) + name = Column(String, nullable=False) + redirect_url = Column(String, nullable=False) - # It should probably be 1:1 client token to application, so we only need one table + user = relationship("User") - token = Column(String, primary_key=True, nullable=False) - name = Column(String, nullable=False) - expiration = Column(BigInteger) + @staticmethod + def get_by_id(client_id): + local_session = get_session() + return local_session.query(ClientApplication).filter(ClientApplication.id == client_id).first() + diff --git a/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py b/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py index 94abb429cc..d079f57ac4 100644 --- a/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py +++ b/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py @@ -102,17 +102,23 @@ def upgrade(): user_repo_insert = sa.sql.text(f"""INSERT INTO "augur_operations"."user_repos" ("group_id", "repo_id") VALUES ({group_id}, {repo_id});""") result = session.execute_sql(user_repo_insert) - op.create_table('client_tokens', + op.create_table('client_applications', + sa.Column('id', sa.String(), nullable=False), + sa.Column('user_id', sa.Integer(), nullable=False), sa.Column('name', sa.String(), nullable=False), - sa.Column('token', sa.String(), nullable=False), - sa.Column('expiration', sa.BigInteger(), nullable=True), - sa.PrimaryKeyConstraint('token'), + sa.Column('redirect_url', sa.String(), nullable=False), + sa.ForeignKeyConstraint(['user_id'], ['augur_operations.users.user_id'], name='client_application_user_id_fkey'), + sa.PrimaryKeyConstraint('id'), schema='augur_operations' ) + op.create_table('user_session_tokens', sa.Column('token', sa.String(), nullable=False), sa.Column('user_id', sa.Integer(), nullable=False), sa.Column('expiration', sa.BigInteger(), nullable=True), + sa.Column('application_id', sa.String(), nullable=True), + + sa.ForeignKeyConstraint(['application_id'], ['augur_operations.client_applications.id'], name='user_session_token_application_id_fkey'), sa.ForeignKeyConstraint(['user_id'], ['augur_operations.users.user_id'], name='user_session_token_user_fk'), sa.PrimaryKeyConstraint('token'), schema='augur_operations' @@ -183,6 +189,6 @@ def downgrade(): session.execute_sql(sa.sql.text(query_text)) op.drop_table('user_session_tokens', schema='augur_operations') - op.drop_table('client_tokens', schema='augur_operations') + op.drop_table('client_applications', schema='augur_operations') # ### end Alembic commands ### diff --git a/augur/application/util.py b/augur/application/util.py new file mode 100644 index 0000000000..2d606804a6 --- /dev/null +++ b/augur/application/util.py @@ -0,0 +1,29 @@ +import logging + +from augur.tasks.github.util.github_task_session import GithubTaskSession +from augur.util.repo_load_controller import RepoLoadController + +logger = logging.getLogger(__name__) + +def get_all_repos(page=0, page_size=25, sort="repo_id", direction="ASC"): + + with GithubTaskSession(logger) as session: + + controller = RepoLoadController(session) + + result = controller.paginate_repos("all", page, page_size, sort, direction) + + return result + +def get_all_repos_count(): + + with GithubTaskSession(logger) as session: + + controller = RepoLoadController(session) + + result = controller.get_repo_count(source="all") + + return result + + + diff --git a/augur/templates/authorization.html b/augur/templates/authorization.html index bdb7b65663..929ee857f7 100644 --- a/augur/templates/authorization.html +++ b/augur/templates/authorization.html @@ -17,10 +17,10 @@

Authorize App

By continuing, you authorize this access, and will be redirected to the following link:

-

{{ application.response_url }}

+

{{ application.redirect_url }}

Make sure you trust the application and this link before proceeding. -
+ diff --git a/augur/templates/groups-table.html b/augur/templates/groups-table.html index abe57a5774..e5ddf094fa 100644 --- a/augur/templates/groups-table.html +++ b/augur/templates/groups-table.html @@ -1,4 +1,4 @@ -{% if groups %} +{# % if groups %}
@@ -30,4 +30,4 @@

Your search did not match any results

{% else %}

Unable to load group information

-{% endif %} +{% endif % #} diff --git a/augur/templates/navbar.html b/augur/templates/navbar.html index e84c639a9b..fe498548a9 100644 --- a/augur/templates/navbar.html +++ b/augur/templates/navbar.html @@ -18,7 +18,7 @@ {% if current_user.is_authenticated %}
    • Profile
      • @@ -43,9 +43,9 @@ -
    • + {#
    • Groups -
      • + #}
    • Collection Status
      • diff --git a/augur/templates/repos-table.html b/augur/templates/repos-table.html index 96e6563b25..9c08224bde 100644 --- a/augur/templates/repos-table.html +++ b/augur/templates/repos-table.html @@ -2,12 +2,12 @@
    • {% for repo in repos %} - + - + {# #} @@ -71,8 +71,8 @@
    {{loop.index + (activePage - 1) * offset}}{{loop.index + (activePage) * offset}} {{ repo.repo_name }}{{ repo.rg_name }}{{ repo.rg_name }}TODO {{ repo.commits_all_time|int }} {{ repo.issues_all_time|int }}
    + {% endfor %} {% else %} -

    No repos selected

    +

    No groups created

    {% endif %}
    @@ -114,7 +115,7 @@

    Add Repos

    event.preventDefault(); var input = document.getElementById("repo_url"); loadingModal.show(); - window.location.replace("{{ url_for('add_user_repo') }}/" + input.value); + window.location.replace("{{ url_for('av_add_user_repo') }}/" + input.value); }); function formError(event, message) { diff --git a/augur/templates/status.html b/augur/templates/status.html index 80a9ff05c9..02b62ed950 100644 --- a/augur/templates/status.html +++ b/augur/templates/status.html @@ -52,7 +52,7 @@

    Commits

    - - - - - - Dasboard - Augur View - - - - - -
    -
    -
    -
    - Dashboard -
    -
    - -
    -
    - - Augur logo - - {# Reserved for future use - - #} -
    -
    - {# Start dashboard content #} -
    -

    Stats

    - {# Start content card #} -
    -
    - {# Start form body #} - - {% for section in sections %} -
    -
    -
    {{ section.title }}
    -
    - {% for setting in section.settings %} -
    -
    - - -
    {{ setting.description or "No description available" }}
    -
    -
    - {% endfor %} -
    - {% endfor %} - {#
    -
    - -
    -
    #} - -
    -
    -

    User Accounts

    - {# Start content card #} -
    -
    -
    - {% for section in sections %} -
    -
    -
    {{ section.title }}
    -
    - {% for setting in section.settings %} -
    -
    - - -
    {{ setting.description or "No description available" }}
    -
    -
    - {% endfor %} -
    - {% endfor %} - {#
    -
    - -
    -
    #} -
    -
    -
    -

    Configuration

    - {# Start content card #} -
    -
    -
    - {% for section in config.items() %} -
    -
    -
    {{ section[0] }}
    -
    - {% for setting in section[1].items() %} -
    -
    - - -
    No description available
    -
    -
    - {% endfor %} -
    - {% endfor %} -
    -
    - -
    -
    -
    -
    -
    -
    -
    -
    - - - - diff --git a/augur/templates/authorization.html b/augur/templates/authorization.html deleted file mode 100644 index 929ee857f7..0000000000 --- a/augur/templates/authorization.html +++ /dev/null @@ -1,41 +0,0 @@ -

    Authorize App

    - -

    {{ application.name }} Sample App is requesting access to your account.

    -

    Authorizing this application will grant it access to the following:

    -
      -
    • Username
      • -
    • Your repo groups
      • -
    • Information collected by Augur, both public and private:
      • -
    • -
        -
      • Issues
        • -
      • Pull requests
        • -
      • Comments
        • -
      • Commit logs
        • -
      -
      • -
    - -

    By continuing, you authorize this access, and will be redirected to the following link:

    -

    {{ application.redirect_url }}

    -Make sure you trust the application and this link before proceeding. - -
    - - - -
    - - - \ No newline at end of file diff --git a/augur/templates/first-time.html b/augur/templates/first-time.html deleted file mode 100644 index c8eb284da8..0000000000 --- a/augur/templates/first-time.html +++ /dev/null @@ -1,211 +0,0 @@ -{# https://www.bootdey.com/snippets/view/dark-profile-settings #} - - - - - - - - - - - - - - -
    -
    - {# Start sidebar #} -
    -
    -
    -
    -
    - -
    -
    -

    First Time Setup

    -

    Take a moment to create or update the configuration for your instance.

    -
    -

    Default values are shown. When you are done updating, click the restart button to save the settings and bring the primary server up.

    -
    - -
    -
    -
    - {% if version %} - Version: {{ version.major }}-{{ version.minor }}-{{ version.series }} - {% else %} - Version: Unspecified - {% endif %} -
    -
    -
    - {# Start form body #} -
    -
    -
    -
    - {% for section in sections %} -
    -
    -
    {{ section.title }}
    -
    - {% for setting in section.settings %} -
    -
    - - -
    {{ setting.description }}
    -
    -
    - {% endfor %} -
    - {% endfor %} -
    -
    -
    Gunicorn Settings
    -
    -
    -
    -
    {{ gunicorn_placeholder }}
    -
    -
    -
    -
    -
    - -
    -
    -
    -
    -
    -
    -
    -
    - - - - - - - diff --git a/augur/templates/groups-table.html b/augur/templates/groups-table.html deleted file mode 100644 index e5ddf094fa..0000000000 --- a/augur/templates/groups-table.html +++ /dev/null @@ -1,33 +0,0 @@ -{# % if groups %} -
    - - - - - - - - - - - - - {% for group in groups %} - - - - - - - - - - {% endfor %} - -
    #Group NameGroup IDDescriptionLast ModifiedData Collection Date
    {{loop.index}}{{ group.rg_name }}{{ group.repo_group_id }}{{ group.rg_description }}{{ group.rg_last_modified }}{{ group.data_collection_date }}TODO
    -
    -{% elif query_key %} -

    Your search did not match any results

    -{% else %} -

    Unable to load group information

    -{% endif % #} diff --git a/augur/templates/index.html b/augur/templates/index.html deleted file mode 100644 index bf73b40f16..0000000000 --- a/augur/templates/index.html +++ /dev/null @@ -1,67 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - {% if title %} - {{title}} - Augur View - {% else %} - Augur View - {% endif %} - - {% if redirect %} - - {% endif %} - - - - - - - {% include 'notifications.html' %} - - {% include 'navbar.html' %} - -
    - {% if invalid %} -

    Invalid API URL

    -

    The API URL [{{ api_url or 'unspecified'}}] is invalid

    - {% elif body %} - {% include '%s.html' % body ignore missing %} - {% else %} -

    404 - Page Not Found

    -

    The page you were looking for isn't here, try clicking one of the navigation links above

    - {% endif %} -
    - -
    -
    -
    -

    This is a beta build of Augur-View. Experimental frontend features may not be fully functional.

    - {#

    Currently serving: {{api_url or 'api_url unspecified'}}

    #} -
    -
    - - Chaos Logo - -
    -
    -
    - - diff --git a/augur/templates/loading.html b/augur/templates/loading.html deleted file mode 100644 index 052af79eab..0000000000 --- a/augur/templates/loading.html +++ /dev/null @@ -1,14 +0,0 @@ -{% if not d %} -

    Uh oh, Something went wrong!

    -

    You were sent to this page because we were loading something for you, but we didn't catch your destination.

    -

    Go back to the previous page and try again. If that doesn't help, submit an issue to https://github.com/chaoss/augur .

    -{% else %} - -

    Give us a moment!

    -

    We are retreiving some data for you, and it may take up to a few seconds to load.

    -

    If you aren't redirected in a few seconds, go back to the previous page and try again.

    - -

    Redirecting to: {{url_for('root', path=d)}}

    -{% endif %} diff --git a/augur/templates/login.html b/augur/templates/login.html deleted file mode 100644 index c71d02d50f..0000000000 --- a/augur/templates/login.html +++ /dev/null @@ -1,155 +0,0 @@ -
    -
    - -
    -
    - - - - \ No newline at end of file diff --git a/augur/templates/navbar.html b/augur/templates/navbar.html deleted file mode 100644 index fe498548a9..0000000000 --- a/augur/templates/navbar.html +++ /dev/null @@ -1,67 +0,0 @@ - diff --git a/augur/templates/notice.html b/augur/templates/notice.html deleted file mode 100644 index 46ed7ead66..0000000000 --- a/augur/templates/notice.html +++ /dev/null @@ -1,6 +0,0 @@ -{% if messageTitle %} -

    {{messageTitle}}

    -{% endif %} -{% if messageBody %} -

    {{messageBody}}

    -{% endif %} diff --git a/augur/templates/notifications.html b/augur/templates/notifications.html deleted file mode 100644 index b59c673391..0000000000 --- a/augur/templates/notifications.html +++ /dev/null @@ -1,79 +0,0 @@ -{% with messages = get_flashed_messages() %} - -
    - {% if messages %} - {% for message in messages %} - - {% endfor %} - {% endif %} -
    - - - - -{% endwith %} - diff --git a/augur/templates/repo-commits.html b/augur/templates/repo-commits.html deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/augur/templates/repo-info.html b/augur/templates/repo-info.html deleted file mode 100644 index 311daa45f7..0000000000 --- a/augur/templates/repo-info.html +++ /dev/null @@ -1,128 +0,0 @@ - - -
    -
    - {% if repo.repo_id %} -

    Report for: {{ repo.repo_name|title }}

    -

    {{ repo.repo_git }}

    - {% for report in reports %} -

    {{ report|replace("_", " ")|title }}

    - {% for image in images[report] %} -
    -
    -
    -
    -
    -
    - {{ image['description'] }} -
    -
    -
    - {% endfor %} - {% endfor %} - {% else %} -

    Repository {{ repo_id }} not found

    - {% endif %} -

    -
    -{% if repo.repo_id %} -{# Wait for cache response: - This method queries the server from the client, asking for confirmation - of which images are available on the server. The server will asynchronously - download the requested images as the page is loading, then once the page - loads, the client will query a locking endpoint on the server and wait - for a response. -#} - -{% endif %} - - - - - - diff --git a/augur/templates/repos-card.html b/augur/templates/repos-card.html deleted file mode 100644 index 9bd6cc4f38..0000000000 --- a/augur/templates/repos-card.html +++ /dev/null @@ -1,27 +0,0 @@ -{% if repos %} -
    -
    - {% for repo in repos %} -
    -
    -
    -
    -
    {{ repo.repo_name }}
     -

    Repository Status: {{ repo.repo_status }}

    -

    All Time Commits: {{ repo.commits_all_time|int }}

    -

    All Time Issues: {{ repo.issues_all_time|int }}

    -
    -
    - Repository ID: {{ repo.repo_id }} -
    -
    -
    -
    - {% endfor %} -
    -
    -{% elif query_key %} -

    Your search did not match any repositories

    -{% else %} -

    Unable to load repository information

    -{% endif %} diff --git a/augur/templates/repos-table.html b/augur/templates/repos-table.html deleted file mode 100644 index 9c08224bde..0000000000 --- a/augur/templates/repos-table.html +++ /dev/null @@ -1,95 +0,0 @@ -{% if repos %} - - - -{# Create the header row for the repo table: - Here we dynamically generate the header row by defining a dictionary list - which contains the titles of each column, accompanied by an optional "key" - item. If a column definition contains a "key" item, that column is assumed - to be sortable, sorting links for that data are generated using the given - key. It is done this way because the client does not receive the full data - each time they load the page, and instead the server sorts the full data. -#} -{# "title" : "Group", "key" : "rg_name"}, #} -{%- set tableHeaders = - [{"title" : "#"}, - {"title" : "Repo Name", "key" : "repo_name"}, - {"title" : "Reports"}, - {"title" : "Commits", "key" : "commits_all_time"}, - {"title" : "Issues", "key" : "issues_all_time"}, - {"title" : "Change Requests"}] -%} -
    - - - - - {%- for header in tableHeaders -%} - {% if header.key %} - {%- if sorting == header.key -%} - {%- set sorting_link = url_for(PS, q=query_key, p=activePage, s=header.key, r= not reverse) -%} - {%- else -%} - {%- set sorting_link = url_for(PS, q=query_key, p=activePage, s=header.key) -%} - {%- endif -%} - - {% else -%} - - {% endif %} {%- endfor -%} - - - - - {% for repo in repos %} - - - - {# #} - - - - - - {% endfor %} - -
    {{ header.title }} - {%- if sorting == header.key and reverse %} ▲ {% elif sorting == header.key %} ▼ {% endif %}{{ header.title }}
    {{loop.index + (activePage) * offset}}{{ repo.repo_name }}{{ repo.rg_name }}TODO{{ repo.commits_all_time|int }}{{ repo.issues_all_time|int }}TODO
    -
    - -
    - -{% elif query_key %} -

    Your search did not match any repositories

    -{% elif current_user.is_authenticated %} -

    No Repos Tracked

    -

    Add repos to your personal tracker in your profile page

    -{% elif activePage != 0 %} -

    Invalid Page

    -Click here to go back -{% else %} -

    Unable to load repository information

    -{% endif %} diff --git a/augur/templates/settings.html b/augur/templates/settings.html deleted file mode 100644 index 6ce1e051fa..0000000000 --- a/augur/templates/settings.html +++ /dev/null @@ -1,140 +0,0 @@ -
    -
    -
    -
    -
    -

    {{ current_user.id }}

    - Delete Account -
    -
    - User Profile -
    -
    -
    -
    -

    Update Password

    - -
    -
    -
    -
    -
    -

    Your Repo Groups

    - {%- set groups = current_user.get_groups()["groups"] -%} - {% if groups %} - {% for group in groups %} - {%- set tableHeaders = - [{"title" : "Group ID"}, - {"title" : "Group Name"}] - -%} -
    - - - - - {%- for header in tableHeaders -%} - - {%- endfor -%} - - - - - {% for repo in repos %} - - - - - {% endfor %} - -
    {{ header.title }}
    {{ group.group_id }}{{ group.name }}
    -
    - {% endfor %} - {% else %} -

    No groups created

    - {% endif %} -
    -
    -
    -

    Add Repos

    - -
    -
    -
    - - - \ No newline at end of file diff --git a/augur/templates/status.html b/augur/templates/status.html deleted file mode 100644 index 02b62ed950..0000000000 --- a/augur/templates/status.html +++ /dev/null @@ -1,233 +0,0 @@ - - - -

    Collection Status

    -
    -
    -
    -

    Pull Requests

    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -

    Issues

    -
    -
    -
    -
    -
    -
    -
    -

    Time between most recently collected issue and last collection run

    -
    -
    -
    -
    -
    -
    -
    -

    Commits

    -
    -
    -
    -
    -
    -
    -
    - -
    -
    - - diff --git a/augur/templates/toasts.html b/augur/templates/toasts.html deleted file mode 100644 index cf707754f2..0000000000 --- a/augur/templates/toasts.html +++ /dev/null @@ -1,60 +0,0 @@ -{% with messages = get_flashed_messages() %} -
    - {% if messages %} - {% for message in messages %} - - {% endfor %} - {% endif %} -
    - -{% endwith %} - - - - diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index 118d03f13d..be68b90f80 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -249,7 +249,7 @@ def add_user_group(self, user_id:int, group_name:str) -> dict: """ if not isinstance(user_id, int) or not isinstance(group_name, str): - return {"status": "Invalid input"} + return False, {"status": "Invalid input"} user_group_data = { "name": group_name, @@ -259,13 +259,14 @@ def add_user_group(self, user_id:int, group_name:str) -> dict: try: result = self.session.insert_data(user_group_data, UserGroup, ["name", "user_id"], return_columns=["group_id"]) except s.exc.IntegrityError: - return {"status": "Error: User id does not exist"} + return False, {"status": "Error: User id does not exist"} if result: - return {"status": "Group created"} - else: - return {"status": "Error while creating group"} + return True, {"status": "Group created"} + + + return False, {"status": "Error while creating group"} def remove_user_group(self, user_id: int, group_name: str) -> dict: """ Delete a users group of repos. @@ -282,7 +283,7 @@ def remove_user_group(self, user_id: int, group_name: str) -> dict: # convert group_name to group_id group_id = self.convert_group_name_to_id(user_id, group_name) if group_id is None: - return {"status": "WARNING: Trying to delete group that does not exist"} + return False, {"status": "WARNING: Trying to delete group that does not exist"} group = self.session.query(UserGroup).filter(UserGroup.group_id == group_id).one() @@ -295,7 +296,7 @@ def remove_user_group(self, user_id: int, group_name: str) -> dict: self.session.commit() - return {"status": "Group deleted"} + return True, {"status": "Group deleted"} def convert_group_name_to_id(self, user_id: int, group_name: str) -> int: @@ -348,27 +349,27 @@ def add_frontend_repo(self, url: List[str], user_id: int, group_name=None, group """ if group_name and group_id: - return {"status": "Pass only the group name or group id not both"} + return False, {"status": "Pass only the group name or group id not both"} if group_id is None: group_id = self.convert_group_name_to_id(user_id, group_name) if group_id is None: - return {"status": "Invalid group name"} + return False, {"status": "Invalid group name"} if not valid_repo and not self.is_valid_repo(url): - return {"status": "Invalid repo", "repo_url": url} + return False, {"status": "Invalid repo", "repo_url": url} repo_id = self.add_repo_row(url, DEFAULT_REPO_GROUP_IDS[0], "Frontend") if not repo_id: - return {"status": "Repo insertion failed", "repo_url": url} + return False, {"status": "Repo insertion failed", "repo_url": url} result = self.add_repo_to_user_group(repo_id, group_id) if not result: - return {"status": "repo_user insertion failed", "repo_url": url} + return False, {"status": "repo_user insertion failed", "repo_url": url} - return {"status": "Repo Added", "repo_url": url} + return True, {"status": "Repo Added", "repo_url": url} def remove_frontend_repo(self, repo_id:int, user_id:int, group_name:str) -> dict: """ Remove repo from a users group. @@ -383,17 +384,17 @@ def remove_frontend_repo(self, repo_id:int, user_id:int, group_name:str) -> dict """ if not isinstance(repo_id, int) or not isinstance(user_id, int) or not isinstance(group_name, str): - return {"status": "Invalid types"} + return False, {"status": "Invalid types"} group_id = self.convert_group_name_to_id(user_id, group_name) if group_id is None: - return {"status": "Invalid group name"} + return False, {"status": "Invalid group name"} # delete rows from user repos with group_id self.session.query(UserRepo).filter(UserRepo.group_id == group_id, UserRepo.repo_id == repo_id).delete() self.session.commit() - return {"status": "Repo Removed"} + return True, {"status": "Repo Removed"} def add_frontend_org(self, url: List[str], user_id: int, group_name: int): @@ -405,12 +406,12 @@ def add_frontend_org(self, url: List[str], user_id: int, group_name: int): """ group_id = self.convert_group_name_to_id(user_id, group_name) if group_id is None: - return {"status": "Invalid group name"} + return False, {"status": "Invalid group name"} repos = self.retrieve_org_repos(url) if not repos: - return {"status": "Invalid org", "org_url": url} + return False, {"status": "Invalid org", "org_url": url} # try to get the repo group with this org name # if it does not exist create one @@ -426,9 +427,9 @@ def add_frontend_org(self, url: List[str], user_id: int, group_name: int): failed_count = len(failed_repos) if failed_count > 0: # this should never happen because an org should never return invalid repos - return {"status": f"{failed_count} repos failed", "repo_urls": failed_repos, "org_url": url} + return False, {"status": f"{failed_count} repos failed", "repo_urls": failed_repos, "org_url": url} - return {"status": "Org repos added", "org_url": url} + return True, {"status": "Org repos added"} def add_cli_repo(self, repo_data: Dict[str, Any], valid_repo=False): """Add list of repos to specified repo_groups @@ -520,42 +521,39 @@ def paginate_repos(self, source, page=0, page_size=25, sort="repo_id", direction if not source: print("Func: paginate_repos. Error: Source Required") - return None + return None, {"status": "Source Required"} if source not in ["all", "user", "group"]: print("Func: paginate_repos. Error: Invalid source") - return None + return None, {"Invalid source"} if direction and direction != "ASC" and direction != "DESC": print("Func: paginate_repos. Error: Invalid direction") - # return {"status": "Invalid direction"} - return None + return None, {"status": "Invalid direction"} try: page = int(page) if page else 0 page_size = int(page_size) if page else 25 except TypeError: print("Func: paginate_repos. Error: Page size and page should be integers") - # return {"status": "Page size and page should be integers"} - return None + return None, {"status": "Page size and page should be integers"} if page < 0 or page_size < 0: print("Func: paginate_repos. Error: Page size and page should be positive") - # return {"status": "Page size and page should be postive"} - return None + return None, {"status": "Page size and page should be postive"} order_by = sort if sort else "repo_id" order_direction = direction if direction else "ASC" query = self.generate_repo_query(source, count=False, order_by=order_by, direction=order_direction, page=page, page_size=page_size, **kwargs) - if not query: - return None + if not query[0]: + return None, {"status": query[1]["status"]} - if query == "No data": - return [] + if query[1]["status"] == "No data": + return [], {"status": "No data"} - get_page_of_repos_sql = s.sql.text(query) + get_page_of_repos_sql = s.sql.text(query[0]) results = pd.read_sql(get_page_of_repos_sql, create_database_engine()) results['url'] = results['url'].apply(lambda datum: datum.split('//')[1]) @@ -567,33 +565,33 @@ def paginate_repos(self, source, page=0, page_size=25, sort="repo_id", direction data = results.to_dict(orient="records") - return data + return data, {"status": "success"} def get_repo_count(self, source, **kwargs): if not source: print("Func: get_repo_count. Error: Source Required") - return None + return None, {"status": "Source Required"} if source not in ["all", "user", "group"]: print("Func: get_repo_count. Error: Invalid source") - return None + return None, {"status": "Invalid source"} user = kwargs.get("user") group_name = kwargs.get("group_name") query = self.generate_repo_query(source, count=True, user=user, group_name=group_name) - if not query: - return None + if not query[0]: + return None, query[1] - if query == "No data": - return [] + if query[1]["status"] == "No data": + return 0, {"status": "No data"} - get_page_of_repos_sql = s.sql.text(query) + get_page_of_repos_sql = s.sql.text(query[0]) result = self.session.fetchall_data_from_sql_text(get_page_of_repos_sql) - return result[0]["count"] + return result[0]["count"], {"status": "success"} def generate_repo_query(self, source, count, **kwargs): @@ -625,12 +623,12 @@ def generate_repo_query(self, source, count, **kwargs): user = kwargs.get("user") if not user: print("Func: generate_repo_query. Error: User not passed when trying to get user repos") - return None + return None, {"status": "User not passed when trying to get user repos"} group_ids = tuple(group.group_id for group in user.groups) if not group_ids: - return "No data" + return None, {"status": "No data"} if len(group_ids) == 1: group_ids_str = str(group_ids)[:-2] + ")" @@ -649,16 +647,17 @@ def generate_repo_query(self, source, count, **kwargs): user = kwargs.get("user") if not user: print("Func: generate_repo_query. Error: User not specified") + return None, {"status": "User not specified"} group_name = kwargs.get("group_name") if not group_name: print("Func: generate_repo_query. Error: Group name not specified") - return None + return None, {"status": "Group name not specified"} group_id = controller.convert_group_name_to_id(user.user_id, group_name) if group_id is None: print("Func: generate_repo_query. Error: Group does not exist") - return None + return None, {"status": "Group does not exists"} query += "\t\t JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id\n" query += f"\t\t WHERE augur_operations.user_repos.group_id = {group_id}\n" @@ -673,5 +672,5 @@ def generate_repo_query(self, source, count, **kwargs): query += f"\t LIMIT {page_size}\n" query += f"\t OFFSET {page*page_size};\n" - return query + return query, {"status": "success"} From 4dbad5accbf25a5ee52304d263aae769e734bf9d Mon Sep 17 00:00:00 2001 From: Ulincsys <28362836a@gmail.com> Date: Tue, 10 Jan 2023 08:36:11 -0600 Subject: [PATCH 067/150] Track templates directory Signed-off-by: Ulincsys <28362836a@gmail.com> --- augur/templates/admin-dashboard.j2 | 178 +++++++++ augur/templates/authorization.j2 | 52 +++ augur/templates/first-time.j2 | 211 +++++++++++ augur/templates/groups-table.j2 | 27 ++ augur/templates/index.j2 | 67 ++++ augur/templates/loading.j2 | 14 + augur/templates/login.j2 | 155 ++++++++ augur/templates/navbar.j2 | 67 ++++ augur/templates/new_settings.j2 | 347 ++++++++++++++++++ augur/templates/notice.j2 | 6 + augur/templates/notifications.j2 | 79 ++++ augur/templates/repo-commits.j2 | 0 augur/templates/repo-info.j2 | 128 +++++++ augur/templates/repos-card.j2 | 30 ++ augur/templates/repos-table.j2 | 95 +++++ augur/templates/settings.j2 | 421 ++++++++++++++++++++++ augur/templates/settings_old.j2 | 140 +++++++ augur/templates/status.j2 | 233 ++++++++++++ augur/templates/toasts.j2 | 60 +++ augur/templates/user-group-repos-table.j2 | 113 ++++++ 20 files changed, 2423 insertions(+) create mode 100644 augur/templates/admin-dashboard.j2 create mode 100644 augur/templates/authorization.j2 create mode 100644 augur/templates/first-time.j2 create mode 100644 augur/templates/groups-table.j2 create mode 100644 augur/templates/index.j2 create mode 100644 augur/templates/loading.j2 create mode 100644 augur/templates/login.j2 create mode 100644 augur/templates/navbar.j2 create mode 100644 augur/templates/new_settings.j2 create mode 100644 augur/templates/notice.j2 create mode 100644 augur/templates/notifications.j2 create mode 100644 augur/templates/repo-commits.j2 create mode 100644 augur/templates/repo-info.j2 create mode 100644 augur/templates/repos-card.j2 create mode 100644 augur/templates/repos-table.j2 create mode 100644 augur/templates/settings.j2 create mode 100644 augur/templates/settings_old.j2 create mode 100644 augur/templates/status.j2 create mode 100644 augur/templates/toasts.j2 create mode 100644 augur/templates/user-group-repos-table.j2 diff --git a/augur/templates/admin-dashboard.j2 b/augur/templates/admin-dashboard.j2 new file mode 100644 index 0000000000..a24829c99f --- /dev/null +++ b/augur/templates/admin-dashboard.j2 @@ -0,0 +1,178 @@ + + + + + + + + + + + + + + + + + + + + + Dasboard - Augur View + + + + + +
    +
    +
    +
    + Dashboard +
    +
    + +
    +
    + + Augur logo + + {# Reserved for future use + + #} +
    +
    + {# Start dashboard content #} +
    +

    Stats

    + {# Start content card #} +
    +
    + {# Start form body #} +
    + {% for section in sections %} +
    +
    +
    {{ section.title }}
    +
    + {% for setting in section.settings %} +
    +
    + + +
    {{ setting.description or "No description available" }}
    +
    +
    + {% endfor %} +
    + {% endfor %} + {#
    +
    + +
    +
    #} +
    +
    +
    +

    User Accounts

    + {# Start content card #} +
    +
    +
    + {% for section in sections %} +
    +
    +
    {{ section.title }}
    +
    + {% for setting in section.settings %} +
    +
    + + +
    {{ setting.description or "No description available" }}
    +
    +
    + {% endfor %} +
    + {% endfor %} + {#
    +
    + +
    +
    #} +
    +
    +
    +

    Configuration

    + {# Start content card #} +
    +
    +
    + {% for section in config.items() %} +
    +
    +
    {{ section[0] }}
    +
    + {% for setting in section[1].items() %} +
    +
    + + +
    No description available
    +
    +
    + {% endfor %} +
    + {% endfor %} +
    +
    + +
    +
    +
    +
    +
    +
    +
    +
    + + + + diff --git a/augur/templates/authorization.j2 b/augur/templates/authorization.j2 new file mode 100644 index 0000000000..d792fa3d69 --- /dev/null +++ b/augur/templates/authorization.j2 @@ -0,0 +1,52 @@ +

    Authorize App

    + +

    {{ app.name }} is requesting access to your account.

    +

    Authorizing this application will grant it access to the following:

    +
      +
    • Username
      • +
    • Your repo groups
      • +
    • Information collected by Augur, both public and private:
      • +
    • +
        +
      • Issues
        • +
      • Pull requests
        • +
      • Comments
        • +
      • Commit logs
        • +
      +
      • +
    + +

    By continuing, you authorize this access, and will be redirected to the following link:

    +

    {{ app.redirect_url }}

    +Make sure you trust the application and this link before proceeding. + +
    + + +
    +
    + +
    +
    + + \ No newline at end of file diff --git a/augur/templates/first-time.j2 b/augur/templates/first-time.j2 new file mode 100644 index 0000000000..c8eb284da8 --- /dev/null +++ b/augur/templates/first-time.j2 @@ -0,0 +1,211 @@ +{# https://www.bootdey.com/snippets/view/dark-profile-settings #} + + + + + + + + + + + + + + +
    +
    + {# Start sidebar #} +
    +
    +
    +
    +
    + +
    +
    +

    First Time Setup

    +

    Take a moment to create or update the configuration for your instance.

    +
    +

    Default values are shown. When you are done updating, click the restart button to save the settings and bring the primary server up.

    +
    + +
    +
    +
    + {% if version %} + Version: {{ version.major }}-{{ version.minor }}-{{ version.series }} + {% else %} + Version: Unspecified + {% endif %} +
    +
    +
    + {# Start form body #} +
    +
    +
    +
    + {% for section in sections %} +
    +
    +
    {{ section.title }}
    +
    + {% for setting in section.settings %} +
    +
    + + +
    {{ setting.description }}
    +
    +
    + {% endfor %} +
    + {% endfor %} +
    +
    +
    Gunicorn Settings
    +
    +
    +
    +
    {{ gunicorn_placeholder }}
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    +
    +
    + + + + + + + diff --git a/augur/templates/groups-table.j2 b/augur/templates/groups-table.j2 new file mode 100644 index 0000000000..ccc0e2a3f3 --- /dev/null +++ b/augur/templates/groups-table.j2 @@ -0,0 +1,27 @@ +{#% if groups %} +
    + + + + + + + + + + {% for group in groups %} + + + + + + + {% endfor %} + +
    #Group NameData Collectio
    {{loop.index}}{{ group.name }}{{ group.data_collection_date }}TODO
    +
    +{% elif query_key %} +

    Your search did not match any results

    +{% else %} +

    Unable to load group information

    +{% endif %#} diff --git a/augur/templates/index.j2 b/augur/templates/index.j2 new file mode 100644 index 0000000000..89cd6734c3 --- /dev/null +++ b/augur/templates/index.j2 @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + {% if title %} + {{title}} - Augur View + {% else %} + Augur View + {% endif %} + + {% if redirect %} + + {% endif %} + + + + + + + {% include 'notifications.j2' %} + + {% include 'navbar.j2' %} + +
    + {% if invalid %} +

    Invalid API URL

    +

    The API URL [{{ api_url or 'unspecified'}}] is invalid

    + {% elif body %} + {% include '%s.j2' % body ignore missing %} + {% else %} +

    404 - Page Not Found

    +

    The page you were looking for isn't here, try clicking one of the navigation links above

    + {% endif %} +
    + +
    +
    +
    +

    This is a beta build of Augur-View. Experimental frontend features may not be fully functional.

    + {#

    Currently serving: {{api_url or 'api_url unspecified'}}

    #} +
    +
    + + Chaos Logo + +
    +
    +
    + + diff --git a/augur/templates/loading.j2 b/augur/templates/loading.j2 new file mode 100644 index 0000000000..052af79eab --- /dev/null +++ b/augur/templates/loading.j2 @@ -0,0 +1,14 @@ +{% if not d %} +

    Uh oh, Something went wrong!

    +

    You were sent to this page because we were loading something for you, but we didn't catch your destination.

    +

    Go back to the previous page and try again. If that doesn't help, submit an issue to https://github.com/chaoss/augur .

    +{% else %} + +

    Give us a moment!

    +

    We are retreiving some data for you, and it may take up to a few seconds to load.

    +

    If you aren't redirected in a few seconds, go back to the previous page and try again.

    + +

    Redirecting to: {{url_for('root', path=d)}}

    +{% endif %} diff --git a/augur/templates/login.j2 b/augur/templates/login.j2 new file mode 100644 index 0000000000..c71d02d50f --- /dev/null +++ b/augur/templates/login.j2 @@ -0,0 +1,155 @@ +
    +
    + +
    +
    + + + + \ No newline at end of file diff --git a/augur/templates/navbar.j2 b/augur/templates/navbar.j2 new file mode 100644 index 0000000000..fe498548a9 --- /dev/null +++ b/augur/templates/navbar.j2 @@ -0,0 +1,67 @@ + diff --git a/augur/templates/new_settings.j2 b/augur/templates/new_settings.j2 new file mode 100644 index 0000000000..74a14ed575 --- /dev/null +++ b/augur/templates/new_settings.j2 @@ -0,0 +1,347 @@ + + + + + + + + + + + + + + + + + + + + + + Settings - Augur View + + + + + + {% include 'notifications.j2' %} +
    +
    +
    +
    + Settings +
    +
    + +
    +
    + + Augur logo + + {# Reserved for future use + + #} +
    +
    + {# Start dashboard content #} +
    +
    +

    Profile

    + {# Start content card #} +
    +
    + {# Start form body #} +
    +
    +
    +
    +

    {{ current_user.id }}

    + Delete Account +
    +
    + User Profile +
    +
    +
    +
    +

    Update Password

    + +
    +
    +
    +
    +
    + + +
    +
    +
    + + + + + + + \ No newline at end of file diff --git a/augur/templates/notice.j2 b/augur/templates/notice.j2 new file mode 100644 index 0000000000..46ed7ead66 --- /dev/null +++ b/augur/templates/notice.j2 @@ -0,0 +1,6 @@ +{% if messageTitle %} +

    {{messageTitle}}

    +{% endif %} +{% if messageBody %} +

    {{messageBody}}

    +{% endif %} diff --git a/augur/templates/notifications.j2 b/augur/templates/notifications.j2 new file mode 100644 index 0000000000..b59c673391 --- /dev/null +++ b/augur/templates/notifications.j2 @@ -0,0 +1,79 @@ +{% with messages = get_flashed_messages() %} + +
    + {% if messages %} + {% for message in messages %} + + {% endfor %} + {% endif %} +
    + + + + +{% endwith %} + diff --git a/augur/templates/repo-commits.j2 b/augur/templates/repo-commits.j2 new file mode 100644 index 0000000000..e69de29bb2 diff --git a/augur/templates/repo-info.j2 b/augur/templates/repo-info.j2 new file mode 100644 index 0000000000..311daa45f7 --- /dev/null +++ b/augur/templates/repo-info.j2 @@ -0,0 +1,128 @@ + + +
    +
    + {% if repo.repo_id %} +

    Report for: {{ repo.repo_name|title }}

    +

    {{ repo.repo_git }}

    + {% for report in reports %} +

    {{ report|replace("_", " ")|title }}

    + {% for image in images[report] %} +
    +
    +
    +
    +
    +
    + {{ image['description'] }} +
    +
    +
    + {% endfor %} + {% endfor %} + {% else %} +

    Repository {{ repo_id }} not found

    + {% endif %} +

    +
    +{% if repo.repo_id %} +{# Wait for cache response: + This method queries the server from the client, asking for confirmation + of which images are available on the server. The server will asynchronously + download the requested images as the page is loading, then once the page + loads, the client will query a locking endpoint on the server and wait + for a response. +#} + +{% endif %} + + + + + + diff --git a/augur/templates/repos-card.j2 b/augur/templates/repos-card.j2 new file mode 100644 index 0000000000..04e4ed3871 --- /dev/null +++ b/augur/templates/repos-card.j2 @@ -0,0 +1,30 @@ +{% if repos %} +
    +
    + {% for repo in repos %} +
    +
    +
    +
    +
    {{ repo.repo_name }}
     +

    Repository Status: {{ repo.repo_status }}

    +

    All Time Commits: {{ repo.commits_all_time|int }}

    +

    All Time Issues: {{ repo.issues_all_time|int }}

    +
    +
    + Repository ID: {{ repo.repo_id }} +
    +
    +
    +
    + {% endfor %} +
    +
    +{% elif query_key %} +

    Your search did not match any repositories

    +{% elif current_user.is_authenticated %} +

    No Repos Tracked

    +

    Add repos to your personal tracker in your profile page

    +{% else %} +

    Unable to load repository information

    +{% endif %} diff --git a/augur/templates/repos-table.j2 b/augur/templates/repos-table.j2 new file mode 100644 index 0000000000..9c08224bde --- /dev/null +++ b/augur/templates/repos-table.j2 @@ -0,0 +1,95 @@ +{% if repos %} + + + +{# Create the header row for the repo table: + Here we dynamically generate the header row by defining a dictionary list + which contains the titles of each column, accompanied by an optional "key" + item. If a column definition contains a "key" item, that column is assumed + to be sortable, sorting links for that data are generated using the given + key. It is done this way because the client does not receive the full data + each time they load the page, and instead the server sorts the full data. +#} +{# "title" : "Group", "key" : "rg_name"}, #} +{%- set tableHeaders = + [{"title" : "#"}, + {"title" : "Repo Name", "key" : "repo_name"}, + {"title" : "Reports"}, + {"title" : "Commits", "key" : "commits_all_time"}, + {"title" : "Issues", "key" : "issues_all_time"}, + {"title" : "Change Requests"}] -%} +
    + + + + + {%- for header in tableHeaders -%} + {% if header.key %} + {%- if sorting == header.key -%} + {%- set sorting_link = url_for(PS, q=query_key, p=activePage, s=header.key, r= not reverse) -%} + {%- else -%} + {%- set sorting_link = url_for(PS, q=query_key, p=activePage, s=header.key) -%} + {%- endif -%} + + {% else -%} + + {% endif %} {%- endfor -%} + + + + + {% for repo in repos %} + + + + {# #} + + + + + + {% endfor %} + +
    {{ header.title }} + {%- if sorting == header.key and reverse %} ▲ {% elif sorting == header.key %} ▼ {% endif %}{{ header.title }}
    {{loop.index + (activePage) * offset}}{{ repo.repo_name }}{{ repo.rg_name }}TODO{{ repo.commits_all_time|int }}{{ repo.issues_all_time|int }}TODO
    +
    + +
    + +{% elif query_key %} +

    Your search did not match any repositories

    +{% elif current_user.is_authenticated %} +

    No Repos Tracked

    +

    Add repos to your personal tracker in your profile page

    +{% elif activePage != 0 %} +

    Invalid Page

    +Click here to go back +{% else %} +

    Unable to load repository information

    +{% endif %} diff --git a/augur/templates/settings.j2 b/augur/templates/settings.j2 new file mode 100644 index 0000000000..aa09f265fe --- /dev/null +++ b/augur/templates/settings.j2 @@ -0,0 +1,421 @@ + + + + + + + + + + + + + + + + + + + + + + Settings - Augur View + + + + + + {% include 'notifications.j2' %} +
    +
    +
    +
    + Settings +
    +
    + +
    +
    + + Augur logo + + {# Reserved for future use + + #} +
    +
    + {# Start dashboard content #} +
    +
    +

    Profile

    + {# Start content card #} +
    +
    + {# Start form body #} +
    +
    +
    +
    +

    {{ current_user.id }}

    + Delete Account +
    +
    + User Profile +
    +
    +
    +
    +

    Update Password

    + +
    +
    +
    +
    +
    + + +
    +
    +
    + + + + + + + + \ No newline at end of file diff --git a/augur/templates/settings_old.j2 b/augur/templates/settings_old.j2 new file mode 100644 index 0000000000..f62a066ab7 --- /dev/null +++ b/augur/templates/settings_old.j2 @@ -0,0 +1,140 @@ +
    +
    +
    +
    +
    +

    {{ current_user.id }}

    + Delete Account +
    +
    + User Profile +
    +
    +
    +
    +

    Update Password

    + +
    +
    +
    +
    +
    +

    Your Repo Groups

    + {%- set groups = current_user.get_groups()["groups"] -%} + {% if groups %} + {% for group in groups %} + {%- set tableHeaders = + [{"title" : "Group ID"}, + {"title" : "Group Name"}] + -%} +
    + + + + + {%- for header in tableHeaders -%} + + {%- endfor -%} + + + + + {% for repo in repos %} + + + + + {% endfor %} + +
    {{ header.title }}
    {{ group.group_id }}{{ group.name }}
    +
    + {% endfor %} + {% else %} +

    No groups created

    + {% endif %} +
    +
    +
    +

    Add Repos

    + +
    +
    +
    + + + \ No newline at end of file diff --git a/augur/templates/status.j2 b/augur/templates/status.j2 new file mode 100644 index 0000000000..02b62ed950 --- /dev/null +++ b/augur/templates/status.j2 @@ -0,0 +1,233 @@ + + + +

    Collection Status

    +
    +
    +
    +

    Pull Requests

    +
    +
    +
    +
    +
    +
    +
    +
    +
    +
    +
    +
    +
    +
    +
    +
    +

    Issues

    +
    +
    +
    +
    +
    +
    +
    +

    Time between most recently collected issue and last collection run

    +
    +
    +
    +
    +
    +
    +
    +

    Commits

    +
    +
    +
    +
    +
    +
    +
    + +
    +
    + + diff --git a/augur/templates/toasts.j2 b/augur/templates/toasts.j2 new file mode 100644 index 0000000000..cf707754f2 --- /dev/null +++ b/augur/templates/toasts.j2 @@ -0,0 +1,60 @@ +{% with messages = get_flashed_messages() %} +
    + {% if messages %} + {% for message in messages %} + + {% endfor %} + {% endif %} +
    + +{% endwith %} + + + + diff --git a/augur/templates/user-group-repos-table.j2 b/augur/templates/user-group-repos-table.j2 new file mode 100644 index 0000000000..0b3adefc25 --- /dev/null +++ b/augur/templates/user-group-repos-table.j2 @@ -0,0 +1,113 @@ +{% if repos %} + +

    {{ group }}

    + + +{# Create the header row for the repo table: + Here we dynamically generate the header row by defining a dictionary list + which contains the titles of each column, accompanied by an optional "key" + item. If a column definition contains a "key" item, that column is assumed + to be sortable, sorting links for that data are generated using the given + key. It is done this way because the client does not receive the full data + each time they load the page, and instead the server sorts the full data. +#} +{# "title" : "Group", "key" : "rg_name"}, #} +{%- set tableHeaders = + [{"title" : "#"}, + {"title" : "Repo Name", "key" : "repo_name"}, + {"title" : "Reports"}, + {"title" : "Commits", "key" : "commits_all_time"}, + {"title" : "Issues", "key" : "issues_all_time"}, + {"title" : "Change Requests"}, + {"title" : "Remove"}] -%} +
    + + + + + {%- for header in tableHeaders -%} + {% if header.key %} + {%- if sorting == header.key -%} + {%- set sorting_link = url_for(PS, q=query_key, p=activePage, s=header.key, r= not reverse) -%} + {%- else -%} + {%- set sorting_link = url_for(PS, q=query_key, p=activePage, s=header.key) -%} + {%- endif -%} + + {% else -%} + + {% endif %} {%- endfor -%} + + + + + {% for repo in repos %} + + + + {# #} + + + + + + + {% endfor %} + +
    {{ header.title }} + {%- if sorting == header.key and reverse %} ▲ {% elif sorting == header.key %} ▼ {% endif %}{{ header.title }}
    {{loop.index + (activePage) * offset}}{{ repo.repo_name }}{{ repo.rg_name }}TODO{{ repo.commits_all_time|int }}{{ repo.issues_all_time|int }}TODO
    +
    + +
    + +{% elif query_key %} +

    Your search did not match any repositories

    +{% elif current_user.is_authenticated %} +

    No Repos Tracked

    +

    Add repos to your personal tracker in your profile page

    +{% elif activePage != 0 %} +

    Invalid Page

    +Click here to go back +{% else %} +

    No repos in group

    +

    Add repos to this group in your profile page

    +{% endif %} + + From fdfa7b9b45655cb2e8556e7f2d7a5157d3cbc6ba Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 10 Jan 2023 14:54:35 -0600 Subject: [PATCH 068/150] Make default group allowed, and return user group exists if it does Signed-off-by: Andrew Brain --- augur/application/db/models/augur_operations.py | 7 ++----- augur/util/repo_load_controller.py | 4 ++++ 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index 5c5d6f7f54..854a6189d4 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -288,8 +288,8 @@ def create_user(username: str, password: str, email: str, first_name:str, last_n local_session.add(user) local_session.commit() - result = user.add_group(f"{username}_default")[0] - if not result: + result = user.add_group("default") + if not result[0] and result[1]["status"] != "Group already exists": return False, {"status": "Failed to add default group for the user"} return True, {"status": "Account successfully created"} @@ -371,9 +371,6 @@ def update_username(self, new_username): def add_group(self, group_name): from augur.util.repo_load_controller import RepoLoadController - - if group_name == "default": - return False, {"status": "Reserved Group Name"} local_session = get_session() diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index be68b90f80..55e8c32feb 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -256,6 +256,10 @@ def add_user_group(self, user_id:int, group_name:str) -> dict: "user_id": user_id } + user_group = self.session.query(UserGroup).filter(UserGroup.user_id == user_id, UserGroup, UserGroup.name == group_name).first() + if user_group: + return False, {"status": "Group already exists"} + try: result = self.session.insert_data(user_group_data, UserGroup, ["name", "user_id"], return_columns=["group_id"]) except s.exc.IntegrityError: From 8efebe27c814b06114e7d3120d21e167ac99250f Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Tue, 10 Jan 2023 15:24:19 -0600 Subject: [PATCH 069/150] Change celery task scheduling to not scale proportionally to the amount of repos Signed-off-by: Isaac Milarsky --- augur/tasks/github/detect_move/tasks.py | 2 +- augur/tasks/github/events/tasks.py | 44 ++++++++++--------- augur/tasks/github/issues/tasks.py | 36 ++++++++------- augur/tasks/github/messages/tasks.py | 31 ++++++------- .../pull_requests/commits_model/tasks.py | 19 ++++---- .../github/pull_requests/files_model/tasks.py | 19 ++++---- augur/tasks/github/pull_requests/tasks.py | 29 ++++++------ augur/tasks/github/repo_info/tasks.py | 20 +++++---- augur/tasks/start_tasks.py | 28 ++++++++---- 9 files changed, 124 insertions(+), 104 deletions(-) diff --git a/augur/tasks/github/detect_move/tasks.py b/augur/tasks/github/detect_move/tasks.py index 2acc440747..f47d800b82 100644 --- a/augur/tasks/github/detect_move/tasks.py +++ b/augur/tasks/github/detect_move/tasks.py @@ -6,7 +6,7 @@ @celery.task -def detect_github_repo_move(repo_git_identifiers : str) -> None: +def detect_github_repo_move(repo_git_identifiers : [str]) -> None: logger = logging.getLogger(detect_github_repo_move.__name__) logger.info(f"Starting repo_move operation with {repo_git_identifiers}") diff --git a/augur/tasks/github/events/tasks.py b/augur/tasks/github/events/tasks.py index 78f356d915..cb8c175e91 100644 --- a/augur/tasks/github/events/tasks.py +++ b/augur/tasks/github/events/tasks.py @@ -15,31 +15,33 @@ @celery.task -def collect_events(repo_git: str): +def collect_events(repo_git_identifiers: [str]): logger = logging.getLogger(collect_events.__name__) - # define GithubTaskSession to handle insertions, and store oauth keys - with GithubTaskSession(logger) as session: - - query = session.query(Repo).filter(Repo.repo_git == repo_git) - repo_obj = execute_session_query(query, 'one') - repo_id = repo_obj.repo_id - - owner, repo = get_owner_repo(repo_git) - - logger.info(f"Collecting Github events for {owner}/{repo}") - - url = f"https://api.github.com/repos/{owner}/{repo}/issues/events" - - event_data = retrieve_all_event_data(repo_git, logger) - - if event_data: - - process_events(event_data, f"{owner}/{repo}: Event task", repo_id, logger) - else: - logger.info(f"{owner}/{repo} has no events") + for repo_git in repo_git_identifiers: + # define GithubTaskSession to handle insertions, and store oauth keys + with GithubTaskSession(logger) as session: + + query = session.query(Repo).filter(Repo.repo_git == repo_git) + repo_obj = execute_session_query(query, 'one') + repo_id = repo_obj.repo_id + + owner, repo = get_owner_repo(repo_git) + + logger.info(f"Collecting Github events for {owner}/{repo}") + + url = f"https://api.github.com/repos/{owner}/{repo}/issues/events" + + event_data = retrieve_all_event_data(repo_git, logger) + + if event_data: + + process_events(event_data, f"{owner}/{repo}: Event task", repo_id, logger) + + else: + logger.info(f"{owner}/{repo} has no events") def retrieve_all_event_data(repo_git: str, logger): diff --git a/augur/tasks/github/issues/tasks.py b/augur/tasks/github/issues/tasks.py index d75c86c279..83dbbb02bb 100644 --- a/augur/tasks/github/issues/tasks.py +++ b/augur/tasks/github/issues/tasks.py @@ -18,27 +18,29 @@ development = get_development_flag() @celery.task -def collect_issues(repo_git: str) -> None: +def collect_issues(repo_git_identifiers: [str]) -> None: logger = logging.getLogger(collect_issues.__name__) - owner, repo = get_owner_repo(repo_git) - # define GithubTaskSession to handle insertions, and store oauth keys - with GithubTaskSession(logger) as session: - - query = session.query(Repo).filter(Repo.repo_git == repo_git) - repo_obj = execute_session_query(query, 'one') - repo_id = repo_obj.repo_id + for repo_git in repo_git_identifiers: + owner, repo = get_owner_repo(repo_git) + + # define GithubTaskSession to handle insertions, and store oauth keys + with GithubTaskSession(logger) as session: + + query = session.query(Repo).filter(Repo.repo_git == repo_git) + repo_obj = execute_session_query(query, 'one') + repo_id = repo_obj.repo_id + + + issue_data = retrieve_all_issue_data(repo_git, logger) + + if issue_data: - - issue_data = retrieve_all_issue_data(repo_git, logger) - - if issue_data: - - process_issues(issue_data, f"{owner}/{repo}: Issue task", repo_id, logger) - - else: - logger.info(f"{owner}/{repo} has no issues") + process_issues(issue_data, f"{owner}/{repo}: Issue task", repo_id, logger) + + else: + logger.info(f"{owner}/{repo} has no issues") def retrieve_all_issue_data(repo_git, logger) -> None: diff --git a/augur/tasks/github/messages/tasks.py b/augur/tasks/github/messages/tasks.py index 26a4769494..89ea3e1c6e 100644 --- a/augur/tasks/github/messages/tasks.py +++ b/augur/tasks/github/messages/tasks.py @@ -17,24 +17,25 @@ @celery.task -def collect_github_messages(repo_git: str) -> None: +def collect_github_messages(repo_git_identifiers: [str]) -> None: logger = logging.getLogger(collect_github_messages.__name__) - with GithubTaskSession(logger, engine) as session: - - repo_id = session.query(Repo).filter( - Repo.repo_git == repo_git).one().repo_id - - owner, repo = get_owner_repo(repo_git) - message_data = retrieve_all_pr_and_issue_messages(repo_git, logger) - - if message_data: - - process_messages(message_data, f"{owner}/{repo}: Message task", repo_id, logger) - - else: - logger.info(f"{owner}/{repo} has no messages") + for repo_git in repo_git_identifiers: + with GithubTaskSession(logger, engine) as session: + + repo_id = session.query(Repo).filter( + Repo.repo_git == repo_git).one().repo_id + + owner, repo = get_owner_repo(repo_git) + message_data = retrieve_all_pr_and_issue_messages(repo_git, logger) + + if message_data: + + process_messages(message_data, f"{owner}/{repo}: Message task", repo_id, logger) + + else: + logger.info(f"{owner}/{repo} has no messages") def retrieve_all_pr_and_issue_messages(repo_git: str, logger) -> None: diff --git a/augur/tasks/github/pull_requests/commits_model/tasks.py b/augur/tasks/github/pull_requests/commits_model/tasks.py index 9a9c834e9c..e50ea9b4ea 100644 --- a/augur/tasks/github/pull_requests/commits_model/tasks.py +++ b/augur/tasks/github/pull_requests/commits_model/tasks.py @@ -7,14 +7,15 @@ @celery.task -def process_pull_request_commits(repo_git: str) -> None: +def process_pull_request_commits(repo_git_identifiers: [str]) -> None: logger = logging.getLogger(process_pull_request_commits.__name__) - with GithubTaskSession(logger) as session: - query = session.query(Repo).filter(Repo.repo_git == repo_git) - repo = execute_session_query(query, 'one') - try: - pull_request_commits_model(repo.repo_id, logger) - except Exception as e: - logger.error(f"Could not complete pull_request_commits_model!\n Reason: {e} \n Traceback: {''.join(traceback.format_exception(None, e, e.__traceback__))}") - raise e + for repo_git in repo_git_identifiers: + with GithubTaskSession(logger) as session: + query = session.query(Repo).filter(Repo.repo_git == repo_git) + repo = execute_session_query(query, 'one') + try: + pull_request_commits_model(repo.repo_id, logger) + except Exception as e: + logger.error(f"Could not complete pull_request_commits_model!\n Reason: {e} \n Traceback: {''.join(traceback.format_exception(None, e, e.__traceback__))}") + raise e diff --git a/augur/tasks/github/pull_requests/files_model/tasks.py b/augur/tasks/github/pull_requests/files_model/tasks.py index 6ed40811a9..fbe29795ac 100644 --- a/augur/tasks/github/pull_requests/files_model/tasks.py +++ b/augur/tasks/github/pull_requests/files_model/tasks.py @@ -6,14 +6,15 @@ from augur.application.db.util import execute_session_query @celery.task -def process_pull_request_files(repo_git: str) -> None: +def process_pull_request_files(repo_git_identifiers: str) -> None: logger = logging.getLogger(process_pull_request_files.__name__) - with GithubTaskSession(logger) as session: - query = session.query(Repo).filter(Repo.repo_git == repo_git) - repo = execute_session_query(query, 'one') - try: - pull_request_files_model(repo.repo_id, logger) - except Exception as e: - logger.error(f"Could not complete pull_request_files_model!\n Reason: {e} \n Traceback: {''.join(traceback.format_exception(None, e, e.__traceback__))}") - #raise e \ No newline at end of file + for repo_git in repo_git_identifiers: + with GithubTaskSession(logger) as session: + query = session.query(Repo).filter(Repo.repo_git == repo_git) + repo = execute_session_query(query, 'one') + try: + pull_request_files_model(repo.repo_id, logger) + except Exception as e: + logger.error(f"Could not complete pull_request_files_model!\n Reason: {e} \n Traceback: {''.join(traceback.format_exception(None, e, e.__traceback__))}") + #raise e \ No newline at end of file diff --git a/augur/tasks/github/pull_requests/tasks.py b/augur/tasks/github/pull_requests/tasks.py index 848a78f5b7..2b3383bcc7 100644 --- a/augur/tasks/github/pull_requests/tasks.py +++ b/augur/tasks/github/pull_requests/tasks.py @@ -17,22 +17,23 @@ @celery.task -def collect_pull_requests(repo_git: str) -> None: +def collect_pull_requests(repo_git_identifiers: [str]) -> None: logger = logging.getLogger(collect_pull_requests.__name__) - - with GithubTaskSession(logger, engine) as session: - - repo_id = session.query(Repo).filter( - Repo.repo_git == repo_git).one().repo_id - - owner, repo = get_owner_repo(repo_git) - pr_data = retrieve_all_pr_data(repo_git, logger) - - if pr_data: - process_pull_requests(pr_data, f"{owner}/{repo}: Pr task", repo_id, logger) - else: - logger.info(f"{owner}/{repo} has no pull requests") + + for repo_git in repo_git_identifiers: + with GithubTaskSession(logger, engine) as session: + + repo_id = session.query(Repo).filter( + Repo.repo_git == repo_git).one().repo_id + + owner, repo = get_owner_repo(repo_git) + pr_data = retrieve_all_pr_data(repo_git, logger) + + if pr_data: + process_pull_requests(pr_data, f"{owner}/{repo}: Pr task", repo_id, logger) + else: + logger.info(f"{owner}/{repo} has no pull requests") # TODO: Rename pull_request_reviewers table to pull_request_requested_reviewers diff --git a/augur/tasks/github/repo_info/tasks.py b/augur/tasks/github/repo_info/tasks.py index 010b2114a0..c739cb49d0 100644 --- a/augur/tasks/github/repo_info/tasks.py +++ b/augur/tasks/github/repo_info/tasks.py @@ -5,16 +5,18 @@ import traceback @celery.task -def collect_repo_info(repo_git: str): +def collect_repo_info(repo_git_identifiers: [str]): logger = logging.getLogger(collect_repo_info.__name__) with GithubTaskSession(logger, engine) as session: - query = session.query(Repo).filter(Repo.repo_git == repo_git) - repo = execute_session_query(query, 'one') - try: - repo_info_model(session, repo) - except Exception as e: - session.logger.error(f"Could not add repo info for repo {repo.repo_id}\n Error: {e}") - session.logger.error( - ''.join(traceback.format_exception(None, e, e.__traceback__))) \ No newline at end of file + + for repo_git in repo_git_identifiers: + query = session.query(Repo).filter(Repo.repo_git == repo_git) + repo = execute_session_query(query, 'one') + try: + repo_info_model(session, repo) + except Exception as e: + session.logger.error(f"Could not add repo info for repo {repo.repo_id}\n Error: {e}") + session.logger.error( + ''.join(traceback.format_exception(None, e, e.__traceback__))) \ No newline at end of file diff --git a/augur/tasks/start_tasks.py b/augur/tasks/start_tasks.py index f8c02cc95d..561b3005ce 100644 --- a/augur/tasks/start_tasks.py +++ b/augur/tasks/start_tasks.py @@ -62,20 +62,30 @@ def repo_collect_phase(): with DatabaseSession(logger) as session: query = session.query(Repo) repos = execute_session_query(query, 'all') - #Just use list comprehension for simple group - repo_info_tasks = [collect_repo_info.si(repo.repo_git) for repo in repos] - for repo in repos: - first_tasks_repo = group(collect_issues.si(repo.repo_git),collect_pull_requests.si(repo.repo_git)) - second_tasks_repo = group(collect_events.si(repo.repo_git), - collect_github_messages.si(repo.repo_git),process_pull_request_files.si(repo.repo_git), process_pull_request_commits.si(repo.repo_git)) - repo_chain = chain(first_tasks_repo,second_tasks_repo) - issue_dependent_tasks.append(repo_chain) + all_repo_git_identifiers = [repo.repo_git for repo in repos] + + #Pool the tasks for collecting repo info. + repo_info_tasks = create_grouped_task_load(dataList=all_repo_git_identifiers, task=collect_repo_info).tasks + + #pool the repo collection jobs that should be ran first and have deps. + primary_repo_jobs = group( + *create_grouped_task_load(dataList=all_repo_git_identifiers, task=collect_issues).tasks, + *create_grouped_task_load(dataList=all_repo_git_identifiers, task=collect_pull_requests).tasks + ) + + secondary_repo_jobs = group( + *create_grouped_task_load(dataList=all_repo_git_identifiers, task=collect_events).tasks, + *create_grouped_task_load(dataList=all_repo_git_identifiers,task=collect_github_messages).tasks, + *create_grouped_task_load(dataList=all_repo_git_identifiers, task=process_pull_request_files).tasks, + *create_grouped_task_load(dataList=all_repo_git_identifiers, task=process_pull_request_commits).tasks + ) + repo_task_group = group( *repo_info_tasks, - chain(group(*issue_dependent_tasks),process_contributors.si()), + chain(primary_repo_jobs,secondary_repo_jobs,process_contributors.si()), generate_facade_chain(logger), collect_releases.si() ) From e79980a3a36699a1f0c6617b121395c5f30afb96 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 10 Jan 2023 15:43:14 -0600 Subject: [PATCH 070/150] Fix errors in the api Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 12 +++++---- augur/util/repo_load_controller.py | 43 +++++++++++++++++------------- 2 files changed, 31 insertions(+), 24 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index ebae5c94f7..a011c64163 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -124,13 +124,11 @@ def user_authorize(): def generate_session(application): code = request.args.get("code") if not code: - print("Passed empty code") return jsonify({"status": "Invalid authorization code"}) username = redis.get(code) redis.delete(code) if not username: - print("Could not find in redis") return jsonify({"status": "Invalid authorization code"}) user = User.get_user(username) @@ -253,7 +251,7 @@ def add_user_group(): return jsonify(result[1]) - @server.app.route(f"/{AUGUR_API_VERSION}/user/remove_group", methods=['GET', 'POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/group/remove", methods=['GET', 'POST']) @login_required def remove_user_group(): if not development and not request.is_secure: @@ -288,7 +286,11 @@ def remove_user_repo(): group_name = request.args.get("group_name") - repo_id = request.args.get("repo_id") + + try: + repo_id = int(request.args.get("repo_id")) + except TypeError: + return {"status": "Repo id must be and integer"} result = current_user.remove_repo(group_name, repo_id) @@ -360,7 +362,7 @@ def group_repo_count(): group_name = request.args.get("group_name") - result = current_user.group_repo_count(group_name) + result = current_user.get_group_repo_count(group_name) result_dict = result[1] if result[0] is not None: diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index 55e8c32feb..99cce626ea 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -86,9 +86,12 @@ def is_valid_repo(self, url: str) -> bool: True if repo url is valid and False if not """ + if not self.session.oauths.list_of_keys: + return False, {"status": "No valid github api keys to retrieve data with"} + owner, repo = parse_repo_url(url) if not owner or not repo: - return False + return False, {"status":"Invalid repo url"} url = REPO_ENDPOINT.format(owner, repo) @@ -103,9 +106,9 @@ def is_valid_repo(self, url: str) -> bool: # if there was an error return False if "message" in result.json().keys(): - return False + return False, {"status": f"Github Error: {result.json()['message']}"} - return True + return True, {"status": "Valid repo"} def retrieve_org_repos(self, url: str) -> List[str]: @@ -123,13 +126,16 @@ def retrieve_org_repos(self, url: str) -> List[str]: owner = parse_org_url(url) if not owner: - return [] + return None, {"status": "Invalid owner url"} url = ORG_REPOS_ENDPOINT.format(owner) repos = [] with GithubTaskSession(logger) as session: + if not session.oauths.list_of_keys: + return None, {"status": "No valid github api keys to retrieve data with"} + for page_data, page in GithubPaginator(url, session.oauths, logger).iter_pages(): if page_data is None: @@ -139,7 +145,7 @@ def retrieve_org_repos(self, url: str) -> List[str]: repo_urls = [repo["html_url"] for repo in repos] - return repo_urls + return repo_urls, {"status": "Invalid owner url"} def is_valid_repo_group_id(self, repo_group_id: int) -> bool: @@ -284,12 +290,9 @@ def remove_user_group(self, user_id: int, group_name: str) -> dict: """ - # convert group_name to group_id - group_id = self.convert_group_name_to_id(user_id, group_name) - if group_id is None: - return False, {"status": "WARNING: Trying to delete group that does not exist"} - - group = self.session.query(UserGroup).filter(UserGroup.group_id == group_id).one() + group = self.session.query(UserGroup).filter(UserGroup.name == group_name, UserGroup.user_id == user_id).first() + if not group: + return False, {"status": "WARNING: Trying to delete group that does not exist"} # delete rows from user repos with group_id for repo in group.repos: @@ -361,8 +364,10 @@ def add_frontend_repo(self, url: List[str], user_id: int, group_name=None, group if group_id is None: return False, {"status": "Invalid group name"} - if not valid_repo and not self.is_valid_repo(url): - return False, {"status": "Invalid repo", "repo_url": url} + if not valid_repo: + result = self.is_valid_repo(url) + if not result[0]: + return False, {"status": result[1]["status"], "repo_url": url} repo_id = self.add_repo_row(url, DEFAULT_REPO_GROUP_IDS[0], "Frontend") if not repo_id: @@ -412,11 +417,11 @@ def add_frontend_org(self, url: List[str], user_id: int, group_name: int): if group_id is None: return False, {"status": "Invalid group name"} - repos = self.retrieve_org_repos(url) - - if not repos: - return False, {"status": "Invalid org", "org_url": url} + result = self.retrieve_org_repos(url) + if not result[0]: + return False, result[1] + repos = result[0] # try to get the repo group with this org name # if it does not exist create one failed_repos = [] @@ -425,7 +430,7 @@ def add_frontend_org(self, url: List[str], user_id: int, group_name: int): result = self.add_frontend_repo(repo, user_id, group_id=group_id, valid_repo=True) # keep track of all the repos that failed - if result["status"] != "Repo Added": + if not result[0]: failed_repos.append(repo) failed_count = len(failed_repos) @@ -445,7 +450,7 @@ def add_cli_repo(self, repo_data: Dict[str, Any], valid_repo=False): url = repo_data["url"] repo_group_id = repo_data["repo_group_id"] - if valid_repo or self.is_valid_repo(url): + if valid_repo or self.is_valid_repo(url)[0]: # if the repo doesn't exist it adds it # if the repo does exist it updates the repo_group_id From 03fd23ab01eaa00697c8af6947e47ac2f9073acb Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 10 Jan 2023 16:45:55 -0600 Subject: [PATCH 071/150] User function improvements Signed-off-by: Andrew Brain --- augur/util/repo_load_controller.py | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index 99cce626ea..550ca41568 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -524,8 +524,6 @@ def get_user_repo_ids(self, user_id: int) -> List[int]: return list(all_repo_ids) - - def paginate_repos(self, source, page=0, page_size=25, sort="repo_id", direction="ASC", **kwargs): if not source: @@ -574,6 +572,9 @@ def paginate_repos(self, source, page=0, page_size=25, sort="repo_id", direction data = results.to_dict(orient="records") + for row in data: + row["repo_name"] = re.search(r"github\.com\/[A-Za-z0-9 \- _]+\/([A-Za-z0-9 \- _ .]+)$", row["url"]).groups()[0] + return data, {"status": "success"} def get_repo_count(self, source, **kwargs): @@ -595,8 +596,11 @@ def get_repo_count(self, source, **kwargs): if query[1]["status"] == "No data": return 0, {"status": "No data"} + + # surround query with count query so we just get the count of the rows + final_query = f"SELECT count(*) FROM ({query[0]}) a;" - get_page_of_repos_sql = s.sql.text(query[0]) + get_page_of_repos_sql = s.sql.text(final_query) result = self.session.fetchall_data_from_sql_text(get_page_of_repos_sql) @@ -606,10 +610,11 @@ def get_repo_count(self, source, **kwargs): def generate_repo_query(self, source, count, **kwargs): if count: - select = "count(*)" + # only query for repos ids so the query is faster for getting the count + select = " DISTINCT(augur_data.repo.repo_id)" else: - select = """ augur_data.repo.repo_id, - augur_data.repo.repo_name, + + select = """ DISTINCT(augur_data.repo.repo_id), augur_data.repo.description, augur_data.repo.repo_git AS url, augur_data.repo.repo_status, @@ -634,18 +639,12 @@ def generate_repo_query(self, source, count, **kwargs): print("Func: generate_repo_query. Error: User not passed when trying to get user repos") return None, {"status": "User not passed when trying to get user repos"} - group_ids = tuple(group.group_id for group in user.groups) - - if not group_ids: + if not user.groups: return None, {"status": "No data"} - if len(group_ids) == 1: - group_ids_str = str(group_ids)[:-2] + ")" - else: - group_ids_str = str(group_ids) - query += "\t\t JOIN augur_operations.user_repos ON augur_data.repo.repo_id = augur_operations.user_repos.repo_id\n" - query += f"\t\t WHERE augur_operations.user_repos.group_id in {group_ids_str}\n" + query += "\t\t JOIN augur_operations.user_groups ON augur_operations.user_repos.group_id = augur_operations.user_groups.group_id\n" + query += f"\t\t WHERE augur_operations.user_groups.user_id = {user.user_id}\n" elif source == "group": From eceab1baa4d425faa44c4cfa2e0e29b972e3420b Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Wed, 11 Jan 2023 08:13:20 -0600 Subject: [PATCH 072/150] Remove print Signed-off-by: Andrew Brain --- augur/api/view/augur_view.py | 1 - augur/util/repo_load_controller.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/augur/api/view/augur_view.py b/augur/api/view/augur_view.py index 79adad6334..56a562eb8e 100644 --- a/augur/api/view/augur_view.py +++ b/augur/api/view/augur_view.py @@ -71,7 +71,6 @@ def load_user_request(request): with DatabaseSession(logger) as session: token = session.query(UserSessionToken).filter(UserSessionToken.token == token).first() - print(token) if token: user = token.user diff --git a/augur/util/repo_load_controller.py b/augur/util/repo_load_controller.py index 550ca41568..9c0317cee6 100644 --- a/augur/util/repo_load_controller.py +++ b/augur/util/repo_load_controller.py @@ -262,7 +262,7 @@ def add_user_group(self, user_id:int, group_name:str) -> dict: "user_id": user_id } - user_group = self.session.query(UserGroup).filter(UserGroup.user_id == user_id, UserGroup, UserGroup.name == group_name).first() + user_group = self.session.query(UserGroup).filter(UserGroup.user_id == user_id, UserGroup.name == group_name).first() if user_group: return False, {"status": "Group already exists"} From a33e7ff25658763791cdd47d89eacc9a79f6b259 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Wed, 11 Jan 2023 13:58:14 -0600 Subject: [PATCH 073/150] analysis sequence pooling for facade scaling Signed-off-by: Isaac Milarsky --- augur/tasks/git/facade_tasks.py | 146 +++++++++++++++++++------------- augur/tasks/util/worker_util.py | 2 + 2 files changed, 89 insertions(+), 59 deletions(-) diff --git a/augur/tasks/git/facade_tasks.py b/augur/tasks/git/facade_tasks.py index fbe4783b01..7ab3878b1c 100644 --- a/augur/tasks/git/facade_tasks.py +++ b/augur/tasks/git/facade_tasks.py @@ -70,17 +70,18 @@ def facade_analysis_init_facade_task(): session.log_activity('Info',f"Beginning analysis.") @celery.task -def grab_comitters(repo_id,platform="github"): +def grab_comitters(repo_id_list,platform="github"): logger = logging.getLogger(grab_comitters.__name__) - try: - grab_committer_list(GithubTaskSession(logger), repo_id,platform) - except Exception as e: - logger.error(f"Could not grab committers from github endpoint!\n Reason: {e} \n Traceback: {''.join(traceback.format_exception(None, e, e.__traceback__))}") - + for repo_id in repo_id_list: + try: + grab_committer_list(GithubTaskSession(logger), repo_id,platform) + except Exception as e: + logger.error(f"Could not grab committers from github endpoint!\n Reason: {e} \n Traceback: {''.join(traceback.format_exception(None, e, e.__traceback__))}") + @celery.task -def trim_commits_facade_task(repo_id): +def trim_commits_facade_task(repo_id_list): logger = logging.getLogger(trim_commits_facade_task.__name__) session = FacadeSession(logger) @@ -96,39 +97,39 @@ def update_analysis_log(repos_id,status): except: pass + for repo_id in repo_id_list: + session.inc_repos_processed() + update_analysis_log(repo_id,"Beginning analysis.") + # First we check to see if the previous analysis didn't complete - session.inc_repos_processed() - update_analysis_log(repo_id,"Beginning analysis.") - # First we check to see if the previous analysis didn't complete + get_status = s.sql.text("""SELECT working_commit FROM working_commits WHERE repos_id=:repo_id + """).bindparams(repo_id=repo_id) - get_status = s.sql.text("""SELECT working_commit FROM working_commits WHERE repos_id=:repo_id - """).bindparams(repo_id=repo_id) + try: + working_commits = session.fetchall_data_from_sql_text(get_status) + except: + working_commits = [] - try: - working_commits = session.fetchall_data_from_sql_text(get_status) - except: - working_commits = [] - - # If there's a commit still there, the previous run was interrupted and - # the commit data may be incomplete. It should be trimmed, just in case. - for commit in working_commits: - trim_commit(session, repo_id,commit['working_commit']) - - # Remove the working commit. - remove_commit = s.sql.text("""DELETE FROM working_commits - WHERE repos_id = :repo_id AND - working_commit = :commit""").bindparams(repo_id=repo_id,commit=commit['working_commit']) - session.execute_sql(remove_commit) - session.log_activity('Debug',f"Removed working commit: {commit['working_commit']}") - - # Start the main analysis + # If there's a commit still there, the previous run was interrupted and + # the commit data may be incomplete. It should be trimmed, just in case. + for commit in working_commits: + trim_commit(session, repo_id,commit['working_commit']) - update_analysis_log(repo_id,'Collecting data') - logger.info(f"Got past repo {repo_id}") + # Remove the working commit. + remove_commit = s.sql.text("""DELETE FROM working_commits + WHERE repos_id = :repo_id AND + working_commit = :commit""").bindparams(repo_id=repo_id,commit=commit['working_commit']) + session.execute_sql(remove_commit) + session.log_activity('Debug',f"Removed working commit: {commit['working_commit']}") + + # Start the main analysis + + update_analysis_log(repo_id,'Collecting data') + logger.info(f"Got past repo {repo_id}") @celery.task -def trim_commits_post_analysis_facade_task(repo_id,commits): +def trim_commits_post_analysis_facade_task(commits): logger = logging.getLogger(trim_commits_post_analysis_facade_task.__name__) session = FacadeSession(logger) @@ -142,24 +143,32 @@ def update_analysis_log(repos_id,status): session.execute_sql(log_message) + repo_ids = [] - update_analysis_log(repo_id,'Data collection complete') - - update_analysis_log(repo_id,'Beginning to trim commits') - - session.log_activity('Debug',f"Commits to be trimmed from repo {repo_id}: {len(commits)}") - for commit in commits: - trim_commit(session,repo_id,commit) - set_complete = s.sql.text("""UPDATE repo SET repo_status='Complete' WHERE repo_id=:repo_id and repo_status != 'Empty' - """).bindparams(repo_id=repo_id) + for commit in commits: + repo_id = commit[1] + if repo_id not in repo_ids: + update_analysis_log(repo_id,'Data collection complete') + + update_analysis_log(repo_id,'Beginning to trim commits') + + session.log_activity('Debug',f"Commits to be trimmed from repo {repo_id}: {len(commits)}") + + repo_ids.append(repo_id) + + trim_commit(session,repo_id,commit[0]) - session.execute_sql(set_complete) + for repo_id in repo_ids: + set_complete = s.sql.text("""UPDATE repo SET repo_status='Complete' WHERE repo_id=:repo_id and repo_status != 'Empty' + """).bindparams(repo_id=repo_id) + + session.execute_sql(set_complete) - update_analysis_log(repo_id,'Commit trimming complete') + update_analysis_log(repo_id,'Commit trimming complete') - update_analysis_log(repo_id,'Complete') + update_analysis_log(repo_id,'Complete') @celery.task def facade_analysis_end_facade_task(): @@ -178,20 +187,26 @@ def facade_start_contrib_analysis_task(): #enable celery multithreading @celery.task -def analyze_commits_in_parallel(queue: list, repo_id: int, repo_location: str, multithreaded: bool)-> None: +def analyze_commits_in_parallel(queue: list, multithreaded: bool)-> None: """Take a large list of commit data to analyze and store in the database. Meant to be run in parallel with other instances of this task. """ #create new session for celery thread. logger = logging.getLogger(analyze_commits_in_parallel.__name__) - session = FacadeSession(logger) logger.info(f"Got to analysis!") - for analyzeCommit in queue: + for commitTuple in queue: + session = FacadeSession(logger) + + session.query(Repo).filter(Repo.repo_id == commitTuple[1]) + repo = execute_session_query(query,'one') + + + repo_loc = (f"{session.repo_base_directory}{repo.repo_group_id}/{repo.repo_path}{repo.repo_name}/.git") + + analyze_commit(session, repo_id, repo_loc, commitTuple[0]) - analyze_commit(session, repo_id, repo_location, analyzeCommit) - logger.info("Analysis complete") @celery.task @@ -241,12 +256,20 @@ def generate_analysis_sequence(logger): start_date = session.get_setting('start_date') + repo_ids = [repo['repo_id'] for repo in repos] + analysis_sequence.append(facade_analysis_init_facade_task.si().on_error(facade_error_handler.s())) + + analysis_sequence.append(create_grouped_task_load(dataList=repo_ids,task=grab_comitters).link_error(facade_error_handler.s())) + + analysis_sequence.append(create_grouped_task_load(dataList=repo_ids,task=trim_commits_facade_task).link_error(facade_error_handler.s())) + + all_missing_commits = [] + all_trimmed_commits = [] + + for repo in repos: session.logger.info(f"Generating sequence for repo {repo['repo_id']}") - analysis_sequence.append(grab_comitters.si(repo['repo_id']).on_error(facade_error_handler.s())) - #grab_comitters.si(repo.repo_id), - analysis_sequence.append(trim_commits_facade_task.si(repo['repo_id'])) #Get the huge list of commits to process. @@ -289,17 +312,22 @@ def generate_analysis_sequence(logger): if len(missing_commits) > 0: #session.log_activity('Info','Type of missing_commits: %s' % type(missing_commits)) - #Split commits into mostly equal queues so each process starts with a workload and there is no - # overhead to pass into queue from the parent. - contrib_jobs = create_grouped_task_load(repo['repo_id'],repo_loc,True,dataList=list(missing_commits),task=analyze_commits_in_parallel) - contrib_jobs.link_error(facade_error_handler.s()) - analysis_sequence.append(contrib_jobs) + #encode the repo_id with the commit. + commits_with_repo_tuple = [(commit,repo['repo_id']) for commit in list(missing_commits)] + #Get all missing commits into one large list to split into task pools + all_missing_commits.extend(commits_with_repo_tuple) # Find commits which are out of the analysis range trimmed_commits = existing_commits - parent_commits - analysis_sequence.append(trim_commits_post_analysis_facade_task.si(repo['repo_id'],list(trimmed_commits))) + + trimmed_commits_with_repo_tuple = [(commit,repo['repo_id']) for commit in list(trimmed_commits)] + all_trimmed_commits.extend(trimmed_commits_with_repo_tuple) + + analysis_sequence.append(create_grouped_task_load(True,dataList=all_missing_commits,task=analyze_commits_in_parallel).link_error(facade_error_handler.s())) + + analysis_sequence.append(create_grouped_task_load(dataList=all_trimmed_commits,task=trim_commits_post_analysis_facade_task).link_error(facade_error_handler.s())) analysis_sequence.append(facade_analysis_end_facade_task.si().on_error(facade_error_handler.s())) #print(f"Analysis sequence: {analysis_sequence}") diff --git a/augur/tasks/util/worker_util.py b/augur/tasks/util/worker_util.py index 8efac1db7b..427017143a 100644 --- a/augur/tasks/util/worker_util.py +++ b/augur/tasks/util/worker_util.py @@ -29,6 +29,8 @@ def create_grouped_task_load(*args,processes=8,dataList=[],task=None): return jobs + + def wait_child_tasks(ids_list): for task_id in ids_list: prereq = AsyncResult(str(task_id)) From 81dfe6601e2de7edbed219175c3b540917d9d109 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Wed, 11 Jan 2023 16:01:13 -0600 Subject: [PATCH 074/150] need to fix issues with accessing redis Signed-off-by: Isaac Milarsky --- augur/tasks/git/facade_tasks.py | 22 +++++++++++++--------- augur/tasks/github/releases/core.py | 2 +- 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/augur/tasks/git/facade_tasks.py b/augur/tasks/git/facade_tasks.py index 7ab3878b1c..9750c307a5 100644 --- a/augur/tasks/git/facade_tasks.py +++ b/augur/tasks/git/facade_tasks.py @@ -199,13 +199,13 @@ def analyze_commits_in_parallel(queue: list, multithreaded: bool)-> None: for commitTuple in queue: session = FacadeSession(logger) - session.query(Repo).filter(Repo.repo_id == commitTuple[1]) + query = session.query(Repo).filter(Repo.repo_id == commitTuple[1]) repo = execute_session_query(query,'one') repo_loc = (f"{session.repo_base_directory}{repo.repo_group_id}/{repo.repo_path}{repo.repo_name}/.git") - analyze_commit(session, repo_id, repo_loc, commitTuple[0]) + analyze_commit(session, commitTuple[1], repo_loc, commitTuple[0]) logger.info("Analysis complete") @@ -258,11 +258,11 @@ def generate_analysis_sequence(logger): repo_ids = [repo['repo_id'] for repo in repos] - analysis_sequence.append(facade_analysis_init_facade_task.si().on_error(facade_error_handler.s())) + analysis_sequence.append(facade_analysis_init_facade_task.si()) - analysis_sequence.append(create_grouped_task_load(dataList=repo_ids,task=grab_comitters).link_error(facade_error_handler.s())) + analysis_sequence.append(create_grouped_task_load(dataList=repo_ids,task=grab_comitters)) - analysis_sequence.append(create_grouped_task_load(dataList=repo_ids,task=trim_commits_facade_task).link_error(facade_error_handler.s())) + analysis_sequence.append(create_grouped_task_load(dataList=repo_ids,task=trim_commits_facade_task)) all_missing_commits = [] all_trimmed_commits = [] @@ -325,12 +325,15 @@ def generate_analysis_sequence(logger): all_trimmed_commits.extend(trimmed_commits_with_repo_tuple) - analysis_sequence.append(create_grouped_task_load(True,dataList=all_missing_commits,task=analyze_commits_in_parallel).link_error(facade_error_handler.s())) + if all_missing_commits: + analysis_sequence.append(create_grouped_task_load(True,dataList=all_missing_commits,task=analyze_commits_in_parallel)) - analysis_sequence.append(create_grouped_task_load(dataList=all_trimmed_commits,task=trim_commits_post_analysis_facade_task).link_error(facade_error_handler.s())) - analysis_sequence.append(facade_analysis_end_facade_task.si().on_error(facade_error_handler.s())) + if all_trimmed_commits: + analysis_sequence.append(create_grouped_task_load(dataList=all_trimmed_commits,task=trim_commits_post_analysis_facade_task)) + + analysis_sequence.append(facade_analysis_end_facade_task.si()) - #print(f"Analysis sequence: {analysis_sequence}") + logger.info(f"Analysis sequence: {analysis_sequence}") return analysis_sequence @@ -420,5 +423,6 @@ def generate_facade_chain(logger): if not limited_run or (limited_run and rebuild_caches): facade_sequence.append(rebuild_unknown_affiliation_and_web_caches_facade_task.si().on_error(facade_error_handler.s()))#rebuild_unknown_affiliation_and_web_caches(session.cfg) + #logger.info(f"Facade sequence: {facade_sequence}") return chain(*facade_sequence) diff --git a/augur/tasks/github/releases/core.py b/augur/tasks/github/releases/core.py index c4fdd96782..093a899a02 100644 --- a/augur/tasks/github/releases/core.py +++ b/augur/tasks/github/releases/core.py @@ -184,7 +184,7 @@ def releases_model(session, repo_git, repo_id): session.logger.info(f"Ran into problem when fetching data for repo {repo_git}: {e}") return - session.logger.info("repository value is: {}\n".format(data)) + #session.logger.info("repository value is: {}\n".format(data)) if 'releases' in data: if 'edges' in data['releases'] and data['releases']['edges']: for n in data['releases']['edges']: From 452bb358c147af215197e52ef8396c22571d7132 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Wed, 11 Jan 2023 17:04:59 -0600 Subject: [PATCH 075/150] don't create so many sessions Signed-off-by: Isaac Milarsky --- augur/tasks/git/facade_tasks.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/augur/tasks/git/facade_tasks.py b/augur/tasks/git/facade_tasks.py index 9750c307a5..c1cbbef7a7 100644 --- a/augur/tasks/git/facade_tasks.py +++ b/augur/tasks/git/facade_tasks.py @@ -195,9 +195,9 @@ def analyze_commits_in_parallel(queue: list, multithreaded: bool)-> None: logger = logging.getLogger(analyze_commits_in_parallel.__name__) logger.info(f"Got to analysis!") - + session = FacadeSession(logger) for commitTuple in queue: - session = FacadeSession(logger) + query = session.query(Repo).filter(Repo.repo_id == commitTuple[1]) repo = execute_session_query(query,'one') From 0425666d63bb99dfd3f5521674f21e15e6f45ea8 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 12 Jan 2023 09:49:02 -0600 Subject: [PATCH 076/150] Add database changes and fixes to the api Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 41 ++++++++++++++++--- .../application/db/models/augur_operations.py | 37 +++++++++++++++++ .../versions/2_added_user_groups_and_login.py | 21 ++++++++++ 3 files changed, 94 insertions(+), 5 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index a011c64163..e5b35264d6 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -296,15 +296,13 @@ def remove_user_repo(): return jsonify(result[1]) - @server.app.route(f"/{AUGUR_API_VERSION}/user/group/repos", methods=['GET', 'POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/group/repos/", methods=['GET', 'POST']) @login_required def group_repos(): """Select repos from a user group by name Arguments ---------- - username : str - The username of the user making the request group_name : str The name of the group to select page : int = 0 -> [>= 0] @@ -333,9 +331,14 @@ def group_repos(): result = current_user.get_group_repos(group_name, page, page_size, sort, direction) + result_dict = result[1] if result[0] is not None: - result_dict.update({"repos": result[0]}) + + for repo in result[0]: + repo["base64_url"] = str(repo["base64_url"].decode()) + + result_dict.update({"repos": result[0]}) return jsonify(result_dict) @@ -370,7 +373,7 @@ def group_repo_count(): return jsonify(result_dict) - @server.app.route(f"/{AUGUR_API_VERSION}/user/groups", methods=['GET', 'POST']) + @server.app.route(f"/{AUGUR_API_VERSION}/user/groups/names", methods=['GET', 'POST']) @login_required def get_user_groups(): """Get a list of user groups by username @@ -393,4 +396,32 @@ def get_user_groups(): return jsonify({"status": "success", "group_names": result[0]}) + @server.app.route(f"/{AUGUR_API_VERSION}/user/groups/repos/ids", methods=['GET', 'POST']) + @login_required + def get_user_groups_and_repos(): + """Get a list of user groups and their repos + + Returns + ------- + list + A list with this strucutre : [{"": Date: Thu, 12 Jan 2023 11:14:05 -0500 Subject: [PATCH 077/150] Added refresh endpoint Signed-off-by: Ulincsys --- augur/api/routes/user.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index e5b35264d6..b68408cb9c 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -148,6 +148,14 @@ def generate_session(application): return jsonify({"status": "Validated", "username": username, "access_token": user_session_token, "token_type": "Bearer", "expires": seconds_to_expire}) + @server.app.route(f"/{AUGUR_API_VERSION}/user/session/refresh") + @api_key_required + def refresh_session(): + refresh_token = request.args.get("refresh_token") + + if not refresh_token: + return jsonify({"status": "Invalid refresh token"}) + @server.app.route(f"/{AUGUR_API_VERSION}/user/query", methods=['POST']) def query_user(): if not development and not request.is_secure: From feea0fb292d0c5002d2d1297777725c2477a3873 Mon Sep 17 00:00:00 2001 From: Isaac Milarsky Date: Thu, 12 Jan 2023 10:23:24 -0600 Subject: [PATCH 078/150] Update Signed-off-by: Isaac Milarsky --- augur/tasks/data_analysis/__init__.py | 13 +++++++------ .../facade_worker/facade03analyzecommit.py | 2 +- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/augur/tasks/data_analysis/__init__.py b/augur/tasks/data_analysis/__init__.py index 69c2e690d8..3324137668 100644 --- a/augur/tasks/data_analysis/__init__.py +++ b/augur/tasks/data_analysis/__init__.py @@ -1,9 +1,3 @@ -from augur.tasks.data_analysis.clustering_worker.tasks import clustering_model -from augur.tasks.data_analysis.contributor_breadth_worker.contributor_breadth_worker import contributor_breadth_model -from augur.tasks.data_analysis.discourse_analysis.tasks import discourse_analysis_model -from augur.tasks.data_analysis.insight_worker.tasks import insight_model -from augur.tasks.data_analysis.message_insights.tasks import message_insight_model -from augur.tasks.data_analysis.pull_request_analysis_worker.tasks import pull_request_analysis_model from augur.application.db.session import DatabaseSession from augur.application.db.models import Repo from augur.application.db.util import execute_session_query @@ -13,6 +7,13 @@ @celery.task def machine_learning_phase(): + from augur.tasks.data_analysis.clustering_worker.tasks import clustering_model + from augur.tasks.data_analysis.contributor_breadth_worker.contributor_breadth_worker import contributor_breadth_model + from augur.tasks.data_analysis.discourse_analysis.tasks import discourse_analysis_model + from augur.tasks.data_analysis.insight_worker.tasks import insight_model + from augur.tasks.data_analysis.message_insights.tasks import message_insight_model + from augur.tasks.data_analysis.pull_request_analysis_worker.tasks import pull_request_analysis_model + logger = logging.getLogger(machine_learning_phase.__name__) diff --git a/augur/tasks/git/util/facade_worker/facade_worker/facade03analyzecommit.py b/augur/tasks/git/util/facade_worker/facade_worker/facade03analyzecommit.py index d6914cb97f..8aecdbd829 100644 --- a/augur/tasks/git/util/facade_worker/facade_worker/facade03analyzecommit.py +++ b/augur/tasks/git/util/facade_worker/facade_worker/facade03analyzecommit.py @@ -165,7 +165,7 @@ def store_commit(repos_id,commit,filename, raise e - session.log_activity('Debug',f"Stored commit: {commit}") + #session.log_activity('Debug',f"Stored commit: {commit}") ### The real function starts here ### From c4e7c701d10608bbbdd6cc610a679c69f19b1c46 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Thu, 12 Jan 2023 10:59:48 -0600 Subject: [PATCH 079/150] Add code for refresh tokens Signed-off-by: Andrew Brain --- augur/api/routes/user.py | 24 +++++++++- .../application/db/models/augur_operations.py | 46 +++++++++++++++++-- .../versions/2_added_user_groups_and_login.py | 12 +++++ 3 files changed, 75 insertions(+), 7 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index b68408cb9c..50dfd1bce3 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -23,7 +23,7 @@ from augur.api.util import get_bearer_token from augur.api.util import get_client_token -from augur.application.db.models import User, UserRepo, UserGroup, UserSessionToken, ClientApplication +from augur.application.db.models import User, UserRepo, UserGroup, UserSessionToken, ClientApplication, RefreshToken from augur.application.config import get_development_flag from augur.tasks.init.redis_connection import redis_connection as redis @@ -151,10 +151,30 @@ def generate_session(application): @server.app.route(f"/{AUGUR_API_VERSION}/user/session/refresh") @api_key_required def refresh_session(): - refresh_token = request.args.get("refresh_token") + refresh_token_str = request.args.get("refresh_token") + if not refresh_token_str: + return jsonify({"status": "Invalid refresh token"}) + + session = Session() + refresh_token = session.query(RefreshToken).filter(RefreshToken.id == refresh_token_str).first() if not refresh_token: return jsonify({"status": "Invalid refresh token"}) + + user_session = refresh_token.user_session + user = user_session.user + + new_user_session = UserSessionToken.create(user.user_id, user_session.application.id) + new_refresh_token = RefreshToken.create(new_user_session.token) + + if refresh_token.delete() != 1: + return jsonify({"status": "Error deleting refresh token"}) + + if user_session.delete() != 1: + return jsonify({"status": "Error deleting user session"}) + + return jsonify({"refresh_token": new_refresh_token.id, "session": new_user_session.token}) + @server.app.route(f"/{AUGUR_API_VERSION}/user/query", methods=['POST']) def query_user(): diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index 9ef2cc75c2..05f8c45786 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -539,11 +539,6 @@ def add_app(self, name, redirect_url): return True - - - - - class UserGroup(Base): group_id = Column(BigInteger, primary_key=True) user_id = Column(Integer, @@ -597,6 +592,21 @@ class UserSessionToken(Base): user = relationship("User") application = relationship("ClientApplication") + @staticmethod + def create(user_id, application_id): + import time + + user_session_token = secrets.token_hex() + seconds_to_expire = 86400 + expiration = int(time.time()) + seconds_to_expire + + local_session = get_session() + user_session = UserSessionToken(token=user_session_token, user_id=user_id, application_id = application_id, expiration=expiration) + + local_session.add(user_session) + local_session.commit() + + return user_session class ClientApplication(Base): __tablename__ = "client_applications" @@ -652,6 +662,32 @@ class SubscriptionType(Base): subscriptions = relationship("Subscription") +class RefreshToken(Base): + __tablename__ = "refresh_tokens" + __table_args__ = ( + UniqueConstraint('user_session_token', name='refresh_token_user_session_token_id_unique'), + {"schema": "augur_operations"} + ) + + id = Column(String, primary_key=True) + user_session_token = Column(ForeignKey("augur_operations.user_session_tokens.token", name="refresh_token_session_token_id_fkey"), nullable=False) + + user_session = relationship("UserSessionToken") + + @staticmethod + def create(user_session_token_id): + + refresh_token_id = secrets.token_hex() + + local_session = get_session() + refresh_token = RefreshToken(id=refresh_token_id, user_session_token=user_session_token_id) + + local_session.add(refresh_token) + local_session.commit() + + return refresh_token + + diff --git a/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py b/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py index 1fac147a10..009268ab6e 100644 --- a/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py +++ b/augur/application/schema/alembic/versions/2_added_user_groups_and_login.py @@ -143,12 +143,24 @@ def upgrade(): ) op.add_column('user_groups', sa.Column('favorited', sa.Boolean(), server_default=sa.text('FALSE'), nullable=False), schema='augur_operations') + + + op.create_table('refresh_tokens', + sa.Column('id', sa.String(), nullable=False), + sa.Column('user_session_token', sa.String(), nullable=False), + sa.ForeignKeyConstraint(['user_session_token'], ['augur_operations.user_session_tokens.token'], name='refresh_token_session_token_id_fkey'), + sa.PrimaryKeyConstraint('id'), + sa.UniqueConstraint('user_session_token', name='refresh_token_user_session_token_id_unique'), + schema='augur_operations' + ) # ### end Alembic commands ### def downgrade(): # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('refresh_tokens', schema='augur_operations') + op.drop_column('user_groups', 'favorited', schema='augur_operations') op.drop_table('subscriptions', schema='augur_operations') From e4b30a9c5b54f4fb9bb8f056c720e553d76e8f82 Mon Sep 17 00:00:00 2001 From: Ulincsys Date: Thu, 12 Jan 2023 12:46:59 -0500 Subject: [PATCH 080/150] Update auth requirements Signed-off-by: Ulincsys --- augur/api/routes/user.py | 18 ++++++++++++++---- augur/templates/settings.j2 | 12 ++++++++++++ 2 files changed, 26 insertions(+), 4 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 50dfd1bce3..a598fd552a 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -122,9 +122,11 @@ def user_authorize(): @server.app.route(f"/{AUGUR_API_VERSION}/user/session/generate", methods=['POST']) @api_key_required def generate_session(application): - code = request.args.get("code") - if not code: + if not (code := request.args.get("code")): return jsonify({"status": "Invalid authorization code"}) + + if request.args.get("grant_type") != "code": + return jsonify({"status": "Invalid grant type"}) username = redis.get(code) redis.delete(code) @@ -142,11 +144,16 @@ def generate_session(application): session = Session() user_session = UserSessionToken(token=user_session_token, user_id=user.user_id, application_id = application.id, expiration=expiration) + refresh_token = RefreshToken.create(user_session_token) + session.add(user_session) session.commit() session.close() - - return jsonify({"status": "Validated", "username": username, "access_token": user_session_token, "token_type": "Bearer", "expires": seconds_to_expire}) + + response = jsonify({"status": "Validated", "username": username, "access_token": user_session_token, "refresh_token" : refresh_token.id, "token_type": "Bearer", "expires": seconds_to_expire}) + response.headers["Cache-Control"] = "no-store" + + return response @server.app.route(f"/{AUGUR_API_VERSION}/user/session/refresh") @api_key_required @@ -155,6 +162,9 @@ def refresh_session(): if not refresh_token_str: return jsonify({"status": "Invalid refresh token"}) + + if request.args.get("grant_type") != "refresh_token": + return jsonify({"status": "Invalid grant type"}) session = Session() refresh_token = session.query(RefreshToken).filter(RefreshToken.id == refresh_token_str).first() diff --git a/augur/templates/settings.j2 b/augur/templates/settings.j2 index aa09f265fe..eb29a2798e 100644 --- a/augur/templates/settings.j2 +++ b/augur/templates/settings.j2 @@ -21,6 +21,7 @@ + Settings - Augur View @@ -128,6 +129,7 @@ {%- set tableHeaders = [{"title" : "Group"}, {"title" : "Number of repos"}, + {"title" : "Favorite"} {"title" : ""}] -%}
    @@ -146,6 +148,7 @@ {{ group.name }} {{ group.repos | length }} + {% endfor %} @@ -370,6 +373,15 @@ button.classList.add("btn-outline-danger"); } } + var toggleFavorite = function(button) { + if(button.classList.contains("bi-star-fill")) { + button.classList.remove("bi-star-fill"); + button.classList.add("bi-star"); + } else { + button.classList.remove("bi-star"); + button.classList.add("bi-star-fill"); + } + }