Allow current postgres config to run on GAE (#210)

* Set file permissions for postgres container scripts

* Use different schema name to db name

It looks like on the GAE if you use a 'pixl'
schema in a pixl database, then orthanc raw
thinks the database is corrupted

.pre-commit-config.yaml

@@ -29,4 +29,4 @@ repos:
         pass_filenames: false
         entry: mypy
         args: ['--config-file=setup.cfg']
-        additional_dependencies: ['mypy', 'types-PyYAML', 'types-requests', 'types-python-slugify']
+        additional_dependencies: ['mypy', 'types-PyYAML', 'types-requests', 'types-python-slugify', 'types-psycopg2']

cli/tests/conftest.py

@@ -60,7 +60,7 @@ def db_engine(monkeymodule) -> Engine:
     :returns Engine: Engine for use in other setup fixtures
     """
     # SQLite doesnt support schemas, so remove pixl schema from engine options
-    execution_options = {"schema_translate_map": {"pixl": None}}
+    execution_options = {"schema_translate_map": {"pipeline": None}}
     engine = create_engine(
         "sqlite:///:memory:",
         execution_options=execution_options,

docker/postgres/Dockerfile

@@ -34,7 +34,7 @@ COPY --chmod=0755 ./postgres/postgres.conf /etc/postgresql/postgresql.conf
 
 COPY --chmod=0777 ./postgres/pixl-db_init.sh /docker-entrypoint-initdb.d/pixl-db_init.sh
 
-COPY ./postgres/create_pixl_tbls.py /pixl/create_pixl_tbls.py
+COPY --chmod=0777 ./postgres/create_pixl_tbls.py /pixl/create_pixl_tbls.py
 
 COPY ./pixl_core/ /pixl/pixl_core
 

pixl_core/src/core/database.py

@@ -24,7 +24,7 @@
 class Base(DeclarativeBase):
     """sqlalchemy base class"""
 
-    metadata = MetaData(schema="pixl")
+    metadata = MetaData(schema="pipeline")
 
 
 class Extract(Base):

postgres/create_pixl_tbls.py

@@ -29,7 +29,7 @@
 engine = create_engine(url, echo=True, echo_pool="debug")
 
 with engine.connect() as connection:
-    connection.execute(CreateSchema("pixl", if_not_exists=True))
+    connection.execute(CreateSchema("pipeline", if_not_exists=True))
     connection.commit()
 
 Base.metadata.create_all(engine)