files: configure Invenio files REST

* Upgrades Invenio to version 3.2 (alpha 9).
* Configures Invenio files REST.
* Creates default location for storing files.
* Removes unnecessary entries (setup_requires and tests_require) in setup.py.
* Closes #81

Co-Authored-by: Sébastien Délèze <sebastien.deleze@rero.ch>

Pipfile

@@ -6,7 +6,7 @@ name = "pypi"
 [packages]
 Babel = ">=2.4.0"
 Flask-BabelEx = ">=0.9.3"
-invenio = {version = "==3.1.0",extras = ["base", "metadata", "postgresql", "auth", "elasticsearch6" ]}
+invenio = {version = "==3.2.0a9",extras = ["base", "metadata", "files", "postgresql", "auth", "elasticsearch6" ]}
 # TODO: remove this contraint once it is solved in invenio
 raven = {version = ">=6.0",extras = ["flask"]}
 uwsgi = ">=2.0"
@@ -17,6 +17,7 @@ orcid = "*"
 python-slugify = "*"
 python3-saml = "*"
 xmltodict = "*"
+marshmallow = "<=3.0.0b6"
 
 [dev-packages]
 Flask-Debugtoolbar = ">=0.10.1"
@@ -29,7 +30,7 @@ marshmallow = ">=2.15.1,<3.0.0"
 pydocstyle = ">=2.0.0"
 pytest = ">=3.3.1"
 pytest-cov = ">=2.5.1"
-pytest-invenio = ">=1.0.2,<1.1.0"
+pytest-invenio = ">=1.2.1,<1.3.0"
 pytest-mock = ">=1.6.0"
 pytest-pep8 = ">=1.0.6"
 pytest-random-order = ">=0.5.4"

scripts/setup

@@ -39,4 +39,5 @@ pipenv run invenio access allow admin-access role moderator
 pipenv run invenio fixtures institutions import
 pipenv run invenio fixtures users import $(pipenv --where)/data/users.json
 pipenv run invenio fixtures documents import hevs
-pipenv run invenio fixtures documents import usi
+pipenv run invenio fixtures documents import usi
+pipenv run invenio fixtures deposits create

setup.py

@@ -129,11 +129,5 @@
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.6',
         'Development Status :: 3 - Alpha',
-    ],
-    setup_requires=[
-        'pytest-runner>=3.0.0,<5',
-    ],
-    tests_require=[
-        'pytest-invenio>=1.0.0,<1.1.0',
     ]
 )

sonar/config.py

@@ -464,3 +464,6 @@ def _(x):
 REST_ENABLE_CORS = True
 """Enable CORS to make it possible to do request to API from other
 applications."""
+
+FILES_REST_PERMISSION_FACTORY = \
+    'sonar.modules.permissions.files_permission_factory'

sonar/modules/cli.py

@@ -19,6 +19,7 @@
 
 import click
 
+from .deposits.cli import deposits
 from .documents.cli import documents
 from .institutions.cli import institutions
 from .users.cli import users
@@ -31,3 +32,4 @@ def fixtures():
 fixtures.add_command(documents)
 fixtures.add_command(institutions)
 fixtures.add_command(users)
+fixtures.add_command(deposits)

sonar/modules/deposits/__init__.py

@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+#
+# Swiss Open Access Repository
+# Copyright (C) 2019 RERO
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, version 3 of the License.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+"""Deposit module."""
+
+from __future__ import absolute_import, print_function

sonar/modules/deposits/cli.py

@@ -0,0 +1,64 @@
+# -*- coding: utf-8 -*-
+#
+# Swiss Open Access Repository
+# Copyright (C) 2019 RERO
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, version 3 of the License.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""Deposit CLI commands."""
+
+import shutil
+from os import makedirs
+from os.path import exists, join
+
+import click
+from flask import current_app
+from flask.cli import with_appcontext
+from invenio_db import db
+from invenio_files_rest.models import Bucket, FileInstance, Location, \
+    ObjectVersion
+
+
+@click.group()
+def deposits():
+    """Deposits CLI commands."""
+
+
+@deposits.command('create')
+@with_appcontext
+def create():
+    """Create a location and a bucket for uploading files."""
+    click.secho('Creating default location for importing files', bold=True)
+
+    # Directory where files are stored
+    directory = join(current_app.instance_path, 'files')
+
+    if exists(directory):
+        shutil.rmtree(directory)
+
+    makedirs(directory)
+
+    # Remove stored data
+    ObjectVersion.query.delete()
+    Bucket.query.delete()
+    FileInstance.query.delete()
+    Location.query.delete()
+    db.session.commit()
+
+    # Create location
+    loc = Location(name='local', uri=directory, default=True)
+    db.session.add(loc)
+    db.session.commit()
+
+    click.secho('Location #{id} created successfully'.format(id=loc.id),
+                fg='green')

sonar/modules/permissions.py

@@ -26,8 +26,10 @@
 from invenio_records_rest.utils import check_elasticsearch
 
 superuser_access_permission = Permission(ActionNeed('superuser-access'))
-admin_access_permission = Permission(RoleNeed('librarian'), RoleNeed('admin'))
+admin_access_permission = Permission(RoleNeed('moderator'), RoleNeed('admin'))
 moderator_access_permission = Permission(ActionNeed('admin-access'))
+user_access_permission = Permission(RoleNeed('user'),
+                                    RoleNeed('moderator'), RoleNeed('admin'))
 
 
 def has_admin_access():
@@ -89,3 +91,8 @@ def decorated_view(*args, **kwargs):
 def admin_permission_factory(admin_view):
     """Admin permission factory."""
     return superuser_access_permission
+
+
+def files_permission_factory(*kwargs):
+    """Files rest permission factory."""
+    return user_access_permission

tests/ui/test_permissions.py

@@ -23,7 +23,8 @@
 from sonar.modules.documents.api import DocumentRecord
 from sonar.modules.permissions import can_create_record_factory, \
     can_delete_record_factory, can_list_record_factory, \
-    can_read_record_factory, can_update_record_factory
+    can_read_record_factory, can_update_record_factory, \
+    files_permission_factory
 
 
 def test_has_admin_access(app, db, client, admin_user_fixture):
@@ -64,3 +65,11 @@ def test_can_list_record_factory(app, client, admin_user_fixture):
         }, dbcommit=True)
 
     assert can_read_record_factory(record)
+
+
+def test_files_permission_factory(client, admin_user_fixture):
+    """Test files permission factory."""
+    login_user_via_view(client,
+                        email=admin_user_fixture.email,
+                        password='123456')
+    assert files_permission_factory().can()