global: initial alembic recipes

* Adds alembic recipe (closes #19).

* Updates dependencies in order to have correct alembic upgrade.

Signed-off-by: Nicolas Harraudeau <nicolas.harraudeau@cern.ch>

.travis.yml

@@ -35,10 +35,33 @@ matrix:
 cache:
   - pip
 
+services:
+    - mysql
+    - postgresql
+
+# Note: dist/sudo/api is required for MySQL 5.6 which adds support for
+# fractional seconds in datetime columns.
+dist: trusty
+sudo: required
+addons:
+  postgresql: "9.4"
+  apt:
+    packages:
+      - mysql-server-5.6
+      - mysql-client-core-5.6
+      - mysql-client-5.6
+
+
 env:
-  - REQUIREMENTS=lowest
-  - REQUIREMENTS=release DEPLOY=true
-  - REQUIREMENTS=devel
+  - REQUIREMENTS=lowest EXTRAS=mysql SQLALCHEMY_DATABASE_URI="mysql+pymysql://travis@localhost:3306/invenio"
+  - REQUIREMENTS=lowest EXTRAS=postgresql SQLALCHEMY_DATABASE_URI="postgresql+psycopg2://postgres@localhost:5432/invenio"
+  - REQUIREMENTS=lowest EXTRAS=sqlite SQLALCHEMY_DATABASE_URI="sqlite:///test.db"
+  - REQUIREMENTS=release EXTRAS=mysql SQLALCHEMY_DATABASE_URI="mysql+pymysql://travis@localhost:3306/invenio"
+  - REQUIREMENTS=release EXTRAS=postgresql SQLALCHEMY_DATABASE_URI="postgresql+psycopg2://postgres@localhost:5432/invenio" DEPLOY=true
+  - REQUIREMENTS=release EXTRAS=sqlite SQLALCHEMY_DATABASE_URI="sqlite:///test.db"
+  - REQUIREMENTS=devel EXTRAS=mysql SQLALCHEMY_DATABASE_URI="mysql+pymysql://travis@localhost:3306/invenio"
+  - REQUIREMENTS=devel EXTRAS=postgresql SQLALCHEMY_DATABASE_URI="postgresql+psycopg2://postgres@localhost:5432/invenio"
+  - REQUIREMENTS=devel EXTRAS=sqlite SQLALCHEMY_DATABASE_URI="sqlite:///test.db"
 
 python:
   - "2.7"
@@ -47,13 +70,15 @@ python:
 before_install:
   - "travis_retry pip install --upgrade pip setuptools py"
   - "travis_retry pip install twine wheel coveralls requirements-builder"
-  - "requirements-builder --level=min setup.py > .travis-lowest-requirements.txt"
-  - "requirements-builder --level=pypi setup.py > .travis-release-requirements.txt"
-  - "requirements-builder --level=dev --req requirements-devel.txt setup.py > .travis-devel-requirements.txt"
+  - "requirements-builder -e records,indexer,${EXTRAS} --level=min setup.py > .travis-lowest-requirements.txt"
+  - "requirements-builder -e records,indexer,${EXTRAS} --level=pypi setup.py > .travis-release-requirements.txt"
+  - "requirements-builder -e records,indexer,${EXTRAS} --level=dev --req requirements-devel.txt setup.py > .travis-devel-requirements.txt"
+  - "mysql -e 'CREATE DATABASE IF NOT EXISTS invenio;' -uroot"
+  - "psql -c 'CREATE DATABASE invenio;' -U postgres"
 
 install:
   - "travis_retry pip install -r .travis-${REQUIREMENTS}-requirements.txt"
-  - "travis_retry pip install -e .[all]"
+  - "travis_retry pip install -e .[all,${EXTRAS}]"
 
 script:
   - "./run-tests.sh"

invenio_pidrelations/alembic/1d4e361b7586_create_pidrelations_tables.py

@@ -0,0 +1,63 @@
+#
+# This file is part of Invenio.
+# Copyright (C) 2017 CERN.
+#
+# Invenio is free software; you can redistribute it
+# and/or modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of the
+# License, or (at your option) any later version.
+#
+# Invenio 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
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Invenio; if not, write to the
+# Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
+# MA 02111-1307, USA.
+#
+# In applying this license, CERN does not
+# waive the privileges and immunities granted to it by virtue of its status
+# as an Intergovernmental Organization or submit itself to any jurisdiction.
+
+"""Create pidrelations tables."""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = '1d4e361b7586'
+down_revision = '2216c32d7059'  # Create branch
+branch_labels = ()
+depends_on = None
+
+
+def upgrade():
+    """Upgrade database."""
+    op.create_table(
+        'pidrelations_pidrelation',
+        sa.Column('created', sa.DateTime(), nullable=False),
+        sa.Column('updated', sa.DateTime(), nullable=False),
+        sa.Column('parent_id', sa.Integer(), nullable=False),
+        sa.Column('child_id', sa.Integer(), nullable=False),
+        sa.Column('relation_type', sa.SmallInteger(), nullable=False),
+        sa.Column('index', sa.Integer(), nullable=True),
+        sa.ForeignKeyConstraint(
+            ['child_id'], ['pidstore_pid.id'],
+            name=op.f('fk_pidrelations_pidrelation_child_id_pidstore_pid'),
+            onupdate='CASCADE', ondelete='CASCADE'
+        ),
+        sa.ForeignKeyConstraint(
+            ['parent_id'], ['pidstore_pid.id'],
+            name=op.f('fk_pidrelations_pidrelation_parent_id_pidstore_pid'),
+            onupdate='CASCADE', ondelete='CASCADE'),
+        sa.PrimaryKeyConstraint(
+            'parent_id', 'child_id', name=op.f('pk_pidrelations_pidrelation')
+        )
+    )
+
+
+def downgrade():
+    """Downgrade database."""
+    op.drop_table('pidrelations_pidrelation')

invenio_pidrelations/alembic/2216c32d7059_create_pidrelations_branch.py

@@ -0,0 +1,40 @@
+#
+# This file is part of Invenio.
+# Copyright (C) 2017 CERN.
+#
+# Invenio is free software; you can redistribute it
+# and/or modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of the
+# License, or (at your option) any later version.
+#
+# Invenio 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
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Invenio; if not, write to the
+# Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
+# MA 02111-1307, USA.
+#
+# In applying this license, CERN does not
+# waive the privileges and immunities granted to it by virtue of its status
+# as an Intergovernmental Organization or submit itself to any jurisdiction.
+
+"""Create pidrelations branch."""
+
+import sqlalchemy as sa
+from alembic import op
+
+revision = '2216c32d7059'
+down_revision = None
+branch_labels = (u'invenio_pidrelations',)
+depends_on = '999c62899c20'  # invenio-pidstore create tables
+
+
+def upgrade():
+    """Upgrade database."""
+
+
+def downgrade():
+    """Downgrade database."""

setup.py

@@ -48,26 +48,37 @@
     ],
     'tests': tests_require,
     'mysql': [
-        'invenio-db[mysql]>=1.0.0b1',
+        'invenio-db[mysql,versioning]>=1.0.0b3',
     ],
     'postgresql': [
-        'invenio-db[postgresql]>=1.0.0b1',
+        'invenio-db[postgresql,versioning]>=1.0.0b3',
     ],
     'sqlite': [
-        'invenio-db>=1.0.0b1',
+        'invenio-db[versioning]>=1.0.0b3',
     ],
     'records': [
         'invenio-deposit>=1.0.0a7',
-        'invenio-records-files>=1.0.0a8',
         'invenio-records>=1.0.0b1',
+        # FIXME: Added because requirements-builder does not search
+        # recursively lowest dependencies.
+        'invenio-records-ui>=1.0.0a8',
+        'invenio-records-rest>=1.0.0a17',
+        'invenio-accounts>=1.0.0b5',
+        'Flask-WTF>=0.13.1',
+        # Needed in order to have correct alembic upgrade.
+        'invenio-oauth2server>=1.0.0a14',
+        'invenio-records-files>=1.0.0a9',
+        'invenio-files-rest>=1.0.0a15',
     ],
     'indexer': [
         'invenio-indexer>=1.0.0a9',
     ],
 }
 
 extras_require['all'] = []
-for reqs in extras_require.values():
+for name, reqs in extras_require.items():
+    if name in ('mysql', 'postgresql', 'sqlite'):
+        continue
     extras_require['all'].extend(reqs)
 
 setup_requires = [
@@ -114,6 +125,9 @@
         'invenio_base.api_apps': [
             'invenio_pidrelations = invenio_pidrelations:InvenioPIDRelations',
         ],
+        'invenio_db.alembic': [
+            'invenio_pidrelations = invenio_pidrelations:alembic',
+        ],
         'invenio_db.models': [
             'invenio_pidrelations = invenio_pidrelations.models',
         ],

tests/conftest.py

@@ -43,7 +43,8 @@
 from invenio_records import InvenioRecords, Record
 from invenio_search import InvenioSearch, current_search, current_search_client
 from marshmallow import fields
-from sqlalchemy_utils.functions import create_database, database_exists
+from sqlalchemy_utils.functions import create_database, database_exists, \
+    drop_database
 
 from invenio_pidrelations import InvenioPIDRelations
 from invenio_pidrelations.config import RelationType
@@ -105,12 +106,17 @@ def es(app):
 @pytest.yield_fixture()
 def db(app):
     """Database fixture."""
-    if not database_exists(str(db_.engine.url)):
-        create_database(str(db_.engine.url))
+    if database_exists(str(db_.engine.url)):
+        db_.session.remove()
+        drop_database(str(db_.engine.url))
+    create_database(str(db_.engine.url))
     db_.create_all()
     yield db_
     db_.session.remove()
-    db_.drop_all()
+    drop_database(db_.engine.url)
+    # Dispose the engine in order to close all connections. This is
+    # needed for sqlite in memory databases.
+    db_.engine.dispose()
 
 
 @pytest.fixture()

tests/test_invenio_pidrelations.py

@@ -26,6 +26,7 @@
 
 from __future__ import absolute_import, print_function
 
+import pytest
 from flask import Flask
 
 from invenio_pidrelations import InvenioPIDRelations
@@ -48,3 +49,22 @@ def test_init():
     assert 'invenio-pidrelations' not in app.extensions
     ext.init_app(app)
     assert 'invenio-pidrelations' in app.extensions
+
+
+def test_alembic(app, db):
+    """Test alembic recipes."""
+    ext = app.extensions['invenio-db']
+
+    if db.engine.name == 'sqlite':
+        raise pytest.skip('Upgrades are not supported on SQLite.')
+
+    assert not ext.alembic.compare_metadata()
+    db.drop_all()
+    ext.alembic.upgrade()
+
+    assert not ext.alembic.compare_metadata()
+    ext.alembic.stamp()
+    ext.alembic.downgrade(target='96e796392533')
+    ext.alembic.upgrade()
+
+    assert not ext.alembic.compare_metadata()