Test database migrations

migrations/env.py

@@ -53,25 +53,23 @@ def run_migrations_online():
     and associate a connection with the context.
 
     """
-    alembic_config = config.get_section(config.config_ini_section)
-    alembic_config['sqlalchemy.url'] = settings.DATABASE_URI
-
-    engine = engine_from_config(
-                alembic_config,
-                prefix='sqlalchemy.',
-                poolclass=pool.NullPool)
-
-    connection = engine.connect()
-    context.configure(
-                connection=connection,
-                target_metadata=target_metadata
-                )
-
-    try:
+    # Enable reusing an existing connection.
+    # http://alembic.readthedocs.org/en/latest/cookbook.html#sharing-a-connection-with-a-series-of-migration-commands-and-environments
+    connectable = config.attributes.get('connection', None)
+
+    if connectable is None:
+        alembic_config = config.get_section(config.config_ini_section)
+        alembic_config['sqlalchemy.url'] = settings.DATABASE_URI
+        connectable = engine_from_config(alembic_config,
+                                         prefix='sqlalchemy.',
+                                         poolclass=pool.NullPool)
+
+    with connectable.connect() as connection:
+        context.configure(connection=connection,
+                          target_metadata=target_metadata)
         with context.begin_transaction():
             context.run_migrations()
-    finally:
-        connection.close()
+
 
 if context.is_offline_mode():
     run_migrations_offline()

migrations/versions/ea660b66f26_initial_schema.py

-"""initial schema
+"""Initial schema
 
 Revision ID: ea660b66f26
 Revises: None
@@ -17,8 +17,132 @@ import sqlalchemy as sa
 
 
 def upgrade():
-    pass
+    ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('assemblies',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.String(length=30), nullable=False),
+    sa.Column('alias', sa.String(length=10), nullable=True),
+    sa.Column('taxonomy_id', sa.Integer(), nullable=False),
+    sa.Column('taxonomy_common_name', sa.String(length=50), nullable=False),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('alias'),
+    sa.UniqueConstraint('name'),
+    mysql_charset='utf8',
+    mysql_engine='InnoDB'
+    )
+    op.create_table('batch_jobs',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('email', sa.String(length=200), nullable=True),
+    sa.Column('download_url', sa.String(length=200), nullable=True),
+    sa.Column('job_type', sa.Enum('name-checker', 'syntax-checker', 'position-converter', 'snp-converter', name='job_type'), nullable=False),
+    sa.Column('argument', sa.String(length=20), nullable=True),
+    sa.Column('result_id', sa.String(length=50), nullable=False),
+    sa.Column('added', sa.DateTime(), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
+    mysql_charset='utf8',
+    mysql_engine='InnoDB'
+    )
+    op.create_index(op.f('ix_batch_jobs_result_id'), 'batch_jobs', ['result_id'], unique=True)
+    op.create_table('references',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('accession', sa.String(length=20), nullable=False),
+    sa.Column('checksum', sa.String(length=32), nullable=False),
+    sa.Column('geninfo_identifier', sa.String(length=13), nullable=True),
+    sa.Column('slice_accession', sa.String(length=20), nullable=True),
+    sa.Column('slice_start', sa.Integer(), nullable=True),
+    sa.Column('slice_stop', sa.Integer(), nullable=True),
+    sa.Column('slice_orientation', sa.Enum('forward', 'reverse', name='slice_orentation'), nullable=True),
+    sa.Column('download_url', sa.String(length=255), nullable=True),
+    sa.Column('added', sa.DateTime(), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
+    mysql_charset='utf8',
+    mysql_engine='InnoDB'
+    )
+    op.create_index(op.f('ix_references_accession'), 'references', ['accession'], unique=True)
+    op.create_index(op.f('ix_references_checksum'), 'references', ['checksum'], unique=True)
+    op.create_index(op.f('ix_references_download_url'), 'references', ['download_url'], unique=True)
+    op.create_index(op.f('ix_references_geninfo_identifier'), 'references', ['geninfo_identifier'], unique=True)
+    op.create_index('reference_slice', 'references', ['slice_accession', 'slice_start', 'slice_stop', 'slice_orientation'], unique=True)
+    op.create_table('transcript_protein_links',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('transcript_accession', sa.String(length=20), nullable=False),
+    sa.Column('protein_accession', sa.String(length=20), nullable=True),
+    sa.Column('added', sa.DateTime(), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
+    mysql_charset='utf8',
+    mysql_engine='InnoDB'
+    )
+    op.create_index(op.f('ix_transcript_protein_links_protein_accession'), 'transcript_protein_links', ['protein_accession'], unique=False)
+    op.create_index(op.f('ix_transcript_protein_links_transcript_accession'), 'transcript_protein_links', ['transcript_accession'], unique=True)
+    op.create_table('batch_queue_items',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('batch_job_id', sa.Integer(), nullable=False),
+    sa.Column('item', sa.String(length=200), nullable=False),
+    sa.Column('flags', sa.String(length=20), nullable=False),
+    sa.ForeignKeyConstraint(['batch_job_id'], ['batch_jobs.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id'),
+    mysql_charset='utf8',
+    mysql_engine='InnoDB'
+    )
+    op.create_index('batch_queue_item_with_batch_job', 'batch_queue_items', ['batch_job_id', 'id'], unique=False)
+    op.create_table('chromosomes',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('assembly_id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.String(length=30), nullable=False),
+    sa.Column('accession', sa.String(length=30), nullable=False),
+    sa.Column('organelle', sa.Enum('nucleus', 'mitochondrion', name='organelle'), nullable=True),
+    sa.ForeignKeyConstraint(['assembly_id'], ['assemblies.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id'),
+    mysql_charset='utf8',
+    mysql_engine='InnoDB'
+    )
+    op.create_index('chromosome_accession', 'chromosomes', ['assembly_id', 'accession'], unique=True)
+    op.create_index('chromosome_name', 'chromosomes', ['assembly_id', 'name'], unique=True)
+    op.create_table('transcript_mappings',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('chromosome_id', sa.Integer(), nullable=False),
+    sa.Column('reference_type', sa.Enum('refseq', 'lrg', name='reference_type'), nullable=False),
+    sa.Column('accession', sa.String(length=20), nullable=False),
+    sa.Column('version', sa.Integer(), nullable=True),
+    sa.Column('gene', sa.String(length=30), nullable=False),
+    sa.Column('transcript', sa.Integer(), nullable=False),
+    sa.Column('orientation', sa.Enum('forward', 'reverse', name='orentation'), nullable=False),
+    sa.Column('start', sa.Integer(), nullable=False),
+    sa.Column('stop', sa.Integer(), nullable=False),
+    sa.Column('cds_start', sa.Integer(), nullable=True),
+    sa.Column('cds_stop', sa.Integer(), nullable=True),
+    sa.Column('exon_starts', sa.Text(), nullable=False),
+    sa.Column('exon_stops', sa.Text(), nullable=False),
+    sa.Column('select_transcript', sa.Boolean(), nullable=False),
+    sa.Column('source', sa.Enum('ucsc', 'ncbi', 'reference', name='source'), nullable=False),
+    sa.ForeignKeyConstraint(['chromosome_id'], ['chromosomes.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id'),
+    mysql_charset='utf8',
+    mysql_engine='InnoDB'
+    )
+    op.create_index('transcript_mapping_transcript', 'transcript_mappings', ['accession', 'version', 'gene', 'transcript', 'chromosome_id'], unique=True)
+    ### end Alembic commands ###
 
 
 def downgrade():
-    pass
+    ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index('transcript_mapping_transcript', table_name='transcript_mappings')
+    op.drop_table('transcript_mappings')
+    op.drop_index('chromosome_name', table_name='chromosomes')
+    op.drop_index('chromosome_accession', table_name='chromosomes')
+    op.drop_table('chromosomes')
+    op.drop_index('batch_queue_item_with_batch_job', table_name='batch_queue_items')
+    op.drop_table('batch_queue_items')
+    op.drop_index(op.f('ix_transcript_protein_links_transcript_accession'), table_name='transcript_protein_links')
+    op.drop_index(op.f('ix_transcript_protein_links_protein_accession'), table_name='transcript_protein_links')
+    op.drop_table('transcript_protein_links')
+    op.drop_index('reference_slice', table_name='references')
+    op.drop_index(op.f('ix_references_geninfo_identifier'), table_name='references')
+    op.drop_index(op.f('ix_references_download_url'), table_name='references')
+    op.drop_index(op.f('ix_references_checksum'), table_name='references')
+    op.drop_index(op.f('ix_references_accession'), table_name='references')
+    op.drop_table('references')
+    op.drop_index(op.f('ix_batch_jobs_result_id'), table_name='batch_jobs')
+    op.drop_table('batch_jobs')
+    op.drop_table('assemblies')
+    ### end Alembic commands ###

tests/test_migrations.py

+"""
+Test database migrations.
+"""
+
+
+from __future__ import unicode_literals
+
+import os
+
+import alembic.autogenerate
+import alembic.command
+import alembic.config
+from alembic.migration import MigrationContext
+from sqlalchemy import create_engine
+
+from mutalyzer import db
+
+
+def test_migrations():
+    """
+    Run all migrations and assert the result is up to date with the model
+    definitions.
+
+    We don't use `utils.MutalyzerTest` here, or `mutalyzer.db.session` in any
+    way for that matter, since it will bootstrap the database schema.
+    """
+    database_uri = os.getenv('MUTALYZER_TEST_DATABASE_URI', 'sqlite://')
+
+    alembic_config = alembic.config.Config('migrations/alembic.ini')
+    engine = create_engine(database_uri)
+
+    with engine.begin() as connection:
+        # http://alembic.readthedocs.org/en/latest/cookbook.html#sharing-a-connection-with-a-series-of-migration-commands-and-environments
+        alembic_config.attributes['connection'] = connection
+
+        if database_uri != 'sqlite://':
+            db.Base.metadata.drop_all(connection)
+
+        # TODO: We might also want to test this with data. An implementation
+        #   might look like this:
+        #
+        #   1. Create initial schema by running the first migration.
+        #   2. Add some database content.
+        #   3. Run the remaining migrations.
+
+        alembic.command.upgrade(alembic_config, 'head')
+
+        context = MigrationContext.configure(connection)
+        assert not alembic.autogenerate.compare_metadata(
+            context, db.Base.metadata)
+
+    engine.dispose()

tests/utils.py

@@ -48,6 +48,8 @@ class TestEnvironment(object):
         """
         Destroy all storage defined in the current environment.
         """
+        db.session.remove()
+
         shutil.rmtree(self.cache_dir)
         os.unlink(self.log_file)