From 141aa09ec595a9114a868544a6c07a33298186e9 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 29 Sep 2015 23:55:51 +0200
Subject: [PATCH] Test database migrations
---
migrations/env.py | 32 ++---
.../versions/ea660b66f26_initial_schema.py | 130 +++++++++++++++++-
tests/test_migrations.py | 52 +++++++
tests/utils.py | 2 +
4 files changed, 196 insertions(+), 20 deletions(-)
create mode 100644 tests/test_migrations.py
diff --git a/migrations/env.py b/migrations/env.py
index 251d6155..1625aef4 100644
--- a/migrations/env.py
+++ b/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()
diff --git a/migrations/versions/ea660b66f26_initial_schema.py b/migrations/versions/ea660b66f26_initial_schema.py
index eec6ce6a..bd3c1483 100644
--- a/migrations/versions/ea660b66f26_initial_schema.py
+++ b/migrations/versions/ea660b66f26_initial_schema.py
@@ -1,4 +1,4 @@
-"""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 ###
diff --git a/tests/test_migrations.py b/tests/test_migrations.py
new file mode 100644
index 00000000..c6f4cb72
--- /dev/null
+++ b/tests/test_migrations.py
@@ -0,0 +1,52 @@
+"""
+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()
diff --git a/tests/utils.py b/tests/utils.py
index aa90a1fd..6743804f 100644
--- a/tests/utils.py
+++ b/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)
--
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