genome / ptero-workflow

Client-facing API for the PTero system
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Revert "Service data to save feature" #258

Closed mkiwala closed 8 years ago

mkiwala commented 8 years ago

Reverts genome/ptero-workflow#256

The database migration in PR #256 fails in the staging environment because the staging database has entries in the job table which violate the NOT NULL constraint on the new column created by this migration.

Traceback (most recent call last):
  File "/app/ptero_workflow/api/application.py", line 38, in before_request
    flask.g.backend = factory.create_backend()
  File "/app/.heroku/src/ptero-common/ptero_common/factories/bigfactory.py", line 23, in create_backend
    self._initialize()
  File "/app/.heroku/src/ptero-common/ptero_common/factories/bigfactory.py", line 32, in _initialize
    self._initialize_database()
  File "/app/.heroku/src/ptero-common/ptero_common/factories/dbfactorymixin.py", line 23, in _initialize_database
    alembic_upgrade(self.alembic_config, self.engine)
  File "/app/.heroku/src/ptero-common/ptero_common/factories/dbfactorymixin.py", line 34, in alembic_upgrade
    command.upgrade(alembic_config, "head")
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/command.py", line 174, in upgrade
    script.run_env()
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/script/base.py", line 397, in run_env
    util.load_python_file(self.dir, 'env.py')
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/util/pyfiles.py", line 81, in load_python_file
    module = load_module_py(module_id, path)
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/util/compat.py", line 79, in load_module_py
    mod = imp.load_source(module_id, path, fp)
  File "/app/ptero_workflow/alembic/env.py", line 67, in <module>
    run_migrations_online()
  File "/app/ptero_workflow/alembic/env.py", line 62, in run_migrations_online
    context.run_migrations()
  File "<string>", line 8, in run_migrations
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/runtime/environment.py", line 797, in run_migrations
    self.get_context().run_migrations(**kw)
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/runtime/migration.py", line 312, in run_migrations
    step.migration_fn(**kw)
  File "/app/ptero_workflow/alembic/versions/89b1fb28bb6c_store_service_data.py", line 20, in upgrade
    op.add_column('job', sa.Column('service_data_to_save', postgresql.JSON(), nullable=False))
  File "<string>", line 8, in add_column
  File "<string>", line 3, in add_column
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/operations/ops.py", line 1535, in add_column
    return operations.invoke(op)
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/operations/base.py", line 318, in invoke
    return fn(self, operation)
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/operations/toimpl.py", line 123, in add_column
    schema=schema
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/ddl/impl.py", line 172, in add_column
    self._exec(base.AddColumn(table_name, column, schema=schema))
  File "/app/.heroku/python/lib/python2.7/site-packages/alembic/ddl/impl.py", line 118, in _exec
    return conn.execute(construct, *multiparams, **params)
  File "/app/.heroku/python/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute
    return meth(self, multiparams, params)
  File "/app/.heroku/python/lib/python2.7/site-packages/sqlalchemy/sql/ddl.py", line 68, in _execute_on_connection
    return connection._execute_ddl(self, multiparams, params)
  File "/app/.heroku/python/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 968, in _execute_ddl
    compiled
  File "/app/.heroku/python/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context
    context)
  File "/app/.heroku/python/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception
    exc_info
  File "/app/.heroku/python/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 200, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb)
  File "/app/.heroku/python/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context
    context)
  File "/app/.heroku/python/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute
    cursor.execute(statement, parameters)
IntegrityError: (psycopg2.IntegrityError) column "service_data_to_save" contains null values
 [SQL: 'ALTER TABLE job ADD COLUMN service_data_to_save JSON NOT NULL']
coveralls commented 8 years ago

Coverage Status

Coverage increased (+0.02%) to 88.577% when pulling 4c08b6427522fc5e15c5b997933818817975454a on revert-256-service_data_to_save_feature into f80079c1bf70f059eea7b7100ab6f259fccfd171 on master.