""" Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and \ (b) add table for doing individual and community tagging of workflows. SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so this script will generate error messages when run against \ SQLite; however, script does execute successfully against SQLite. """ from sqlalchemy import * from sqlalchemy.orm import * from migrate import * from migrate.changeset import * import logging log = logging.getLogger( __name__ ) metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) StoredWorkflowTagAssociation_table = Table( "stored_workflow_tag_association", metadata, Column( "id", Integer, primary_key=True ), Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "user_tname", Unicode(255), index=True), Column( "value", Unicode(255), index=True), Column( "user_value", Unicode(255), index=True) ) WorkflowTagAssociation_table = Table( "workflow_tag_association", metadata, Column( "id", Integer, primary_key=True ), Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "user_tname", Unicode(255), index=True), Column( "value", Unicode(255), index=True), Column( "user_value", Unicode(255), index=True) ) def upgrade(): print __doc__ metadata.reflect() # Create user_id column in history_tag_association table. HistoryTagAssociation_table = Table( "history_tag_association", metadata, autoload=True ) c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) try: c.create( HistoryTagAssociation_table ) assert c is HistoryTagAssociation_table.c.user_id except Exception, e: # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. print str(e) log.debug( "Adding user_id column to history_tag_association table failed: %s" % str( e ) ) # Create user_id index for history_tag_association table. try: i = Index( "ix_history_tag_association_user_id", HistoryTagAssociation_table.c.user_id ) i.create() except: # Mysql doesn't have a named index, but alter should work HistoryTagAssociation_table.c.user_id.alter( unique=False ) # Populate column so that user_id is the id of the user who owns the history (and, up to now, was the only person able to tag the history). if c is HistoryTagAssociation_table.c.user_id: db_session.execute( "UPDATE history_tag_association SET user_id=( SELECT user_id FROM history WHERE history_tag_association.history_id = history.id )" ) # Create user_id column in history_dataset_association_tag_association table. HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, autoload=True ) c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) try: c.create( HistoryDatasetAssociationTagAssociation_table ) assert c is HistoryDatasetAssociationTagAssociation_table.c.user_id except Exception, e: # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. print str(e) log.debug( "Adding user_id column to history_dataset_association_tag_association table failed: %s" % str( e ) ) # Create user_id index for history_dataset_association_tag_association table. try: i = Index( "ix_history_dataset_association_tag_association_user_id", HistoryDatasetAssociationTagAssociation_table.c.user_id ) i.create() except: # Mysql doesn't have a named index, but alter should work HistoryDatasetAssociationTagAssociation_table.c.user_id.alter( unique=False ) # Populate column so that user_id is the id of the user who owns the history_dataset_association (and, up to now, was the only person able to tag the page). if c is HistoryDatasetAssociationTagAssociation_table.c.user_id: db_session.execute( "UPDATE history_dataset_association_tag_association SET user_id=( SELECT history.user_id FROM history, history_dataset_association WHERE history_dataset_association.history_id = history.id AND history_dataset_association.id = history_dataset_association_tag_association.history_dataset_association_id)" ) # Create user_id column in page_tag_association table. PageTagAssociation_table = Table( "page_tag_association", metadata, autoload=True ) c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) try: c.create( PageTagAssociation_table ) assert c is PageTagAssociation_table.c.user_id except Exception, e: # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. print str(e) log.debug( "Adding user_id column to history_tag_association table failed: %s" % str( e ) ) # Create user_id index for page_tag_association table. try: i = Index( "ix_page_tag_association_user_id", PageTagAssociation_table.c.user_id ) i.create() except: # Mysql doesn't have a named index, but alter should work PageTagAssociation_table.c.user_id.alter( unique=False ) # Populate column so that user_id is the id of the user who owns the page (and, up to now, was the only person able to tag the page). if c is PageTagAssociation_table.c.user_id: db_session.execute( "UPDATE page_tag_association SET user_id=( SELECT user_id FROM page WHERE page_tag_association.page_id = page.id )" ) # Create stored_workflow_tag_association table. try: StoredWorkflowTagAssociation_table.create() except Exception, e: print str(e) log.debug( "Creating stored_workflow_tag_association table failed: %s" % str( e ) ) # Create workflow_tag_association table. try: WorkflowTagAssociation_table.create() except Exception, e: print str(e) log.debug( "Creating workflow_tag_association table failed: %s" % str( e ) ) def downgrade(): metadata.reflect() # Drop user_id column from history_tag_association table. HistoryTagAssociation_table = Table( "history_tag_association", metadata, autoload=True ) try: HistoryTagAssociation_table.c.user_id.drop() except Exception, e: print str(e) log.debug( "Dropping column user_id from history_tag_association table failed: %s" % str( e ) ) # Drop user_id column from history_dataset_association_tag_association table. HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, autoload=True ) try: HistoryDatasetAssociationTagAssociation_table.c.user_id.drop() except Exception, e: print str(e) log.debug( "Dropping column user_id from history_dataset_association_tag_association table failed: %s" % str( e ) ) # Drop user_id column from page_tag_association table. PageTagAssociation_table = Table( "page_tag_association", metadata, autoload=True ) try: PageTagAssociation_table.c.user_id.drop() except Exception, e: print str(e) log.debug( "Dropping column user_id from page_tag_association table failed: %s" % str( e ) ) # Drop stored_workflow_tag_association table. try: StoredWorkflowTagAssociation_table.drop() except Exception, e: print str(e) log.debug( "Dropping stored_workflow_tag_association table failed: %s" % str( e ) ) # Drop workflow_tag_association table. try: WorkflowTagAssociation_table.drop() except Exception, e: print str(e) log.debug( "Dropping workflow_tag_association table failed: %s" % str( e ) )