/lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 182 lines · 178 code · 0 blank · 4 comment · 0 complexity · 09e9c397a6b6217b0dda8f591c4a86a4 MD5 · raw file
- """
- 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()
- 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(migrate_engine):
- metadata.bind = migrate_engine
- print __doc__
- metadata.reflect()
- # Create user_id column in history_tag_association table.
- HistoryTagAssociation_table = Table( "history_tag_association", metadata, autoload=True )
- if migrate_engine.name != 'sqlite':
- c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True )
- try:
- c.create( HistoryTagAssociation_table, index_name='ix_history_tag_association_user_id')
- 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 ) )
- else:
- c = Column( "user_id", Integer)
- 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 ) )
- # 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:
- migrate_engine.execute(
- "UPDATE history_tag_association SET user_id=( SELECT user_id FROM history WHERE history_tag_association.history_id = history.id )"
- )
- if migrate_engine.name != 'sqlite':
- # 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, index_name='ix_history_dataset_association_tag_association_user_id')
- 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 ) )
- else:
- #In sqlite, we can no longer quietly fail to add foreign key.
- # 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)
- 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 ) )
- # 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:
- migrate_engine.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)"
- )
- if migrate_engine.name != 'sqlite':
- # 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, index_name='ix_page_tag_association_user_id')
- 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 page_tag_association table failed: %s" % str( e ) )
- else:
- # Create user_id column in page_tag_association table.
- PageTagAssociation_table = Table( "page_tag_association", metadata, autoload=True )
- c = Column( "user_id", Integer )
- 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 page_tag_association table failed: %s" % str( e ) )
- # 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:
- migrate_engine.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(migrate_engine):
- metadata.bind = migrate_engine
- 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 ) )