/lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 48 lines · 36 code · 5 blank · 7 comment · 2 complexity · 661f256c2ab8d7adbb89d51aa4dd1da6 MD5 · raw file

  1. """
  2. This script adds the filename_override_metadata column to the JobExternalOutputMetadata table,
  3. allowing existing metadata files to be written when using external metadata and a cluster
  4. set up with read-only access to database/files
  5. """
  6. from sqlalchemy import *
  7. from sqlalchemy.orm import *
  8. from migrate import *
  9. from migrate.changeset import *
  10. import datetime
  11. now = datetime.datetime.utcnow
  12. import sys, logging
  13. # Need our custom types, but don't import anything else from model
  14. from galaxy.model.custom_types import *
  15. log = logging.getLogger( __name__ )
  16. log.setLevel(logging.DEBUG)
  17. handler = logging.StreamHandler( sys.stdout )
  18. format = "%(name)s %(levelname)s %(asctime)s %(message)s"
  19. formatter = logging.Formatter( format )
  20. handler.setFormatter( formatter )
  21. log.addHandler( handler )
  22. metadata = MetaData()
  23. def display_migration_details():
  24. print "========================================"
  25. print "This script adds the filename_override_metadata column to the JobExternalOutputMetadata table,"
  26. print" allowing existing metadata files to be written when using external metadata and a cluster"
  27. print "set up with read-only access to database/files"
  28. print "========================================"
  29. def upgrade(migrate_engine):
  30. metadata.bind = migrate_engine
  31. display_migration_details()
  32. # Load existing tables
  33. metadata.reflect()
  34. try:
  35. job_external_output_metadata = Table( "job_external_output_metadata", metadata, autoload=True )
  36. col = Column( "filename_override_metadata", String( 255 ) )
  37. col.create( job_external_output_metadata )
  38. assert col is job_external_output_metadata.c.filename_override_metadata
  39. except Exception, e:
  40. log.debug( "Adding column 'filename_override_metadata' to job_external_output_metadata table failed: %s" % ( str( e ) ) )
  41. def downgrade(migrate_engine):
  42. metadata.bind = migrate_engine
  43. pass