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Source code for galaxy.model.migrate.versions.0127_output_collection_adjustments
"""
Migration script updating collections tables for output collections.
"""
import logging
from sqlalchemy import (
Column,
ForeignKey,
Integer,
MetaData,
Table,
TEXT,
Unicode
)
from galaxy.model.custom_types import TrimmedString
from galaxy.model.migrate.versions.util import (
add_column,
create_table,
drop_column,
drop_table
)
log = logging.getLogger(__name__)
metadata = MetaData()
JobToImplicitOutputDatasetCollectionAssociation_table = Table(
"job_to_implicit_output_dataset_collection", metadata,
Column("id", Integer, primary_key=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("dataset_collection_id", Integer, ForeignKey("dataset_collection.id"), index=True),
Column("name", Unicode(255))
)
[docs]def upgrade(migrate_engine):
print(__doc__)
metadata.bind = migrate_engine
metadata.reflect()
create_table(JobToImplicitOutputDatasetCollectionAssociation_table)
dataset_collection_table = Table("dataset_collection", metadata, autoload=True)
# need server_default because column in non-null
populated_state_column = Column('populated_state', TrimmedString(64), default='ok', server_default="ok", nullable=False)
add_column(populated_state_column, dataset_collection_table, metadata)
populated_message_column = Column('populated_state_message', TEXT, nullable=True)
add_column(populated_message_column, dataset_collection_table, metadata)
[docs]def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_table(JobToImplicitOutputDatasetCollectionAssociation_table)
dataset_collection_table = Table("dataset_collection", metadata, autoload=True)
drop_column('populated_state', dataset_collection_table)
drop_column('populated_state_message', dataset_collection_table)