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Source code for galaxy.model.migrate.versions.0037_samples_library

This migration script removes the library_id & folder_id fields in the 'request' table and
adds the same to the 'sample' table. This also adds a 'datatx' column to request_type table
to store the sequencer login information. Finally, this adds a 'dataset_files' column to
the sample table.
from __future__ import print_function

import datetime
import logging

from sqlalchemy import (

from galaxy.model.custom_types import (
from galaxy.model.migrate.versions.util import (

log = logging.getLogger(__name__)
now = datetime.datetime.utcnow
metadata = MetaData()

[docs]def upgrade(migrate_engine): print(__doc__) metadata.bind = migrate_engine metadata.reflect() # Add the datatx_info column in 'request_type' table col = Column("datatx_info", JSONType()) add_column(col, 'request_type', metadata) # Delete the library_id column in 'request' table Request_table = Table("request", metadata, autoload=True) # TODO: Dropping a column used in a foreign key fails in MySQL, need to remove the FK first. drop_column('library_id', Request_table) # Delete the folder_id column in 'request' table # TODO: Dropping a column used in a foreign key fails in MySQL, need to remove the FK first. drop_column('folder_id', Request_table) # Add the dataset_files column in 'sample' table Sample_table = Table("sample", metadata, autoload=True) col = Column("dataset_files", JSONType()) add_column(col, Sample_table, metadata) # Add the library_id column in 'sample' table col = Column("library_id", Integer, ForeignKey("library.id"), index=True) add_column(col, Sample_table, metadata, index_name='ix_sample_library_id') # Add the library_id column in 'sample' table col = Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True) add_column(col, Sample_table, metadata, index_name='ix_sample_library_folder_id')
[docs]def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() Sample_table = Table("sample", metadata, autoload=True) drop_column('folder_id', Sample_table) drop_column('library_id', Sample_table) drop_column('dataset_files', Sample_table) Request_table = Table("request", metadata, autoload=True) col = Column('folder_id', Integer, ForeignKey('library_folder.id'), index=True) add_column(col, Request_table, metadata, index_name='ix_request_folder_id') col = Column('library_id', Integer, ForeignKey("library.id"), index=True) add_column(col, Request_table, metadata, index_name='ix_request_library_id') drop_column('datatx_info', 'request_type', metadata)