This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.model.migrate.versions.0059_sample_dataset_file_path

Migration script to modify the 'file_path' field type in 'sample_dataset' table
to 'TEXT' so that it can support large file paths exceeding 255 characters
from __future__ import print_function

import logging

from sqlalchemy import Column, MetaData, Table, TEXT
from sqlalchemy.exc import NoSuchTableError

log = logging.getLogger(__name__)
metadata = MetaData()

[docs]def upgrade(migrate_engine): metadata.bind = migrate_engine print(__doc__) metadata.reflect() try: SampleDataset_table = Table("sample_dataset", metadata, autoload=True) except NoSuchTableError: SampleDataset_table = None log.debug("Failed loading table 'sample_dataset'") if SampleDataset_table is not None: cmd = "SELECT id, file_path FROM sample_dataset" result = migrate_engine.execute(cmd) filepath_dict = {} for r in result: id = int(r[0]) filepath_dict[id] = r[1] # remove the 'file_path' column try: SampleDataset_table.c.file_path.drop() except Exception: log.exception("Deleting column 'file_path' from the 'sample_dataset' table failed.") # create the column again try: col = Column("file_path", TEXT) col.create(SampleDataset_table) assert col is SampleDataset_table.c.file_path except Exception: log.exception("Creating column 'file_path' in the 'sample_dataset' table failed.") for id, file_path in filepath_dict.items(): cmd = "update sample_dataset set file_path='%s' where id=%i" % (file_path, id) migrate_engine.execute(cmd)
[docs]def downgrade(migrate_engine): pass