This document is for an old release 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.0052_sample_dataset_table

Migration script to add the sample_dataset table and remove the 'dataset_files' column
from the 'sample' table

import datetime
import logging
from json import loads

from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
from sqlalchemy.exc import NoSuchTableError

from galaxy.model.custom_types import TrimmedString
from galaxy.model.migrate.versions.util import localtimestamp, nextval

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

SampleDataset_table = Table('sample_dataset', metadata,
                            Column("id", Integer, primary_key=True),
                            Column("create_time", DateTime, default=now),
                            Column("update_time", DateTime, default=now, onupdate=now),
                            Column("sample_id", Integer, ForeignKey("sample.id"), index=True),
                            Column("name", TrimmedString(255), nullable=False),
                            Column("file_path", TrimmedString(255), nullable=False),
                            Column("status", TrimmedString(255), nullable=False),
                            Column("error_msg", TEXT),
                            Column("size", TrimmedString(255)))

[docs]def upgrade(migrate_engine): print(__doc__) metadata.bind = migrate_engine metadata.reflect() try: SampleDataset_table.create() except Exception: log.exception("Creating sample_dataset table failed.") cmd = "SELECT id, dataset_files FROM sample" result = migrate_engine.execute(cmd) for r in result: sample_id = r[0] if r[1]: dataset_files = loads(r[1]) for df in dataset_files: if isinstance(df, dict): cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')" cmd = cmd % (nextval(migrate_engine, 'sample_dataset'), localtimestamp(migrate_engine), localtimestamp(migrate_engine), str(sample_id), df.get('name', ''), df.get('filepath', ''), df.get('status', '').replace('"', '').replace("'", ""), "", df.get('size', '').replace('"', '').replace("'", "").replace(df.get('filepath', ''), '').strip()) migrate_engine.execute(cmd) # Delete the dataset_files column in the Sample table try: Sample_table = Table("sample", metadata, autoload=True) except NoSuchTableError: Sample_table = None log.debug("Failed loading table sample") if Sample_table is not None: try: Sample_table.c.dataset_files.drop() except Exception: log.exception("Deleting column 'dataset_files' from the 'sample' table failed.")
[docs]def downgrade(migrate_engine): pass