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
from __future__ import print_function

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(""), 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