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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.")