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Source code for galaxy.model.migrate.versions.0147_job_messages

"""
Add structured failure reason column to jobs table
"""

import logging

from sqlalchemy import (
    Column,
    MetaData,
    Table,
    TEXT
)

from galaxy.model.custom_types import JSONType
from galaxy.model.migrate.versions.util import (
    add_column,
    alter_column,
    drop_column
)

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


[docs]def upgrade(migrate_engine): print(__doc__) metadata.bind = migrate_engine metadata.reflect() jobs_table = Table("job", metadata, autoload=True) job_messages_column = Column("job_messages", JSONType, nullable=True) add_column(job_messages_column, jobs_table, metadata) job_job_stdout_column = Column("job_stdout", TEXT, nullable=True) add_column(job_job_stdout_column, jobs_table, metadata) job_job_stderr_column = Column("job_stderr", TEXT, nullable=True) add_column(job_job_stderr_column, jobs_table, metadata) tasks_table = Table("task", metadata, autoload=True) task_job_messages_column = Column("job_messages", JSONType, nullable=True) add_column(task_job_messages_column, tasks_table, metadata) task_job_stdout_column = Column("job_stdout", TEXT, nullable=True) add_column(task_job_stdout_column, tasks_table, metadata) task_job_stderr_column = Column("job_stderr", TEXT, nullable=True) add_column(task_job_stderr_column, tasks_table, metadata) for table in [jobs_table, tasks_table]: alter_column('stdout', table, name='tool_stdout') alter_column('stderr', table, name='tool_stderr')
[docs]def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() jobs_table = Table("job", metadata, autoload=True) tasks_table = Table("task", metadata, autoload=True) for colname in ["job_messages", "job_stdout", "job_stderr"]: drop_column(colname, jobs_table) drop_column(colname, tasks_table) for table in [jobs_table, tasks_table]: alter_column('tool_stdout', table, name='stdout') alter_column('tool_stderr', table, name='stderr')