def upgrade(migrate_engine):
print(__doc__)
metadata.bind = migrate_engine
metadata.reflect()
if migrate_engine.name in ['postgres', 'postgresql']:
subworkflow_id_column = Column("subworkflow_id", Integer, ForeignKey("workflow.id"), nullable=True)
input_subworkflow_step_id_column = Column("input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), nullable=True)
parent_workflow_id_column = Column("parent_workflow_id", Integer, ForeignKey("workflow.id"), nullable=True)
else:
subworkflow_id_column = Column("subworkflow_id", Integer, nullable=True)
input_subworkflow_step_id_column = Column("input_subworkflow_step_id", Integer, nullable=True)
parent_workflow_id_column = Column("parent_workflow_id", Integer, nullable=True)
add_column(subworkflow_id_column, "workflow_step", metadata)
add_column(input_subworkflow_step_id_column, "workflow_step_connection", metadata)
add_column(parent_workflow_id_column, "workflow", metadata)
workflow_output_label_column = Column("label", TrimmedString(255))
workflow_output_uuid_column = Column("uuid", UUIDType, nullable=True)
add_column(workflow_output_label_column, "workflow_output", metadata)
add_column(workflow_output_uuid_column, "workflow_output", metadata)
# Make stored_workflow_id nullable, since now workflows can belong to either
# a stored workflow or a parent workflow.
alter_column("stored_workflow_id", "workflow", metadata, nullable=True)
for table in TABLES:
# Indexes are automatically created when the tables are.
create_table(table)
def upgrade(migrate_engine):
print(__doc__)
metadata.bind = migrate_engine
metadata.reflect()
# Make workflow_step_id nullable to allow for PJAs to be created for
# individual jobs.
alter_column("workflow_step_id",
"post_job_action",
metadata,
nullable=True)
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')
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')