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Source code for galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules
"""
Migration script to support subworkflows and workflow request input parameters
"""
import logging
from sqlalchemy import Column, ForeignKey, ForeignKeyConstraint, Index, Integer, MetaData, Table
from galaxy.model.custom_types import JSONType, TrimmedString, UUIDType
from galaxy.model.migrate.versions.util import add_column, alter_column, create_table, drop_column, drop_table
log = logging.getLogger(__name__)
metadata = MetaData()
WorkflowInvocationToSubworkflowInvocationAssociation_table = Table(
"workflow_invocation_to_subworkflow_invocation_association", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_id", Integer),
Column("subworkflow_invocation_id", Integer),
Column("workflow_step_id", Integer),
ForeignKeyConstraint(['workflow_invocation_id'], ['workflow_invocation.id'], name='fk_wfi_swi_wfi'),
ForeignKeyConstraint(['subworkflow_invocation_id'], ['workflow_invocation.id'], name='fk_wfi_swi_swi'),
ForeignKeyConstraint(['workflow_step_id'], ['workflow_step.id'], name='fk_wfi_swi_ws')
)
WorkflowRequestInputStepParameter_table = Table(
"workflow_request_input_step_parameter", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_id", Integer),
Column("workflow_step_id", Integer),
Column("parameter_value", JSONType),
ForeignKeyConstraint(['workflow_invocation_id'], ['workflow_invocation.id'], name='fk_wfreq_isp_wfi'),
ForeignKeyConstraint(['workflow_step_id'], ['workflow_step.id'], name='fk_wfreq_isp_ws')
)
TABLES = [
WorkflowInvocationToSubworkflowInvocationAssociation_table,
WorkflowRequestInputStepParameter_table,
]
INDEXES = [
Index("ix_wfinv_swfinv_wfi", WorkflowInvocationToSubworkflowInvocationAssociation_table.c.workflow_invocation_id),
Index("ix_wfinv_swfinv_swfi", WorkflowInvocationToSubworkflowInvocationAssociation_table.c.subworkflow_invocation_id),
Index("ix_wfreq_inputstep_wfi", WorkflowRequestInputStepParameter_table.c.workflow_invocation_id)
]
[docs]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)
[docs]def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column("subworkflow_id", "workflow_step", metadata)
drop_column("parent_workflow_id", "workflow", metadata)
drop_column("input_subworkflow_step_id", "workflow_step_connection", metadata)
drop_column("label", "workflow_output", metadata)
drop_column("uuid", "workflow_output", metadata)
for table in TABLES:
drop_table(table)