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Source code for galaxy.model.migrate.versions.0145_add_workflow_step_input
"""
Migration script for workflow step input table.
"""
from __future__ import print_function
import logging
from migrate import ForeignKeyConstraint as MigrateForeignKeyConstraint
from sqlalchemy import (
Boolean,
Column,
ForeignKey,
Index,
Integer,
MetaData,
Table,
TEXT,
)
from galaxy.model.custom_types import JSONType
from galaxy.model.migrate.versions.util import (
create_table,
drop_index,
drop_table
)
log = logging.getLogger(__name__)
metadata = MetaData()
WorkflowStepInput_table = Table(
"workflow_step_input", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
Column("name", TEXT),
Column("merge_type", TEXT),
Column("scatter_type", TEXT),
Column("value_from", JSONType),
Column("value_from_type", TEXT),
Column("default_value", JSONType),
Column("default_value_set", Boolean, default=False),
Column("runtime_value", Boolean, default=False),
Index('ix_workflow_step_input_workflow_step_id_name_unique', "workflow_step_id", "name", unique=True, mysql_length={'name': 200}),
)
[docs]def upgrade(migrate_engine):
print(__doc__)
metadata.bind = migrate_engine
metadata.reflect()
OldWorkflowStepConnection_table = Table("workflow_step_connection", metadata, autoload=True)
for fkc in OldWorkflowStepConnection_table.foreign_key_constraints:
mfkc = MigrateForeignKeyConstraint([_.parent for _ in fkc.elements], [_.column for _ in fkc.elements], name=fkc.name)
try:
mfkc.drop()
except Exception:
log.exception("Dropping foreign key constraint '%s' from table '%s' failed", mfkc.name, OldWorkflowStepConnection_table)
for index in OldWorkflowStepConnection_table.indexes:
drop_index(index, OldWorkflowStepConnection_table)
OldWorkflowStepConnection_table.rename("workflow_step_connection_preupgrade145")
# Try to deregister that table to work around some caching problems it seems.
OldWorkflowStepConnection_table.deregister()
metadata._remove_table("workflow_step_connection", metadata.schema)
metadata.reflect()
NewWorkflowStepConnection_table = Table(
"workflow_step_connection", metadata,
Column("id", Integer, primary_key=True),
Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
Column("input_step_input_id", Integer, ForeignKey("workflow_step_input.id"), index=True),
Column("output_name", TEXT),
Column("input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
)
for table in (WorkflowStepInput_table, NewWorkflowStepConnection_table):
create_table(table)
insert_step_inputs_cmd = \
"INSERT INTO workflow_step_input (workflow_step_id, name) " + \
"SELECT DISTINCT input_step_id, input_name FROM workflow_step_connection_preupgrade145"
migrate_engine.execute(insert_step_inputs_cmd)
insert_step_connections_cmd = \
"INSERT INTO workflow_step_connection (output_step_id, input_step_input_id, output_name, input_subworkflow_step_id) " + \
"SELECT wsc.output_step_id, wsi.id, wsc.output_name, wsc.input_subworkflow_step_id " + \
"FROM workflow_step_connection_preupgrade145 AS wsc JOIN workflow_step_input AS wsi ON wsc.input_step_id = wsi.workflow_step_id AND wsc.input_name = wsi.name ORDER BY wsc.id"
migrate_engine.execute(insert_step_connections_cmd)
drop_table(OldWorkflowStepConnection_table)
[docs]def downgrade(migrate_engine):
metadata.bind = migrate_engine
NewWorkflowStepConnection_table = Table("workflow_step_connection", metadata, autoload=True)
for fkc in NewWorkflowStepConnection_table.foreign_key_constraints:
mfkc = MigrateForeignKeyConstraint([_.parent for _ in fkc.elements], [_.column for _ in fkc.elements], name=fkc.name)
try:
mfkc.drop()
except Exception:
log.exception("Dropping foreign key constraint '%s' from table '%s' failed", mfkc.name, NewWorkflowStepConnection_table)
for index in NewWorkflowStepConnection_table.indexes:
drop_index(index, NewWorkflowStepConnection_table)
NewWorkflowStepConnection_table.rename("workflow_step_connection_predowngrade145")
# Try to deregister that table to work around some caching problems it seems.
NewWorkflowStepConnection_table.deregister()
metadata._remove_table("workflow_step_connection", metadata.schema)
metadata.reflect()
OldWorkflowStepConnection_table = Table(
"workflow_step_connection", metadata,
Column("id", Integer, primary_key=True),
Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
Column("input_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
Column("output_name", TEXT),
Column("input_name", TEXT),
Column("input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
)
create_table(OldWorkflowStepConnection_table)
insert_step_connections_cmd = \
"INSERT INTO workflow_step_connection (output_step_id, input_step_id, output_name, input_name, input_subworkflow_step_id) " + \
"SELECT wsc.output_step_id, wsi.workflow_step_id, wsc.output_name, wsi.name, wsc.input_subworkflow_step_id " + \
"FROM workflow_step_connection_predowngrade145 AS wsc JOIN workflow_step_input AS wsi ON wsc.input_step_input_id = wsi.id ORDER BY wsc.id"
migrate_engine.execute(insert_step_connections_cmd)
for table in (NewWorkflowStepConnection_table, WorkflowStepInput_table):
drop_table(table)