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Merge branch 'release_16.01' into dev

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This commit is contained in:
Dannon Baker
2016-03-22 09:18:55 -04:00
parent 35403f2a91 30750c32e4
commit 45c1731888
1 changed files with 29 additions and 18 deletions
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lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py → lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
+29 -18
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@@ -4,7 +4,7 @@ Migration script to support subworkflows and workflow request input parameters
import datetime
import logging
from sqlalchemy import Column, Integer, ForeignKey, MetaData, Table
from sqlalchemy import Column, Integer, ForeignKey, MetaData, Table, Index, ForeignKeyConstraint
from galaxy.model.custom_types import TrimmedString, UUIDType, JSONType
@@ -15,22 +15,33 @@ metadata = MetaData()
WorkflowInvocationToSubworkflowInvocationAssociation_table = Table(
"workflow_invocation_to_subworkflow_invocation_association", metadata,
Column( "id", Integer, primary_key=True ),
Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
Column( "subworkflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
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')
)
WorkflowRequestInputStepParmeter_table = Table(
WorkflowRequestInputStepParameter_table = Table(
"workflow_request_input_step_parameter", metadata,
Column( "id", Integer, primary_key=True ),
Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
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,
WorkflowRequestInputStepParmeter_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)
]
@@ -38,16 +49,17 @@ def upgrade(migrate_engine):
metadata.bind = migrate_engine
print __doc__
metadata.reflect()
subworkflow_id_column = Column( "subworkflow_id", Integer, ForeignKey("workflow.id"), nullable=True )
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 )
input_subworkflow_step_id_column = Column( "input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), nullable=True )
__add_column( input_subworkflow_step_id_column, "workflow_step_connection", metadata )
parent_workflow_id_column = Column( "parent_workflow_id", Integer, ForeignKey("workflow.id"), nullable=True )
__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 )
@@ -58,6 +70,7 @@ def upgrade(migrate_engine):
__alter_column("workflow", "stored_workflow_id", metadata, nullable=True)
for table in TABLES:
# Indexes are automatically created when the tables are.
__create(table)
@@ -66,15 +79,13 @@ def downgrade(migrate_engine):
metadata.reflect()
__drop_column( "subworkflow_id", "workflow_step", metadata )
__drop_column( "parent_workflow_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 )
__alter_column("workflow", "stored_workflow_id", metadata, nullable=False)
for table in TABLES:
__drop(table)