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Bugfix for loading subworkflows from workflow descriptions. #4394

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merged 1 commit into from Aug 14, 2017

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commented Aug 9, 2017

Sometimes unrelated workflow steps can be flushed in a half complete state and violate integrity constraints when a subworkflow step causes a flush of during the load of a different step. This fixes that by preloading all subworkflows during workflow import.

IntegrityError: (sqlite3.IntegrityError) NOT NULL constraint failed: workflow_step.workflow_id [SQL: u'INSERT INTO workflow_step (create_time, update_time, workflow_id, subworkflow_id, type, tool_id, tool_version, tool_hash, tool_inputs, tool_errors, position, config, order_index, uuid, label) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)'] [parameters: ('2017-08-06 17:11:40.611716', '2017-08-06 17:11:40.611720', None, 1, 'subworkflow', None, None, None, None, None, <read-only buffer for 0x115a97fb0, size -1, offset 0 at 0x115a97e70>, None, None, '494d856ec0fc453688e8c6d464305d7b', u'metrics_markduplicates')]\n", "err_msg": "Uncaught exception in exposed API method:", "err_code": 0}

This PR doesn't include a test case but one will be included if the CWL branch is merged at a later date (xref common-workflow-language/common-workflow-language@cd1dc66).

Bugfix for loading subworkflows from workflow descriptions.
Sometimes unrelated workflow steps can be flushed in a half complete state and violate integrity constraints when a subworkflow step causes a flush of during the load of a different step. This fixes that by preloading all subworkflows during workflow import.

This PR doesn't include a test case but one will be included if the CWL branch is merged at a later date (xref common-workflow-language/common-workflow-language@cd1dc66).

@mvdbeek mvdbeek merged commit e594152 into galaxyproject:dev Aug 14, 2017

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commented Aug 14, 2017

Should we port this back to 17.05/17.01 ?

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