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Merge pull request #8418 from jmchilton/fix_too_many_records

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[19.05] Try to fix too many workflow step output associations.
This commit is contained in:
Nate Coraor
2019-08-07 15:35:49 -04:00
committed by GitHub
parent c4fa198d0b f4388a3d11
commit 9071402e31
2 changed files with 3 additions and 14 deletions
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lib/galaxy/workflow/modules.py
+1 -12
View File
@@ -594,7 +594,7 @@ class InputModule(WorkflowModule):
progress.set_outputs_for_input(invocation_step, step_outputs)
def recover_mapping(self, invocation_step, progress):
progress.set_outputs_for_input(invocation_step)
progress.set_outputs_for_input(invocation_step, already_persisted=True)
class InputDataModule(InputModule):
@@ -1305,17 +1305,6 @@ class ToolModule(WorkflowModule):
return complete
def recover_mapping(self, invocation_step, progress):
outputs = {}
for output_dataset_assoc in invocation_step.output_datasets:
outputs[output_dataset_assoc.output_name] = output_dataset_assoc.dataset
for output_dataset_collection_assoc in invocation_step.output_dataset_collections:
outputs[output_dataset_collection_assoc.output_name] = output_dataset_collection_assoc.dataset_collection
progress.set_step_outputs(invocation_step, outputs)
def _effective_post_job_actions(self, step):
effective_post_job_actions = step.post_job_actions[:]
for key, value in self.runtime_post_job_actions.items():
lib/galaxy/workflow/run.py
+2 -2
View File
@@ -405,7 +405,7 @@ class WorkflowProgress(object):
else:
return step_outputs[output_name]
def set_outputs_for_input(self, invocation_step, outputs=None):
def set_outputs_for_input(self, invocation_step, outputs=None, already_persisted=False):
step = invocation_step.workflow_step
if outputs is None:
@@ -420,7 +420,7 @@ class WorkflowProgress(object):
elif step_id in self.inputs_by_step_id:
outputs['output'] = self.inputs_by_step_id[step_id]
self.set_step_outputs(invocation_step, outputs)
self.set_step_outputs(invocation_step, outputs, already_persisted=already_persisted)
def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
step = invocation_step.workflow_step