Feature #1745

Person

BMPS: Results for user-created workflows

Added by Hervé Ménager about 7 years ago. Updated about 7 years ago.

Status:AssignedStart date:06/14/2013
Priority:NormalDue date:
Assignee:PersonJennifer Dommer% Done:

60%

Category:-
Target version:1.5.2

Description

Requested by NIAID (Jennifer) for HPCWeb project:
Users should be able to view and download the results of a workflow when it is executed. After discussion, the solution will be the following:
- users annotate the workflow at design time in the BMPS interface,
- the serialized GraphML is annotated to mention which task results should be top-level,
- the server-side BMPSWorkflow produces the corresponding output parameters in the workflow definition.

History

#1 Person Updated by Hervé Ménager about 7 years ago

Expected GraphML sent by BMPS should look like this:

<port name="alignmentout">
  <data key="type">pipeOut</data>
  <data key="status">active</data>
  <data key="output">true</data>
  <port key="prompt">Alignment</port>
</port>

Here, the added part <data key="output">true</data> tells that this task output is a "main workflow output". If set to false, or not present, the output is not a workflow output.

#2 Person Updated by Hervé Ménager about 7 years ago

  • Subject changed from Results for BMPS-created workflows to BMPS: Results for user-created workflows

#3 Person Updated by Hervé Ménager about 7 years ago

  • % Done changed from 0 to 60

first code to tag all outputs as workflow outputs by Jennifer: r380
server-side implementation to generate the corresponding Mobyle Workflow XML: r4452

#4 Person Updated by Hervé Ménager about 7 years ago

  • Target version changed from 1.5.1 to 1.5.2

#5 Person Updated by Hervé Ménager about 7 years ago

  • Status changed from Assigned to Feedback

important side-effect of this modification:
1) all task output are now tagged as workflow outputs by default
2) however an output of a Mobyle XML can be or not be produced by the run
3) the current code (see here:https://projets.pasteur.fr/projects/mobyle/repository/revisions/4452/annotate/trunk/Src/Mobyle/WorkflowJob.py#L545) raises an error if a linked task output does not produce an output.

Try for instance to run a single dnapars with the current code, without any seqboot: an error message is raised and the workflow fails because the seqboot output has not been produced.

#6 Person Updated by Hervé Ménager about 7 years ago

  • Status changed from Feedback to Assigned

add workaround for this side effect in r4463

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