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Fix Reexecute #902

Merged
merged 32 commits into from
Sep 6, 2024
Merged

Fix Reexecute #902

merged 32 commits into from
Sep 6, 2024

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kabir-vats
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… all workflows

Kabir Bradman Vats - 397552 and others added 24 commits July 8, 2024 14:58
…er. Can definitely see a lot of reworking in terms of the interfaces & will have to go to drawing board for that
Accidental save from vim
… central code. Load containers in foreground, will change to background later
Restructure dep_manager and separate container, redis, and neo4j from…
@kabir-vats kabir-vats added the WIP (no-ci) Don't run any CI for this PR label Aug 19, 2024
@kabir-vats kabir-vats self-assigned this Aug 19, 2024
@kabir-vats kabir-vats changed the base branch from Multiple-Workflows-One-Database to develop August 20, 2024 17:15
@kabir-vats kabir-vats changed the base branch from develop to Multiple-Workflows-One-Database August 20, 2024 17:30
@kabir-vats kabir-vats changed the base branch from Multiple-Workflows-One-Database to develop August 29, 2024 14:06
@kabir-vats kabir-vats added WIP Work in progress and removed WIP (no-ci) Don't run any CI for this PR labels Aug 29, 2024
@kabir-vats kabir-vats removed the WIP Work in progress label Sep 3, 2024
@kabir-vats kabir-vats requested a review from rstyd September 3, 2024 17:11
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This looks great and worked well for me.
@kabir-vats What is the file that has the name of the workflow that appears in the archive?
total 5
-rw-rw-r-- 1 pagrubel pagrubel 912 Sep 4 15:16 bee.conf
-rw-rw-r-- 1 pagrubel pagrubel 3 Sep 4 15:16 bee_wf_name
-rw-rw-r-- 1 pagrubel pagrubel 8 Sep 4 15:16 bee_wf_status
drwxrwxr-x 2 pagrubel pagrubel 4096 Sep 4 15:16 bee_workflow
drwxrwxr-x 2 pagrubel pagrubel 4096 Sep 4 15:16 cat-174318f74bf24b6bab36a1c4f6068519
-rw-rw-r-- 1 pagrubel pagrubel 2159 Sep 4 15:16 cat-grep-tar
drwxrwxr-x 2 pagrubel pagrubel 4096 Sep 4 15:16 grep0-8dd6f1b3a2074a1280561718f31f7c06
drwxrwxr-x 2 pagrubel pagrubel 4096 Sep 4 15:16 grep1-e4fa3ccb9fbf4cf492ca69505725d2e3
-rw-rw-r-- 1 pagrubel pagrubel 211 Sep 4 15:16 submit_command_args.yaml
drwxrwxr-x 2 pagrubel pagrubel 4096 Sep 4 15:16 tar-83bb47ee861d4d0cb0fbb5cf1f836f19

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pagrubel commented Sep 4, 2024

The submit command I used was:
beeflow submit cgt cat-grep-tar cat-grep-tar/workflow.cwl cat-grep-tar/input.yml .

so I'm asking about the cat-grep-tar file

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The submit command I used was: beeflow submit cgt cat-grep-tar cat-grep-tar/workflow.cwl cat-grep-tar/input.yml .

so I'm asking about the cat-grep-tar file

If you mean the file that holds all the cwl files, that should be bee_workflow.

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pagrubel commented Sep 5, 2024

The submit command I used was: beeflow submit cgt cat-grep-tar cat-grep-tar/workflow.cwl cat-grep-tar/input.yml .
so I'm asking about the cat-grep-tar file

If you mean the file that holds all the cwl files, that should be bee_workflow.

No there is an extra binary file with the name of the workflow, in this case cat-grep-tar. It doesn't appear when running using the current develop branch.

@@ -121,7 +117,7 @@ def post(self):
return make_response(jsonify(msg='Workflow uploaded', status='ok',
wf_id=wf_id), 201)

def put(self):
def put(self): # This method can be deleted / deprecated
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Why not delete it now?

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pagrubel commented Sep 5, 2024

@kabir-vats This looks great. Thank you for streamlining code.

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This looks very good Kabir, thank you.

@pagrubel pagrubel merged commit 602bb72 into develop Sep 6, 2024
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@pagrubel pagrubel deleted the fix-reexecute branch September 6, 2024 05:01
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2 participants