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reanahub / reana-workflow-engine-snakemake

REANA Workflow Engine Snakemake
MIT License
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fix job status reporting #6

Closed tiborsimko closed 3 years ago

tiborsimko commented 3 years ago

Similarly to #5, another observed issue is that the workflow executes fine, and finishes fine, and is reported as finished, but its job in the logs is still reported as running:

$ reana-client status -w helloworld-snakemake-kubernetes
NAME                              RUN_NUMBER   CREATED               STARTED               ENDED                 STATUS  
helloworld-snakemake-kubernetes   3            2021-08-12T13:39:43   2021-08-12T13:39:56   2021-08-12T13:40:26   finished

$ reana-client  ls -w helloworld-snakemake-kubernetes 
NAME                                                    SIZE   LAST-MODIFIED      
results/greetings.txt                                   34     2021-08-12T13:40:06
data/names.txt                                          20     2021-08-12T13:39:44
code/helloworld.py                                      3253   2021-08-12T13:39:44
.snakemake/metadata/cmVzdWx0cy9ncmVldGluZ3MudHh0        1029   2021-08-12T13:40:06
.snakemake/log/2021-08-12T133956.052424.snakemake.log   1283   2021-08-12T13:40:26
workflow/snakemake/inputs.yaml                          70     2021-08-12T13:39:44
workflow/snakemake/Snakefile                            1043   2021-08-12T13:39:44

$ reana-client logs -w helloworld-snakemake-kubernetes
...
==> Job logs
==> Step: helloworld
==> Workflow ID: ba3d416a-e1a5-4f07-bb2d-4a2713618b46
==> Compute backend: Kubernetes
==> Job ID: reana-run-job-fc3b2701-5b41-42ea-992e-be37f1736794
==> Docker image: python:2.7-slim
==> Command: python code/helloworld.py --inputfile data/names.txt --outputfile results/greetings.txt --sleeptime 0
==> Status: running
==> Started: 2021-08-12T13:39:56
==> Logs:
job: :
 2021-08-12T13:39:57 INFO     Parameters: inputfile=data/names.txt outputfile=results/greetings.txt sleeptime=0.0

Completed

(note ==> Status: running)