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obophenotype / ontology-kg-preprocessing-kit

Simple preprocessing kit for beating a set of ontologies into shape for KG ingestion
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Jenkins of covid ingest stopped functioning #2

Open matentzn opened 4 years ago

matentzn commented 4 years ago

https://build.obolibrary.io/job/obophenotype/job/covid-kg-ontology-preprocessing/job/master/23/console

I had this problem before on Monarch Jenkins, no idea whats causing it.. @kltm Is there any way I can delete the job and start over (it was added by your automated obophenotype repo scan)?

kltm commented 4 years ago

Without digging in, my guess is that this is due to a container leaking information onto the host system's file system. Assuming so, the issue is that your container is running as root and/or has incompatible permissions with the jenkins host, causing any file produced from the container and placed into the host workspace to have issues when touched by a not-that-container process, including the jenkins host.

ERROR: Failed to clean the workspace
Suppressed: java.nio.file.FileSystemException: /var/lib/jenkins/workspace/kg-ontology-preprocessing_master@2/ontologies/hp/hp_finished.owl: Operation not permitted
kltm commented 4 years ago

I think this is likely to be the same constellation of issues from the "Docker path" email thread in mid-November. I believe that as a temporary workaround one could remove the Jenkinsfile or branch. Otherwise, one could maybe try to manually remove the .git/ directory from that space before beginning operations.

matentzn commented 4 years ago

Yeah, sounds like you are right! Thanks.