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PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
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DepMap 04-drug_dosage_and_curves.py Script failing on CCLE file download #108

Closed jjacobson95 closed 8 months ago

jjacobson95 commented 9 months ago

Continuous integration failing on 04-drug_dosage_and_curves.py script. This script passes "CCLE" to 04a-drugResponseData.R which maps it to "CCLE_2015" which is passed to this command dset<<-downloadPSet(f,saveDir='.',timeout=10000). This is the command which is failing.

Error starts on this line. I have not been able to reproduce the issue locally. All of the other files are downloading fine within CI but this one has been consistently been failing.

Once the DepMap scripts are working (and all is aligned to updated schema), the continuous integration pipeline should be cleared!

sgosline commented 9 months ago

OK, I'll debug in my local build branch, hopefully over the weekend.

jjacobson95 commented 8 months ago

Sounds great. It is now looking like it may simply be a storage space issue. Deleting each file after use may do it? Hopefully that makes it easier to resolve.

jjacobson95 commented 8 months ago

Just an update, the CI pipeline is still blocked on this script. The error message can be seen here. CPTAC, HCMI, BeatAML are building. MPNST will be added after this is resolved.

For more info - this is running on the JJ_Builder_branch which has the latest changes to the depmap scripts (pulled from local_build_script).

sgosline commented 8 months ago

Again, the CI will be broken for a while, focus on the poster for now, once we have a working package we can revisit the CI

sgosline commented 8 months ago

This works in local build - python scripts/build_locally.py --exp