fix: A requesting top variably expressed genes, no longer limit to CG…

stjude / proteinpaint

Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.

https://proteinpaint.stjude.org/

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fix: A requesting top variably expressed genes, no longer limit to CG… #1743

Closed xzhou82 closed 2 weeks ago

xzhou82 commented 2 weeks ago

…C set

Description

Congyu please test with local ~~GFF~~ PP against new api currently in qa; you need to connect gdc vpn please find out time taken, and assess gene sets returned for all cases, gliomas, HGG, if they makes sense

Checklist

Check each task that has been performed or verified to be not applicable.

[ ] Tests: added and/or passed unit and integration tests, or N/A
[ ] Todos: commented or documented, or N/A
[ ] Notable Changes: updated release.txt, prefixed a commit message with "fix:" or "feat:", added to an internal tracking document, or N/A

congyu-lu commented 2 weeks ago

…C set

Description

Congyu please test with local GFF against new api currently in qa; you need to connect gdc vpn please find out time taken, and assess gene sets returned for all cases, gliomas, HGG, if they makes sense

Checklist

Check each task that has been performed or verified to be not applicable.

[ ] Tests: added and/or passed unit and integration tests, or N/A

[ ] Todos: commented or documented, or N/A

[ ] Notable Changes: updated release.txt, prefixed a commit message with "fix:" or "feat:", added to an internal tracking document, or N/A

Tested with local GFF using qa-orange VPN

all cases: took about 70 seconds to Loading genes that are top variably expressed in current cohort... (until showing "Processing data...")
After adding glioma filter:

congyu-lu commented 2 weeks ago

…C set

Description

Congyu please test with local GFF against new api currently in qa; you need to connect gdc vpn please find out time taken, and assess gene sets returned for all cases, gliomas, HGG, if they makes sense

Checklist

Check each task that has been performed or verified to be not applicable.

[ ] Tests: added and/or passed unit and integration tests, or N/A

[ ] Todos: commented or documented, or N/A

[ ] Notable Changes: updated release.txt, prefixed a commit message with "fix:" or "feat:", added to an internal tracking document, or N/A

Tested with local GFF using qa-orange VPN

all cases: took about 70 seconds to Loading genes that are top variably expressed in current cohort... (until showing "Processing data...")

After adding glioma filter:

Need to update the legend label here, it still shows CGC genes only

xzhou82 commented 2 weeks ago

70s is not okay.. how much time is it for gliomas? and this doesn't seem right. Phil has indicated the new api should be much faster than this. please doublecheck if it is querying against the qa environment. also i don't think you have to test it with local GFF. just pp at http://localhost:3000/ should be good

congyu-lu commented 2 weeks ago

70s is not okay.. how much time is it for gliomas? and this doesn't seem right. Phil has indicated the new api should be much faster than this. please doublecheck if it is querying against the qa environment. also i don't think you have to test it with local GFF. just pp at http://localhost:3000/ should be good

Tested with qa-orange VPN, for both local GFF and http://localhost:3000: from "Loading genes that are top variably expressed in current cohort" to "Processing data...": All cases took about 70s, glioma took about 60s.

Also in here this note needs to be updated: Genes are selected from 738 Cancer Gene Census genes.

xzhou82 commented 2 weeks ago

thanks will remember to fix those once the api performance issue is resolved

xzhou82 commented 2 weeks ago

close this PR since api is not fast and cannot be the default; still use cgc as default but will allow user to deselect it