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: create minified msigdb and associate to hg38-test for CI #1734

Closed xzhou82 closed 2 weeks ago

xzhou82 commented 2 weeks ago

Description

i have the new db file locally at tp/anno/msigdb/termdbtest/db and it works at termdbtest matrix

test at http://localhost:3000/?termdb={%22vocab%22:{%22dslabel%22:%22msigdb%22,%22genome%22:%22hg38-test%22}}

and matrix

Checklist

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

siosonel commented 2 weeks ago

@xzhou82 "i don't know how to auto copy it from repo to local so CI can work" EDIT 2: this should already be handled correctly when using server/test/serverconfig.json, I'm testing locally EDIT: may need to handle this as a separate symlink. I think it should be okay to save the test msigdb file under test/tp/files/hg38/TermdbTest, and point to that location. The symlink is already automatically created when server/dataset/termdb.test.js is loaded, by copyDataFilesFromRepo2Tp() in that js file

termdbs: {
        msigdb: {
            label: 'MSigDB',
            cohort: {
                db: { file: 'tp/files/hg38-test/TermdbTest/msigdb' },
                termdb: {
                    isGeneSetTermdb: true
                }
            }
        }
    },
xzhou82 commented 2 weeks ago

i moved it to test/tp/files/hg38/TermdbTest/msigdb/db and it works. please test