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Fixed validation issue with different geneset_def_version #6817

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merged 2 commits into from Nov 18, 2019

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dianab0
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@dianab0 dianab0 commented Nov 14, 2019

The current validation process of cBioPortal does not throw an error when the property geneset_def_version is different in the study from the one in the database. This leads to an error throwing when cBioPortal tries to load the study.
Fixed it by first adding the geneset version from database to the API and also to PortalInfo, then retrieving it in the validateData.py script and comparing it to geneset_def_version in the study.

Fix # (see https://help.github.com/en/articles/closing-issues-using-keywords)

Describe changes proposed in this pull request:

  • Updated the API to include the geneset version at /api/genesets/version
  • Updated the DumpPortalInfo script to get the geneset from API
  • Updated the validateData.py to get the geneset version from either portal info or API, compare it to the geneset_def_version in the study and return error if different.

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  • Runs on heroku
  • Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
  • The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.
  • Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!

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The current validation process of cBioPortal studies does not throw an
error when the property geneset_def_version is different in the study
from the one in the database. This leads to an error throwing when
cBioPortal tries to load the study.
Fixed it by first adding the geneset version from database to the API
and also to PortalInfo, then retrieving it in the validateData.py script
and comparing it to geneset_def_version in the study.
@jjgao jjgao temporarily deployed to cbioportal-geneset-vers-uq2ige November 14, 2019 15:45 Inactive
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@oplantalech oplantalech left a comment

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Thank you, @dianab0! Good work!

Updated the test folder so the python test scripts will run with the new
changes.
@jjgao jjgao temporarily deployed to cbioportal-geneset-vers-uq2ige November 18, 2019 11:29 Inactive
@dianab0
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dianab0 commented Nov 18, 2019

Pushed a second commit to include the necessary changes to the test_data folder so the test scripts will work.

@n1zea144 n1zea144 merged commit c0b8d89 into cBioPortal:master Nov 18, 2019
@inodb inodb added the bug label Nov 22, 2019
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5 participants