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Allow Seed Database Scripts To Run From cBioPortal Core #1171

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jamesqo opened this issue Mar 25, 2024 · 1 comment
Open

Allow Seed Database Scripts To Run From cBioPortal Core #1171

jamesqo opened this issue Mar 25, 2024 · 1 comment

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@jamesqo
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jamesqo commented Mar 25, 2024

Some scripts used to import data from the seed DB have been moved to cbioportal-core but still reference properties files in the main cbioportal repo. Enable them to be run via building the cbioportal-core repo only and update the public documentation.

@jamesqo
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jamesqo commented Mar 25, 2024

For example, the script used to import microRNA data is here: https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/scripts/ImportGeneData.java but it references a database properties files that is still in cbioportal: https://github.com/cBioPortal/cbioportal/blob/master/src/main/resources/application.properties.EXAMPLE#L8-L11

The DB migration script has also been moved to the core repo: https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/resources/scripts/migrate_db.py

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