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knowledgesystems / cmo-pipelines

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Allow Seed Database Scripts To Run From cBioPortal Core #1171

Open jamesqo opened 5 months ago

jamesqo commented 5 months ago

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 commented 5 months ago

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