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cBioPortal / datahub

A centralized location for storing curated data from cBioPortal
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Circle CI bug: database creating/dropping issue between commits #1617

Open yichaoS opened 2 years ago

yichaoS commented 2 years ago

Validation error in PR https://github.com/cBioPortal/datahub/pull/1613

In Circle CI test server local database, the row with value null in info table, possibly from one of earlier seedDB.sql.gz commits, didn't get dropped after a later commit with a new seedDB.sql.gz. Thus there are two rows in Circle CI DB info table, which causes a validation error.

In seedDB.sql.gz

Screen Shot 2022-02-28 at 4 29 23 PM

In Circle CI DB image

Validation error

Screen Shot 2022-03-01 at 3 23 05 PM
yichaoS commented 2 years ago

The temporary solution we have for now, for seedDB release is:

Manually change the just created seedDB dumped sql file to fix gene set version validation error.o remove duplicate records in info table when importing cgds.sql and then seedDB.sql Change line INSERT INTO info VALUES ('2.XX.XX','msigdb_XXXX'); into UPDATE info SET GENESET_VERSION="msigdb_XXX";