cBioPortal / cbioportal-core

Externalized cBioPortal Core
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(1/7) RFC 79: Implement incremental upload of tab delimited data. #45

Closed forus closed 5 months ago

forus commented 5 months ago

This loader covers the following data types:

Note: We do not support incremental upload of GSVA data although tab-delimited uploader covers this type with non-interactive upload. The incremental upload for GSVA data will throw an error. We decided to exclude GSVA as there is unclarity from our part on whether GSVA scores of existing samples need to be recalculated when a new sample is added to the data.

This PR makes the tab. delimited data loader run in a single transaction to escape corruption of tsv rows (e.g. sample has been added to the header, but not to the info rows).

The first commit (https://github.com/cBioPortal/cbioportal-core/pull/38/commits/b2c1c21665496f77fe91addb6521e8eb674438e2) contains the code improvements. It could be handy to review it first.

======= Please review https://github.com/cBioPortal/cbioportal-core/pull/44 next.

Please note, to avoid the costly process of rebasing all pull requests (PRs), all feedback will be incorporated into the final PR.