RFC79: Incremental Upload of Data Entries #48
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To make the dataset look like real data in the database
Apperently, the flag does not change anything. But we add it anyway as the tests for "incremental" data upload.
adding to the all case list and case list specified with command arguments is supported
From case lists that is not _all case list and not specified with --add-to-case-lists option
with a reference to the ticket
We changed them to work for the demo. Mutation numbers did not change on demo.
Not it was easy to be confused where sample and clinical_sample (attributes), patient and clinical_patient (attributes) related code
This flag for command to upload molecular profile data
pieterlukasse
previously approved these changes
Jun 27, 2024
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I will try to review this. One quick comment - when it comes time to merge this PR I hope we use "squash and merge" rather than merging in the individual changesets. |
Make it explicity that function will delete any matching records "if they exist"
…tribute Specify that sampleIds is optional and can be set to null
increase incapsulation
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sheridancbio
approved these changes
Jul 16, 2024
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This looks good. Legacy functionality is supported and new functionality is enabled through command line arguments. Changes are described in the approved RFC-79 document and code follows that closely.
The remainder of the java code (after my part 4 partial review) was reviewed by @forus and I interactively yesterday. My review did not cover the test case data, but testing approaches (including python script "called" java methods) was discussed as well.
The MSK importer has not yet been tested with these changes, but I believe that any problems which are observed can be addressed in the MSK codebase itself (which mainly wraps/depends on the DAO classes here)
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See also RFC79
The solution involves extending the current
metaImport.pyscript and java data loader commands with additional flags to support the incremental upload of entries. This approach allows users to add patients, samples, and molecular data without having to reupload the entire study.Read more in docs cBioPortal/cbioportal#10816
To review in logical parts and see previous discussions about the implementation, you might want to check the chain of closed PRs this PR consists of: