Incremental data upload for mutations, case lists, patient and sample attributes #32
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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
haynescd
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Apr 22, 2024
src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java
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src/main/java/org/mskcc/cbio/portal/scripts/UpdateCaseListsSampleIds.java
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- change location of the files - make sure assertions could work on the seed mini db - get rid from absent cbioportal dependencies
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Make process_data_directory(...) smaller
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Incremental data upload for mutations, case lists, patient and sample attributes
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What is done in this PR:
Enhancements to the DAO Layer: Introduced new methods in the Data Access Object (DAO) layer to enable:
Reversion of Method Deprecations: Reinstated previously deprecated methods for retrieving mutations.
Data Import Extension:
--overwrite-existingflag for theImportClinicalDataandImportProfileDatascripts, allowing for the re-upload of entries if they already exist in the database.Python scripts Extension
Testing Enhancements: Added integration tests to verify the incremental upload functionality for sample and mutation data.
Demo (you can download high-quality video here):
study_es_0_incfolder data description (the green = new entries; the yellow = updated entries; the light blue = existing in db):