RFC84: Data Entries Removal #46
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forus
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JREastonMarks,
pieterlukasse and
haynescd
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JREastonMarks
src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfileSamples.java
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pieterlukasse
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Jun 28, 2024
src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticAlteration.java
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src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCnaDiscreteLongData.java
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This was referenced Jun 28, 2024
Add command to remove sample to python wrapper Implment sample removal command Remove sample from the tab delimited tables as well Do samples removal in a transaction Move removing sample everywhere in study to respective DAOs To be able to reuse this functionality Refactor sample removal test by using stream of Test and fix edge cases of sample removal command Add command to remove patient to python wrapper Add java command to remove patient in a study Increase test independence Adding or removing profile/sample should break only one test Fix patient id to sample ids mapping bug Throw exception when sample with GSVA is removed Throw exception when generic profile samples list is empty Refactor patient and sample removal code Remove unused logger and imports Remove unused code from cna discrete long data tests
pieterlukasse
approved these changes
Jul 17, 2024
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In the current implementation of cBioPortal, the functionality for data management is limited to the deletion of entire studies, as documented here. This approach lacks granularity and does not provide users with the ability to selectively remove individual entries associated with a study, such as patients, samples, or specific molecular data profiles. This limitation restricts the flexibility needed for detailed data management and maintenance, leading to potential inefficiencies and challenges in study data handling.
To address this limitation, this PR extends the capabilities of the
cbioportalImporter.pyscript and includes additional commands to the java tool that allow for the selective removal of patient or sample.See more details in the RFC84 Data Entries Removal document.
Reminder: Do not forget to enable the following PR cBioPortal/cbioportal#10820