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RFC79: Incremental Upload of Data Entries #48

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RFC79: Incremental Upload of Data Entries #48

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Commits on Apr 14, 2024

  1. Add clinical_attribute_meta records to the seed mini 

    To make the dataset look like real data in the database
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  2. Implement sample attribute rewriting flag

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  3. Add --overwrite-existing for the rest of test cases 

    Apperently, the flag does not change anything.
But we add it anyway as the tests for "incremental" data upload.
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  4. Test that mutations stay after updating the sample attributes

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  5. Add overwrite-existing support for mutations data

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  6. Fix --overwirte-existing flag description for importer of profile data

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  7. Add loader command to update case list with sample ids 

    adding to the all case list and case list specified with command arguments is supported
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  8. Add option to remove sample ids from the remaining case lists 

    From case lists that is not _all case list and not specified with --add-to-case-lists option
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  9. Make removing sample ids from not mentioned case lists a default beha… 

    …viour
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  10. Make update case list command to read case lists files

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  11. Fix test clinical data headers

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  12. Test incremental patient upload

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  13. Add flag to reload patient clinical attributes

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  14. Add TODO comment to remove MIXED_ATTRIBUTES data type 

    with a reference to the ticket
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  15. WIP adopt py script to incremental upload

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  16. Fix java.sql.SQLException: Generated keys not requested

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  17. Clean alteration_driver_annotation during mutations inc. upload

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  18. Fix validator and importer py scripts for inc. upload

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  19. Add test/demo data for incremental loading of study_es_0 study

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  20. Rename and move incremental tests to incementalTest folder

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  21. Update TODO comment how to deal with multiple sample files

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  22. Move study_es_0_inc to the new test data folder

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  23. Fix removing patient attributes on samples inc. upload

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  24. Change study_es_0_inc to contain more diverse data 

    We changed them to work for the demo.
Mutation numbers did not change on demo.
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  25. Specify that data_directory for incremental data

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  26. Disambiguate clinical data constants names 

    Not it was easy to be confused where sample and clinical_sample (attributes),
patient and clinical_patient (attributes) related code
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  27. Remove not necessary TODO comments

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  28. Remove MSK copyright mistakenly copy-pasted

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  29. Fix comment of UpdateCaseListsSampleIds.run() method

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  30. Make --overwrite-existing flag description more generic 

    This flag for command to upload molecular profile data
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  31. Add TODO comments for possible reuse of the code

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  32. Update case lists for multiple clinical sample files 

    Potentially for different studies
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  33. Extract and reuse common logic to read and validate case lists

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Commits on Apr 30, 2024

  1. Fix TestIntegrationTest 

    - 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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  2. Revert RESOURCE_DEFINITION_DICTIONARY initialsation to empty set

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  3. Minor improvments. Apply PRs feedback

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Commits on May 1, 2024

  1. Make tests fail the build. Conduct exit status of tests correctly

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  2. Write Validation complete only in case of successful validation

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  3. Add python tests for incremental/full data import

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  4. Add unit test for incremental data validation

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Commits on May 3, 2024

  1. Test rough order of importer commands. Remove sorting in the script t… 

    …o guarantee that
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  2. Extract smaller functions from the big one in py script 

    Make process_data_directory(...) smaller
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Commits on May 15, 2024

  1. Merge pull request #32 from se4bio/inc-data-upload-poc 

    Incremental data upload for mutations, case lists, patient and sample attributes
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  2. Refactor tab delim. data importer 

    - Calculate number of lines in the file in the loader
- Remove unused imports and fields
- Reuse constructors
- Reuse common parsing logic in tab delimiter importer
- Show full stacktrace which helps in dinding where tests errored out
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  3. Implement incremental upload of mRNA data

    @forus
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  4. Add RPPA test

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  5. Add normal sample to thest data to test skipping

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  6. Add rows with more columns then in header to skip

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  7. Skip rows that don't have enough sample columns

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  8. Test for invalid entrez id

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  9. Extract common code from inc. tab. delim. tests

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  10. Implement incremntal upload of cna data via tab. delim. loader

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  11. Blanken values for genes not mentioned in the file

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  12. Remove unused code

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  13. Throw unsupported operation exception for GENESET_SCORE incremental u… 

    …pload
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  14. Add generic assay data incremental upload test

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  15. Fix integration tests

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  16. Make tab. delimiter data uploader transactional

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  17. Check for illegal state in tab delim. data update 

    It's dangerous as we would further mess up the data in the row
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  18. Wire incremental tab delim. data upload to cli commands

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  19. Expand README with section on how to run incremental upload

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  20. Address TODOs in tab delim. importer

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  21. Add more data types to incremental data upload folder

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  22. Remove obsolete TODO comment

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Commits on May 16, 2024

  1. Reuse genetic_profile record if it exists in db already 

    Do it for all data types, not only MAF
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  2. Test incremental upload of tab delim. data types from umbrella script 

    - Split big tab. delim test to multiple tests based on data type.

- Use ImportProfileData instead of ImportTabDelimData for testing.
  - We cover more logic with such tests.
  - This is more stable interface. ImportTabDelimData can be refactored.
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  3. Move counting lines if file inside generic assay patient level data u… 

    …ploader
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Commits on May 17, 2024

  1. Give error that generic asssay patient level data is not supported

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  2. Clean sample_cna_event despite whether it has alteration_driver_annot… 

    …ation rows or not
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Commits on May 28, 2024

  1. Fix cbioportalImport script execution 

    args variable was not declared
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  2. Remove not needed spring context initialisation 

    that caused different errors to occur
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  3. Make error message more informative when gene panel is not found 

    Do not throw NPE, but NSEE with error message that mentions panel id
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  4. Add more genes to the mini seed to load study_es_0

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  5. Make study_es_0_inc data pass validation

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  6. Document in README how to load study_es_0 study

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  7. Implement incremental upload for timeline data

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  8. Implement incremental upload of CNA DISCRETE long data

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  9. Add data type sanity check for tsv uploded

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  10. Move storing/dedup logic of genetic alteration values to importer

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  11. Move all inc. upload logic for tab delim. data types to GeneticAltera… 

    …tionImporter
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  12. Add CNA DISCRETE LONG to study_es0_inc test dataset

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  13. Remove unused code

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  14. Make validation to pass for CNA long and study_es_0_inc data

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  15. Implement incremental upload for gene panel matrix 

    The uploader was working in incremental manner already.
I had to add tests for those only.
I had to implement incremental upload for gene panel matrix
from differend data (CNA, Mutations) uploaders though.
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  16. Make validation of study_es_0_inc data to pass

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  17. Implement incremental upload of structural variants data 

    I removed DaoGeneticProfileSamples.addGeneticProfileSamples(geneticProfileId, orderedSampleList);
as it does not seem to be needed.
it does not make any sense to store samples in genetic_profile_samples, if you don't use genetic_alteration table at all.
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  18. Implement incremental upload of CNA segmented data

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Commits on Jun 4, 2024

  1. Make it explicit that timeline uploader support bulk mode only

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  2. Fix number of columns in SV tsv data file

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Commits on Jun 11, 2024

  1. Update paragraph on inc. upload in README

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  2. Rename validation method to better describe it's purpose 

    To really validate entrez id, we need to look it up
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  3. Fix cleaning alteration_driver_annotation table for specific sample

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  4. DRY tab separated value string parsing

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  5. Reuse FileUtil.isInfoLine(String line) throughout the code

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  6. Extract ensuring header and row match to tsv utility class

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  7. Simplify delete sql. Rely on cascade delete instead.

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  8. Generalise overwrite-existing flag description to make it more accurate

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  9. Rename updateMode to isIncrementalUpdateMode flag

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  10. Improve description of overwrite-existing flag for gene panel profile… 

    … map
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  11. Implement more optimal way to update sample profile

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  12. Optimize code by always using batch upsert for sample profile

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  13. Recognise that SEG importer always use bulkLoad

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  14. Organise bulk mode flushing for SEG importer

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  15. Ignore case for bulkLoad load mode option as everywhere in the code

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Commits on Jun 13, 2024

  1. add comma to README

    @pieterlukasse
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  2. improve order comments for INCREMENTAL_UPLOAD_SUPPORTED_META_TYPES

    @pieterlukasse
    pieterlukasse committed Jun 13, 2024
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  3. Add join by GENETIC_PROFILE_ID column for sample_cna_event and altera… 

    …tion_driver_annotaiton tables
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    forus committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. Check for inconsistency in sample ids and values while reading geneti… 

    …c alterations
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  2. Make method name to initialise transaction clearer

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    forus committed Jun 14, 2024
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  3. Remove TODOs that were done

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    forus committed Jun 14, 2024
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  4. Rename isInfoLine util. method to isDataLine 

    I got feedback that "info line" sounds like the header metadata lines starting with #
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    forus committed Jun 14, 2024
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  5. Simplify code by using inheritence instead of composition

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Commits on Jun 19, 2024

  1. Optimize removing genetic alterations 

    by removing them for the whole genetic profile at once.

one sql statment instead of N
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    forus committed Jun 19, 2024
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  2. Access inherited variables with this. intead of super. 

    the confusion that triggered the change: The use of super. indicates that the subclass also declares one with the same name, but you are trying to not set that somehow?
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    forus committed Jun 19, 2024
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  3. Merge pull request #45 from cBioPortal/inc-tab-delimited-uploader 

    (1/7) RFC 79: Implement incremental upload of tab delimited data.
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    forus committed Jun 19, 2024
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  4. Merge pull request #44 from cBioPortal/make_study_es_0_to_load 

    (2/7) RFC79: Make study_es_0_inc data pass validation
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  5. Merge pull request #43 from cBioPortal/inc-timeline-uploader 

    (3/7) RFC79: Implement incremental upload for timeline data
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    forus committed Jun 19, 2024
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  6. Merge pull request #42 from cBioPortal/inc-cna-discrete-long 

    (4/7) RFC79: Implement incremental upload of CNA DISCRETE long data
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    forus committed Jun 19, 2024
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  7. Merge pull request #41 from cBioPortal/inc-gene-panel-matrix 

    (5/7) RFC79: Implement incremental upload for gene panel matrix
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  8. Merge pull request #40 from cBioPortal/inc-sv 

    (6/7) RFC79: Implement incremental upload of structural variants data
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  9. Merge pull request #39 from cBioPortal/inc-seg 

    (7/7) RFC79: Implement incremental upload of CNA segmented data
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    forus committed Jun 19, 2024
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  10. Merge pull request #47 from cBioPortal/rfc79-feedback 

    RFC79: Implement feedback from previous 7 PRs
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    forus committed Jun 19, 2024
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Commits on Jun 21, 2024

  1. Remove unused code from DaoSampleList.addSampleList()

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    forus committed Jun 21, 2024
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  2. Remove extra semicolons at the end of java statements

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    forus committed Jun 21, 2024
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  3. Rename upsertSampleProfiles to upsertSampleToProfileMapping 

    method in DaoSampleProfile
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    forus committed Jun 21, 2024
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  4. Use java 8 way to convert typed list to array in GeneticAlterationInc… 

    …rementalImporter
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    forus committed Jun 21, 2024
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  5. Improve doc comments for TsvUtil.isDataLine(String line)

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    forus committed Jun 21, 2024
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Commits on Jun 27, 2024

  1. Rename and codument better method to updateCaseLists

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    forus committed Jun 27, 2024
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