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reimplement /data_objects/study/{study_id} using alldocs #608

Merged
merged 44 commits into from
Aug 21, 2024
Merged

reimplement /data_objects/study/{study_id} using alldocs #608

merged 44 commits into from
Aug 21, 2024

Commits on Jul 23, 2024

  1. reimplement /data_objects/study/{study_id} using alldocs

    @sujaypatil96
    sujaypatil96 committed Jul 23, 2024
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Commits on Aug 2, 2024

  1. make output of /data_objects/study/{study_id} endpoint look more JSON… 

    …-like
    @sujaypatil96
    sujaypatil96 committed Aug 2, 2024
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  2. return full DataObjects instead of just DataObject ids

    @sujaypatil96
    sujaypatil96 committed Aug 2, 2024
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Commits on Aug 8, 2024

  1. get DataObjects for /data_objects/study/{study_id} from data_object_set

    @sujaypatil96
    sujaypatil96 committed Aug 8, 2024
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  2. feat: refactor notebook and supporting code

    @dwinston
    dwinston committed Aug 8, 2024
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  3. fix: Ensure extra_kwargs is optional

    @dwinston
    dwinston committed Aug 8, 2024
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  4. fix: no trying **extra_kwargs until needed

    @dwinston
    dwinston committed Aug 8, 2024
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  5. feat: speed up nb 

    relevant tot #576
    @dwinston
    dwinston committed Aug 8, 2024
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  6. populate library attributes in SRA <Action> blocks

    @sujaypatil96 @dwinston
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  7. pull in library_name into NCBI XML

    @sujaypatil96 @dwinston
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  8. fix tests/test_data/test_ncbi_xml.py test file

    @sujaypatil96 @dwinston
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  9. use only file basename to populate file_path attribute in SRA <Action… 

    …> blocks
    @sujaypatil96 @dwinston
    sujaypatil96 authored and dwinston committed Aug 8, 2024
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  10. Upgrade to nmdc-schema 10.7.0

    @pkalita-lbl @dwinston
    pkalita-lbl authored and dwinston committed Aug 8, 2024
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  11. doc: clarify that user must be site admin to POST /sites/{site_id}:ge… 

    …nerateCredentials

fix #606
    @dwinston
    dwinston committed Aug 8, 2024
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  12. style: reformat

    @dwinston
    github-actions authored and dwinston committed Aug 8, 2024
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  13. Update nmdc_runtime/api/endpoints/sites.py 

    Co-authored-by: eecavanna <[email protected]>
    @dwinston @eecavanna
    dwinston and eecavanna committed Aug 8, 2024
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  14. Update nmdc_runtime/api/endpoints/sites.py 

    Co-authored-by: eecavanna <[email protected]>
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  15. chore: clean up a bit

    @dwinston
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  16. fix: changesheet can update bytes-ranged slot 

    close #613
    @dwinston
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  17. fix: ensure doc for changesheet

    @dwinston
    dwinston committed Aug 8, 2024
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  18. add broker name as custom NCBI <Attribute>

    @sujaypatil96 @dwinston
    sujaypatil96 authored and dwinston committed Aug 8, 2024
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  19. expand abbreviated NMDC

    @sujaypatil96 @dwinston
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  20. pull in value for SRA Attribute library_construction_protocol

    @sujaypatil96 @dwinston
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  21. update tests in test_ncbi_xml.py to check library_construction_protoc… 

    …ol information
    @sujaypatil96 @dwinston
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  22. fix: part1 for builtins

    @dwinston
    dwinston committed Aug 8, 2024
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  23. add test file

    @dwinston
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  24. fix: ensure regression test, and expand code documentation 

    fixes #616
    @dwinston
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  25. fix: typo

    @dwinston
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  26. infer SRA <DataType> from DataObject URL/file path

    @sujaypatil96 @dwinston
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  27. change <DataType> from fastq to sra-fun-fastq

    @sujaypatil96 @dwinston
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  28. not all schema collections suffix with _sets (#620) 

    * fix: allow "update" of non-`id`-having document collections

interpret as simple insertion. leave note in code about decision to insist on schema-supplied uniqueness signal.

fix #611

* refactor to add test

* fix: rm abandoned candidate test

* Update nmdc_runtime/site/ops.py

Co-authored-by: eecavanna <[email protected]>

---------

Co-authored-by: eecavanna <[email protected]>
    @dwinston @eecavanna
    dwinston and eecavanna committed Aug 8, 2024
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  29. feat: test dependent on alldocs materialization 

    towards #608
    @dwinston
    dwinston committed Aug 8, 2024
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  30. Merge branch 'main' into issue-401-reimplement-data-objects-study-id-… 

    …endpoint
    @dwinston
    dwinston authored Aug 8, 2024
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  31. style: reformat

    github-actions committed Aug 8, 2024
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  32. fix: ensure extract_to dir

    @dwinston
    dwinston committed Aug 8, 2024
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Commits on Aug 15, 2024

  1. docstring for get_classname_from_typecode() in `nmdc_runtime/api/en… 

    …dpoints/find.py`

Co-authored-by: eecavanna <[email protected]>
    @sujaypatil96 @eecavanna
    sujaypatil96 and eecavanna authored Aug 15, 2024
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  2. docstring for mongorestore_collection() in `nmdc_runtime/api/db/mon… 

    …go.py`

Co-authored-by: eecavanna <[email protected]>
    @sujaypatil96 @eecavanna
    sujaypatil96 and eecavanna authored Aug 15, 2024
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  3. style: reformat

    github-actions committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. make output of /data_objects/study/{study_id} look more JSON-like

    @sujaypatil96
    sujaypatil96 committed Aug 16, 2024
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Commits on Aug 21, 2024

  1. Merge branch 'main' into issue-401-reimplement-data-objects-study-id-… 

    …endpoint
    @dwinston
    dwinston committed Aug 21, 2024
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  2. doc: add docstring

    @dwinston
    dwinston committed Aug 21, 2024
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  3. fix: reassert type

    @dwinston
    dwinston committed Aug 21, 2024
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  4. chore: remove unused imports

    @dwinston
    dwinston committed Aug 21, 2024
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  5. style: rename

    @dwinston
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