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F gaps in int columns

Merged Florian Spreckelsen requested to merge f-gaps-in-int-columns into dev
All threads resolved!

Summary

For #126 (closed). Adds support for empty values in integer columns and Pandas-specific datatypes. This is needed for https://gitlab.indiscale.com/caosdb/customers/geomar/management/-/issues/269.

Focus

The most important part is to use the dtype argument in Pandas' read_csv function. We also replace the np.issubdtype and isinstance functions in the datatype checks by helper functions that support the relevant Pandas datatypes.

Test Environment

For the actual bug, the new unit test should be sufficient. Also use this branch in the Geomar server-profile and the bis-custom submodule in branch f-nan-in-int and test a sample upload with empty fields in, e.g., the integer-valued AphiaID.

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Edited by Daniel Hornung

Merge request reports

Pipeline #52563 passed

Pipeline passed for 7787203e on f-gaps-in-int-columns

Merged by Daniel HornungDaniel Hornung 11 months ago (Jun 28, 2024 10:12am UTC)

Merge details

  • Changes merged into dev with 0a6e5c5d.
  • Deleted the source branch.
  • Auto-merge enabled

Pipeline #52852 passed

Pipeline passed for 0a6e5c5d on dev

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  • Florian Spreckelsen
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  • added 1 commit

    • 6e41fd1d - MAINT: Remove debugging output

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  • Florian Spreckelsen marked the checklist item Reference related issues as completed

    marked the checklist item Reference related issues as completed

  • Florian Spreckelsen marked the checklist item Up-to-date CHANGELOG.md (or not necessary) as completed

    marked the checklist item Up-to-date CHANGELOG.md (or not necessary) as completed

  • Florian Spreckelsen marked the checklist item Up-to-date JSON schema (or not necessary) as completed

    marked the checklist item Up-to-date JSON schema (or not necessary) as completed

  • Florian Spreckelsen marked the checklist item Appropriate user and developer documentation (or not necessary) as completed

    marked the checklist item Appropriate user and developer documentation (or not necessary) as completed

  • Florian Spreckelsen marked the checklist item Annotations in code (Gitlab comments) as completed

    marked the checklist item Annotations in code (Gitlab comments) as completed

  • Florian Spreckelsen marked the checklist item All automated tests pass as completed

    marked the checklist item All automated tests pass as completed

  • Florian Spreckelsen changed the description

    changed the description

  • added 1 commit

    • 7787203e - DOC: Some rewording and typos.

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  • Daniel Hornung resolved all threads

    resolved all threads

  • Daniel Hornung marked the checklist item I understand the intent of this MR as completed

    marked the checklist item I understand the intent of this MR as completed

  • Daniel Hornung marked the checklist item Up-to-date CHANGELOG.md (or not necessary) as completed

    marked the checklist item Up-to-date CHANGELOG.md (or not necessary) as completed

  • Daniel Hornung marked the checklist item Appropriate user and developer documentation (or not necessary) as completed

    marked the checklist item Appropriate user and developer documentation (or not necessary) as completed

  • Daniel Hornung marked the checklist item The test environment setup works and the intended behavior is reproducible in the test as completed

    marked the checklist item The test environment setup works and the intended behavior is reproducible in the test as completed

  • Daniel Hornung marked the checklist item In-code documentation and comments are up-to-date. as completed

    marked the checklist item In-code documentation and comments are up-to-date. as completed

  • Daniel Hornung enabled an automatic merge when the pipeline for 7787203e succeeds

    enabled an automatic merge when the pipeline for 7787203e succeeds

  • Daniel Hornung canceled the automatic merge

    canceled the automatic merge

  • Daniel Hornung enabled an automatic merge when the pipeline for 7787203e succeeds

    enabled an automatic merge when the pipeline for 7787203e succeeds

  • mentioned in commit 0a6e5c5d

  • Daniel Hornung marked the checklist item All automated tests pass as completed

    marked the checklist item All automated tests pass as completed

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