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Map TCGA old UUID with new UUID to fix data module #346

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Merged
ernestoarbitrio merged 9 commits into from
Nov 10, 2021
Merged

Map TCGA old UUID with new UUID to fix data module #346

ernestoarbitrio merged 9 commits into from
Nov 10, 2021

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@alessiamarcolini alessiamarcolini commented Nov 9, 2021 •
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Description

Finally, the TCGA portal allows for downloading the slides, but with the new release they changed all the UUIDs of the files.

This PR also saves the files in the cache with its original TCGA name instead of the UUID, so it can be easier to recover from if there are other changes from the TCGA side in the future.

Types of Changes

  • Core
  • Bugfix
  • New feature
  • Enhancement/optimization
  • Documentation

Issues Fixed or Closed by This PR

Checklist

  • My code follows the code style of this project.
  • My change requires a change to the documentation.
  • I have updated the documentation accordingly.
  • I have read the CONTRIBUTING document.
  • I have added tests to cover my changes.
  • I have tested the changes and verified that they work and don't break anything (as well as I can manage).

@alessiamarcolini alessiamarcolini requested review from ernestoarbitrio and nicolebussola and removed request for ernestoarbitrio November 9, 2021 12:19
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alessiamarcolini commented Nov 9, 2021

Good news is that for the TCGA example in examples/TCGA, the file with metadata clinical_csv_example.csv did not include UUIDs of files but only the case_id, which remained the same between the two releases, so there is no need to update it

@alessiamarcolini alessiamarcolini marked this pull request as ready for review November 9, 2021 12:30
@alessiamarcolini alessiamarcolini added this to the 0.3.1 milestone Nov 9, 2021
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codecov bot commented Nov 9, 2021 •
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Codecov Report

Merging #346 (9fe8b04) into master (94ec6cb) will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff            @@
##            master      #346   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           17        17           
  Lines         1324      1324           
  Branches       128       128           
=========================================
  Hits          1324      1324
Impacted Files Coverage Δ
histolab/data/__init__.py 100.00% <ø> (ø)
histolab/data/_registry.py 100.00% <ø> (ø)

Continue to review full report at Codecov.

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ernestoarbitrio
ernestoarbitrio approved these changes Nov 9, 2021
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❤️

nicolebussola
nicolebussola approved these changes Nov 9, 2021
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LGTM

@ernestoarbitrio ernestoarbitrio merged commit 21e626d into master Nov 10, 2021
@ernestoarbitrio ernestoarbitrio deleted the tcga-data branch November 10, 2021 10:18
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@ernestoarbitrio ernestoarbitrio ernestoarbitrio approved these changes

@nicolebussola nicolebussola nicolebussola approved these changes

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Getting issue with TCGA

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