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bokulich-lab / q2-fondue

Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere
BSD 3-Clause "New" or "Revised" License
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ENH: Full support sample and experiment IDs #122

Closed adamovanja closed 2 years ago

adamovanja commented 2 years ago

This PR closes #117 by introducing support for fetching metadata and sequences also when given a set of experiment or sample IDs. Furthermore, it fixes that sequences are also correctly fetched from study IDs.

Testing

  1. Scrape a collection of your choice with scrape-collection
  2. Fetch metadata and sequences for all non-empty output artifacts with get-all, get-metadata and/or get-sequences.

To try out scraping a collection that also contains the newly supported sample and experiment IDs, you can add these two publications to your collection:

codecov-commenter commented 2 years ago

Codecov Report

Merging #122 (d5de5d4) into main (cb924d4) will increase coverage by 0.25%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #122      +/-   ##
==========================================
+ Coverage   95.28%   95.53%   +0.25%     
==========================================
  Files          15       15              
  Lines        1123     1121       -2     
  Branches      206      204       -2     
==========================================
+ Hits         1070     1071       +1     
+ Misses         28       27       -1     
+ Partials       25       23       -2
Impacted Files Coverage Δ
q2_fondue/plugin_setup.py 100.00% <ø> (ø)
q2_fondue/entrezpy_clients/_pipelines.py 100.00% <100.00%> (+4.54%) :arrow_up:
q2_fondue/metadata.py 100.00% <100.00%> (+2.85%) :arrow_up:
q2_fondue/scraper.py 99.20% <100.00%> (ø)
q2_fondue/sequences.py 96.19% <100.00%> (ø)
q2_fondue/utils.py 91.66% <100.00%> (ø)

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adamovanja commented 2 years ago

thank you for your review and the suggestions @lina-kim 🚀