ENH: Fetch restricted access sequences with a repository key

[adamovanja]

closes #155

Testing

Using the freely available test key prj_phs710EA_test.ngc try and fetch the accession ID SRR1219902: 1) Download the key from here. 2) Import the above run ID as a NCBIAccessionIDs artifact. 3) Follow the instructions in the README here.

Beware, the download might take rather long (in my case it was ~1-2 hrs) as the freely available key matches a sequencing file of 13.8 GB.

Note: The GitHub action is failing due to a temporarily expired certificate for packages.qiime2.org.

[codecov[bot]]

Codecov Report

Merging #156 (809f679) into main (d5167a9) will increase coverage by 0.02%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #156      +/-   ##
==========================================
+ Coverage   98.62%   98.64%   +0.02%     
==========================================
  Files          29       29              
  Lines        2980     3035      +55     
==========================================
+ Hits         2939     2994      +55     
  Misses         41       41              

Impacted Files	Coverage Δ
q2_fondue/plugin_setup.py	100.00% <ø> (ø)
q2_fondue/tests/test_get_all.py	98.68% <ø> (ø)
q2_fondue/sequences.py	98.55% <100.00%> (+0.07%)	:arrow_up:
q2_fondue/tests/test_sequences.py	98.32% <100.00%> (+0.17%)	:arrow_up:

:mega: We’re building smart automated test selection to slash your CI/CD build times. Learn more

[lina-kim]

Thanks for the update @adamovanja! I gave it a whirl, and according to the log the download finished in a few hours. While I got a "download finished" message, no output directory has appeared :( I'll try running it again.

[adamovanja]

hi @lina-kim, thanks for trying it out. Actually after this message it might take 30 to 45 min for the downloaded sequences to be written to Q2 artifacts. So I suggest you just wait for a bit longer.

[nbokulich]

maybe another print statement is needed to avoid confusion, e.g., Validating data...