ENH: add an action to search for run IDs using a text query

[misialq]

This PR adds a new action allowing retrieval of SRA run IDs using a text search query which will be executed on the BioSample database. The output of the action will then be a single NCBIAccessionIDs artifact that can be used to fetch corresponding sequences and/or metadata.

Additionally, a little refactor is included in the Entrezpy pipelines submodule: the ESearch part is separated from the rest of the pipeline to allow fetching more than 10000 UIDs (particularly important for the action introduced in this PR) - see the expanded comments in the code.

Testing:
To test, you can run something like:

qiime fondue get-ids-from-query --p-email <your email> --p-n-jobs 4 --p-query "txid410656[Organism] AND \"public\"[Filter] AND (chicken OR poultry)" --o-ids ids-from-query.qza --verbose 

Please also verify that fetching metadata using run and aggregate IDs works correctly as these parts are influenced by changes in this PR (so, ideally: run, BioProject and study/experiment/sample IDs).

Note:
This PR should be merged after #138 - it already has its changes incorporated (otherwise the CI is broken). Also, it would be easier to review after the other one.

[codecov]

Codecov Report

Merging #136 (1efba49) into main (4d9fc11) will decrease coverage by 0.00%.
The diff coverage is 98.73%.

❗ Current head 1efba49 differs from pull request most recent head 88d2680. Consider uploading reports for the commit 88d2680 to get more accurate results

@@            Coverage Diff             @@
##             main     #136      +/-   ##
==========================================
- Coverage   98.58%   98.57%   -0.01%     
==========================================
  Files          27       29       +2     
  Lines        2895     2955      +60     
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+ Hits         2854     2913      +59     
- Misses         41       42       +1     

Impacted Files	Coverage Δ
q2_fondue/metadata.py	98.63% <ø> (ø)
q2_fondue/sequences.py	98.55% <ø> (ø)
q2_fondue/tests/test_sequences.py	98.09% <ø> (ø)
q2_fondue/tests/test_query.py	94.11% <94.11%> (ø)
q2_fondue/entrezpy_clients/_esearch.py	97.77% <100.00%> (+0.05%)	⬆️
q2_fondue/entrezpy_clients/_pipelines.py	100.00% <100.00%> (ø)
q2_fondue/plugin_setup.py	100.00% <100.00%> (ø)
q2_fondue/query.py	100.00% <100.00%> (ø)
q2_fondue/tests/test_metadata.py	99.68% <100.00%> (+0.01%)	⬆️

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[adamovanja]

Thanks for this neatly implemented addition @misialq 🥇.

I added my code comments inline. Could you also add a description of the new action to the ReadMe and maybe also the tutorial?

I tested the new get-ids-from-query action with one query [1] and it worked like a charm. Also, fetching metadata for run, bioproject and study IDs still worked as expected [2].

---

[1] Command tested: qiime fondue get-ids-from-query --p-email my@mail.com --p-n-jobs 4 --p-query "human gut metagenome[Organism] AND public[Filter] AND (infant OR baby) " --o-ids ids-from-query.qza --verbose

[2] Tested run ID = ERR184806, study ID = SRP132205 and bioproject ID = PRJEB16321

[adamovanja]

thanks for the changes. this looks great to me 🚀