FIX: correct E-Direct param setting when fetching metadata

[misialq]

This PR changes how we are using some of the entrezpy functionalities in order to make better use of their built-in ways of handling E-Direct pipelines and multi-threaded requests.

The big change is in the inheritance of our ESearch/EFetch classes (both Result and Analyzer): instead of inheriting from EutilsResult/EutilsAnalyzer, they will now inherit from EsearchResult/EsearchAnalyzer/EfetchAnalyzer (please mind that EFetchResult still inherits from the EutilsResult as most of the functionality needs to be implemented from scratch there). The reason for this change is that those "new" base classes provide more handy functionalities out-of-the-box, allowing us to better/easier use pipelines and automatically handle large requests (> 10000 run IDs) without the need for batching/looping/other workarounds.

To test this change, try fetching metadata with get-metadata using any BioProject ID and a list of run IDs. Importantly, those should contain more than 10000 (run) IDs to check that the "new" batching works properly.

Closes #132.

[codecov]

Codecov Report

Merging #135 (7998f21) into main (89a59dd) will increase coverage by 0.08%.
The diff coverage is 91.66%.

@@            Coverage Diff             @@
##             main     #135      +/-   ##
==========================================
+ Coverage   95.62%   95.71%   +0.08%     
==========================================
  Files          15       14       -1     
  Lines        1165     1096      -69     
  Branches      216      213       -3     
==========================================
- Hits         1114     1049      -65     
+ Misses         26       22       -4     
  Partials       25       25              

Impacted Files	Coverage Δ
q2_fondue/utils.py	92.72% <ø> (ø)
q2_fondue/metadata.py	96.96% <86.66%> (-3.04%)	⬇️
q2_fondue/entrezpy_clients/_esearch.py	95.45% <93.33%> (+1.25%)	⬆️
q2_fondue/entrezpy_clients/_efetch.py	89.91% <100.00%> (-0.05%)	⬇️
q2_fondue/entrezpy_clients/_pipelines.py	100.00% <100.00%> (ø)
q2_fondue/sequences.py	96.15% <100.00%> (-0.04%)	⬇️

Help us with your feedback. Take ten seconds to tell us how you rate us.

[adamovanja]

thanks @misialq for clean refactor 🚀. I added some comments inline. Also, I tested it on the BioProject ID PRJEB11419 that is linked with 39'504 run IDs and it fetched all the metadata correctly in 1:20 hrs 🎉 .

[adamovanja]

Thanks for addressing the comments. Could you remove issue #91 from the PR description? Then we are ready to merge 😊.

This PR looks great to me. I'm glad you found this clean solution 🥇.