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refactor filtering of user specified strains #178

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merged 8 commits into from
Dec 14, 2023
Merged

refactor filtering of user specified strains #178

merged 8 commits into from
Dec 14, 2023

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CunliangGeng
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@CunliangGeng CunliangGeng commented Nov 14, 2023 •
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Based on the new loading pipeline, the filtering of user strains is conducted just after loading strain mappings, which will simplify the upcoming loading pipeline. The change of loading process looks like below:
Before: load strain mappings --> load BGC, GCF, spectra and MF --> filter user strains
Now: load strain mappings --> filter user strains --> load BGC, GCF, spectra and MF

Major Changes:

  • create strain_loader.py and add function load_user_strains
  • add schema for json file of user specified strains (now we require user to provide strains in a JSON file)
  • update the use of load_user_strains in loader.py
  • remove test_loader.py (the whole loading pipeline is ongoing, and tests will be added later)

@CunliangGeng
update docstring
5043c1f
@CunliangGeng
refactor reading and filtering of user specified strains
a7668e7 
- remove `_filter_user_strains` method
- remove reading user strains file from `_load_optional` method
- add `_load_user_strains` method
- update `_load_strain_mappings` method to include the reading and filtering of user specified strains after loading strain mappings
@CunliangGeng CunliangGeng marked this pull request as draft November 15, 2023 15:16
@CunliangGeng CunliangGeng marked this pull request as ready for review November 15, 2023 15:21
@CunliangGeng CunliangGeng marked this pull request as draft November 16, 2023 09:59
@CunliangGeng
Delete test_loader.py
affeea1
@CunliangGeng
add schema for user strains JSON file
e70b5fd 
Users are required to provide their specified strains in a JSON file. Here the schema of that JSON file is added.
@CunliangGeng
Create strain_loader.py
1e5ab2f 
Create an independent `load_user_strains` function.
@CunliangGeng
Create test_strain_loader.py
9528404
@CunliangGeng
use new load function of user strains in loader.py
09cc141
@CunliangGeng CunliangGeng marked this pull request as ready for review November 17, 2023 12:02
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CunliangGeng commented Nov 20, 2023 •
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Current dependencies on/for this PR:

This stack of pull requests is managed by Graphite.

This was referenced Nov 20, 2023
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@CunliangGeng CunliangGeng mentioned this pull request Dec 5, 2023
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gcroci2
gcroci2 approved these changes Dec 11, 2023
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src/nplinker/strain_loader.py Outdated Show resolved Hide resolved
@CunliangGeng @gcroci2
fix typo
50f4de0 
Co-authored-by: Giulia Crocioni <55382553+gcroci2@users.noreply.github.com>
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CunliangGeng commented Dec 14, 2023 •
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Merge activity

@CunliangGeng CunliangGeng merged commit bd45807 into dev Dec 14, 2023
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@CunliangGeng CunliangGeng deleted the filter_user_strains branch December 14, 2023 10:34
This was referenced Dec 20, 2023
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@gcroci2 gcroci2 gcroci2 approved these changes

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@CunliangGeng @gcroci2