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Updates to WormBase processor #1472

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Updates to WormBase processor #1472

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934c4f2
Create wormbase module
Bradley-Buchner Jan 27, 2025
46aa210
Make wormbase agents
Bradley-Buchner Jan 30, 2025
305ad9a
Modify _make_agent
Bradley-Buchner Jan 30, 2025
99e051d
Modify _download_wormbase_data and _read_wormbase_csv
Bradley-Buchner Jan 30, 2025
e9f1b49
Add test_print_agent_data_in_init
Bradley-Buchner Jan 30, 2025
9e9b0e8
Added test for agent info extraction (name, db_refs)
Bradley-Buchner Jan 30, 2025
fc6974d
Modified test_download_wormbase_data and test for agent info extraction
Bradley-Buchner Jan 30, 2025
18aaf12
Fix url usage
Bradley-Buchner Jan 31, 2025
2e11451
Modify _download_wormbase_data and _read_wormbase_data
Bradley-Buchner Jan 31, 2025
93bed0c
Delete parse_wormbase.py
Bradley-Buchner Jan 31, 2025
cdb7dd5
Add description
Bradley-Buchner Jan 31, 2025
511d788
Add "Make statements" section
Bradley-Buchner Feb 3, 2025
b01befb
Add assertions for statements, Remove test for _download_wormbase_data
Bradley-Buchner Feb 3, 2025
40d6dbc
Merge remote-tracking branch 'upstream/master'
Bradley-Buchner Feb 5, 2025
b4c84d3
Update __init__.py
Bradley-Buchner Feb 5, 2025
fac5e19
Update processor.py
Bradley-Buchner Feb 5, 2025
2a09e33
Modify statement creation to handle molecular interaction data
Bradley-Buchner Feb 8, 2025
4c5364d
Update test file
Bradley-Buchner Feb 8, 2025
94c04b7
Incorporate wormbase-to-entrez ID mappings to ensure agents have an e…
Bradley-Buchner Feb 9, 2025
230d8bb
Update Statement creation test
Bradley-Buchner Feb 9, 2025
bc79efd
Move data loading into api
Bradley-Buchner Feb 11, 2025
89e9da0
Decouple data loading and WormBase processor
Bradley-Buchner Feb 11, 2025
09ed482
Clean up some of the API and processor
bgyori Feb 11, 2025
e3e19ee
Refactor processor for processing rows
bgyori Feb 11, 2025
b2606a1
Improve code styling
bgyori Feb 11, 2025
c474930
Refactor processor into reusable functions
bgyori Feb 11, 2025
7e0d05d
Improve processor source_ids
bgyori Feb 12, 2025
5056484
Remove NA handling from pd.read_csv()
Bradley-Buchner Feb 13, 2025
97f75e2
Add get_agent_role_info(), replace Activation/Inhibition with Increas…
Bradley-Buchner Feb 13, 2025
c69faa6
Update test file to use process_from_files() instead of WormBaseProce…
Bradley-Buchner Feb 13, 2025
e8e90a9
Misc. updates
Bradley-Buchner Feb 16, 2025
26547df
Clean up test_statement_creation
Bradley-Buchner Feb 16, 2025
5d0294f
Add test files
Bradley-Buchner Feb 16, 2025
9cefe12
Add functionality for new data source
Bradley-Buchner May 29, 2025
d396e63
Create c_elegans_all_genes.txt
Bradley-Buchner May 29, 2025
c13f037
Merge branch 'master' into wormbase
Bradley-Buchner Oct 20, 2025
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