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refactoring signor #283

Merged
merged 3 commits into from
Feb 4, 2025
Merged

refactoring signor #283

merged 3 commits into from
Feb 4, 2025

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EvanDietzMorris
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SIGNOR refactor:

  • The main issue was that qualifiers cannot be lists, I changed the single values to strings, and split edges when >1 (anatomical context qualifier)
  • It was calling get_latest_source_version in the constructor, we never want to do that but here it didn't even have a purpose
  • It was reading/parsing the node mapping file from disk for every single node mapping (that's sloooow and inefficient)
  • The mapping file we create was generated in get_data, that should really go in parse_data (get_data should only download source data, any manipulation or parsing of the source that is subject to change needs to go in parse_data or it won't run again with a new parser release)
  • The way extractor was used doesn't really use the features of extractor and complicates things some so I just took it out

nitpicky stuff:

  • main data file was saved as getLatestRelease.php, changed that to a .tsv file
  • flattened unnecessary loop in get_data
  • make_datafile() and signor_data.json were a bit ambiguous, changed their names to make_signor_type_map()
  • changed get_node() to fix_node_curie_prefix()
  • cleaned up the function that returned subject and object ids

@github-actions github-actions bot added the Biological Context QC Require validation of biological context to ensure accuracy and consistency label Feb 3, 2025
@EvanDietzMorris EvanDietzMorris merged commit e5a8c8b into master Feb 4, 2025
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@EvanDietzMorris EvanDietzMorris deleted the signor_refactor branch February 4, 2025 17:52
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