Commits · 9df8d5d286de18026eafdd4ea9520b83d3cd74cd · meldb / concepts-processing

Project 'el7g15/uos-latex-template-instructions' was moved to 'uos-latex-group/uos-latex-template-instructions'. Please update any links and bookmarks that may still have the old path.

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Mar 06, 2025
- (fix) Changed the versioning of phenotypes to semantic versioning using the... · 9df8d5d2
  mjbonifa authored 4 months ago
  9df8d5d2
- (refactor) Changed codes to concepts directory for alignment with OMOP. Closes #52 · 1e099555
  mjbonifa authored 4 months ago
  
  1e099555
Feb 27, 2025
- fix: readded metadata to phen output. This is now done after the translation... · 7ccf8657
  mjbonifa authored 4 months ago
  7ccf8657
- fix: started to add the metadata back in, the translation function is trickly... · 5b3b1d29
  mjbonifa authored 4 months ago
  5b3b1d29
- fix: moved omop export to concept-sets, moved concept set csv files to... · 7fdebb00
  mjbonifa authored 4 months ago
  7fdebb00
- fix: added version message to publish · e6ab6fbc
  mjbonifa authored 4 months ago
  
  e6ab6fbc
Feb 26, 2025
- fix: yaml library dump strips all quotes from the output and there's no... · 4b77e5d3
  mjbonifa authored 4 months ago
  4b77e5d3
- feature: added -r option to connect to a remote repo on publication. This is a... · 820b8677
  mjbonifa authored 4 months ago
  820b8677
- fix: added map definition to the config.yaml so that we know which maps are... · e549bf4b
  mjbonifa authored 4 months ago
  e549bf4b
- fix: had to resolve the phen_path to full path rather than using the relative... · 28fde5f6
  mjbonifa authored 4 months ago
  28fde5f6
- test: added tests for diff between config 1, 2, 3 in test_diff. Updated the... · ba8a7ccb
  mjbonifa authored 4 months ago
  ba8a7ccb
Feb 25, 2025
- fix: error writing .gitignore with spaces before *.db and other lines. Closes #39 · 7221405d
  mjbonifa authored 4 months ago
  
  7221405d
- fix. removed contributing.md from mkdocs · 900c4949
  mjbonifa authored 4 months ago
  
  900c4949
- fix: added schema validation using Cerberus to the validation in phen. Closes #16 · 8bda4c7c
  mjbonifa authored 4 months ago
  
  8bda4c7c
Feb 24, 2025
- started the precommit hook work, but seems more complex as it requires some... · 3a7d715c
  mjbonifa authored 4 months ago
  3a7d715c
- refactor: tidied up the action code for categories but still not opimimal as... · 49d78a3f
  mjbonifa authored 4 months ago
  49d78a3f
- refactor: completed refactoring of config to combine codes within concept... · ca41792b
  mjbonifa authored 4 months ago
  ca41792b
- test: added new config3.yaml that includes hanlon. had to refactor phen map to... · 6ecf468f
  mjbonifa authored 4 months ago
  6ecf468f
- refactor: converted all examples to yaml and added test for config2. Updated... · 78e6fcd6
  mjbonifa authored 4 months ago
  78e6fcd6
- refactor: converted all examples to yaml and added test for config2. Updated... · 9eca4250
  mjbonifa authored 4 months ago
  9eca4250
Feb 23, 2025
- added gitignore to phen init. closes #4 · 60973bce
  mjbonifa authored 4 months ago
  
  60973bce
- test: run mypc to check types and add annotations. run black and reformatted... · 829bb6c2
  mjbonifa authored 4 months ago
  829bb6c2
- refactor:trud and omop versions are now written in yaml format. When map is... · 08006e0c
  mjbonifa authored 4 months ago
  08006e0c
Feb 21, 2025
- not dumped all database tables to file on export so they can be versioned · ac87eca9
  mjbonifa authored 5 months ago
  
  ac87eca9
- implemented first part of export to create the omop database refactoring setup... · 4cbcdfe5
  mjbonifa authored 5 months ago
  4cbcdfe5
- added exepected output to readme · 289d4d48
  mjbonifa authored 5 months ago
  
  289d4d48
- refactord build directory. Moved trud and omop to a vocab directory. Moved... · e6fa6be4
  mjbonifa authored 5 months ago
  e6fa6be4
Feb 20, 2025
- moved code types to a CodeTypeParser class they depend on the existance of the... · 8e356322
  mjbonifa authored 5 months ago
  8e356322
- added initial pyproject.toml and testing creating package without conda.yaml,... · f51e056a
  mjbonifa authored 5 months ago
  f51e056a
- added logging errors back in phen code, and not nested in the lambda function of parse · 09d928c9
  mjbonifa authored 5 months ago
  
  09d928c9
- added exceptions in phen · 25fa78ab
  mjbonifa authored 5 months ago
  
  25fa78ab
- added exceptions in phen · 1e8776a8
  mjbonifa authored 5 months ago
  
  1e8776a8
- refactored process codes in phen, moved into a single function · 7bc070b1
  mjbonifa authored 5 months ago
  
  7bc070b1
- removed the translate flag from teh phen code, not necessary and made the... · e7c14011
  mjbonifa authored 5 months ago
  e7c14011
- removed the translate from map and convert codes, fixed covert codes so that... · 3c02f68f
  mjbonifa authored 5 months ago
  3c02f68f
- fixed empty output exception as it did not print the config file path · 8ab33d12
  mjbonifa authored 5 months ago
  
  8ab33d12
- changed code types to objectives not classes so don't need to instantiate them... · 315be709
  mjbonifa authored 5 months ago
  315be709
- standardised code_type import in phen · 305237d5
  mjbonifa authored 5 months ago
  
  305237d5
- standardised code_type import in phen · 19918ce3
  mjbonifa authored 5 months ago
  
  19918ce3
Feb 19, 2025
- moved metadata to preprocess function · 8c8ce07c
  mjbonifa authored 5 months ago
  
  8c8ce07c