Commits · 767dfd1cd34b4310f77f767c963b23a74b56444c · meldb / concepts-processing · GitLab

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Feb 18, 2025
- added initial pytests for basic workflow · 767dfd1c
  mjbonifa authored 4 months ago
  
  767dfd1c
- added OMOP versioning · 28aecd75
  mjbonifa authored 4 months ago
  
  28aecd75
- shorted all the _code references removing _code as not needed and maps API and configuration easier · c87d1411
  mjbonifa authored 4 months ago
  
  c87d1411
- moved publish.py to the output of the map function ratehr than a separate... · 74638822
  mjbonifa authored 4 months ago
  74638822
- changed phen/output directory to phen/map and added concept-sets directory · e5cbdbd2
  mjbonifa authored 4 months ago
  
  e5cbdbd2
- tidied phen init · 66f7c9e9
  mjbonifa authored 4 months ago
  
  66f7c9e9
- fixed the version from commit, supports an empty repo or a repo that's been... · dd623973
  mjbonifa authored 4 months ago
  dd623973
- added ACMC_GITHUB_PAT and ACMC_GITLAB_PAT as environmnet variables and... · 43cba163
  mjbonifa authored 4 months ago
  43cba163
- moved trud api key to an environment variable; stored trud versions in file... · 43692665
  mjbonifa authored 4 months ago
  43692665
Feb 17, 2025
- tested with remote repo in github and gitlab soton · 80685c23
  mjbonifa authored 4 months ago
  
  80685c23
- added support for initialising from a remote repository · 0a65ea76
  mjbonifa authored 4 months ago
  
  0a65ea76
- added version control through a git repository; changed init to create the git... · e50447ea
  mjbonifa authored 4 months ago
  e50447ea
Feb 16, 2025
- added phen validate as a command to validate the configuration in a specified directory · 8c0be40f
  mjbonifa authored 4 months ago
  
  8c0be40f
- refactored trud constants from MAPS to TRUD · c156c2d0
  mjbonifa authored 4 months ago
  
  c156c2d0
- refactored map to phen; refactored to standard directories for phenotypes that... · 95c3d5cf
  mjbonifa authored 4 months ago
  95c3d5cf
Feb 15, 2025
- fixed hard coded mapping for codes mapping files in map.py · 42564803
  mjbonifa authored 4 months ago
  
  42564803
- the _code suffix makes a difference to a lot of thigns, need to work that out · cb24de86
  mjbonifa authored 4 months ago
  
  cb24de86
- added example based on clinicalcodes.org, needs more work to demonstrate... · 3a6da0b8
  mjbonifa authored 4 months ago
  3a6da0b8
- fixed default output and error files · 945ff7ca
  mjbonifa authored 4 months ago
  
  945ff7ca
- changed trud map directory to trud to align with the naming convention used... · 24c5944e
  mjbonifa authored 4 months ago
  24c5944e
- added acmc command line wrapper for entire toolkit moving parameter passing... · 9c72a9b3
  mjbonifa authored 4 months ago
  9c72a9b3
Feb 13, 2025
- changed directory checks for this script to focus on maps directory and not... · 33134b3e
  mjbonifa authored 4 months ago
  33134b3e
- updated mjb conda nad tested it can recreate the env · 38716126
  mjbonifa authored 4 months ago
  
  38716126
- renamed trud_api.py to trud.py; fixed error for r3->snomed as missed the file path · 47aeae38
  mjbonifa authored 4 months ago
  
  47aeae38
- added temporary conda environment · 83694229
  mjbonifa authored 4 months ago
  
  83694229
- updated readme; updated handling of build directories as these were not created automatically · b613e078
  mjbonifa authored 4 months ago
  
  b613e078
Feb 06, 2025
- Update README · d6a686c1
  Jakub Dylag authored 4 months ago
  
  d6a686c1
- move summary excel into json config · 8f8b5119
  Jakub Dylag authored 4 months ago
  
  8f8b5119
Jan 24, 2025
- rename JSON "meldb_phenotypes" -> "concept_set" · 28f44a19
  Jakub Dylag authored 5 months ago
  
  28f44a19
- Update README · bf5af2c1
  Jakub Dylag authored 5 months ago
  
  bf5af2c1
- Update README · 38fc682b
  Jakub Dylag authored 5 months ago
  
  38fc682b
Jan 22, 2025
- Export Conda Environment with Instructions · 55bbd31a
  Jakub Dylag authored 5 months ago
  
  55bbd31a
Jan 21, 2025
- Re-write README · 3876e7cd
  Jakub Dylag authored 5 months ago
  
  3876e7cd
- omop installation script · 5b98129c
  Jakub Dylag authored 5 months ago
  
  5b98129c
Jan 10, 2025
- rename error log columns, moved omop code definitions to parse.py · 850bd595
  Jakub Dylag authored 5 months ago
  
  850bd595
Jan 08, 2025
- Rename "code" -> "CONCEPT" and "MELDB_concept" -> "CONCEPT_SET" · 3c0f4c4a
  Jakub Dylag authored 5 months ago
  
  3c0f4c4a
- publish output to db · 4d8cbf8a
  Jakub Dylag authored 5 months ago
  
  4d8cbf8a
Nov 15, 2024
- Remove MELDB External source files · a4c7db06
  Jakub Dylag authored 7 months ago
  
  a4c7db06
Nov 01, 2024
- Auto Download and Extract TRUD Code Tables · 7389291c
  Jakub Dylag authored 8 months ago
  
  7389291c
Oct 31, 2024
- Summary Sheet to CSV and filepath in JSON file · 4929dd79
  Jakub Dylag authored 8 months ago
  
  4929dd79