Commits · ac87eca98575b4478252cd1b8d038a38bc86b00c · meldb / concepts-processing · GitLab

Snippets Groups Projects

Feb 21, 2025
- not dumped all database tables to file on export so they can be versioned · ac87eca9
  mjbonifa authored 4 months ago
  
  ac87eca9
- implemented first part of export to create the omop database refactoring setup... · 4cbcdfe5
  mjbonifa authored 4 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
- checked metadata_df · 633702e3
  mjbonifa authored 5 months ago
  
  633702e3
- fixed state but between test and running from the command line · 75615a67
  mjbonifa authored 5 months ago
  
  75615a67
- removed -verify from option as always should be doing this and added some... · ab787128
  mjbonifa authored 5 months ago
  ab787128
- Refactored base into logging; moved raise_ to raise_exception in parse as more... · 131f74ac
  mjbonifa authored 5 months ago
  131f74ac
Feb 18, 2025
- refactored files into the module acmc and sorted all the imports · 5e1fdfc4
  mjbonifa authored 5 months ago
  
  5e1fdfc4
- changed all print statements for logging, and configured the default level... · 7de89272
  mjbonifa authored 5 months ago
  7de89272
- added initial logging setup but not updated any of the print statements yet as... · dbb536f0
  mjbonifa authored 5 months ago
  dbb536f0
- added initial pytests for basic workflow · 767dfd1c
  mjbonifa authored 5 months ago
  
  767dfd1c
- added OMOP versioning · 28aecd75
  mjbonifa authored 5 months ago
  
  28aecd75
- shorted all the _code references removing _code as not needed and maps API and configuration easier · c87d1411
  mjbonifa authored 5 months ago
  
  c87d1411
- moved publish.py to the output of the map function ratehr than a separate... · 74638822
  mjbonifa authored 5 months ago
  74638822
- changed phen/output directory to phen/map and added concept-sets directory · e5cbdbd2
  mjbonifa authored 5 months ago
  
  e5cbdbd2
- tidied phen init · 66f7c9e9
  mjbonifa authored 5 months ago
  
  66f7c9e9
- fixed the version from commit, supports an empty repo or a repo that's been... · dd623973
  mjbonifa authored 5 months ago
  dd623973
- added ACMC_GITHUB_PAT and ACMC_GITLAB_PAT as environmnet variables and... · 43cba163
  mjbonifa authored 5 months ago
  43cba163
Feb 17, 2025
- tested with remote repo in github and gitlab soton · 80685c23
  mjbonifa authored 5 months ago
  
  80685c23
- added support for initialising from a remote repository · 0a65ea76
  mjbonifa authored 5 months ago
  
  0a65ea76
- added version control through a git repository; changed init to create the git... · e50447ea
  mjbonifa authored 5 months ago
  e50447ea
Feb 16, 2025
- added phen validate as a command to validate the configuration in a specified directory · 8c0be40f
  mjbonifa authored 5 months ago
  
  8c0be40f
- refactored trud constants from MAPS to TRUD · c156c2d0
  mjbonifa authored 5 months ago
  
  c156c2d0
- refactored map to phen; refactored to standard directories for phenotypes that... · 95c3d5cf
  mjbonifa authored 5 months ago
  95c3d5cf
Feb 15, 2025
- fixed hard coded mapping for codes mapping files in map.py · 42564803
  mjbonifa authored 5 months ago
  
  42564803
- the _code suffix makes a difference to a lot of thigns, need to work that out · cb24de86
  mjbonifa authored 5 months ago
  
  cb24de86