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meldb
concepts-processing
Commits
Commits · 5bba5a98cbc007ace67ee307c07cce735f795309
5bba5a98cbc007ace67ee307c07cce735f795309
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concepts-processing
acmc
phen.py
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Feb 27, 2025
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
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
4 months ago
289d4d48
refactord build directory. Moved trud and omop to a vocab directory. Moved...
· e6fa6be4
mjbonifa
authored
4 months ago
e6fa6be4
Feb 20, 2025
moved code types to a CodeTypeParser class they depend on the existance of the...
· 8e356322
mjbonifa
authored
4 months ago
8e356322
added initial pyproject.toml and testing creating package without conda.yaml,...
· f51e056a
mjbonifa
authored
4 months ago
f51e056a
added logging errors back in phen code, and not nested in the lambda function of parse
· 09d928c9
mjbonifa
authored
4 months ago
09d928c9
added exceptions in phen
· 25fa78ab
mjbonifa
authored
4 months ago
25fa78ab
added exceptions in phen
· 1e8776a8
mjbonifa
authored
4 months ago
1e8776a8
refactored process codes in phen, moved into a single function
· 7bc070b1
mjbonifa
authored
4 months ago
7bc070b1
removed the translate flag from teh phen code, not necessary and made the...
· e7c14011
mjbonifa
authored
4 months ago
e7c14011
removed the translate from map and convert codes, fixed covert codes so that...
· 3c02f68f
mjbonifa
authored
4 months ago
3c02f68f
fixed empty output exception as it did not print the config file path
· 8ab33d12
mjbonifa
authored
4 months ago
8ab33d12
changed code types to objectives not classes so don't need to instantiate them...
· 315be709
mjbonifa
authored
4 months ago
315be709
standardised code_type import in phen
· 305237d5
mjbonifa
authored
4 months ago
305237d5
standardised code_type import in phen
· 19918ce3
mjbonifa
authored
4 months ago
19918ce3
Feb 19, 2025
moved metadata to preprocess function
· 8c8ce07c
mjbonifa
authored
4 months ago
8c8ce07c
checked metadata_df
· 633702e3
mjbonifa
authored
4 months ago
633702e3
fixed state but between test and running from the command line
· 75615a67
mjbonifa
authored
4 months ago
75615a67
removed -verify from option as always should be doing this and added some...
· ab787128
mjbonifa
authored
4 months ago
ab787128
Refactored base into logging; moved raise_ to raise_exception in parse as more...
· 131f74ac
mjbonifa
authored
4 months ago
131f74ac
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