v1.0.0
What's Changed
Feature
- allow use of visit_detail table for episode of care in
720ca89
Fix
- fixed converter for new FHIR Timing definition in
94ac078
Chore
- updated requirements-dev.txt in
804d05c
Ci
Refactor
- updated to pendulum 3.0.0 in
2bd6c46
Tests
- omop.concepts in
20bc847
Unknown
- Bump fastapi from 0.105.0 to 0.108.0 in
ac06aa1 - Bump httpx from 0.25.2 to 0.26.0 in
d708b6d - Bump uvicorn[standard] from 0.24.0.post1 to 0.25.0 in
43f39f1 - Bump psycopg[binary] from 3.1.15 to 3.1.16 in
6c4e1d8 - Bump fastapi from 0.104.1 to 0.105.0 in
ff2f635 - Bump psycopg[binary] from 3.1.14 to 3.1.15 in
6d983e7 - Bump psycopg[binary] from 3.1.13 to 3.1.14 in
2ebdf7c - Update test.yml in
6da47e0 - Bump pandas from 2.1.3 to 2.1.4 in
da354bc - Bump pytest-env from 1.1.1 to 1.1.3 in
fa3e240 - Bump httpx from 0.25.1 to 0.25.2 in
5d61190 - skipping peep test in
6ca5e01 - all values per day must be true in
fe352bb - added pytest instructions in
0234e77 - test all values per day valid in
acc06ec - Bump psycopg[binary] from 3.1.12 to 3.1.13 in
2409e43 - quoting user/pass in db conn str in
4d53bac - Bump pandas from 2.1.1 to 2.1.3 in
fbc3404 - Bump httpx from 0.25.0 to 0.25.1 in
77b7504 - Bump sqlalchemy from 2.0.22 to 2.0.23 in
77f6f5e - Bump uvicorn[standard] from 0.23.2 to 0.24.0.post1 in
b2eef85 - Update pydantic requirement from <2.0.0 to <3.0.0 in
049c25d - Bump pytest-env from 1.1.0 to 1.1.1 in
1f10cfa - Bump fastapi from 0.104.0 to 0.104.1 in
134e9a5 - fixed tests in
ebbf806 - set pydantic to <2 in
90a0567 - version bumps in
ed263bc - refactoring, tests for commenting added in
513ced6 - updated readme in
50a677b - Bump tqdm from 4.65.0 to 4.66.1 in
b687e70 - Bump fastapi from 0.100.1 to 0.101.1 in
25632b6 - Bump uvicorn[standard] from 0.23.0 to 0.23.2 in
20df49f - Bump fastapi from 0.100.0 to 0.100.1 in
5bd8062 - Bump uvicorn[standard] from 0.22.0 to 0.23.0 in
556d13a - Bump fastapi from 0.97.0 to 0.100.0 in
b7161a2 - Bump pytest from 7.3.2 to 7.4.0 in
801633d - fixed exception reporting in
b7210a3 - added exception handling for tx server in
da68a90 - removed thrombocytopenia from test in
9ffcfc0 - fixed converter test in
cbd4d95 - Bump pytest-env from 0.8.1 to 0.8.2 in
5148063 - updated tests in
2fcef61 - fixed wrong field usage in Quantity.unit in
39c8b9b - updated testdata: added tinzaparin in
2f92574 - Bump pytest from 7.3.1 to 7.3.2 in
bae2528 - Bump fastapi from 0.95.2 to 0.97.0 in
bb99b0f - refactored fastapi app, added comments in
ed0f222 - fixed execution map test in
06836d6 - fixed rowcount logging in
0d94823 - test different cte in
1408530 - added index to recommendation_result table in
e5beaf0 - only using python3.11 in tests in
dbded94 - improved exclusion statement in
6f379c6 - improved exclusion statement in
0592e57 - improved logging in
d0964de - adapted tests to new exclusion strategy in
8eb3411 - moved exclusion to combination statements in
bf38afc - changed result db structure, added query description in
5a65e2f - added indices in
878c691 - fixed drug exposure: zero length exposure in
11a33cc - added psycopg binary requirements in
b32a917 - renamed test recommendation base file in
2b7eef2 - code cleanup in
7f26670 - added recommendation tests in
ca5940e - changed precision requirement in
ba0a22c - fixed ValueNumber tests in
bf1e033 - added tidal volume criterion tests in
3b3d231 - changed ValueNumber for floating point comparisons in
5752922 - removed duplicate code in
a8490c8 - fixed duration calculation in
d7fb3fe - updated omop testdata ref in
dfcb6d6 - fixed sepsis m1 test in
737d65e - fixed tidal volume per body weight calc in
5bd20f2 - Bump pytest-cov from 4.0.0 to 4.1.0 in
bc7766f - implemented rec36b tests in
7da4989 - implemented sepsis m1 tests in
2d78ecb - reduced test number in
8f78842 - implemented rec36a tests in
1166a4a - implemented rec36a tests in
6b0f3f3 - implemented rec35 tests in
1955317 - fixed goal exclusion if no action is specified in
11dcd56 - fixed active patients test in
234fae8 - added parameters in
b9211e1 - implemented rec18 tests in
eacc678 - fixed goal exclusion in
9d38f2f - fixed criterion tests in
8f1c672 - added env to github workflow in
d443495 - implemented rec17 tests in
2c595e6 - added result mismatch reporting in
1bd0f53 - moved common code into TestRecommendationBase in
e4cb60d - added separate sql query logger in
9afc7a3 - Bump pytest-postgresql from 4.1.1 to 5.0.0 in
66e525c - Bump fastapi from 0.95.1 to 0.95.2 in
f9cfe0f - Bump httpx from 0.24.0 to 0.24.1 in
b699ea9 - Bump uvicorn[standard] from 0.21.1 to 0.22.0 in
67757e5 - added combination (db) test in
3576ff8 - multiple person test: drug_exp, meas, obs in
a6f42b9 - added multiple person test to active_patients in
f5048bd - added multiple person test to occurrences in
73a51f0 - fixed rec15 test in
32967a6 - updated testdata in
7b2a7b9 - added visit_occurrence tests in
0cfad35 - fixed interval in
1737d78 - updated testdata in
11ad3e4 - fixed drug exposure frequencies, boundaries & added tests in
d5ea84f - adjusted test cases to edge values in
746e0e3 - added drug exposure explicit tests in
84d2921 - Update dependabot.yml in
a61a3c9 - fixed value test in
a414cab - fixed recommendation test in
b96d011 - added value concept tests in
ed70693 - added value concept tests in
b283e71 - added observation tests (numeric only) in
32cba40 - created value criterion test suite in
67dc7d6 - added measurement tests in
2abf94b - update omop testdata in
368448e - add ValueNumber.parse function in
93bf75f - added procedure_occurrence tests in
a237bae - restricting output date ranges to observation period in
1247857 - db: changed to timezone-aware datetime columns in
b4a8e33 - renamed criterion->condition in
da95023 - updated testdata in
14cb62b - added condition_occurrence single patient tests in
6957b8d - fixed active patients during period selection in
b10f3a3 - added fastapi tests in
8bdedc8 - restructured tests & added converter tests in
d5b48e2 - added fhir.util tests in
1f169aa - added FHIRClient tests in
b97a782 - added terminology tests in
c96292a - fixed db setup/teardown in
1669945 - restructured tests dir in
2acac73 - fixed database connection in tests in
594b2df - fixed tests in
759688c - added CriterionCombination tests in
f1ec6e5 - added execution map tests in
7446036 - additional coverage for utiL in
b55be64 - added recommendation tests to gh workflow in
8277f8a - recommendation test stubs in
cf3dc71 - added recommendation test run cli option in
37c7668 - added ee.utils tests in
c25e263 - added codecov in
c224630 - fixed workflow in
86c1663 - added slow tests markers in
d6826d6 - added dependabot in
e63b321 - rec server as service in
e63c77f - added recommendation server building in
9aeb28c - expose ports in
584e945 - added postgres environment variables in
23447b1 - updated to psycopg3 in
b82ae13 - added pytest github workflow in
b7eede3 - added submodule in
d2c1264 - moved fixtures into separate directory in
7a10ebd - removed session in
8f12fca - migrated table defs to new style in
701a39d - sqlalchemy 2 declarative tables in
1ba1ccf - migrate to sqlalchemy 2.0 (updated lib) in
f91f372 - migrate to sqlalchemy 2.0 in
3dd9c3e - removed ExecutionEngine from main module import in
b2acfb4 - added vocabulary logger in
28d08e0 - implemented drug frequency in
bba6f0f - dirty test implementation in
a0dc4c4 - fix drug_exposure valid_to in
3c26fef - calculate drug quantity per interval in
a2aef53 - body_weight as static criterion in
4be73c9 - filtering datetime by datetime_end also in
4d7297c - select visit_occurrence id & datetime in
f144d21 - fixed ProcedureOccurrence constructor in
ccc3cac - fixed exclusion for drug administration extensions in
4e8b560 - fixed valid range for static vars in
c75677f - autodetect allergies in
2938b15 - updated to FHIR R5 in
d876153 - added static parameter to criteria/characteristics in
f724253 - fixed person_id join in
9197dae - implemented per day output in
5e17f53 - removed patient data result table in
ecde5dd - updated precommit in
514129d - updated readme in
84a0390 - added drug concept, end datetimes, description in
038d359 - fixed api in
a18ae07 - added title and name to recommendation in
596db60 - added criteria names, sqlalchemy in
b9b7a7b - implementing fastapi interface in
70cb734 - fixed tidal volume in
d6637a1 - fixed exclusion in
60576b7 - added compiled statement logging in
1daac46 - changed from active patients to patients during period in
24cba4b - updated requirements in
169ff3e - updated README in
2916361 - fixed negative criteria (exclude) in
83182ad - same base criterion for all cohort defs in
43ed2cc - fixed combination query in
04a8a9c - fixed multiple selection of person_id in
316076d - fixed cohort def hashing & distinct persons in
48bef20 - implemented select data for custom criterion in
98994ec - add configuration in
818bb08 - saving basetable (active patients) to results in
0ab3dcf - moved OMOP concepts to constants in
c3ec58d - implemented patient data result in
46ead45 - modified pre-commit in
e2f9ad2 - fixed sql generation in
722ad4f - adapted queries for result table in
81e3f92 - fixed hashing in
9651a04 - implemented dict / from_dict in
ae4f8b1 - starting insert into result tables in
599adb3 - added Criterion.category in
2927273 - added result tables in
b1673bd - added check for base table join in
ad55c52 - removed unused imports in
3ba4750 - updated pre-commit conf in
cd3f502 - sqlachemied ExecutionMap in
e6870e7 - implemented recommendation collection in
fdb40a5 - fixed sql in
53af529 - updated OMOP CDM to 5.4 in
c22de43 - fixing sql statements in
84a657b - using sqlalchemy models in
4edaed7 - added select into statements in
bf2fe3c - added procedure duration in
2991f3c - implemented datetime window in
60080fc - added explicit ucum unit names in
4923462 - added custom concept in
8db3667 - updated readme in
81c4158 - added dose-condition-extension in
a95b019 - error for unimplemented selection behavior in
ca5f235 - body positioning action in
bd6edcc - ventilator mgmt goal in
ee36064 - implemented laboratory value goal in
d110d50 - added goals & single factory class in
5db856b - refactoring in
9ab413a - implemented one-or-more selection behavior in
d99599d - drug administration continued in
7fccc16 - implementing drug administration action in
b9b90be - added values for measurement in
2cf1364 - added conversion to criterion in
427fe8e - code cleanup in
b19308a - added compopsition of sql statements in
45d1747 - type hinting python 3.10 style in
a939885 - clean up in
67d8ffb - merge json-cohort-def in
99f7c44 - removed cohort definition (json) code in
1e270dc - current status - unverified in
efd2800 - reading all recommendations in
d57956b - exclude is assumed to be False by default in
91d069c - added search workaround in
28c0859 - corrected laboratory & added ventilation mgmt in
d68a165 - updated init.py in
5b6d9d7 - implemented additional criteria in
6eb4135 - added exclusion handling in
843da24 - updated readme in
c144033 - implemented cohort definition for conditions in
8bacf1d - continued development in
97904fd - initial commit in
514025d