- fix: comment fixes (
32df5a4) - fix: recommendation and criterion ids are (de)serialized less incorrectly (
0a9c8ff) - fix: use commnon style for Recommendation._base_criterion serialization (
2c660fa) - fix: include _root attribute in (de)serialization of CriterionCombination (
a8f770f) - fix: widen type signature of Serializable.from_json to include bytes (
ab8564a) - fix: random minor fixes (
8d8523e) - fix: filter intervention criteria by population (
03c3902) - fix: unpickling of temporal count (
0cd4e04) - fix(plot): sort criteria, give proper titles, and group (
afac6b1) - fix: cohort logic reduction (
c530621) - fix: processing of temporal criteria (
55801d4) - fix: graph node display of temporal combinations (
cff71cf) - fix: (de)serialize PopulationInterventionPair.{population,intervention} with class info (
76bf3b8) - fix: serialize NonCommutativeLogicalCriterionCombination.{left,right} with class information (
23f3643) - fix: allow deserializing a Timing instance as ProcedureOccurrence.timing (
e94790b) - fix: use of visit_detail in ActivePatients (
7b33c6b) - fix: cytoscape graph for non-concept criteria (
a5a0f91)
- chore(deps): bump path-to-regexp and express in /apps/viz-frontend (
32f8da7) - chore(deps): bump nanoid from 3.3.7 to 3.3.8 in /apps/viz-frontend (
a7b4b46) - chore(deps): bump the dependencies group with 4 updates (
5ab168d) - chore: update submodule (
3fc9d59) - chore(deps): bump the dependencies group with 3 updates (
7cf9f3d) - chore(deps): bump the dependencies group with 4 updates (
abc94ce) - chore(deps): bump cross-spawn from 7.0.3 to 7.0.6 in /apps/viz-frontend (
8ab7aff) - chore(deps): bump the dependencies group with 2 updates (
a2d21a6) - chore(deps): bump the dependencies group with 2 updates (
765df8b) - chore(deps): bump the dependencies group with 4 updates (
5d0fbdf) - chore(deps): bump the dependencies group with 2 updates (
bd186bb) - chore(deps): bump http-proxy-middleware in /apps/viz-frontend (
d7863ab) - chore(deps): bump the dependencies group with 5 updates (
15ed84f) - chore(deps): bump the dependencies group with 10 updates (
570acd9) - chore(deps): bump uvicorn[standard] from 0.31.0 to 0.31.1 (
c09c50f) - chore(deps): update rollup (
72dd535) - chore: update deps (
6978695) - chore(deps): bump body-parser and express in /apps/viz-frontend (
33e1dd3) - chore(deps): bump send and express in /apps/viz-frontend (
66a4e5a) - chore(deps): bump serve-static and express in /apps/viz-frontend (
f7a6538) - chore(deps): bump path-to-regexp and express in /apps/viz-frontend (
9cfbc2b) - chore(deps): bump express from 4.19.2 to 4.21.0 in /apps/viz-frontend (
58049a6) - chore(deps): bump sympy from 1.13.0 to 1.13.2 (
4b45f40) - chore(deps): bump sqlalchemy from 2.0.30 to 2.0.35 (
0634cc1) - chore(deps): bump pydantic-settings from 2.3.4 to 2.5.2 (
a262a35) - chore(deps): bump micromatch from 4.0.5 to 4.0.8 in /apps/viz-frontend (
b118011) - chore(deps): bump webpack from 5.89.0 to 5.94.0 in /apps/viz-frontend (
8a9bd5a) - chore(deps): bump pyyaml from 6.0.1 to 6.0.2 (
35f2338) - chore(deps-dev): bump tqdm from 4.66.4 to 4.66.5 (
91d005f)
- ci: fix semantic release (
a933fe3) - ci: update pre-commit (
09ef28f) - ci(dependabot): bump codecov/codecov-action from 4 to 5 (
86182aa) - ci: dependabot validation (
da94b07) - ci: dependabot grouped updates (
ac34af8)
- feat: remove intervention sink (
751dce2) - feat: add AnyTime temporal criterion (
de284b7) - feat: add PointInTimeCriterion.forward_fill property (
b0440f0) - feat: falling back to non-standard concepts when standard is not found (
4ddaf53)
- refactor: remove exclude attribute (
01eecd1) - refactor: use logical not criterion combination instead of exclude=True (
79b5791)
- revert: removed not-applicable view (
d4b181b)
- test: fixed vocabulary test (
013e009)
- tests: remove insert_criterion exclude tests (
78a0237) - tests: adapt to new population filtering behavior (
85e73b1)
- create enum types in public schema to facility data exchange between schemas (
ae0c373) - reduce log output (
3db23cb)
- fix(graph): dose info in nodes (
0848d88) - fix: interval ffill until observation_window end (
4c9ade1) - fix(viz): display of 0 sec entries (
51d5304) - fix: tidal volume for <110 cm height (
7833827) - fix(viz): displaying recommendation name (
2b4c5a5) - fix(viz-backend): database timezone setting (
5c00d67) - fix(viz-frontend): colors, sorting, display (
531c6ab)
- perf(viz-backend): interval per person (
99c7d51)
- test: adapted to measurement value forward filling until end of observation window (
a27eef6) - test: ffill with observation window (
14e6187)
- fix: type hints (
d0358f5) - fix: made TimeIntervalType serializable (
c6ee140) - fix: overlapping intervals for adjacent windows (
c95bdd6)
- chore(deps): bump fastapi from 0.111.0 to 0.112.0 (
284f4d4) - chore(deps): bump setuptools from 70.0.0 to 72.1.0 (
71524cd) - chore(deps-dev): bump pytest from 8.2.1 to 8.3.2 (
c29961b) - chore(deps): bump numpy from 1.26.4 to 2.0.1 (
d0169bc) - chore(deps): bump psycopg[binary] from 3.1.19 to 3.2.1 (
1a0a7a1) - chore: added default value for settings time interval (
bef1b4b)
- docs: added time interval configuration (
72f20b0)
- feat: added conditional filter (for dosage condition ext) (
c98e6e0) - feat: dynamic graph display app (
a5cdd54) - feat: added static graph display app (
9dd5450) - feat: added execution graph json to database (
7b7bb92) - feat: dynamic handling of time interval types (e.g. shifts) (
c2bddd3) - feat: implemented find_overlapping_windows (
a7e6e9b) - feat: implemented temporal aggregation combination (
7b3c3d8)
- refactor: renamed CriterionCombination to LogicalCriterionCombination (
eb5c576)
- revert: no explicit adding of negative intervals (
abb94dd)
- test(rectangle): fix naive create windows test (
80d7e56) - test: implemented temporal combination tests (
579e423)
- tests: fixed missing timezone parameter in create_time_intervals (
266390c)
- fix: loading both ventilation observable vs (
6b95b54) - fix: observation vs loading (
587d112) - fix: added default ee builder (
4ecec00) - fix: static datetime column labels (
51a9f29) - fix: import error (
c2f4b4f) - fix(drug_exposure): division by zero weight (
93757f5) - fix: parallel runner exception handling (
e7f5bcf) - fix: parallel runner exception handling (
b35af88) - fix: removed name from assessment (
b5f5b94)
- chore(deps): bump braces from 3.0.2 to 3.0.3 in /apps/viz-frontend (
9fbf591) - chore(deps): bump pydantic from 2.7.1 to 2.8.2 (
84c4c6b) - chore(deps): bump sympy from 1.12 to 1.13.0 (
8882bc4) - chore: update requirements (
f47e74d) - chore(pandas): prevent downcasting warning (
6a9e1e1) - chore(pydantic): updated use of deprecated methods (
c675ebc) - chore: update pre-commit (
8f5bd42)
- ci: fix semantic-release (
81cda94) - ci(depandabot): set main target branch (
73d6c37) - ci: manual triggering of workflow (
194cc53) - ci: fixed workflow (
10b1503)
- feat: add quick methods for creating CombinationCriterion (
6549c18) - feat: set person_id to BigInt (
449381b) - feat: allow override value required (
8f1d63b) - feat: add register() method to StandardVocabulary (
2670c6e) - feat: implemented ventilation observable characteristic (
273407f) - feat: implemented updated observation characteristic (
d165075) - feat: add builder to allow individual configurations (
f964dd1)
- refactor: removed ventilation-observable characteristic (
0cb5ab2) - refactor: removed abstract methods from Criterion (
a7ac65d) - refactor: add type check for converters (
ffb2672) - refactor: parser version independent from recommendation (
c7df6b2)
- fix: criterion duplicate detection (removed "name" from eq) (
e971dc4) - fix: drug_administration exclude flag for dosages (
4f77591) - fix: task processing of empty base data intervals (
22ce873) - fix: repr of expressions (
fa6c816) - fix: double exclusion of drug dosages (
8e89340) - fix: wrong attribute name (
dcd8392) - fix: missing default parameter (
d2949d0) - fix: checking for existence of schema first (
548b593) - fix(cohort_logic): unpickling of BaseExpr objects (
72d44f4) - fix: preserving NO_DATA intervals after counting (
cbe4986) - fix(cohort_logic): infinite recursion due to new/init (
02bb73c) - fix: action parser v2 (
bbf21ba) - fix: explicit version in app (
ea6f5c6) - fix: count rectangle logic (
578b300) - fix: handling of Count expr (
6598630) - fix(drug_exposure): default dose: Any >1/Day (
e3324b5) - fix: pandas behavior for chained assignment, downcasting (
ddf3c83) - fix(drug_exposure): using value_min=1 instead of value=1 for no frequency (
b1e5b63) - fix: fixed paths in execute.py (
626563c) - fix: creation of celida views (
43bf5a6) - fix: index creation with descending column (
dec2db4) - fix: active patients selection (
dfb9b44) - fix: added base criterion & datetime filtering to criteria queries (
632cd1b) - fix: recommendation creation from database (
a9c315d) - fix: filtering negative duration intervals (
8066ed8) - fix: tidal volume per ideal body weight query (
942d36f) - fix: parallel runner could not pickle namedtuple from pyx (
9ecaa5e) - fix: interval normalization for storage (
d5948c9) - fix: interval normalization for storage (
4389d80) - fix: rectangle processing (
3dcb20f) - fix: parallel task runner (
d8cc157) - fix: static criteria in PointInTimeCriterion (
c5aa33e) - fix: priority order when merging criterion intervals (
0af15a6) - fix(drug_exposure): incorrect type expected (
37f13fe) - fix: fixed converter for new FHIR Timing definition (
94ac078) - fix: forward fill not removing last second (
0b2b61a) - fix: unique task name (
58c2ec5) - fix: added Criterion/Expr eq/hash (
ab84a1c)
- chore(pydantic): updated to pydantic v2 (
83d5706) - chore(deps-dev): bump tqdm from 4.66.2 to 4.66.4 (
ff0d73a) - chore(deps): bump fastapi from 0.110.2 to 0.111.0 (
b75d1ec) - chore(deps): bump sqlalchemy from 2.0.29 to 2.0.30 (
2b83a93) - chore(deps-dev): bump pytest from 8.1.1 to 8.2.0 (
1d3948a) - chore(deps): bump ejs from 3.1.9 to 3.1.10 in /apps/viz-frontend (
e8c6bd1) - chore(deps): bump networkx from 3.2.1 to 3.3 (
0a9f3da) - chore(deps): bump pandas from 2.2.1 to 2.2.2 (
150ce04) - chore(deps): bump setuptools from 69.2.0 to 69.5.1 (
b984b45) - chore(deps): bump fastapi from 0.110.0 to 0.110.2 (
251383c) - chore(deps): bump cython from 3.0.9 to 3.0.10 (
ba7cd26) - chore(deps): bump express from 4.18.2 to 4.19.2 in /apps/viz-frontend (
570be21) - chore(deps-dev): bump pytest-cov from 4.1.0 to 5.0.0 (
16735f1) - chore(deps): bump sqlalchemy from 2.0.28 to 2.0.29 (
85a051a) - chore(deps): bump uvicorn[standard] from 0.28.0 to 0.29.0 (
7ee1dde) - chore(deps): bump webpack-dev-middleware in /apps/viz-frontend (
c6078f7) - chore(deps): bump setuptools from 69.1.1 to 69.2.0 (
19c52c0) - chore(deps): bump follow-redirects in /apps/viz-frontend (
d97f64b) - chore: updaqted pytest, pytest-postgres (
bf0e9c9) - chore: updated uvicorn, cython, sqlachemy (
1804bc5) - chore(deps): bump es5-ext from 0.10.62 to 0.10.63 in /apps/viz-frontend (
bb813ec) - chore(deps-dev): bump httpx from 0.26.0 to 0.27.0 (
05f0f85) - chore(deps): bump setuptools from 69.1.0 to 69.1.1 (
bedb04b) - chore(deps-dev): bump pytest from 8.0.1 to 8.0.2 (
70c211d) - chore(deps): bump pandas from 2.2.0 to 2.2.1 (
923d1ba) - chore(deps): bump fastapi from 0.109.2 to 0.110.0 (
8f08334) - chore(deps-dev): bump pytest from 8.0.0 to 8.0.1 (
2de8565) - chore(deps): bump sqlalchemy from 2.0.26 to 2.0.27 (
32c1f25) - chore: removed pyinterval from requirements (
3be202d) - chore(deps-dev): bump tqdm from 4.66.1 to 4.66.2 (
d59baa4) - chore(deps): bump numpy from 1.26.3 to 1.26.4 (
7d55d4e) - chore(deps): bump setuptools from 69.0.3 to 69.1.0 (
60d83ae) - chore(deps): bump sqlalchemy from 2.0.25 to 2.0.26 (
13a90db) - chore(deps): bump uvicorn[standard] from 0.27.0.post1 to 0.27.1 (
520cfcf) - chore(deps): bump fastapi from 0.109.1 to 0.109.2 (
20b19c2) - chore(deps): bump psycopg[binary] from 3.1.17 to 3.1.18 (
db32fdc) - chore(deps): bump pytz from 2023.4 to 2024.1 (
82e0403) - chore(deps): bump fastapi from 0.109.0 to 0.109.1 (
b700696) - chore(deps-dev): bump pytest-postgresql from 5.0.0 to 5.1.0 (
fbce1ce) - chore(deps): bump pytz from 2023.3.post1 to 2023.4 (
6e35cf8) - chore(deps): bump uvicorn[standard] from 0.26.0 to 0.27.0.post1 (
9fc2fb2) - chore(deps): bump python-dotenv from 0.21.1 to 1.0.1 (
64228ad) - chore(deps-dev): bump pytest from 7.4.4 to 8.0.0 (
56cd920) - chore(deps): bump uvicorn[standard] from 0.25.0 to 0.26.0 (
882fee5) - chore(deps): bump numpy from 1.26.2 to 1.26.3 (
027d841) - chore(deps): bump pandas from 2.1.4 to 2.2.0 (
80f7d25) - chore(deps): bump setuptools from 68.0.0 to 69.0.3 (
fba4a83) - chore(deps): bump follow-redirects in /apps/viz-frontend (
4ce519c) - chore: ignoring .c files in task/process (
50c1db9) - chore: version bump to 2.0.0-rc1 (
9825042) - chore: updated requirements (
1aea8c7) - chore: updated sample.env (
d1a529f) - chore: updated requirements-dev.txt (
804d05c)
- style: removed unnecessary context manager (
f4ebc00) - style: comment cleanup (
bf4225c) - style: changed criteria description format (
d474ba4)
- ci: merge into single workflow (
b628de9) - ci: add main to semantic-release action (
239b94f) - ci: changed target branch to dev (
c863756) - ci: fixed release notes (
1729d62) - ci: specified dev branch (
f5faa04) - ci: added semantic-release action (
9e48390) - ci: init semantic release (
6f09151) - ci: changed rec server test url (
54caf6f) - ci(dependabot): bump codecov/codecov-action from 3 to 4 (
23b1fd6) - ci: fixed env variable names in gh action (
0e02746) - ci: updated recommendation-server env variables (
84b78f9) - ci: added build before test (
5e939a3) - ci: set new env variables in test.yml (
828a889) - ci(dependabot): bump actions/setup-python from 4 to 5 (
163ce9e)
- feat: implemented invalid_combinations for test v2 (
947e2de) - feat: implemented assessment action & scale goal (
e490083) - feat: added weight-related dosage query (
c10a1cc) - feat: allowing multiple dosages per drug action (
aabc4a8) - feat: set recommendation versions back to latest (
9dd5097) - feat: added version-specific ebm-cpg parsers (
0d9e7a4) - feat: added version compare function (
22dbe5e) - feat: added drug route selection (
82098e6) - feat: added handling of additional operators (
9fc3489) - feat: improved code, added pyx (
9057739) - feat: added additional operators (
0094e21) - feat(rectangle_python): added union with count (
96b438d) - feat: made settings configurable (
39e6164) - feat: added versioning to recommendations/tests (
79966a7) - feat: added debug & query logging (
e4dde1f) - feat: checking for available interval_start/interval_end (
ea0ec00) - feat: implemented select_type for interval_portion (
755b4ac) - feat: added pool size parameter (
c1510e6) - feat: intersection priority order: NO_DATA>POSITIVE (
72b1059) - feat: allow use of visit_detail table for episode of care (
720ca89) - feat: added multiprocessing switch (
44c5557) - feat(db): added version, made schema dynamic (
a0174c2) - feat(ExecutionGraph): late import of matplotlib (
8c3b7fe) - feat: interval_result view uses criterion description (
97068ae)
- perf: added indices (
dc9cc1c) - perf: added cython rectangle (
be4b556) - perf: improved recommendation test setup (
a03e263) - perf: changed deepcopy to copy in criterion (
fb7a413) - perf: implemented geometry operations (
f5973e0) - perf: on-demand init of database structure (
ec0cfe2) - perf: removed pandas from tasks (
213cdb2) - perf: removed pandas from process (
2a4be43)
- refactor: removed name from criterion/converters (
6862c9b) - refactor: recommendation test setup code (
40709e4) - refactor: renamed parsers (
dbd6c1c) - refactor: renamed FhirParser (
e74c5cc) - refactor: moved fhir parsing code to own class (
f1a8ef4) - refactor: moved logging messages (
2045870) - refactor: updated to pendulum 3.0.0 (
2bd6c46) - refactor: replaced sympy logic classes by own (
4ffec08)
- revert: removed timing processing from converter (
8e90ba1)
- test: add route concept to tests (
3e33a06) - test: set recommendation package version to latest (
bd3123a) - test: update testdata (
5ed77be) - test: added max/min/exact tests (
ca26cfd) - test: fixed tests (missing package_version) (
79ca60c) - test: running only rec35 & m1 (
4c14fc0) - test: fixed missing data type (
8871acf) - test: fixed task identification (
be42d67) - test: rest_api fixed httpx warning (
2ab3d51) - test: adjusted rec36a expected data (
1abfc0a) - test: fixed missing data type (
113aece) - test: fixed missing data type (
d9f40a3) - test: fixed type of allergy parameters (
28ae25e) - test: fixed tests (
fbc992f) - test: rec36a fixed expectations (
78fc95e) - test: fixed expected data (intervals are now merged) (
7f87f95) - test: using 200 entries instead of 30 for "fast" rec test (
901e19b) - test: removed execution map tests (
9bd0d00) - test: rec36a tests (
9c437a1)
- tests(assessment): implemented tests (
3892f32) - tests(app): fixed recommendation test (
287968f) - tests(drug_exposure): weight related test (
9853bae) - tests: fix cohort logic str tests (
46db84b) - tests: fix tests that included (abstract)criterion name (
9325892) - tests(rec17): implemented v2 tests (
949a022) - tests(rec17): implemented v2 tests (
ecd610e) - tests: fixed heparin,argatroban generators (
bfce919) - tests: fixed ddimer unit (
719508d) - tests(rec18): fixed 1.4 test (
7ecb288) - tests(rec15): implemented tests v2 (
8d33ca4) - tests: fixed combination generation (
1b307ca) - tests: fixed observation generator without value (
e8cbef7) - tests: fixed missing data type of Allergy generators (
69b030a) - tests(rec18): implemented all drugs (
e4306de) - tests(rec18): implemented all dalteparin tests (
4b3f7e7) - tests(rec18): implemented dalteparin test (
14079db) - tests: add definitions (
cfd0821) - tests: fix generators for visit, drug_exposure (
d9d9e49) - tests: add international unit (
7e2f4e0) - tests(rec36a): implemented v2 tests (
fab90c4) - tests(rec36b): started adaptation to test framework v2 (
1deb18c) - tests(rec15-18): added 1.5 test skeletons (
447803d) - tests(rec36b): using new test framework (
c253dc6) - tests(sepsis): using new test framework (
d1e353e) - tests(rec35): removed old implementation (
76bd469) - tests(rec35): implemented test v2 (
d13bd97) - tests: implementing TestRecommendationBase v2 (
eaacc02) - tests: added DataGenerator classes (
c8daf3a) - tests: rec17, rec18 set fixed recommendation version (
698fca6) - tests: updated testdata ref (
eff506c) - tests: added DrugAdministrationAction tests (
a4606bc) - tests: updated testdata ref (
4039e6b) - tests(rec36a): reduced number of tests (
3032aa6) - tests(rec18): Reducing number of tests (
9517733) - tests(rec17): Reducing number of tests (
09f8735) - tests: prevent duplicate criteria in explicit combinations (
4c00f80) - tests: added explicit combination option (
1dc56ac) - tests: fix criterion name (
2f177a4) - tests: fix parsing, random sample, aPTT (
1701411) - tests: different comparators possible (
bdbafe2) - tests: refactored recommendation test code (
96f76b6) - tests(combination): fixed repr/str expectation (
eeaa787) - tests(rec17): set package version to latest (
609b299) - tests(rec18): added atrial fibrillation (
1d62c79) - tests: fixed rec15 test for latest version (using at least) (
cfe5566) - tests: set explicit recommendation version (
28ef74b) - tests: added route test (
335ba48) - tests: rectangle tests for both implementations (
288fff2) - tests: fix import of merge_adjacent_intervals (
ae9bbf2) - tests: added rectangle with count tests (
f75e8ce) - tests(rec15/rec17): added tests for updated recommendations (
e868a9d) - tests: fixed tests (
2a7a0ba) - tests: fixed run_id & active patients (
8a5c6c6) - tests: re-enabled all tests (
cf8f6c2) - tests(rest_api): fix tests (
4ef282e) - tests: fixed cohort logic tests (
90ea5fd) - tests: omop.concepts (
20bc847)
- Update test.yml (
3513e89) - updated testdata ref (
93303e7) - Bump fastapi from 0.108.0 to 0.109.0 (
750d0bd) - Update README.md (
814fcb1) - updated README (
c91c07a) - added execute script (
5b0167e) - Bump fastapi from 0.105.0 to 0.108.0 (
ac06aa1) - Bump httpx from 0.25.2 to 0.26.0 (
d708b6d) - Bump uvicorn[standard] from 0.24.0.post1 to 0.25.0 (
43f39f1) - Bump psycopg[binary] from 3.1.15 to 3.1.16 (
6c4e1d8) - added processing tests (
044e7c2) - updated trigger error message (
a586f0d) - added datetime offset to testdata creation (
6ca22d9) - fixed merging of different interval types (
033ec2c) - added value serialization tests (
5752295) - improved interval overlap trigger error message (
a260063) - clean up (
0c98766) - fixed tests (
44d8654) - added interval merging switch to test_criterion (
e1c5e07) - implemented negative-dominant result merging (
2d62833) - made Task.handle_criterion static (
4671b65) - fixed interval union for different priority order (
a106858) - fixed test teardown (database cleaning) (
8baf4e5) - streamlined postgres trigger disable in tests (
ce37d4a) - fixed dst changes (
5daf527) - implemented procedure timing (
b731b15) - fixed DrugAdministration parsing (
d2e2321) - updated ProcedureOccurrence to Timing (
4b8e941) - fixed drug_exposure at DST changes and tests (
1557295) - fixed tidal volume test: if height is before tv: negative (
d1e40f3) - fixed observation/measurement tests (
8c5786e) - fixed tests (
fe029ad) - fixed trigger test (
0ee2fc6) - updated timing processing (
477b561) - fixed concepts test (
873024e) - fixed check_int (
f4fe238) - fixed imports (
9283ae7) - added process.forward_fill (
fcb15ec) - updated to new Dosage type, added Timing parser (
bb9d855) - re-added ValueCount (
f179ca0) - simplified Timing typ (
2ee7b5e) - added missing files (
edcc091) - added tests (
5b42f1b) - fixed circular import (
6197fc3) - added convenience constructor for Timing (
d96fb03) - implemented additional Value types (
5dde0f3) - moved TimeRange to types (
c92bb65) - changed Concept str/repr (
2a2529d) - fixed expected results of recommendation (
5eb5e2f) - added custom priority orders as contextmanager (
cb8d5ae) - clean up (
831def3) - different intersection priority order in P&I (
c20c8a8) - changed interval intersection priority order (
af3f268) - streamlined tidal volume custom criterion (
3503da3) - removed duration from PointInTime criterion (
e98bd23) - updated DateTime type (
c95e12b) - updated viz apps (
cd595cc) - fixed hard coded schema name (
4aa3495) - fixed drug exposure without dose/interval (
a68ffdc) - fixed interval replace (
bebf1fa) - fixed different expectation re population coverage (full/partial day) (
38d8f29) - added interval_coverage view (
199e6cf) - added psql trigger test (
e5a9626) - fixed interval OR (
4b80ac1) - renamed celida tables (
10d8767) - changed union interval order (
3972a5c) - fixed static criteria (
2be0f52) - fixed rec15 functionality (
88629b5) - added interval result view (
3600dc2) - fixed masking (
d22e3fd) - exchanged interval with interval with type (
aea3f20) - implemented Interval with type (
4c55142) - improved execution graph (
14d5c74) - changed p/i combination to OR (
24d3e35) - fixing multi-pi_plan recommendations (
f38d3fa) - fixed full_day_coverage view (
7986af3) - added execution graph (
1c99c2b) - added handling of P&I combination (
82bc31f) - fixed drug exposure test (
767fa9f) - drug exposure now selecting drugs as subquery during execution (
3d5bc88) - implemented execution map tests (
68ed040) - moved app tests to apps folder (
426bf3b) - fixed visit_occurrence test (
6df38a5) - added viz backend/frontend apps (
e4eb509) - renamed rest_api app (
fcc7948) - fixed value tests (
4c24927) - fixed drug exposure tests (
c0c23c4) - (partially) fixed tests (
76b245c) - fixed active patients test (
1bd22d4) - renamed RecommendationPlan table (
030bfda) - improved concept description (
7835a7d) - renamed CohortDefintion and CohortDefinitionCombination (
e0236b8) - refactored registration process (
af15c86) - updated pendulum to 3.0.0 (
2d7eead) - Bump psycopg[binary] from 3.1.14 to 3.1.15 (
6d983e7) - Bump fastapi from 0.104.1 to 0.105.0 (
ff2f635) - Bump psycopg[binary] from 3.1.13 to 3.1.14 (
2ebdf7c) - Bump pytest-env from 1.1.1 to 1.1.3 (
fa3e240) - Bump pandas from 2.1.3 to 2.1.4 (
da354bc) - Update test.yml (
6da47e0) - Bump httpx from 0.25.1 to 0.25.2 (
5d61190) - fixed package import (
bf254f8) - implemented process tests (
3d0a418) - using DateTimeInterval, fixed no data inversion (
9ff1a7c) - consolidating criterion intervals for logical operators (
6c8d2dd) - implemented combinations (
b49fcb2) - split criteria into p, i; added params to tasks (
89f29a9) - fixed drug exposure (
8bb7cf4) - fixed tidal volume test (
2fba1fb) - dynamic omop schema name (
846da54) - refactored conditional column creation (
4080a0a) - added portion (
6a7eec2) - adapted (partially) tvibw (
1bb7345) - fixed view existence check (
d0b0c15) - fixed tests (
e2bd44a) - fixed tests (
b104fae) - refactoring (
dee356a) - added PointInTime criterion (for Meas, Obs) (
b09ca70) - explicit Enum datatypes (
27c9771) - updated Value.to_sql to use TableClause (
75ba8d6) - adapted procedure occurrence (
2b96d5f) - adapted procedure occurrence (
634c9e3) - fixed test active patients (
8e0c3a2) - implemented interval inversion (
ae68f8f) - fixed active_patients test (
9bc2650) - added partial_day_coverage view (
b239d17) - added full_day_coverage view (
ae85452) - fixed bugs (
4a17178) - refactoring (
1bc6a72) - extended logic (
4cff316) - updated index names (
e2f7789) - split up cohort definition file (
2ad1fef) - split up cohort definition file (
d63c9ca) - changed docstring style (
f7b4d09) - added exception handling (
8494952) - added exception handling (
34b5347) - implemented class scheme for runner (
6abe49d) - fixed multiprocessing (
cdccc85) - added tasks and runner (
6258a9b) - added interval processing (
02e3d12) - current status (
b834fe7) - skipping peep test (
6ca5e01) - Bump psycopg[binary] from 3.1.12 to 3.1.13 (
2409e43) - all values per day must be true (
fe352bb) - added pytest instructions (
0234e77) - test all values per day valid (
acc06ec) - quoting user/pass in db conn str (
4d53bac) - Bump uvicorn[standard] from 0.23.2 to 0.24.0.post1 (
b2eef85) - Bump sqlalchemy from 2.0.22 to 2.0.23 (
77f6f5e) - Bump httpx from 0.25.0 to 0.25.1 (
77b7504) - Bump pandas from 2.1.1 to 2.1.3 (
fbc3404) - Update pydantic requirement from <2.0.0 to <3.0.0 (
049c25d) - Bump pytest-env from 1.1.0 to 1.1.1 (
1f10cfa) - Bump fastapi from 0.104.0 to 0.104.1 (
134e9a5) - fixed tests (
ebbf806) - set pydantic to <2 (
90a0567) - version bumps (
ed263bc) - refactoring, tests for commenting added (
513ced6) - Bump tqdm from 4.65.0 to 4.66.1 (
b687e70) - Bump fastapi from 0.100.1 to 0.101.1 (
25632b6) - Bump uvicorn[standard] from 0.23.0 to 0.23.2 (
20df49f) - Bump fastapi from 0.100.0 to 0.100.1 (
5bd8062) - Bump uvicorn[standard] from 0.22.0 to 0.23.0 (
556d13a) - Bump fastapi from 0.97.0 to 0.100.0 (
b7161a2) - Bump pytest from 7.3.2 to 7.4.0 (
801633d) - updated readme (
50a677b) - fixed exception reporting (
b7210a3) - added exception handling for tx server (
da68a90) - Bump pytest-env from 0.8.1 to 0.8.2 (
5148063) - removed thrombocytopenia from test (
9ffcfc0) - fixed converter test (
cbd4d95) - updated tests (
2fcef61) - fixed wrong field usage in Quantity.unit (
39c8b9b) - updated testdata: added tinzaparin (
2f92574) - Bump pytest from 7.3.1 to 7.3.2 (
bae2528) - Bump fastapi from 0.95.2 to 0.97.0 (
bb99b0f) - refactored fastapi app, added comments (
ed0f222) - fixed execution map test (
06836d6) - fixed rowcount logging (
0d94823) - test different cte (
1408530) - added index to recommendation_result table (
e5beaf0) - only using python3.11 in tests (
dbded94) - improved exclusion statement (
6f379c6) - improved exclusion statement (
0592e57) - improved logging (
d0964de) - adapted tests to new exclusion strategy (
8eb3411) - moved exclusion to combination statements (
bf38afc) - changed result db structure, added query description (
5a65e2f) - added indices (
878c691) - fixed drug exposure: zero length exposure (
11a33cc) - added psycopg binary requirements (
b32a917) - renamed test recommendation base file (
2b7eef2) - code cleanup (
7f26670) - added recommendation tests (
ca5940e) - changed precision requirement (
ba0a22c) - fixed ValueNumber tests (
bf1e033) - added tidal volume criterion tests (
3b3d231) - changed ValueNumber for floating point comparisons (
5752922) - removed duplicate code (
a8490c8) - fixed duration calculation (
d7fb3fe) - implemented rec36b tests (
7da4989) - updated omop testdata ref (
dfcb6d6) - fixed sepsis m1 test (
737d65e) - fixed tidal volume per body weight calc (
5bd20f2) - implemented sepsis m1 tests (
2d78ecb) - reduced test number (
8f78842) - implemented rec36a tests (
1166a4a) - implemented rec36a tests (
6b0f3f3) - Bump pytest-cov from 4.0.0 to 4.1.0 (
bc7766f) - implemented rec35 tests (
1955317) - fixed goal exclusion if no action is specified (
11dcd56) - added parameters (
b9211e1) - implemented rec18 tests (
eacc678) - fixed goal exclusion (
9d38f2f) - fixed active patients test (
234fae8) - fixed criterion tests (
8f1c672) - added env to github workflow (
d443495) - implemented rec17 tests (
2c595e6) - added result mismatch reporting (
1bd0f53) - moved common code into TestRecommendationBase (
e4cb60d) - added separate sql query logger (
9afc7a3) - Bump fastapi from 0.95.1 to 0.95.2 (
f9cfe0f) - Bump pytest-postgresql from 4.1.1 to 5.0.0 (
66e525c) - Bump httpx from 0.24.0 to 0.24.1 (
b699ea9) - Bump uvicorn[standard] from 0.21.1 to 0.22.0 (
67757e5) - added combination (db) test (
3576ff8) - Update dependabot.yml (
a61a3c9) - multiple person test: drug_exp, meas, obs (
a6f42b9) - added multiple person test to active_patients (
f5048bd) - added multiple person test to occurrences (
73a51f0) - fixed rec15 test (
32967a6) - updated testdata (
7b2a7b9) - added visit_occurrence tests (
0cfad35) - fixed interval (
1737d78) - updated testdata (
11ad3e4) - fixed drug exposure frequencies, boundaries & added tests (
d5ea84f) - adjusted test cases to edge values (
746e0e3) - added drug exposure explicit tests (
84d2921) - fixed value test (
a414cab) - fixed recommendation test (
b96d011) - added value concept tests (
ed70693) - added value concept tests (
b283e71) - added observation tests (numeric only) (
32cba40) - created value criterion test suite (
67dc7d6) - added measurement tests (
2abf94b) - update omop testdata (
368448e) - add ValueNumber.parse function (
93bf75f) - added procedure_occurrence tests (
a237bae) - restricting output date ranges to observation period (
1247857) - db: changed to timezone-aware datetime columns (
b4a8e33) - renamed criterion->condition (
da95023) - updated testdata (
14cb62b) - added condition_occurrence single patient tests (
6957b8d) - fixed active patients during period selection (
b10f3a3) - added fastapi tests (
8bdedc8) - restructured tests & added converter tests (
d5b48e2) - added fhir.util tests (
1f169aa) - added FHIRClient tests (
b97a782) - added terminology tests (
c96292a) - fixed db setup/teardown (
1669945) - restructured tests dir (
2acac73) - fixed database connection in tests (
594b2df) - fixed tests (
759688c) - added CriterionCombination tests (
f1ec6e5) - added execution map tests (
7446036) - additional coverage for utiL (
b55be64) - added recommendation tests to gh workflow (
8277f8a) - recommendation test stubs (
cf3dc71) - added recommendation test run cli option (
37c7668) - added ee.utils tests (
c25e263) - added codecov (
c224630) - fixed workflow (
86c1663) - added slow tests markers (
d6826d6) - added dependabot (
e63b321) - rec server as service (
e63c77f) - added recommendation server building (
9aeb28c) - expose ports (
584e945) - added postgres environment variables (
23447b1) - updated to psycopg3 (
b82ae13) - added pytest github workflow (
b7eede3) - added submodule (
d2c1264) - moved fixtures into separate directory (
7a10ebd) - removed session (
8f12fca) - migrated table defs to new style (
701a39d) - sqlalchemy 2 declarative tables (
1ba1ccf) - migrate to sqlalchemy 2.0 (updated lib) (
f91f372) - migrate to sqlalchemy 2.0 (
3dd9c3e) - removed ExecutionEngine from main module import (
b2acfb4) - added vocabulary logger (
28d08e0) - implemented drug frequency (
bba6f0f) - dirty test implementation (
a0dc4c4) - fix drug_exposure valid_to (
3c26fef) - calculate drug quantity per interval (
a2aef53) - body_weight as static criterion (
4be73c9) - filtering datetime by datetime_end also (
4d7297c) - select visit_occurrence id & datetime (
f144d21) - fixed ProcedureOccurrence constructor (
ccc3cac) - fixed exclusion for drug administration extensions (
4e8b560) - fixed valid range for static vars (
c75677f) - autodetect allergies (
2938b15) - updated to FHIR R5 (
d876153) - added static parameter to criteria/characteristics (
f724253) - fixed person_id join (
9197dae) - implemented per day output (
5e17f53) - removed patient data result table (
ecde5dd) - updated precommit (
514129d) - updated readme (
84a0390) - added drug concept, end datetimes, description (
038d359) - fixed api (
a18ae07) - added title and name to recommendation (
596db60) - added criteria names, sqlalchemy (
b9b7a7b) - implementing fastapi interface (
70cb734) - fixed tidal volume (
d6637a1) - fixed exclusion (
60576b7) - added compiled statement logging (
1daac46) - changed from active patients to patients during period (
24cba4b) - updated requirements (
169ff3e) - updated README (
2916361) - fixed negative criteria (exclude) (
83182ad) - same base criterion for all cohort defs (
43ed2cc) - fixed combination query (
04a8a9c) - fixed multiple selection of person_id (
316076d) - fixed cohort def hashing & distinct persons (
48bef20) - implemented select data for custom criterion (
98994ec) - add configuration (
818bb08) - saving basetable (active patients) to results (
0ab3dcf) - moved OMOP concepts to constants (
c3ec58d) - implemented patient data result (
46ead45) - modified pre-commit (
e2f9ad2) - fixed sql generation (
722ad4f) - adapted queries for result table (
81e3f92) - fixed hashing (
9651a04) - implemented dict / from_dict (
ae4f8b1) - starting insert into result tables (
599adb3) - added Criterion.category (
2927273) - added result tables (
b1673bd) - added check for base table join (
ad55c52) - removed unused imports (
3ba4750) - updated pre-commit conf (
cd3f502) - sqlachemied ExecutionMap (
e6870e7) - implemented recommendation collection (
fdb40a5) - fixed sql (
53af529) - updated OMOP CDM to 5.4 (
c22de43) - fixing sql statements (
84a657b) - using sqlalchemy models (
4edaed7) - added select into statements (
bf2fe3c) - added procedure duration (
2991f3c) - implemented datetime window (
60080fc) - added explicit ucum unit names (
4923462) - added custom concept (
8db3667) - updated readme (
81c4158) - added dose-condition-extension (
a95b019) - error for unimplemented selection behavior (
ca5f235) - body positioning action (
bd6edcc) - ventilator mgmt goal (
ee36064) - implemented laboratory value goal (
d110d50) - added goals & single factory class (
5db856b) - refactoring (
9ab413a) - implemented one-or-more selection behavior (
d99599d) - drug administration continued (
7fccc16) - implementing drug administration action (
b9b90be) - added values for measurement (
2cf1364) - added conversion to criterion (
427fe8e) - code cleanup (
b19308a) - added compopsition of sql statements (
45d1747) - type hinting python 3.10 style (
a939885) - clean up (
67d8ffb) - merge json-cohort-def (
99f7c44) - current status - unverified (
efd2800) - removed cohort definition (json) code (
1e270dc) - reading all recommendations (
d57956b) - exclude is assumed to be False by default (
91d069c) - added search workaround (
28c0859) - corrected laboratory & added ventilation mgmt (
d68a165) - updated init.py (
5b6d9d7) - implemented additional criteria (
6eb4135) - added exclusion handling (
843da24) - updated readme (
c144033) - implemented cohort definition for conditions (
8bacf1d) - continued development (
97904fd) - initial commit (
514025d)