Releases: CODEX-CELIDA/execution-engine
Releases · CODEX-CELIDA/execution-engine
v2.4.0
What's Changed
Bug fixes
- comment fixes in
32df5a4
- recommendation and criterion ids are (de)serialized less incorrectly in
0a9c8ff
- use commnon style for Recommendation._base_criterion serialization in
2c660fa
- include _root attribute in (de)serialization of CriterionCombination in
a8f770f
- widen type signature of Serializable.from_json to include bytes in
ab8564a
- random minor fixes in
8d8523e
- filter intervention criteria by population in
03c3902
- unpickling of temporal count in
0cd4e04
- sort criteria, give proper titles, and group in
afac6b1
- cohort logic reduction in
c530621
- processing of temporal criteria in
55801d4
- graph node display of temporal combinations in
cff71cf
- (de)serialize PopulationInterventionPair.{population,intervention} with class info in
76bf3b8
- serialize NonCommutativeLogicalCriterionCombination.{left,right} with class information in
23f3643
- allow deserializing a Timing instance as ProcedureOccurrence.timing in
e94790b
- use of visit_detail in ActivePatients in
7b33c6b
- cytoscape graph for non-concept criteria in
a5a0f91
Chores
- bump path-to-regexp and express in /apps/viz-frontend in
32f8da7
- bump nanoid from 3.3.7 to 3.3.8 in /apps/viz-frontend in
a7b4b46
- bump the dependencies group with 4 updates in
5ab168d
- update submodule in
3fc9d59
- bump the dependencies group with 3 updates in
7cf9f3d
- bump the dependencies group with 4 updates in
abc94ce
- bump cross-spawn from 7.0.3 to 7.0.6 in /apps/viz-frontend in
8ab7aff
- bump the dependencies group with 2 updates in
a2d21a6
- bump the dependencies group with 2 updates in
765df8b
- bump the dependencies group with 4 updates in
5d0fbdf
- bump the dependencies group with 2 updates in
bd186bb
- bump http-proxy-middleware in /apps/viz-frontend in
d7863ab
- bump the dependencies group with 5 updates in
15ed84f
- bump the dependencies group with 10 updates in
570acd9
- bump uvicorn[standard] from 0.31.0 to 0.31.1 in
c09c50f
- update rollup in
72dd535
- update deps in
6978695
- bump body-parser and express in /apps/viz-frontend in
33e1dd3
- bump send and express in /apps/viz-frontend in
66a4e5a
- bump serve-static and express in /apps/viz-frontend in
f7a6538
- bump path-to-regexp and express in /apps/viz-frontend in
9cfbc2b
- bump express from 4.19.2 to 4.21.0 in /apps/viz-frontend in
58049a6
- bump sympy from 1.13.0 to 1.13.2 in
4b45f40
- bump sqlalchemy from 2.0.30 to 2.0.35 in
0634cc1
- bump pydantic-settings from 2.3.4 to 2.5.2 in
a262a35
- bump micromatch from 4.0.5 to 4.0.8 in /apps/viz-frontend in
b118011
- bump webpack from 5.89.0 to 5.94.0 in /apps/viz-frontend in
8a9bd5a
- bump pyyaml from 6.0.1 to 6.0.2 in
35f2338
- bump tqdm from 4.66.4 to 4.66.5 in
91d005f
Continuous integration
- fix semantic release in
a933fe3
- update pre-commit in
09ef28f
- bump codecov/codecov-action from 4 to 5 in
86182aa
- dependabot validation in
da94b07
- dependabot grouped updates in
ac34af8
Documentation
Features
- remove intervention sink in
751dce2
- add AnyTime temporal criterion in
de284b7
- add PointInTimeCriterion.forward_fill property in
b0440f0
- falling back to non-standard concepts when standard is not found in
4ddaf53
Performance improvements
Refactoring
- remove exclude attribute in
01eecd1
- use logical not criterion combination instead of exclude=True in
79b5791
Revert
- removed not-applicable view in
d4b181b
Testing
- fixed vocabulary test in [
013e009
](https://github.com/CODEX-CELIDA/execution-engine/c...
v2.3.0
What's Changed
Feature
Fix
- dose info in nodes in
0848d88
- interval ffill until observation_window end in
4c9ade1
- display of 0 sec entries in
51d5304
- tidal volume for <110 cm height in
7833827
- displaying recommendation name in
2b4c5a5
- database timezone setting in
5c00d67
- colors, sorting, display in
531c6ab
Performance
- interval per person in
99c7d51
Refactor
Test
- adapted to measurement value forward filling until end of observation window in
a27eef6
- ffill with observation window in
14e6187
Unknown
v2.2.0
What's Changed
Feature
- added conditional filter (for dosage condition ext) in
c98e6e0
- dynamic graph display app in
a5cdd54
- added static graph display app in
9dd5450
- added execution graph json to database in
7b7bb92
- dynamic handling of time interval types (e.g. shifts) in
c2bddd3
- implemented find_overlapping_windows in
a7e6e9b
- implemented temporal aggregation combination in
7b3c3d8
Fix
- type hints in
d0358f5
- made TimeIntervalType serializable in
c6ee140
- overlapping intervals for adjacent windows in
c95bdd6
Chore
- bump fastapi from 0.111.0 to 0.112.0 in
284f4d4
- bump setuptools from 70.0.0 to 72.1.0 in
71524cd
- bump pytest from 8.2.1 to 8.3.2 in
c29961b
- bump numpy from 1.26.4 to 2.0.1 in
d0169bc
- bump psycopg[binary] from 3.1.19 to 3.2.1 in
1a0a7a1
- added default value for settings time interval in
bef1b4b
Documentation
- added time interval configuration in
72f20b0
Refactor
- renamed CriterionCombination to LogicalCriterionCombination in
eb5c576
Revert
- no explicit adding of negative intervals in
abb94dd
Test
Tests
- fixed missing timezone parameter in create_time_intervals in
266390c
Unknown
v2.1.0
What's Changed
Feature
- add quick methods for creating CombinationCriterion in
6549c18
- set person_id to BigInt in
449381b
- allow override value required in
8f1d63b
- add register() method to StandardVocabulary in
2670c6e
- implemented ventilation observable characteristic in
273407f
- implemented updated observation characteristic in
d165075
- add builder to allow individual configurations in
f964dd1
Fix
- loading both ventilation observable vs in
6b95b54
- observation vs loading in
587d112
- added default ee builder in
4ecec00
- static datetime column labels in
51a9f29
- import error in
c2f4b4f
- division by zero weight in
93757f5
- parallel runner exception handling in
e7f5bcf
- parallel runner exception handling in
b35af88
- removed name from assessment in
b5f5b94
Chore
- bump braces from 3.0.2 to 3.0.3 in /apps/viz-frontend in
9fbf591
- bump pydantic from 2.7.1 to 2.8.2 in
84c4c6b
- bump sympy from 1.12 to 1.13.0 in
8882bc4
- update requirements in
f47e74d
- prevent downcasting warning in
6a9e1e1
- updated use of deprecated methods in
c675ebc
- update pre-commit in
8f5bd42
Ci
- fix semantic-release in
81cda94
- set main target branch in
73d6c37
- manual triggering of workflow in
194cc53
- fixed workflow in
10b1503
Refactor
- removed ventilation-observable characteristic in
0cb5ab2
- removed abstract methods from Criterion in
a7ac65d
- add type check for converters in
ffb2672
- parser version independent from recommendation in
c7df6b2
Test
Unknown
v2.0.0
What's Changed
Feature
- implemented invalid_combinations for test v2 in
947e2de
- added weight-related dosage query in
c10a1cc
- allowing multiple dosages per drug action in
aabc4a8
- set recommendation versions back to latest in
9dd5097
- added version-specific ebm-cpg parsers in
0d9e7a4
- added version compare function in
22dbe5e
- added drug route selection in
82098e6
- added handling of additional operators in
9fc3489
- improved code, added pyx in
9057739
- added additional operators in
0094e21
- added union with count in
96b438d
- made settings configurable in
39e6164
- added versioning to recommendations/tests in
79966a7
- added debug & query logging in
e4dde1f
- checking for available interval_start/interval_end in
ea0ec00
- implemented select_type for interval_portion in
755b4ac
- added pool size parameter in
c1510e6
- intersection priority order: NO_DATA>POSITIVE in
72b1059
- added multiprocessing switch in
44c5557
- allow use of visit_detail table for episode of care in
720ca89
- added version, made schema dynamic in
a0174c2
- late import of matplotlib in
8c3b7fe
- interval_result view uses criterion description in
97068ae
Fix
- criterion duplicate detection (removed "name" from eq) in
e971dc4
- drug_administration exclude flag for dosages in
4f77591
- task processing of empty base data intervals in
22ce873
- repr of expressions in
fa6c816
- double exclusion of drug dosages in
8e89340
- wrong attribute name in
dcd8392
- missing default parameter in
d2949d0
- checking for existence of schema first in
548b593
- unpickling of BaseExpr objects in
72d44f4
- preserving NO_DATA intervals after counting in
cbe4986
- infinite recursion due to new/init in
02bb73c
- action parser v2 in
bbf21ba
- explicit version in app in
ea6f5c6
- count rectangle logic in
578b300
- handling of Count expr in
6598630
- default dose: Any >1/Day in
e3324b5
- pandas behavior for chained assignment, downcasting in
ddf3c83
- using value_min=1 instead of value=1 for no frequency in
b1e5b63
- fixed paths in execute.py in
626563c
- creation of celida views in
43bf5a6
- index creation with descending column in
dec2db4
- active patients selection in
dfb9b44
- added base criterion & datetime filtering to criteria queries in
632cd1b
- recommendation creation from database in
a9c315d
- filtering negative duration intervals in
8066ed8
- tidal volume per ideal body weight query in
942d36f
- parallel runner could not pickle namedtuple from pyx in
9ecaa5e
- interval normalization for storage in
d5948c9
- interval normalization for storage in
4389d80
- rectangle processing in
3dcb20f
- parallel task runner in
d8cc157
- static criteria in PointInTimeCriterion in
c5aa33e
- priority order when merging criterion intervals in
0af15a6
- incorrect type expected in
37f13fe
- forward fill not removing last second in
0b2b61a
- unique task name in
58c2ec5
- added Criterion/Expr eq/hash in
ab84a1c
- fixed converter for new FHIR Timing definition in
94ac078
Chore
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
](11a33c...