0e88f359f5
Merge remote-tracking branch 'remotes/origin/master' into batch-empi-job
2020-07-29 09:42:12 -07:00
3098affccb
Update path when updating resource links ( #2007 )
...
* fix resource link index reuse bug
* Resolve merge conflicts
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-07-28 21:40:56 -04:00
6a8e09addf
Ensure that parent structuredefinitions are snapshotted before ( #2005 )
...
* Ensure that parent structuredefinitions are snapshotted before
snapshotting child
* Add changelog
2020-07-28 11:46:58 -04:00
82dcc395ec
Merge branch 'master' into batch-empi-job
2020-07-27 14:59:27 -07:00
3a7ac0debc
Correct invalid decimal numbers stored in DB ( #2003 )
...
* Correct invalid decimal numbers stored in DB
* Add changelog
2020-07-27 13:33:27 -04:00
4e66cb6752
Merge pull request #1994 from jamesagnew/fix_mssql_errors
...
Fix mssql errors
2020-07-24 11:26:23 -04:00
296ed963cc
Fix sentence fragment
2020-07-23 12:57:46 -04:00
7b435d6052
changelog for mssql changers
2020-07-23 12:16:11 -04:00
bbe6d5600e
Address review comments
2020-07-22 11:58:08 -07:00
160778d3fd
Empi docs ( #1989 )
...
* Remove lines from image edges. Thanks Max!
* fix case 4 docs
only mark possible match as eid if it was via an eid match
2020-07-21 13:07:49 -04:00
4c4d46008b
Credit for #1848
2020-07-21 05:40:41 -04:00
c13e17b4e6
Add changelog and bump Jetty
2020-07-17 11:50:45 -04:00
ebd6ca4b64
Empi 3 ruleset version ( #1978 )
...
* add rule version
* add rule version
* Rough in model for Golden Record.
* Test Link Rule Version
* add eid match boolean
* added new fields to EmpiLink to provide more information about how the link was created
* add logging to check an edge case
* all tests pass
* wip with failing tests
* tests pass
* FIXME
* optimize imports
* test score in provider output
* FIXME
* FIXME
* Fix jpa test app context
* fix migration string length
* review feedback param name
* review feedback javadoc
* review feedback javadoc
* bean config reorganization for cdr
* add more tests
2020-07-17 08:31:15 -04:00
49c08f31d8
Credit for #1896
2020-07-16 09:26:41 -04:00
077ee02771
Fix validation for enumerated ValueSets ( #1982 )
...
* Allow code validation against enumerated VS
* Work on validation
* Work on this
* Work on tests
* Work on validation
* Work on tests
* Work on validation
* Test fixes
* Add changelog
* For a change
* Test fixes
2020-07-15 13:38:14 -04:00
063bf4237c
Allow ConceptMap with no explicit group source/target ( #1983 )
...
* Allow ConceptMap with no explicit group source/target
* Add changelog
2020-07-15 12:57:10 -04:00
baba4cc240
Avoid version conflicts on current writes ( #1971 )
...
* Add auto retry of transactions
* Experiment in Maven build
* Transaction autoretry
* Work on transaction retries
* Work on transaction retry
* Work on transaction retry
* Fix tests
* Avoid version conflicts
* Add changelog
* Resolve LGTM issue
* FIx transaction scope error
* Test fixes
* Test fix
* Test fixes
* Test fix
* Test fixes
2020-07-13 08:51:13 -04:00
c40d15294d
Credit for #1966
2020-07-08 10:44:52 -04:00
b786006183
Credit for #1878
2020-07-06 13:46:30 -04:00
11ad41d472
Credit for #1893
2020-07-06 05:52:40 -04:00
2b5c834d96
Merge branch 'atlas-grand-rounds' of https://github.com/ConsultingMD/hapi-fhir into ConsultingMD-atlas-grand-rounds
2020-07-06 05:45:19 -04:00
4c883cf741
Added an entry for Ohum/FHIR ( #1930 )
2020-07-06 05:43:20 -04:00
4b1546f002
Add support for ISO 3166 to validator ( #1967 )
...
* Add ISO 3166 support
* Add support for ISO-3166
* Add changelog
* Test fixes
2020-07-06 05:29:48 -04:00
6fb6675b1e
Resolve validation errors to ValueSet with UCUM ( #1948 )
...
* Add tests for validation errors
* Work on validation errors
* Bump core version
* Fix validation errors
* Test fixes
* Add changelog
* Test fix
* Test fix
* Test fix
2020-07-05 19:59:21 -04:00
f356c7c385
Migrate to JUnit5 ( #1952 )
...
* Work on junit
* Work on junit 5
* Work on junit 5
* Bump errorprone vcersion
* Work on tests
* Junit 5 tweaks
* Fixes
* Work on tests
* Work on junit5
* Work on tests
* Test fixes
* Work on junit5
* Test work
* Get junit5 working
* Test fix
* Work on tests
* WOrk on tests
* Work on tests
* fixes
* Compile fix
* One more tweak
* Compile fix
* Add changelog
* Fix compile error
* Compile fix
2020-07-04 18:28:16 -04:00
290577ff3e
Remove unnecessary type predicate ( #1963 )
...
* Remove unnecessary type predicate
* Add changelog
2020-07-03 17:54:25 -04:00
714bd6216e
Empi 70 phonetic indexing ( #1941 )
...
* start with failing test
* test passes with fixmes
* javadoc and config
* pre-review cleanup
* generalize encoding
* test passes, but indexing needs to be optimized
* test passes, but indexing needs to be optimized
* step 1 of optimization. big refactor of all predicates
* step 2 of optimization: determine phonetic encoder at time of RuntimeSearchParam creation
* integrated new phonetic encoders into empi
* phonetic search implemented
* IT passes
* pre-review cleanup
* final pre-review cleanup
* final pre-review cleanup
* Fix compile error
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-06-30 17:36:54 -04:00
fa4bbe3685
Allow search criteria as subscription delivery mechanism ( #1951 )
...
* Terser should create correct Enumeration on create
* Start work
* Work on subscriptions
* Work on seed bundles
* Bundle transmission
* Add changelog
* Test fix
* Fix LGTM warning
2020-06-30 14:29:09 -04:00
072f3a422a
Use read partition for finding update candidate on upsert ( #1945 )
...
* Use read partition for finding update candidate on upsert
* Add changelog
2020-06-29 18:22:27 -04:00
571589d00d
Merge branch 'master' into spring-batch-integration
2020-06-24 13:46:13 -07:00
2bd17806c4
Update changelog
2020-06-24 09:46:56 -07:00
38a2b00663
Empi 69 and candidates ( #1936 )
...
broaden empi blocking searches to support and searchparams as well as ors
2020-06-24 09:12:56 -04:00
bb7a773f41
Merge branch 'master' into spring-batch-integration
2020-06-23 16:02:41 -07:00
e65c264927
Support double _has expressions ( #1939 )
...
* Support nested _has queries
* Add changelog
2020-06-23 17:58:47 -04:00
6825d2fcf0
Reduce DB roundtrips for revincludes ( #1937 )
...
* Reduce DB roundtrips for revincludes
* Add changelog
2020-06-23 16:26:04 -04:00
f88298a1fb
Remote terminology service enhancements ( #1934 )
...
* Remote terminology service enhancements
* Add changelog
2020-06-23 11:35:26 -04:00
67d363f9e1
Add setting to allow validation of reference targets ( #1932 )
...
* Add setting to allow validation of reference targets
* Add changelog
* Add changelog
* License headers
* Plugin version bump
* Experiment with Maven build
2020-06-23 11:35:10 -04:00
ced376f7ba
Add changelog entry; fix typo.
2020-06-22 17:02:08 -04:00
0e86732599
Add changelog
2020-06-19 14:03:22 -07:00
46c00f4efb
Update for Loinc 2.68 ( #1917 )
...
* Work on loinc updates
* Work on loinc upload
* Clean up CLI config
* Add changelog
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
* Clean up imports
* LOINC fixes
* Loinc loader fixes
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
2020-06-18 16:55:11 -04:00
d164e2d450
Empi 28 matchers ( #1918 )
...
* adding matchers
* reorganize resource matching api
* added precision sensitive date matcher
* stricter rules validation
* validate thresholds
* validate paths. with FIXMES
* validate searchparams
* fix merge compile error
* add soundex, validate no duplicate names
* add normalize substring
* add exact field to matcher
* EXACT -> STRING, exact=true
* cleanup test method
* match test passes with fixmes
* fixed vector matching
* fixed vector matching
* updating documentation and fixing tests
* updated rules documentation with latest matchers
* updated rules documentation with latest matchers
* created eid page
* eid documentation
* pre-review cleanup
* clean up beans
* disentangling beans
* checkstyle
* noop to trigger CI
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_rules.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2020-06-14 17:15:56 -04:00
622659cbb3
Add type parameter to resource reindexing operation ( #1921 )
...
* Add type parameter to resource reindexing operation
* Add changelog
* CLean up reindexing
2020-06-12 16:51:18 -04:00
756602183b
Add changelog for https://github.com/hapifhir/org.hl7.fhir.core/pull/237
2020-06-11 14:03:20 -04:00
b8da4f0140
Add package support ( #1911 )
...
* Begin rework of package management
* Work on NPM
* Work on package management
* Work on NPM
* NPM rework
* Work on NPM
* NPM package rework
* Updates
* Updates
* Add license
* Work on package server
* Work on package importing
* Work on package management
* Package rework
* Work on packages
* Work on package manager
* Work on pkgs
* NPM work
* NPM rework
* Work on package cache
* Work on NPM
* Work on NPM
* Package fixes
* Add tests
* Tweaks
* Test fixes
* Add changelog
* Avoid snapshot dep
2020-06-10 05:30:20 -04:00
0d3ad622b5
Correct Validation Performance Regression ( #1895 )
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* Validation performance regression
* Optimize validation
* More cleanup
* Add changelog
* Test fixes
* Build fixes
2020-06-10 05:26:21 -04:00
122bd97344
Changes recommended during code review.
2020-06-09 09:59:03 -04:00
c86e46b196
Add documentation and remove requirement for max parameter (defaulted to 1 now).
2020-06-08 18:08:02 -04:00
dd84846b94
Empi 56 link merged person ( #1902 )
2020-06-05 15:50:50 -04:00
558f419955
Empi 54 not duplicate ( #1900 )
...
add operation to unduplicate persons
2020-06-05 12:21:09 -04:00
21330a0a22
Transaction create performance improvement ( #1899 )
...
* Work on perf issue
* Improve write performance for large bundles with tags
* Add changelog
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1899-improve-write-xact-perf-with-tags.yaml
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
* Test fix
* Test fixes
* Test fixes
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
2020-06-05 05:26:06 -04:00
Tadgh
James Agnew
michelgleeson
Mike G
Ken Stevens
Sumeet Chhetri
Diederik Muylwyk
ianmarshall