Commit Graph

352 Commits

Author SHA1 Message Date
Tadgh dfecca33bc
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_operations.md
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-08-01 11:32:30 -07:00
Tadgh 7299162f10 Update doc phrasing 2020-08-01 11:31:28 -07:00
Tadgh bd22b0239f Add caveat 2020-07-31 09:13:38 -07:00
Gary Graham 9f0af3c21c docs for batch run 2020-07-30 19:25:30 -07:00
Tadgh f731e44303 Partial addition of docs for batch run 2020-07-30 18:21:35 -07:00
Tadgh 07f9e8466b Add documentation for -clear 2020-07-30 15:23:43 -07:00
Tadgh 8b4fa8048f Add changelog 2020-07-30 14:42:25 -07:00
Tadgh 0e88f359f5 Merge remote-tracking branch 'remotes/origin/master' into batch-empi-job 2020-07-29 09:42:12 -07:00
James Agnew 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
James Agnew 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
Tadgh 82dcc395ec Merge branch 'master' into batch-empi-job 2020-07-27 14:59:27 -07:00
James Agnew 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
michelgleeson 4e66cb6752
Merge pull request #1994 from jamesagnew/fix_mssql_errors
Fix mssql errors
2020-07-24 11:26:23 -04:00
jamesagnew 296ed963cc Fix sentence fragment 2020-07-23 12:57:46 -04:00
Mike G 7b435d6052 changelog for mssql changers 2020-07-23 12:16:11 -04:00
Tadgh bbe6d5600e Address review comments 2020-07-22 11:58:08 -07:00
Ken Stevens 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
jamesagnew 4c4d46008b Credit for #1848 2020-07-21 05:40:41 -04:00
jamesagnew c13e17b4e6 Add changelog and bump Jetty 2020-07-17 11:50:45 -04:00
Ken Stevens 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
jamesagnew 49c08f31d8 Credit for #1896 2020-07-16 09:26:41 -04:00
James Agnew 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
James Agnew 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
James Agnew 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
jamesagnew c40d15294d Credit for #1966 2020-07-08 10:44:52 -04:00
jamesagnew b786006183 Credit for #1878 2020-07-06 13:46:30 -04:00
jamesagnew 11ad41d472 Credit for #1893 2020-07-06 05:52:40 -04:00
jamesagnew 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
Sumeet Chhetri 4c883cf741
Added an entry for Ohum/FHIR (#1930) 2020-07-06 05:43:20 -04:00
James Agnew 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
James Agnew 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
James Agnew 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
James Agnew 290577ff3e
Remove unnecessary type predicate (#1963)
* Remove unnecessary type predicate

* Add changelog
2020-07-03 17:54:25 -04:00
Ken Stevens 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
James Agnew 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
James Agnew 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
Tadgh 571589d00d Merge branch 'master' into spring-batch-integration 2020-06-24 13:46:13 -07:00
Tadgh 2bd17806c4 Update changelog 2020-06-24 09:46:56 -07:00
Ken Stevens 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
Tadgh bb7a773f41 Merge branch 'master' into spring-batch-integration 2020-06-23 16:02:41 -07:00
James Agnew e65c264927
Support double _has expressions (#1939)
* Support nested _has queries

* Add changelog
2020-06-23 17:58:47 -04:00
James Agnew 6825d2fcf0
Reduce DB roundtrips for revincludes (#1937)
* Reduce DB roundtrips for revincludes

* Add changelog
2020-06-23 16:26:04 -04:00
James Agnew f88298a1fb
Remote terminology service enhancements (#1934)
* Remote terminology service enhancements

* Add changelog
2020-06-23 11:35:26 -04:00
James Agnew 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
Diederik Muylwyk ced376f7ba Add changelog entry; fix typo. 2020-06-22 17:02:08 -04:00
Tadgh 0e86732599 Add changelog 2020-06-19 14:03:22 -07:00
James Agnew 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
Ken Stevens 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
James Agnew 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
jamesagnew 756602183b Add changelog for https://github.com/hapifhir/org.hl7.fhir.core/pull/237 2020-06-11 14:03:20 -04:00
James Agnew 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
James Agnew 0d3ad622b5
Correct Validation Performance Regression (#1895)
* Validation performance regression

* Optimize validation

* More cleanup

* Add changelog

* Test fixes

* Build fixes
2020-06-10 05:26:21 -04:00
ianmarshall 122bd97344 Changes recommended during code review. 2020-06-09 09:59:03 -04:00
ianmarshall c86e46b196 Add documentation and remove requirement for max parameter (defaulted to 1 now). 2020-06-08 18:08:02 -04:00
Ken Stevens dd84846b94
Empi 56 link merged person (#1902) 2020-06-05 15:50:50 -04:00
Ken Stevens 558f419955
Empi 54 not duplicate (#1900)
add operation to unduplicate persons
2020-06-05 12:21:09 -04:00
James Agnew 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
Ken Stevens 60e420aaa3
resolves #1838 (#1839)
* Added %today that works like %now but with date precision instead of dateTime precision.
2020-06-04 09:52:41 -04:00
Ken Stevens 33753881e2
Empi 55 deactivate merged (#1883) 2020-06-03 13:12:01 -04:00
jamesagnew 201c3a6187 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-06-02 07:47:06 -04:00
jamesagnew 760d19cf89 Prep for 5.0.2 2020-06-02 07:46:57 -04:00
ianmarshall f48214deda Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
# Conflicts:
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
2020-05-29 23:54:11 -04:00
James Agnew 7f72305f57
Improve Period range indexing (#1873)
* Fix #1871 - Handle period range searches better

* Add changelog

* FIx tests

* Add test logging

* Address review comments
2020-05-28 08:56:43 -04:00
Ken Stevens 97a1bd40a1
Added TLS parameters to Java Mail Sender (#1666)
* Added TLS parameters to Java Mail Sender

* changelog
2020-05-27 19:17:01 -04:00
James Agnew 6899604ae4
Correct validation of fragment codesystems (#1865)
* Update validation for fragment codesystem

* Test fixes

* Add changelog

* Test fix
2020-05-25 20:44:09 -04:00
jamesagnew 0175396ee0 Docs fix 2020-05-25 20:28:57 -04:00
ianmarshall b250ac4f3d Add a change log. 2020-05-25 18:42:17 -04:00
jamesagnew 6a4f5b9b3a Credit for #1826 2020-05-24 09:32:44 -04:00
Craig Appl 098c3ad737
Fixing a typo in the performance.md server_jpa doc (#1849) 2020-05-23 17:17:51 -04:00
jamesagnew 9192d41448 Credit for #1637 2020-05-23 17:16:19 -04:00
James Agnew e780a8402e
Use R5 snapshot generator (#1862)
* Use R5 snapshot generator

* Snapshot generator reworking
2020-05-23 12:54:19 -04:00
James Agnew c374383b37
Allow AuthorizationInterceptor to properly authorize GraphQL statements (#1864)
* Allow AuthorizationInterceptor to properly authorize GraphQL statements

* Add changelog
2020-05-22 20:40:37 -04:00
IanMMarshall a1a3d9de38
Merge branch 'master' into im_20200520_cascade_delete 2020-05-22 16:11:38 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857)
EMPI Initial Implementation (still plenty of known gaps)
2020-05-22 15:03:20 -04:00
ianmarshall 6a5c23c36b Adding a proposed change log. 2020-05-22 13:45:17 -04:00
Ken Stevens 2360ed4abe
fix build (#1861) 2020-05-21 19:22:08 -04:00
James Agnew ce5ade53d9
Fix #1855 - StructureDefinition search not working (#1858) 2020-05-21 09:35:37 -04:00
James Agnew e07e071130
Avoid deserialization issues in subscription delivery (#1856)
* Avoid deserialization issues in subscription delivery

* Add changelog
2020-05-21 05:47:39 -04:00
James Agnew 5b2181a563
Implement FHIR Patch (#1850)
* Start working on FHIRPatch

* More work on fhirpatch

* Work on FHIR Patch

* Add patch

* Test fixes

* Test fixes

* Get tests fixed

* Chnage to trigger a build

* Compile fix

* Dependency version fixes

* Test fix

* COmpile fix

* Try to fix build

* Test fix attempt

* Another build attempt

* Another build tweak

* Cleanup
2020-05-20 19:43:55 -04:00
James Agnew 9aaf5ccd63
Fix expunge when using unique search param (#1854)
* Fix expunge when using unique search param

* Add chaneglog
2020-05-20 15:58:53 -04:00
jamesagnew 8ab80e3529 Credit for #1853 2020-05-20 10:54:38 -04:00
James Agnew c9c90b327c
Allow no read interceptor for partition (#1851)
* Allow no read interceptor for partition

* Add changelog

* Test fix
2020-05-19 17:06:56 -04:00
jamesagnew cc92bd7b07 Revert "Start working on FHIRPatch"
This reverts commit b3f6e7d521.
2020-05-17 11:56:50 -04:00
jamesagnew b3f6e7d521 Start working on FHIRPatch 2020-05-17 11:44:06 -04:00
jamesagnew 52c8e3551c Version bump to 5.1.0-SNAPSHOT 2020-05-15 14:43:32 -04:00
jamesagnew fe0e07a313 Bump to 5.0.1 2020-05-15 05:47:01 -04:00
jamesagnew 9b1cd6cd5c Add changelog 2020-05-15 05:45:01 -04:00
James Agnew 79a064dfd9
Optimize chain sql paths (#1844)
* Start cleanup

* Almost workinf

* Possibly working!!

* Fixes

* Test fix

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Add changelog

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-05-15 05:36:12 -04:00
jamesagnew 1d13e29ac0 Version bump to 5.1.0-SNAPSHOT 2020-05-12 20:04:20 -04:00
jamesagnew d631ecff4a Prepare for 5.0.0 2020-05-12 11:49:18 -04:00
jamesagnew c7da4b0914 Build Cleanup 2020-05-11 13:25:58 -04:00
James Agnew 0c13a65871
Bump to latest Core version (#1841)
* Start working on bumping core

* Work on tests

* Work on tests

* Bump core definitions

* Bump R5 defs

* Tweak changelog

* Test fix
2020-05-11 12:37:16 -04:00
jamesagnew 386f395e4b Version bump 2 dependencies 2020-05-10 19:10:18 -04:00
jamesagnew 5ea94abde5 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-05-10 12:10:03 -04:00
James Agnew 9d8bd0d51e
Bump R4 definitions to 4.0.1 (#1837)
* Bump R4 definitions to 4.0.1

* Add changelog

* Test fixes
2020-05-08 19:34:13 -04:00
jamesagnew 7f12f80358 Docs correction 2020-05-08 11:48:26 -04:00
James Agnew 6cc07b6689
Make binary storage work for bulk export (#1836)
* Make binary storage work for bulk export

* Add changelog

* Build fixes

* Test fix

* Test fix

* Test fix
2020-05-07 19:20:22 -04:00
Simon Yun e874abad47 Add Grand Rounds to HAPI FHIR Atlas 2020-05-06 13:47:26 -07:00
James Agnew a77aa6a28e
Multitenancy Ticket 2 - #1813 (#1821)
* Work on multitenancy

* Second ticket started

* More multitenancy work

* Work on tenancy security

* Work on multitenancy

* Test fixes

* Add docs

* cs tweak

* Multitenancy fixes

* Add debug log

* Fix build

* Add headers

* Add partition selection interceptor hook

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Account for review comments

* Resolve FIXMES

* Work on tests

* Test fixes

* A bit more cleanup

* Work on multitenancy

* Update hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientExamples.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Allow disabling text modifier indexing

* Add changelog

* Docs fixes

* Address review comment

* Resolve merge conflicts

* Merge master

* Compile fix

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-05-05 15:12:15 -04:00
James Agnew 35c2b7a2c1
Allow disabling text modifier indexing (#1831)
* Allow disabling text modifier indexing

* Add changelog

* Address review comment

* Resolve merge conflicts
2020-05-05 12:16:55 -04:00