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1807 Commits

Author SHA1 Message Date
Tadgh 3b9f9e6cc3 Rename operation 2020-08-03 21:35:12 -07:00
Tadgh 0ef1665061 Merge branch 'batch-empi-job' of github.com:jamesagnew/hapi-fhir into batch-empi-job 2020-08-01 11:48:27 -07:00
Tadgh 8b378995b2 Doc updates 2020-08-01 11:45:47 -07:00
Tadgh 4c64cec8fa
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 11:40:24 -07:00
Tadgh 9c5b69bb6e
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 11:37:11 -07:00
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
James Agnew 91147cf6b0
Scope tag search to correct resource type (#1829) 
* failing _tag tests

* cleanup

* Scope tag query to correct resource type

* Changelog

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-05-05 11:09:46 -04:00
jamesagnew ceae417d35 Credit for #1710 2020-05-04 05:42:32 -04:00
jamesagnew 394a47b83a Fix YAML error 2020-05-01 13:03:59 -04:00
jamesagnew 586089fc69 Credit for #1749 2020-05-01 07:38:31 -04:00
jamesagnew a786756169 Credit for #1812 2020-05-01 07:27:12 -04:00
jamesagnew 439a901e30 Credit for #1734 2020-05-01 05:56:47 -04:00
James Agnew 3d5a8bb3f8
Add UCUM support (#1824) 
* Add UCUM support

* Add changelog

* Some cleanup

* Test fix

* Add flywayDB callback

* Add hooks to schema migrator
 2020-04-30 15:22:41 -04:00
Tadgh 8f8a8a3dc2 Merge branch 'master' into date-match-bug 2020-04-29 16:17:50 -07:00
jamesagnew 885a18e0d8 Credit for #1788 2020-04-29 09:12:36 -04:00
James Agnew ededcc18d2
Add Partitioning / Multitenancy (#1807) 
* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Add columns

* Work on multitenancy

* Work on muiltitenancy

* Work on multitenancy

* Work on uniques

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* More work on multitenancy

* Work on multitenancy

* Multitenancy work

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Work on multitenancy

* Work on docs

* Work on multitenancy

* Work on docs

* DOcs work

* Tenancy docs

* Work on docs

* Finish docs

* Add changelog

* Rename config

* Add migration tasks

* Fix typo

* Migration fix

* One more migration fix

* A couple more migration fixes

* Docs cleanup

* Work on docs

* Bump boot version

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Work on review comments

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java

Co-Authored-By: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Compile fx

* Test fixes

* One more bugfix

* Update operation name

* Add one more constant

* Roll back a change that was causing test failures

* Test fixes

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-04-24 05:45:11 -04:00
jamesagnew 37aa11182d Docs fixes 2020-04-23 21:05:23 -04:00
Ken Stevens 0b1a64d093
Merge pull request #1809 from jamesagnew/ks-20200420-changelog 
retroactively add changelog for a search database change
 2020-04-23 11:39:24 -04:00
Ken Stevens b728c14b98
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1698-remove-search-last-used-column.yaml 
Co-Authored-By: James Agnew <jamesagnew@gmail.com>
 2020-04-23 11:39:12 -04:00
James Agnew 5f88d87027
Tweak to #1801 - Normalize double leading zeros in database (#1815) 2020-04-23 09:44:08 -04:00
jamesagnew 7efd8a9f6e Merge branch 'ja_20200206_multitenancy' of github.com:jamesagnew/hapi-fhir into ja_20200206_multitenancy 2020-04-21 20:55:09 -04:00
jamesagnew 6226381595 Merge branch 'master' into ja_20200206_multitenancy 2020-04-21 20:54:56 -04:00
jamesagnew 1f37cdd8cf Address review comments 2020-04-21 20:53:10 -04:00
James Agnew 49d15dbbe8
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:32:27 -04:00
James Agnew 45fdd9981e
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:30:50 -04:00
James Agnew 4184268bea
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:30:10 -04:00
James Agnew 50ef7d7afd
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:27:24 -04:00
James Agnew 6e444986bc
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:26:02 -04:00
James Agnew 7d0d7d9ab7
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:20:34 -04:00
James Agnew d10538cdbe
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:20:20 -04:00
James Agnew fb4e620ba8
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:19:50 -04:00
James Agnew 532c830a43
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:19:35 -04:00
James Agnew 4fe7f6e322
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:19:02 -04:00
James Agnew 53695c50a0
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:18:47 -04:00
James Agnew c67cbca8c2
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:18:33 -04:00
jamesagnew c7de85339c Work on review comments 2020-04-21 20:18:06 -04:00
James Agnew 02e5dcb90d
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:17:44 -04:00
James Agnew 138369ede2
Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:17:17 -04:00
jamesagnew 11fade2c2e Bump boot version 2020-04-21 15:55:35 -04:00
jamesagnew 4b93a0d724 Credit for #1806 2020-04-21 15:49:43 -04:00
jamesagnew 1f848dde82 Credit for #1791 2020-04-21 15:30:42 -04:00
James Agnew c716216b34
Adjust return type for fluent delete() operation (#1805) 
* Add cascading delete to client

* Add changelog

* Client delete should return MethodOutcome

* Rerturn more appropriate type for delete operations

* Refactor cascade detection to be reusable
 2020-04-21 15:23:11 -04:00
jamesagnew f218ade480 Credit for #1810 2020-04-21 15:15:04 -04:00
jamesagnew 4abebf2247 Docs cleanup 2020-04-21 09:28:52 -04:00
Ken Stevens 1133c5a6fc retroactively add javadoc for a search database change 2020-04-20 17:24:30 -04:00
jamesagnew e6c806283e Merge branch 'ja_20200206_multitenancy' of github.com:jamesagnew/hapi-fhir into ja_20200206_multitenancy 2020-04-20 16:58:59 -04:00
jamesagnew 544d9fbc6c Add migration tasks 2020-04-20 16:58:48 -04:00
jamesagnew bbab016ca6 Rename config 2020-04-20 12:38:04 -04:00
jamesagnew faddeeb779 Add changelog 2020-04-20 11:15:35 -04:00
jamesagnew 95b77af570 Merge branch 'master' into ja_20200206_multitenancy 2020-04-20 11:07:10 -04:00
jamesagnew 7248b4e18e Finish docs 2020-04-20 11:02:27 -04:00
jamesagnew c412339a05 Merge branch 'ja_20200206_multitenancy' of github.com:jamesagnew/hapi-fhir into ja_20200206_multitenancy 2020-04-19 14:41:26 -04:00
jamesagnew d3479cd093 Work on docs 2020-04-19 14:41:18 -04:00
jamesagnew cd3e1c5e72 Tenancy docs 2020-04-19 10:15:51 -04:00
jamesagnew 6c760c9bff DOcs work 2020-04-18 19:14:02 -04:00
jamesagnew c0965b1be8 Work on docs 2020-04-18 18:54:46 -04:00
jamesagnew 2ddeea37c2 Work on multitenancy 2020-04-18 17:27:06 -04:00
James Agnew 42c8cd0e38
Add cascading delete to client (#1804) 
* Add cascading delete to client

* Add changelog
 2020-04-18 11:16:16 -04:00
jamesagnew bcac2b061c Credit for #1799 2020-04-18 11:14:15 -04:00
jamesagnew 48057b9d8e Merge branch 'master' into ja_20200206_multitenancy 2020-04-17 17:59:48 -04:00
James Agnew 497757501b
Improve search method binding priority (#1802) 
* Work on search method binding priority

* Work on method priority

* Work on binding priority

* Test fixes

* Add changelog

* Test fixes

* compile fix

* One more comple fix

* Test cleanup

* Test fix
 2020-04-17 09:28:33 -04:00
jamesagnew 25cdbb15c2 Work on multitenancy 2020-04-16 15:33:48 -04:00
jamesagnew d822867a4a Merge branch 'master' into ja_20200206_multitenancy 2020-04-15 22:12:20 -04:00
James Agnew f95f619bdc
Correct two JPA processing bugs (#1801) 
* Work on search params on contained

* Add workaround for stored decimals with leading decimal point

* Add changelog

* Cleanup

* Test fix

* Test fix

* One more test fix
 2020-04-15 14:22:47 -04:00
jamesagnew 982b54df57 Work on multitenancy 2020-04-13 11:50:49 -04:00
jamesagnew c26a5553e9 Multitenancy work 2020-04-12 20:47:32 -04:00
jamesagnew e55ccf88fc Work on multitenancy 2020-04-10 20:01:59 -04:00
jamesagnew 219332e9e3 Work on multitenancy 2020-04-10 11:11:29 -04:00
James Agnew 1a3a40b3c9
Merge pull request #1796 from jamesagnew/ja_20200409_report_json_error_attr_name 
Improve error message reporting for invalid json - Fix #1793
 2020-04-09 15:11:57 -04:00
jamesagnew e0fcbe1df2 Merge branch 'master' into ja_20200206_multitenancy 2020-04-09 11:52:27 -04:00
James Agnew fdf6633145
Add validation for currencies to validator (#1797) 
* Add validation for currencies to validator

* Add changelog
 2020-04-09 11:39:30 -04:00
jamesagnew 2a43aa3b6c Improve error message reporting for invalid json - Fix #1793 2020-04-09 09:53:13 -04:00
James Agnew 8cdc3a72ce
Fix #1794 - Client ID and Server ID mode clash (#1795) 
* Fix #1794 - Client ID and Server ID mode clash

* Try to track down intermittent test failure
 2020-04-09 09:31:13 -04:00
jamesagnew 0e44786320 Add changelog 2020-04-08 18:07:36 -04:00
jamesagnew b78205c218 Ongoing cleanup 2020-04-06 17:00:45 -04:00
jamesagnew 6baf1995c9 Work on subscription cleanup 2020-04-02 20:30:19 -04:00
jamesagnew 08c1c28f67 Credit for #1786 2020-03-31 20:08:25 -04:00
jamesagnew 9d09466c21 Add debug logging to CLI 2020-03-31 10:49:16 -04:00
James Agnew fe48313100
Add response size capturing interceptor (#1776) 
* Work on capturing repsonse sizes

* Interceptor complete

* Add changelog

* Test fix
 2020-03-30 11:24:10 -04:00
jamesagnew 62d867902f Work on multitenancy 2020-03-29 18:16:04 -04:00
jamesagnew 691f2c4e9a Work on muiltitenancy 2020-03-29 13:35:20 -04:00
jamesagnew 9df4c58122 Work on multitenancy 2020-03-27 09:22:00 -04:00
jamesagnew ec6fe70acb Merge branch 'master' into ja_20200206_multitenancy 2020-03-27 05:50:08 -04:00
James Agnew b794618e9d
Avoid a crash encoding contained bundle (#1778) 
* Avoid a crash encoding contained bundle

* Add changelog

* Apply same fix to XML

* Fix typo
 2020-03-25 21:20:10 -04:00
jamesagnew 4b5165b5e2 Docs fix 2020-03-24 20:10:14 -04:00
James Agnew eaaddaf7ca
Fix #1763 - Include bundle type in summary=count responses (#1773) 
* Fix #1763 - Include bundle type in summary=count responses

* Test fix
 2020-03-24 16:24:41 -04:00
James Agnew c6d23a8bc6
Add chain on _type parameter (#1772) 
* Add chain on _type parameter

* Add changelog

* Test fix

* Address review comments

* Fix azure yaml

* Correct HTTPs in pom

* One more pom tweak

* Test fix

* Try azure again
 2020-03-24 09:44:57 -04:00
jamesagnew 13f0e5384b Address review comments 2020-03-24 06:02:55 -04:00
jamesagnew fa29f3e8ab Credit for #1770 2020-03-23 19:12:05 -04:00
jamesagnew 7706600a8c Add changelog 2020-03-23 18:05:48 -04:00
jamesagnew 14316147c5 Resolve some docs issues 2020-03-23 10:34:12 -04:00
James Agnew c2ae5a8326
Add FHIRPath evaluation interceptor (#1769) 
* Add FHIRPath evaluation interceptor

* Add changelog
 2020-03-22 12:57:24 -04:00
Jafer Khan b8b8248133 Merge branch 'master' of https://github.com/jaferkhan/hapi-fhir into cleanup-docs-v2 
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/validation/profile_validator.md
 2020-03-22 02:25:11 +05:00
Tadgh ad46c3173a Add missed attribution to changelog 2020-03-18 10:26:33 -07:00
Tadgh 3eb09b15f0 Merge branch 'master' into bugfix/1752-support-chained-parameters-inside-reverse-chained-parameter 2020-03-17 10:32:43 -07:00
James Agnew 22413911bf
Validation api changes (#1719) 
* Validation enhancements

* Work on validation api reworking

* Keep working on validation API

* Keep working on new term API

* Work on validation api

* Ongoing work on validation

* Work on integrating validation

* Work on validation API

* Add to validation API

* Work on validation

* Work on API

* Work on validation

* Work on validation API

* Work on validation API

* Work on validation api

* Work on validation API

* Work on validation api

* Validation API changes

* Work on API

* More work on validationo API

* Work on validation API

* FIxes

* WOrk on validation api

* Work on validation API

* Tests passing!

* More cleanup

* More validation API changes

* Fix intermittent test failure

* Package reorg

* Validation API work

* Work on doocumentation

* Work on API

* More work on new validation API

* Fix errorprone-reported error

* Test fixes

* Documentation updates

* Documentation tweaks

* Work on API

* Bean name adjustments

* Build fixes

* Some test fixes
 2020-03-17 13:28:59 -04:00
Tadgh 77733b59fa Add changelog 2020-03-17 09:33:58 -07:00
James Agnew 288abe4504
Improve efficiency in search deleting (#1759) 
* Improve efficiency in search deleting

* Changelog

* Address review comments
 2020-03-17 12:33:38 -04:00
James Agnew 5867d62d62
Avoid duplicate predicate in _id queries (#1761) 
* Avoid duplicate predicate in _id queries

* Add changelog

* Change to trigger CI

* Address review comments
 2020-03-17 11:12:58 -04:00
James Agnew 1dc5d89013
Optmize forced ID resolution (#1754) 
* Add forced ID caching

* Work on id optimization

* Test fixes

* More optimization work

* Add some docs

* Work on docs

* Test fixes

* Test fixes

* Test fixes

* Address review comments

* Compile fix
 2020-03-12 17:12:50 -04:00
tungdt 46c67d20cc Add VEIG(Vietnam Ehealth Innovation Group) to points.json 2020-03-06 17:43:56 +07:00
Tadgh 828ddd5185 Update docs 2020-03-04 12:14:55 -08:00
James Agnew 58ee76549c Merge branch 'master' into ja_20200206_multitenancy 2020-03-04 08:19:22 -05:00
Ken Stevens 5b5ef08500 Merge remote-tracking branch 'remotes/origin/master' into ks-20200302-near-chain 2020-03-03 09:44:52 -05:00
James Agnew 4a160a2df3 Merge branch 'master' into ja_20200206_multitenancy 2020-03-03 09:25:19 -05:00
James Agnew 58b5bd9664
Limit type on _has query (#1743) 
* Limit type on _has query

* Add changelog
 2020-03-03 08:28:38 -05:00
James Agnew 3c2c1dab2e
Error on missing profile validation (#1742) 
* Error on missing profile validation

* Add changelog

* Test fixes
 2020-03-03 08:28:26 -05:00
Ken Stevens bce1716c6c documentation 2020-03-02 22:13:21 -05:00
James Agnew 8c78e465b1
Defer large term delta adds (#1736) 
* Defer large term delta adds

* Add changelog
 2020-02-28 14:41:15 -05:00
James Agnew 5bc554949b
Remove deleted resources from cached search results (#1732) 
* Remove deleted resources from cached search results

* Add changelog

* Add tests
 2020-02-28 10:57:26 -05:00
James Agnew cb9906580e
Index canonical references (#1728) 
* Index canonical references

* Add changelog

* Fix compile error

* Add whitespace
 2020-02-25 21:45:46 -05:00
Gary Graham df9e86ec66 Merge branch 'master' into date-match-bug 2020-02-25 17:26:53 -05:00
James Agnew b2b0ff22b4
Collapse date joins (#1726) 
* Collapse date joins

* Add changelog

* Address review comments

* Add whitespace

* fix test

Co-authored-by: Ken Stevens <ken.stevens@sympatico.ca>
 2020-02-25 17:17:13 -05:00
Gary Graham 97c98254d0 Extract Common functionality out of CalculateHashesTask, build CalculateOrdinalDatesTask based on it 2020-02-25 16:09:08 -05:00
Gary Graham 512af5b87d Add changelog entry 2020-02-25 14:09:51 -05:00
James Agnew a05c4ce9eb
Don't thrash delta links (#1721) 
* Don't thrash delta links

* Add changelog

* Remove commented out code
 2020-02-19 17:46:54 -05:00
James Agnew ab8dfa5a03
Avoid multi-term for ElasticSearch (#1717) 
* Avoid multi-term for ElasticSearch

* Add changelog

* Remove redundant code
 2020-02-18 16:40:44 -05:00
IanMMarshall fba28950ec
Merge pull request #1693 from jamesagnew/im_20200131_remove_circular_dependency_forcedid 
Changes to schema to loosen dependencies involving Forced ID table
 2020-02-18 14:16:09 -05:00
James Agnew 64f07e4dc0
Includes performance enhancement (#1702) 
* Includes performance enhancement

* Add changelog

* Test fix

* Fix typo

* A few coverage cleanups

* Test fix

* Fix changelog
 2020-02-18 14:11:48 -05:00
ianmarshall 2f4f62b32e Add change log for Resource and Resource History table changes. 2020-02-18 14:09:59 -05:00
James Agnew 60f16dd91d
Update to 4.3.x core JAR (#1715) 
* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Start working on converter

* Account for compile errors

* Test fix

* Work no validator

* Work on getting core working

* Add some test coverage

* Many test fixes

Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
 2020-02-17 14:28:29 -05:00
jamesagnew ddc7b601ee Version bump to 4.3.0-SNAPSHOT 2020-02-16 19:23:22 -05:00
jamesagnew 4fd80cfca7 Bump to 4.2.0 2020-02-16 19:00:15 -05:00
jamesagnew f7ec41ffc5 Work on multitenancy 2020-02-09 08:40:15 -05:00
James Agnew b2d2346228 Work on multitenancy 2020-02-07 15:18:06 -05:00
James Agnew 97289b3a1f Credit for #1692 2020-02-04 17:38:42 -05:00
jamesagnew afd6a2b3a7 Remove entry from atlas 2020-02-01 17:31:57 -05:00
Ken Stevens 2545fc6e3d Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search 
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml
 2020-01-29 17:06:02 -05:00
jamesagnew beab5b3a9c Credit for #1689 2020-01-29 05:56:36 -05:00
dionmcm 95254406bc updated custom narrative generation documentation 
I found that the documented pattern of
 [name].class=[fully qualified classname]
No longer works. The pattern of
 [name].resourceType=[ResourceType]
worked for me, I updated the datatype example as well in kind, but I've not used it that way.

Maybe some extended examples for the other property type extensions would be good - e.g. .profile, .style, .contextPath, .narrative, .title
 2020-01-29 05:53:45 -05:00
James Agnew 471073103f Further reduce memory usage in the terminology delta operations 2020-01-28 14:36:15 -05:00
Ken Stevens cef58b528e added _filter to list of search gaps 2020-01-25 18:46:58 -05:00
Ken Stevens eff4b294df Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search 
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml
 2020-01-25 18:40:55 -05:00
James Agnew ba0048aade
Resolve memory leak (#1685) 
* Work on memory leak

* Work on term delta uploading

* Resolve memoery leak in terminology service

* Fix cache key
 2020-01-25 17:48:26 -05:00
Ken Stevens a63c62b2e1 ensure in-memory matching location search for Dstu3 falls back to a db search 2020-01-25 14:35:20 -05:00
Ken Stevens 78ab01f00b Change log and check in-memory search for location 2020-01-24 21:56:14 -05:00
James Agnew dd01688a90 Credit for #1679 2020-01-24 08:32:19 -05:00
James Agnew 39ff698dd2
Parser performance tweaks (#1660) 
* Parser improvements

* Parser tweaks

* Fix test

* Add changelog

* Bump spring mvc version

* Bump spring version

* Test fix?
 2020-01-22 14:44:12 -05:00
James Agnew 0718f6b52a
Allow schemalocation in XML validation (#1677) 
* Allow schemaLocation declaration in XML when validating

* Add fix for #1676
 2020-01-21 07:14:16 +09:00
James Agnew c0e929dacb
Copy identifiers to placeholder resources (#1675) 
* Copy identifiers to placeholder resources

* Add tests

* Maven cleanup

* Still messing around with azure

* Adding to logging

* More azure work

* One more attempt

* More messing around with azure

* Test fix

* Another caching attempt

* More work on azure pipeline

* Fix pipeline file

* Keep working on pipeline

* More work on azure

* More azure

* More azure work

* More azure
 2020-01-21 06:09:06 +09:00
James Agnew aad5a30a3d
Support count=0 (#1670) 
* Support count=0

* Fix LGTM issue
 2020-01-15 14:52:32 +08:00
James Agnew 201ec34db4
Fix expunge issue when no tags present (#1671) 
* Fix expunge issue when no tags present

* Add changelog

* Try to clean up POMs that are failing CI

* Rework dependencies

* Roll back change that did not work
 2020-01-15 14:47:22 +08:00
James Agnew 1390ea3c06
Update FHIR R5 structures to 4.2.0 version (#1665) 
* Work on upgrading core

* Work on R5 updates

* Work on core updates

* Test fix

* Update model version properties file for R5

* Bump core version

* Test fixes

* Add 4.2.0-SNAPSHOT version to versions page in docs
 2020-01-14 10:27:01 +08:00
James Agnew 62b50f06ad Documentation fix 2020-01-14 04:44:10 +08:00
James Agnew 114e8f5f15 Credit for #1655 2020-01-13 13:39:47 +08:00
James Agnew 0c008e11be License header version bump 2020-01-10 13:15:14 -05:00
James Agnew ca3b4297e1 FIx #1649 - Account for LOINC file format changes in 2.67 2020-01-03 14:19:22 -05:00
James Agnew 2f3018c56e Credit for #1603 2020-01-03 13:43:16 -05:00
James Agnew 82921472d4 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-01-03 13:43:11 -05:00
Diederik Muylwyk e65363f74d Fix typo. 2020-01-03 12:31:11 -05:00
James Agnew 3edcb04fb1 Add atlas entry 2020-01-03 11:08:48 -05:00
Diederik Muylwyk 48f7ee5afb Rolling back previous unnecessary changes. 2019-12-31 09:25:56 -05:00
Diederik Muylwyk 856993edf8 Moved changelog entry, and added clarifying comments to DateRangeParam. 2019-12-30 15:29:35 -05:00
jamesagnew 3788136194 Credit for #1650 2019-12-27 10:02:00 -05:00
James Agnew baa8eaf728
Merge pull request #1650 from jaferkhan/fix-modifier-typo 
Correct typos in code snippets across three different files
 2019-12-27 10:00:33 -05:00
jamesagnew 4c923c6e92 Atlas update 2019-12-27 08:16:17 -05:00
Jafer Khan 27a084f061 Correct typo in code's comment. Fixes gh-1617 2019-12-27 16:25:45 +05:00
Jafer Khan 8039d68608 Fixed various typos and other minor issues in docs 2019-12-26 01:36:18 +05:00
Jafer Khan 35fbe69589 Add more text to the incomplete paragraph. Fixes gh-1638 2019-12-25 20:31:57 +05:00
James Agnew ecb8da7aea Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-12-21 11:57:51 -05:00
James Agnew 5aa961ade7 Docs tweak 2019-12-21 11:56:31 -05:00
jamesagnew c03e470fcd Credit for #1588 2019-12-21 11:37:02 -05:00
jamesagnew 736b066884 Update David's email 2019-12-21 09:35:44 -05:00
James Agnew 8a1fa3ea3c
Merge pull request #1643 from jamesagnew/ja_20191219_improve_validator 
Handle standalone validation of custom VS/CS
 2019-12-19 16:38:29 -05:00
James Agnew d050b7b3c2 Add changelog 2019-12-19 15:03:30 -05:00
jamesagnew d7240019c3 Points update from Jens 2019-12-18 19:26:48 -05:00
jamesagnew 5db231bae1 Add style guide 2019-12-18 05:50:55 -05:00
James Agnew f77428c05b Update text on changelog 2019-12-17 11:16:16 -05:00
James Agnew 04b79a7b6f Documentation updates 2019-12-16 18:52:28 -05:00
James Agnew e1f2d044ed Add errorprone back into build 2019-12-15 09:42:51 -05:00
jamesagnew 89f819ae74 A bit more work on docs 2019-12-15 08:07:23 -05:00
jamesagnew ba8f50f0c8 Docs updates 2019-12-14 18:19:09 -05:00
Jafer Khan a1a50ad257 Fixed typo in docs 2019-12-14 18:55:49 +05:00
jamesagnew d232f4267e Docs tweak 2019-12-12 09:33:00 -05:00
James Agnew 2054b409ff Fix compile error 2019-12-10 16:47:50 -05:00
James Agnew 8049215d07 A couple more docs updates 2019-12-10 16:41:43 -05:00
James Agnew d277d3fed5 Docs updates 2019-12-10 16:10:09 -05:00
Ken Stevens bd1b41ff82 change out-of-order-permitted from environment variablet to flag to work like dont-use-flyway 2019-12-09 16:44:24 -05:00
Ken Stevens 5117b93add document new environment variable 2019-12-09 11:49:43 -05:00
Ken Stevens c1aec7c0e4 document new environment variable 2019-12-09 11:45:30 -05:00
James Agnew 5e69fcdc5f Fix compile error 2019-12-06 17:06:53 -05:00
James Agnew 438ef70fdb Reuse connections in brute force migrator 2019-12-06 16:52:26 -05:00
James Agnew d91617e923
Account for review changes (#1623) 2019-12-05 18:01:45 -05:00
James Agnew b2e2cb88d7 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-12-03 10:53:19 -05:00
James Agnew f277819830 Add map points JSON 2019-12-03 10:53:06 -05:00
James Agnew f58fba6f04
Some test cleanup (#1616) 
* Some test cleanup

* Add test

* More test logging

* More docs cleanup

* Add test logging
 2019-12-02 11:00:18 -05:00
James Agnew 86bd9a28fe
Fix to valueset expansion logic (#1613) 
* Fox to valueset expansion logic

* Work on docs

* Docs tweaks

* Docs tweaks

* Fix test

* Remove unused class

* Add changelog
 2019-12-01 21:21:19 -05:00
Jafer Khan 2115721940 Corrected typos and fixed grammatical mistakes in documentation 2019-12-01 03:35:35 +05:00
James Agnew 5f803f7e68 Documentation updates 2019-11-26 02:00:22 -03:00
James Agnew 5becb613fe Add some documentation 2019-11-24 19:09:34 -05:00
James Agnew 497a96ae68 Version bump for next round of development 2019-11-12 22:09:21 -05:00
jamesagnew f99ad981b5 Version bump to 4.1.0 2019-11-12 16:08:20 -05:00
James Agnew aa0301084b
Don't succeed validation on unknown codesystem (#1575) 
* Don't succeed validation on unknown codesystem

* Test fixes

* Work on error messages

* Work on code validation API

* work on tests

* Work on validation

* Test fix

* Update DSTU3 validation reources

* Upgrade structures

* Test fixes
 2019-11-12 14:35:49 -05:00
John Poth 969174136e Rename org.hl7.fhir.convertors package as it's already used 2019-10-24 12:23:38 -05:00
Stig Rohde Døssing 79e97b24e5 Fix #1481 - Add missing dependency to hapi-fhir-docs 2019-10-17 13:57:58 -04:00
James Agnew 12a74e6cbc
Fix term uploads and validate against valueset recalculation (#1540) 
* Start refactoring terminology delta operations

* Work on delta operations

* Work on concept saving

* Split term services into smaller services

* Work on term delta operations

* Work on term svcs

* Work on term operations

* More work on delta uploader

* Add a test

* Wrk on term service

* Fix compile error

* Some refactoring

* Test fix

* Test fix

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Work on delta

* Work on tests#

* Test fixes

* Improve resequencing logic

* Build test

* More testing

* More build testing

* More work on tests

* CHange test logging

* Fix term service PID issue

* Update src/changes/changes.xml

Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Address review comment

* Some cleanup

* Test fix

* Fix some tests

* Work on upload command

* Test fixes

* Work on validation fixes

* Work on validation against pre-expansion

* Work on direct validation

* A bit of cleanup

* Add some javadoc

* Force another build

* Test fixes

* Fix tests

* Fix tests
 2019-10-15 21:31:29 -04:00
James Agnew c8ce07c40e Deprecate redundant IVersionSpecificBundleProvider method 2019-09-30 09:45:31 -04:00
James Agnew 663431f571 Fix docs issue 2019-09-27 16:57:14 -04:00
James Agnew 27c637b8d7 Docs fix 2019-09-27 14:02:42 -04:00
James Agnew 5f563057c0
Set up CI with Azure Pipelines (#1502) 
* Set up CI with Azure Pipelines

[skip ci]

* Update azure-pipelines.yml for Azure Pipelines

* Skip tests for a build

* Work on pipeline

* Update azure-pipelines.yml for Azure Pipelines

* Interceptors docs

* Test fix

* Disable releases from snapshot repo

* Try disabling jitpack

* Fix dependency issue

* A couple of test fixes

* Change to trigger a build

* Force a change to trigger a build

* Force a build

* FIx test
 2019-09-24 14:38:38 -04:00
James Agnew 004f42cdcc Clean up docs 2019-09-23 15:56:02 -04:00
James Agnew 2bcb1c9c1c Work on docs 2019-09-23 09:56:29 -04:00
James Agnew e05ea676e9 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-22 15:55:06 -04:00
James Agnew 520b50dfdc Ongoing work on docs migration 2019-09-22 15:54:52 -04:00
jamesagnew 936587df6e Work on migrating docs 2019-09-22 15:52:49 -04:00
James Agnew 0a5eca0821 Work on docs 2019-09-22 13:25:50 -04:00
James Agnew d43c1760ef Adjust docs 2019-09-22 08:59:54 -04:00
James Agnew 58b7e3a923 Start splitting docs into separate project 2019-09-22 08:58:17 -04:00