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949 Commits

Author SHA1 Message Date
Nick Goupinets d63c580e82 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-01 13:18:42 -05:00
James Agnew 1e5def260c
Bump woodstox version (#2199) 2020-11-27 19:49:06 -05:00
Nick Goupinets 2a3b72db17 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-11-27 16:54:04 -05:00
jamesagnew da75ff8da2 Credit for #2197 2020-11-26 10:08:56 -05:00
dependabot[bot] 27cff8153b
Bump jetty_version from 9.4.30.v20200611 to 9.4.34.v20201102 (#2176) 
Bumps `jetty_version` from 9.4.30.v20200611 to 9.4.34.v20201102.

Updates `jetty-http` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-servlets` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-io` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-continuation` from 9.4.30.v20200611 to 9.4.34.v20201102

Updates `jetty-security` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-servlet` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-server` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-util` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-webapp` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-xml` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `websocket-api` from 9.4.30.v20200611 to 9.4.34.v20201102

Updates `websocket-client` from 9.4.30.v20200611 to 9.4.34.v20201102

Updates `websocket-server` from 9.4.30.v20200611 to 9.4.34.v20201102

Updates `jetty-maven-plugin` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-11-19 20:20:01 -05:00
NG 4bbe4a3ef7 Merge branch 'gg_20201105-remove-person-references' of https://github.com/jamesagnew/hapi-fhir into gg_20201105-remove-person-references 2020-11-19 14:56:31 -05:00
NG 4378df7dcb Removed more EMPI refs from the docs 2020-11-19 14:56:18 -05:00
Tadgh 953b662827 Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references 2020-11-19 14:24:51 -05:00
Tadgh 75c0c25d7b remove references to EMPI 2020-11-18 19:50:00 -05:00
jamesagnew 0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew 4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -05:00
James Agnew 228e75b501
Bump core to latest versions (#2154) 
* Bump core to latest versions

* Compile fix

* Bump to non snapshot core library
 2020-11-03 15:43:37 -05:00
jamesagnew 6ccb7c8312 Bump HTTPClient version 2020-10-28 10:28:04 -04:00
jamesagnew 783cbb3cf8 Bump postgres driver version 2020-10-26 19:34:50 -04:00
James Agnew 8000d2d0cf
SQL Join Rework (#2086) 
* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* added the other six index links

* trying different annotations

* Start testing

* Update resources on package install

* Add changelog

* Join rework

* CLean up SQL builder

* Add docs

* SP rework

* Join work

* Work on params

* Work on refactor

* Work on chains

* Work on joins

* Rework queries

* Work on queries

* Many more tests passing

* Refs test

* Work on sorting

* Work on tests

* More joins work

* Work on tests

* Work on queries

* Tests passing

* More test fixes

* Test fixes

* Work on SQL

* Tests passing

* Add some tests

* Add some tests

* License headers

* Use entity manager to get datasourcd

* One more fix

* Model cleanup

* Ongoing work

* Fixes

* Fixes

* Work on joins

* Ongoing fixes

* Merge conflict

* Cleanup

* clean up unused fields

* Work on join

* COmpile fix

* Rework querying

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java

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

* Address review comments

* Resolve fixmes

* Test fix

* Test fixes

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-10-26 05:24:26 -04:00
jamesagnew 0fdff3e052 Credit for #2142 2020-10-23 10:33:49 -04:00
James Agnew aa3da9b05f
Bump bootstrap version (#2128) 
* Bump bootstrap version

* Add changelog

* Resolve fixme

* Rmove test code
 2020-10-12 20:47:14 -04:00
jamesagnew 7d150858dc Credit for #2118 2020-10-12 20:45:02 -04:00
jamesagnew bd6feec2f4 Initial credit for #2118 2020-10-12 17:19:15 -04:00
Josh Collins 844624b6dd
RDF Support in HAPI FHIR (#2118) 
* RDF Support in HAPI FHIR

* Ability to read/write FHIR resources as RDF (turtle serialization)
* Test suite to test roundtrip-ability of RDF parser

* Add null checks to appease LGTM

* Correct null check logic
 2020-10-12 17:16:00 -04:00
jamesagnew 576f6efc39 Credit for #1607 2020-10-09 11:58:00 -04:00
jamesagnew e8d844f4f3 Merge branch 'master' into gg_20201008_baddeps 2020-10-09 07:53:19 -04:00
James Agnew 2134d40f1c
Account for timezones in lastUpdated search (#2113) 
* Add test

* Fix

* Add changelog

* Test fixes

* Test fix

* Test fixes

* Resolve fixme

* Test fixes

* Remove debug logs

* Try to get CI tests passing again
 2020-10-09 07:52:46 -04:00
Tadgh 375552ac49 Update hibernate core and validator 2020-10-08 14:15:57 -04:00
Tadgh 5a29fd9945 rollback the elastic changes 2020-10-06 17:20:11 -04:00
dependabot[bot] 6ab7a0bcfe
Bump animal-sniffer-maven-plugin from 1.18 to 1.19 (#2084) 
Bumps [animal-sniffer-maven-plugin](https://github.com/mojohaus/animal-sniffer) from 1.18 to 1.19.
- [Release notes](https://github.com/mojohaus/animal-sniffer/releases)
- [Commits](https://github.com/mojohaus/animal-sniffer/compare/animal-sniffer-parent-1.18...animal-sniffer-parent-1.19)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-09-16 08:02:01 -04:00
jamesagnew ea5fba6dfb Remove maven site plugin 2020-09-15 05:40:19 -04:00
James Agnew 5b6ee4e475
Dependency version bump (#2074) 
* Dependency version bump

* More dependency work

* One more fix
 2020-09-14 08:42:28 -04:00
dependabot[bot] f3d5b69da0
Bump flyway-core from 6.4.1 to 6.5.4 (#2039) 
Bumps [flyway-core](https://github.com/flyway/flyway) from 6.4.1 to 6.5.4.
- [Release notes](https://github.com/flyway/flyway/releases)
- [Commits](https://github.com/flyway/flyway/compare/flyway-6.4.1...flyway-6.5.4)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-08-13 05:47:43 -04:00
jamesagnew 92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew 5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
jamesagnew f0ed640e24 Upgrade core library dependency version 2020-08-10 09:05:04 -04:00
jamesagnew c13e17b4e6 Add changelog and bump Jetty 2020-07-17 11:50:45 -04:00
dependabot[bot] dbe171d658
Bump jetty_version from 9.4.24.v20191120 to 9.4.29.v20200521 (#1890) 
Bumps `jetty_version` from 9.4.24.v20191120 to 9.4.29.v20200521.

Updates `jetty-http` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-servlets` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-io` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-continuation` from 9.4.24.v20191120 to 9.4.29.v20200521

Updates `jetty-security` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-servlet` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-server` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-util` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-webapp` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-xml` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `websocket-api` from 9.4.24.v20191120 to 9.4.29.v20200521

Updates `websocket-client` from 9.4.24.v20191120 to 9.4.29.v20200521

Updates `websocket-server` from 9.4.24.v20191120 to 9.4.29.v20200521

Updates `jetty-maven-plugin` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-07-17 11:47:06 -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 11ad41d472 Credit for #1893 2020-07-06 05:52:40 -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
Tadgh 59659b2802 Move order of modules 2020-06-24 10:11:30 -07:00
Tadgh bb7a773f41 Merge branch 'master' into spring-batch-integration 2020-06-23 16:02:41 -07:00
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
Tadgh a9c704c06e Merge branch 'master' into spring-batch-integration 2020-06-10 12:24:19 -07:00
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
Tadgh 278a1070ae :Merge branch 'master' into spring-batch-integration 2020-06-08 17:16:11 -07:00
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
Diederik Muylwyk 93a1229789 Removing redundant maven-enforcer-plugin execution. 2020-05-27 12:57:11 -04:00
Diederik Muylwyk ed1e103751 Duplicate maven-enforcer-plugin removed, executions consolidated. 2020-05-27 12:39:17 -04:00
Tadgh 35b1533db1 Add new project for spring batch 2020-05-25 22:32:00 -07:00
ianmarshall ee87a2e2d0 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-25 11:37:34 -04:00
jamesagnew 6a4f5b9b3a Credit for #1826 2020-05-24 09:32:44 -04:00
jamesagnew c97ef7adfc A bit more contributors cleanup 2020-05-23 19:45:00 -04:00
jamesagnew 3bf0628436 Updatyes to devs list 2020-05-23 19:17:33 -04:00
jamesagnew d24f075cdb Update some orgs 2020-05-23 17:22:59 -04:00
jamesagnew b60404dbb8 Credit for #1849 2020-05-23 17:18:37 -04:00
jamesagnew 9192d41448 Credit for #1637 2020-05-23 17:16:19 -04:00
ianmarshall 4d378ee0ed Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
#	hapi-fhir-jpaserver-base/pom.xml
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java
 2020-05-22 17:04:01 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857) 
EMPI Initial Implementation (still plenty of known gaps)
 2020-05-22 15:03:20 -04:00
jamesagnew e22549e0c4 Bump MySQL JDBC driver version 2020-05-21 21:21:13 -04:00
jamesagnew 8ff7d5407a Bump core version 2020-05-21 19:22:28 -04:00
Ken Stevens 2360ed4abe
fix build (#1861) 2020-05-21 19:22:08 -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
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
ianmarshall 529e1e1f5e Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-14 12:09:24 -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
ianmarshall 4cced40b54 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
 2020-05-05 17:19:32 -04:00
jamesagnew ceae417d35 Credit for #1710 2020-05-04 05:42:32 -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
jamesagnew 885a18e0d8 Credit for #1788 2020-04-29 09:12:36 -04:00
ianmarshall dd749791db 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
 2020-04-24 16:55:45 -04:00
jamesagnew 6226381595 Merge branch 'master' into ja_20200206_multitenancy 2020-04-21 20:54:56 -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
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 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
ianmarshall 540375a7eb Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-04-17 17:39:27 -04:00
jamesagnew e0b419354f Bump up hamcrest version and force the use of the latest version 2020-04-17 13:59:22 -04:00
jamesagnew a1b3a97acf Work on docs 2020-04-17 09:28:44 -04:00
ianmarshall 925bbbbcdc Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java
#	hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
#	pom.xml
 2020-04-13 18:35:15 -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 e0fcbe1df2 Merge branch 'master' into ja_20200206_multitenancy 2020-04-09 11:52:27 -04:00
jamesagnew 6baf1995c9 Work on subscription cleanup 2020-04-02 20:30:19 -04:00
ianmarshall f891634341 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-03-31 13:30:28 -04:00
jamesagnew 62d867902f Work on multitenancy 2020-03-29 18:16:04 -04:00
jamesagnew ec6fe70acb Merge branch 'master' into ja_20200206_multitenancy 2020-03-27 05:50:08 -04:00
ianmarshall 4e4c8dbd9a Initial commit of changes to support $lastn operation. 2020-03-25 18:02:13 -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 bb4cbb6af5 One more pom tweak 2020-03-24 06:10:29 -04:00
jamesagnew 22e0c7a596 Correct HTTPs in pom 2020-03-24 06:09:03 -04:00
jamesagnew fa29f3e8ab Credit for #1770 2020-03-23 19:12:05 -04:00
jamesagnew 14316147c5 Resolve some docs issues 2020-03-23 10:34:12 -04:00
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
Jens Kristian Villadsen 80139f4800
Update pom.xml (#1709) 
A run on master using https://jeremylong.github.io/DependencyCheck/dependency-check-maven/index.html shows quartz as having a critical security issue in version 2.3.1
 2020-03-17 12:47:12 -04:00
James Agnew 4a160a2df3 Merge branch 'master' into ja_20200206_multitenancy 2020-03-03 09:25:19 -05:00
Gary Graham ed7b9fc6b6 Initial attempt at integrating elastic APM for search performance 2020-02-28 16:09:16 -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
James Agnew ebf395bee9 Merge branch 'master' into ja_20200206_multitenancy 2020-02-09 08:40:29 -05:00
jamesagnew f7ec41ffc5 Work on multitenancy 2020-02-09 08:40:15 -05:00
James Agnew c5c1e3196b Resolve FIXMEs (#1705) 
* Resolve FIXMEs

* Test fixes

* Test fixes

* Clean up unused code

* Add some test coverage

* Test fix

* Test fix

* Avoid intermittent
 2020-02-09 08:39:46 -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 3c965183e7 Checkstyle plugin version bump 2020-02-03 19:45:32 -05:00
dependabot[bot] b5adef43ac Bump checkstyle from 8.18 to 8.29 
Bumps [checkstyle](https://github.com/checkstyle/checkstyle) from 8.18 to 8.29.
- [Release notes](https://github.com/checkstyle/checkstyle/releases)
- [Commits](https://github.com/checkstyle/checkstyle/compare/checkstyle-8.18...checkstyle-8.29)

Signed-off-by: dependabot[bot] <support@github.com>
 2020-02-02 20:36:15 -05:00
jamesagnew beab5b3a9c Credit for #1689 2020-01-29 05:56:36 -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 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
jamesagnew f963906545 Bump postgres version 2019-12-27 09:57:40 -05:00
James Agnew 5cfc75eac2 Test fixes 2019-12-25 13:05:33 -05:00
James Agnew 0a21ab6941 Use datasource for migrator 2019-12-18 14:23:46 -05:00
James Agnew c0c85d7c8c Logging fixes 2019-12-16 10:30:04 -05:00
jamesagnew f2221bcc69 Restore errorprone to the build 2019-12-15 19:11:27 -05:00
James Agnew e1f2d044ed Add errorprone back into build 2019-12-15 09:42:51 -05:00
jamesagnew ba8f50f0c8 Docs updates 2019-12-14 18:19:09 -05:00
Ken Stevens 0b30033b0a upgrade flyway to latest version 
automatically repair failed migrations
 2019-12-09 11:19:18 -05:00
dependabot[bot] fadaad9e96
Bump jetty_version from 9.4.23.v20191118 to 9.4.24.v20191120 
Bumps `jetty_version` from 9.4.23.v20191118 to 9.4.24.v20191120.

Updates `jetty-http` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `jetty-servlets` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `jetty-io` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `jetty-continuation` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `jetty-security` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `jetty-servlet` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `jetty-server` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `jetty-util` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `jetty-webapp` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `jetty-xml` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Updates `websocket-api` from 9.4.23.v20191118 to 9.4.24.v20191120

Updates `websocket-client` from 9.4.23.v20191118 to 9.4.24.v20191120

Updates `websocket-server` from 9.4.23.v20191118 to 9.4.24.v20191120

Updates `jetty-maven-plugin` from 9.4.23.v20191118 to 9.4.24.v20191120
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.23.v20191118...jetty-9.4.24.v20191120)

Signed-off-by: dependabot[bot] <support@github.com>
 2019-12-02 23:16:19 +00:00
Jafer Khan 2115721940 Corrected typos and fixed grammatical mistakes in documentation 2019-12-01 03:35:35 +05:00
Ken Stevens a32c62f83b Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 
# Conflicts:
#	src/changes/changes.xml
 2019-11-24 16:42:23 -05:00
James Agnew dc9650e32c Bump greenmail dep 2019-11-23 20:52:21 +01:00
James Agnew 51b608188b
Some CI surefire improvements (#1602) 
* Some CI surefire improvements

* Build tweak

* More tweak

* Update azure-pipelines.yml for Azure Pipelines

* Update azure-pipelines.yml for Azure Pipelines

* One more CI attempt

* Update azure-pipelines.yml for Azure Pipelines

* Tweak command line

* Another build test fixc

* More build cleanup
 2019-11-23 19:51:02 +01:00
James Agnew a2f77b23d2
Fix #1583 - Index local refs in canonical types (#1593) 
* Fix #1583 - Index local refs in canonical types

* Add fix to pre-expansion

* Test fix

* Rework ID handling

* Test fixes

* Fix test
 2019-11-23 16:32:37 +01:00
Ken Stevens 6543da1470 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 2019-11-15 09:28:30 -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
Ken Stevens 7525e70bbc added message type to channel api. needed by kafka listeners when more than one message type needs to be supported 2019-11-09 18:31:08 -05:00
Jens Kristian Villadsen 37cc5a4a72 Update pom.xml 
Bump version of awaitility (https://github.com/awaitility/awaitility/pull/138) due to issues on Windows
 2019-11-05 05:29:06 -05:00
Ken Stevens 1c4b73b86a pre-review cleanup 2019-11-04 08:27:34 -05:00
Ken Stevens 4c732ce977 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 2019-11-03 21:07:59 -05:00
Ken Stevens 6ff1aaae61 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 2019-11-03 13:46:51 -05:00
James Agnew 60628356a8 Version bump spring 2019-11-03 11:29:22 -05:00
James Agnew ac51098cb3 Version bump H2 2019-11-02 23:48:14 -04:00
Ken Stevens bb0f71f271 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 2019-11-02 21:51:47 -04:00
James Agnew 3b6709e1d1
Merge pull request #1566 from jamesagnew/ja_20190928_rationalize_search_param_extractor 
Rationalize search param extractors across FHIR versions
 2019-11-02 16:18:23 -04:00
Ken Stevens bee993a0ec Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 
# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTask.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropTableTask.java
 2019-11-01 13:37:00 -04:00
Stig Rohde Døssing 80bfb9af37 Issue-1077: Make CapabilityStatementProvider use the closest common superclass of provided resources when generating rest.resource.profile, instead of always using the base definition. 2019-11-01 10:20:16 -04:00
James Agnew e29462bcab Version bump some dependencies 2019-11-01 10:15:27 -04:00
Ken Stevens 9c9193b401 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 2019-10-31 09:38:30 -04:00
James Agnew 97d5edc0b0 Credit for #1538 2019-10-31 08:21:11 -04:00
James Agnew 817f9ae36e Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-27 17:25:20 -04:00
Ken Stevens 18e8604494 Merge remote-tracking branch 'remotes/origin/master' into ks-flyway 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
 2019-10-27 08:29:52 -04:00
James Agnew 464c6c5b45
Upgrade dependencies and addess Semmle issues (#1554) 
* Version bumps

* FIx build issues

* Address a few Semmle issues

* Work on tests

* Some test fixes

* Test fix

* Fix deletions

* Test fix

* Fix intermittent test failure

* One more dependency bump

* Add some test logging

* Remove bad import

* Add some tests

* Test updates
 2019-10-22 17:10:58 -04:00
James Agnew a375f761cb FIx typo in pom 2019-10-22 14:17:25 -04:00
James Agnew 5809457335 Credit for #1526 2019-10-22 14:01:21 -04:00
jelmer.terwal c003047ca9 Split test from example 2019-10-22 13:58:52 -04:00
James Agnew 0af79b84d9
Use webjars instead of including JS deps (#1551) 
* Use webjars instead of including JS deps

* Add changelog
 2019-10-21 07:22:55 -04:00
James Agnew e6ae368424 Credit for #1547 2019-10-18 07:07:02 -04:00
James Agnew 2725797610
Implement Terminology Delta Operations (#1536) 
* 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

* Test fixes
 2019-10-14 19:14:41 -04:00
Ken Stevens 790f655a95 flyway initial implementation (with FIXMEs) 2019-10-06 17:55:10 -04:00
jamesagnew 55491fd1bf Add a couple of exclusions 2019-10-03 07:21:53 -04:00
James Agnew da9efaea0b Credit for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/54 2019-10-01 15:22:03 -04:00
jamesagnew 48d191cbe5 Credit for #1473 2019-10-01 05:32:54 -04:00
James Agnew 557a8ccc66
Add top level support for ElasticSearch (#1514) 
* ElasticSearch work

* Add ElasticSearch properties builder

* Clean up POM

* Remove redundant project

* Try to troubleshoot embedded elasticsearch

* Another test attempt

* Add credentials to elasticsearch config

* Work on lastn

* Address review comments

* A couple of test fixes
 2019-09-30 09:30:39 -04:00
jamesagnew b2c13f3018 Work on codecov integration 2019-09-25 13:25:59 -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
jamesagnew 936587df6e Work on migrating docs 2019-09-22 15:52:49 -04:00
James Agnew 58b7e3a923 Start splitting docs into separate project 2019-09-22 08:58:17 -04:00
James Agnew ad01d7598c Credit for #1489 2019-09-19 20:41:02 -04:00
jamesagnew 170698562a Bump to current org.hl7.fhir.core 2019-09-19 08:11:30 -04:00
James Agnew 4a751cbfc5
Integrate Bulk Export (#1487) 
* Start working on subscription processor

* Work on new scheduler

* Test fixes

* Scheduler refactoring

* Fix test failure

* One more test fix

* Updates to scheduler

* More scheduler work

* Tests now all passing

* Ongoing work on export

* Ongoing scheduler work

* Ongoing testing

* Work on export task

* Sync master

* Ongoing work

* Bump xml patch version

* Work on provider

* Work on bulk

* Work on export scheduler

* More test fies

* More test fixes

* Compile fix

* Reduce logging

* Improve logging

* Reuse bulk export jobs

* Export provider

* Improve logging in bulk export

* Work on bulk export service

* One more bugfix

* Ongoing work on Bulk Data

* Add changelog
 2019-09-17 16:01:35 -04:00
James Agnew 0831feb2c3 Bump xml patch version 2019-09-11 17:33:31 -04:00
jamesagnew c7ec9601fd Bump core version 2019-09-10 13:32:59 -04:00
James Agnew 722c7a8211 Work on GraphQL updates 2019-09-06 14:56:17 -04:00
James Agnew 8ce8f1e864 Credit for #1461 2019-09-01 18:41:17 -04:00
Ken Stevens 37c1ba44fe Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump 2019-08-21 15:04:16 -04:00
James Agnew 9428430822
Add support for Resource.meta.source (#1438) 
* Work on indexing source

* Work on tests

* Refactor query count tests

* Unit test fixes

* Add some tests

* DAO fix

* Fix compile error

* Unit test fix

* Cleanup

* Test fix

* Fix compile error

* One more test fix
 2019-08-21 11:17:43 -04:00
Ken Stevens daf45db2be fixed a test and removed awaitility excludes 
mvn install completed successfully
 2019-08-20 09:14:21 -04:00
Ken Stevens 630bb916b4 awaitility version bump 2019-08-19 12:15:14 -04:00
James Agnew a0cb7beb28 Bump core projects version 2019-08-19 08:15:04 -04:00
James Agnew 4490c9ca09 Correct the eq operator on the _filter parameter 2019-08-14 14:39:40 -04:00
jamesagnew e1b43d811f Version bump to 4.1.0-SNAPSHOT 2019-08-14 14:06:06 -04:00
jamesagnew 3f22456b0f Bump version to 4.0.0 2019-08-14 11:06:26 -04:00
jamesagnew a1e1cf4e56 Credit for #1375 2019-08-13 05:37:40 -04:00
James Agnew 31e374ded8 Credit for #1220 2019-08-12 13:35:27 -04:00
James Agnew 301a8f8432
Merge #1146 - Filter implementation (#1220) 
* Initial commit of _filter keyword implementation.

* - Completed all search parameter types for _filter.
- Implemented handling for _has, _id, _security, language, _profile, _security, and _tag.

* - Changes to support "ne" matching on resource ID for _filter

* Implemented language

* Commit/push before creation of pull request

* Ongoing merge work

* Ongoing merge work

* Merge master in

* Test fix
 2019-08-12 11:59:33 -04:00
jamesagnew 4e1bbe681a Bump supported PGSQL driver 2019-08-08 15:12:29 -04:00
James Agnew dd0cb10dbb
validate operation ignores parameter profile (#1417) 
* This should be working now - need to check tests

* Add a changelog and some docs

* One more test fix

* Tests should be passing

* Fix compile

* Test fixes

* Ignore outdated DSTU2 validation test
 2019-08-07 15:31:59 -04:00
jamesagnew d9247a2021 Account for GPG 1.2 2019-08-07 10:43:30 -04:00
James Agnew 60eab3ad70
Add support for R5 resources (#1416) 
* Work so far on R5 support

* Add support for R5

* Docs changes
 2019-08-06 17:30:31 -04:00
jamesagnew 46c8c61932 Restore build - May need to roll back the RDF changes 2019-08-01 10:14:56 -04:00
jamesagnew 39c2a95ce7 Credit for #1321 2019-08-01 09:29:43 -04:00
James Agnew 0f4738c1b5
Merge branch 'master' into rdf_parser 2019-08-01 09:25:40 -04:00
jamesagnew e20443010d Credit for #1404 2019-08-01 06:38:37 -04:00
James Agnew 7831e8a0ed Add support for $snapshot generation and validation based on snapshots 2019-07-14 16:15:56 -04:00