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282 Commits

Author SHA1 Message Date
jamesagnew 376a84d213 Version bump 2021-06-14 13:12:34 -04:00
James Agnew dc627dc019
Add bulk export authorization layer (#2712) 
* Add bulk export authorization layer

* Add docs

* Version bump

* Authorize any

* Add bulk export - all

* Address lgtm issue
 2021-06-06 20:47:43 -04:00
jamesagnew ff2698d4d1 Merge branch 'rel_5_4' 2021-05-19 09:22:11 -04:00
jamesagnew de56f440cb Version bump 2021-05-18 17:14:14 -04:00
jamesagnew 2068372998 Version bump 2021-05-07 17:43:54 -04:00
jamesagnew 63c4b22cd3 Undo bump 2021-05-07 17:42:50 -04:00
jamesagnew 17e41520a4 Version bump 2021-05-07 17:41:39 -04:00
jamesagnew 5db01f3139 Build fixes 2021-05-03 05:57:45 -04:00
James Agnew 0cea403800
Fix vulnerability warning on maven plugin (#2621) 
* Fix vulnerability warning on maven plugin

* Compile fixes

* Fix bootstrap dep

* Test fix

* Fix tests

* FIx deps
 2021-05-02 12:14:32 -04:00
James Agnew 970a9884f0
Avoid tag definition constraint (#2620) 
* Avoid tag definition constraint failure

* Version bumps

* Add changelog

* Avoid guava issue

* Test fix

* Test fix

* Bump pom
 2021-05-01 17:16:15 -04:00
James Agnew 95d7ba6fa8
Streamline Search SQLs (#2576) 
* Streamline SQL queries

* SQL query tidying

* Add changelog

* Test fixes

* Tests passing

* Ongoing work

* Test fixes

* Test fixes

* Build fix

* Cleanup

* Fixes
 2021-04-28 10:29:09 -04:00
James Agnew 2ba1005762
OpenAPI Support (#2560) 
* Start work on OpenAPI

* Fixes

* Work on OpenAPI

* Cleanup

* Cleanup

* More swagger work

* Build fix

* More work

* More work

* Add documentation

* Docs fixes

* Add changelog

* License updates

* Add API

* Cleanup

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md

Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>

* Work on scripts

* Add docs

* Compile fix

* Work on fixes

* Fix tests

* Test fix

* Test fix

* Build fix

* Tests

* Build fix

* Work on pipeline

* Version bump

* Test fix

* Version bump

* Test fix attempts

* Test fix

* Test fix

* Remove accidentally committed files

* Fixes

* Tets fixes

* Test fix

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fixes

* License header updates

* test fix

* Test fixes

* Test fix

* Test fixes

* Test fix

* Checkstyle bump

Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
 2021-04-25 15:40:50 -04:00
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -04:00
James Agnew ca2088f3ad
Add framework for Bulk Import (#2538) 
* Start work on bul;k import

* Work on bulk import

* Have batch working

* Working

* Working

* More work

* More work on bulk export

* Address fixmes

* License header updates

* Test fixes

* License header updates

* Test fix

* Test fix

* Version bumps

* Work on config

* Test cleanup

* One more version bump

* Version bump

* CLeanup

* A few additions

* Test fixes

* Test fix

* Test fix

* Migration fix

* Test fix

* Test fix
 2021-04-14 17:41:32 -04:00
James Agnew a6cbf7eebd
Add support for hierarchycal valueset expansion (#2525) 
* Add support for hierarchycal valueset expansion

* Add changelog

* Add tests

* Cleanup

* Test fix

* Test fixes
 2021-04-06 17:36:54 -04:00
James Agnew b617c7690d
Search Parameter Infrastructure Cleanup (#2522) 
* Search param service cleanup

* Work on collapsing search param

* Search param cleanup

* Work on build

* Test fix

* Test fixes

* Ongoing work

* Test fix

* Compile fix

* Test fixes

* Test fix

* Test fix

* License header updates

* Remove fixme

* Cleanup

* Cleanup
 2021-04-05 17:40:10 -04:00
James Agnew 0bf746f23b
Add support for revincludes to CapabilityStatement generator (#2521) 
* Add support for revincludes to CapabilotyStatement generator

* Add changelog

* Fixes

* Test fix

* Test fixes

* Test fix

* Test fix

* More fixes to CS cache

* Test fix

* Test fix

* Test fix
 2021-04-05 08:29:04 -04:00
James Agnew 049097e5b4
Improve CapabilityStatement Generation (#2511) 
* Start work

* Work on testing

* Version bump

* Test fix

* Compile fix

* Test Fixes

* Test fix

* Test fix

* Compile fix

* Tst fix

* Test fix

* Test fix

* Test fix
 2021-03-30 05:48:03 -04:00
Diederik Muylwyk b720c32c1d Version bump 2021-03-29 18:23:16 -04:00
James Agnew dc41d5ad61
Add terminology mapping and display population interceptors (#2488) 
* Start work on code mapping interceptors

* Work on generation

* Add terminology mapping and display population interceptors

* Add changelog

* License header updates

* Test fixes

* Fix typo

* Interceptor fixes

* License header update

* Test fixes

* Mapping fixes

* Version bump

* License header updates

* Add null tests

* Add null guard

* Intermittent fix
 2021-03-21 12:03:57 -04:00
Tadgh 9dd42fa605 Remove duplicate constant 2021-03-01 14:00:20 -05:00
Tadgh 27cac16de6 Add custom mimetypes to capability statement 2021-03-01 13:54:21 -05:00
James Agnew 3eda19c65a
Version bump (#2400) 
* Version bump

* Docs changes

* Docs tweaks

* Docs tweak

* Spelling fixes

* Docs tweaks
 2021-02-18 11:07:49 -05:00
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
Michael Buckley 4553ca2708 Fix expected error code. 
500 is a server error.  0 is a failed connection.  This should be a server error.
 2021-02-05 11:32:48 -05:00
jamesagnew d65ed820a5 Javadoc build fix 2021-02-01 12:13:47 -05:00
jamesagnew 656dd33ba8 FIx javadoc build 2021-01-21 08:58:23 -05:00
James Agnew 14b0688f69
Bump core version to 5.2.16 (#2308) 
* Bump core library version

* Test fix

* Build fixes

* Some test fixes

* One more bit of docs

* Build fix

* Test fix

* Test fix

* Docs fix
 2021-01-21 05:30:23 -05:00
Ken Stevens 520400d6ea
added IPagingProvider.canSearchByOffset() (#2281) 
* init rev

* added IPagingProvider.canSearchByOffset()
consolidated parameters in bundle link methods

* fix refactoring error

* add @Nonnull to BundleLinks parameter

* null check

* fix test

* cleanup

* fix refactoring

* final cleanup

* review feedback

* review feedback

* review feedback
 2021-01-11 20:42:41 -05:00
Bill Denton 84d9854e24
OSGi manifest maintenance (#2217) 
* manifest cleanup and delete Fragment-Host

* make hapi-fhir-server-empi into an OSGi bundle
 2020-12-18 16:48:44 -05:00
James Agnew f228b4a167
Fix an error parsing extensions with a value type of UUID (#2258) 2020-12-18 10:57:31 -05:00
James Agnew 1e5def260c
Bump woodstox version (#2199) 2020-11-27 19:49:06 -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 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
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 e780a8402e
Use R5 snapshot generator (#1862) 
* Use R5 snapshot generator

* Snapshot generator reworking
 2020-05-23 12:54:19 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857) 
EMPI Initial Implementation (still plenty of known gaps)
 2020-05-22 15:03:20 -04:00
James Agnew 63ff0ede9c
Make diff operation work securely (#1859) 
* Make diff operation work securely

* Build tweak

* FIx tests
 2020-05-21 19:20:48 -04:00
James Agnew ce5ade53d9
Fix #1855 - StructureDefinition search not working (#1858) 2020-05-21 09:35:37 -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 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
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 14316147c5 Resolve some docs issues 2020-03-23 10:34:12 -04:00
James Agnew f89661526c Missed noe rename in #1769 2020-03-22 13:27:04 -04:00
James Agnew c2ae5a8326
Add FHIRPath evaluation interceptor (#1769) 
* Add FHIRPath evaluation interceptor

* Add changelog
 2020-03-22 12:57:24 -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
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 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 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 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
James Agnew 1a348abaf5 Try to fix 2 intermittent test failures 2019-11-08 08:45:08 -05:00
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
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 817f9ae36e Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-27 17:25:20 -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 c46260f91a Test fix 2019-10-03 09:10:08 -04:00
James Agnew db668d96b9 Add a few tests and remove some dead code 2019-10-03 09:00:14 -04:00
James Agnew 066c9a7fb7 Improvements to AutohrizationInterceptor create handling 2019-09-30 15:07:23 -04:00
James Agnew 0bee7a7b53 Test fix 2019-09-30 10:12:49 -04:00
James Agnew c8ce07c40e Deprecate redundant IVersionSpecificBundleProvider method 2019-09-30 09:45:31 -04:00
James Agnew 8657afb01e
Fix intermittent test failures regarding search (#1509) 
* Add some logging

* Add more test logging

* Work on some test logging

* Fix compile error

* Work on codecov

* Work on codecov

* Remove test debug messages
 2019-09-25 20:15:21 -04:00
James Agnew 520b50dfdc Ongoing work on docs migration 2019-09-22 15:54:52 -04:00
James Agnew 58b7e3a923 Start splitting docs into separate project 2019-09-22 08:58:17 -04:00
James Agnew d3c8962ae6 Add some tests 2019-09-17 14:04:35 -04:00
James Agnew 722c7a8211 Work on GraphQL updates 2019-09-06 14:56:17 -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
James Agnew 0c9e5ec1ea
Support GraphQL for R3/4/5 (#1424) 
* Work on grpahql enhanbcements

* Add some more chars to the sanitizer function

* Add changelog
 2019-08-12 08:24:32 -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