Commit Graph

524 Commits

Author SHA1 Message Date
jamesagnew 190f0ccb22 Add test for #2063 2020-09-01 14:12:57 -04:00
James Agnew dbbff1fd16
Allow HTTP 204 response to transaction (#2051)
* Allow HTTP 204 response to transaction

* Add changelog

* Test fix
2020-08-21 21:00:55 -04:00
James Agnew eab828f47a
Add transactionbuilder (#2041)
* Add transactionbuilder

* Add changelog

* Add creates
2020-08-17 07:47:40 -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
James Agnew 5d9d4070fb
Fix an issue with binary storage not updating correctly if a retry (#2014)
interceptor is present
2020-08-05 09:14:40 -04:00
jamesagnew 5f1078ac13 Cleanup of package installer 2020-07-21 11:43:57 -04:00
christian ohr 1c27726055
#1817: fix problem with missing resource references when extensions are used (#1848)
Co-authored-by: Christian Ohr <christian.ohr@icw.de>
2020-07-21 05:36:25 -04:00
Ibrohim Kholilul Islam 5a79304893
Implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation (#1896)
* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation

* GraphQLQueryBodyParameter to recognize application/graphql

* fix 500 error on method without @GraphQLQueryBody

* refactor to processGraphQlGetRequest and processGraphQlPostRequest

* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest

* fix imports
2020-07-16 09:25:26 -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
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 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 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
jamesagnew 4119cbb0c4 Terser should create correct Enumeration on create 2020-06-17 18:32:27 -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
Martin Zacho Grønhøj 9bde517540
Install external ig package at startup (#1826)
* Do not use deprecated methods in structures-r4 test

* beginning development of feature Implementation Guide installer

* fetch IG, generate snapshots of SDs of and persist conformance resources to db

Missing initialization, error-handling and handling of NameSystems and Subscriptions

* Refactor IgInstaller and implement support for R4 and R5

* Error handling and removed logic for invoking IG installation

IgInstaller should be invoked by applications

* Implement pull request comments in IgInstaller

1) Renamed IgInstaller -> IgInstallerSvc for consistency
2) Use field autowiring and @PostConstruct for consistency
3) Use exceptions instead of boolean flags for success indication
4) Use IValidationSuport to generate snapshots of StructureDefinitions
in a version independent way (less maintenance) instead of SnapshotGenerator.java
5) Read IGs for tests from src/main/resources instead of external URL

* IG installation: Wrap exceptions during resource creation in custom class

* IG installation: Improved logging

* IG installation: Search for existing resources in a version independent way
2020-05-24 09:25:46 -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 ce5ade53d9
Fix #1855 - StructureDefinition search not working (#1858) 2020-05-21 09:35:37 -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 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
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 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
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
jamesagnew 36a7e9c980 Test fixes 2020-04-22 14:56:13 -04:00
jamesagnew 6226381595 Merge branch 'master' into ja_20200206_multitenancy 2020-04-21 20:54:56 -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 33b8e82f79 Compile fix 2020-04-21 09:29:23 -04:00
jamesagnew 544d9fbc6c Add migration tasks 2020-04-20 16:58:48 -04:00
jamesagnew 95b77af570 Merge branch 'master' into ja_20200206_multitenancy 2020-04-20 11:07:10 -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
David Gileadi 461739fb32 Add test for millisecond precision 2020-04-18 11:15:32 -04:00
jamesagnew 48057b9d8e Merge branch 'master' into ja_20200206_multitenancy 2020-04-17 17:59:48 -04:00
jamesagnew e0b419354f Bump up hamcrest version and force the use of the latest version 2020-04-17 13:59:22 -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 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 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 c1d682ed02 Test fixes 2020-04-09 12:36:33 -04:00
jamesagnew 879fbb0bf8 Test fixes 2020-04-09 10:34:18 -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 c0df88739a Intermittent test fix 2020-04-08 19:19:30 -04:00
jamesagnew 40d0c27ae3 Work on subscription cleanup 2020-04-05 18:43:27 -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
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
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
August Langhout 2c1ec8fb0d add test to check that json parsing also fails with identically named contained resources 2020-03-23 19:09:54 -04:00
August Langhout a75bf948c1 Remove personal data 2020-03-23 19:09:54 -04:00
August Langhout 2b23a6f2f0 Fix Xml parse issue: do not override the references with global contained resources if they have already been resolved 2020-03-23 19:09:54 -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 bde7c356fe
Implement Jackson parser/serializer (#1733)
* [dev] Integration of a Jackson serializer and deserializer - first stage

* [fix] Fixed some serializing issues
[improve] Improved the processing, removed the loggers

* [clean] Removed the JacksonSerializer class, replaced all the Gson classes with Jackson classes

* [clean] Small cleanup

* [improve] Throw a ConfigurationException if the JsonGenerator cannot be created

* [improve] Use the ObjectMapper's `readTree` instead of `readValue`

* [dev] Latest fixes and improvements

* [dev] Use the Jackson serializer

* [clean] Removed the ObjectMapper configuration, for now

* [fix] Use the GsonStructure also for the parsing of a FHIR resource

* [clean] Removed the LinkedList usage

* Work on preparing for merge of #1673

* Resolve build errors

* Work on parser integration

* Tests passing

* Resolve fixme

* CLeanup

* Fix dependency

Co-authored-by: Bogdan Solga <bogdan.solga@gmail.com>
2020-03-17 17:27:26 -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 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
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 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 e6d3897700 Add tests 2020-01-30 08:49:40 -05:00
James Agnew a6f3ee8319 Add a unit test 2020-01-29 09:35:22 -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 0e1f03b999 Work on validation 2019-12-19 14:41:35 -05:00
jamesagnew 549b1c85c3 Test fix 2019-12-12 05:43:05 -05:00
James Agnew d277d3fed5 Docs updates 2019-12-10 16:10:09 -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 7745dc4ad4 Don't require fhir core javadocs by default 2019-11-26 02:22:09 -03:00
James Agnew 5f803f7e68 Documentation updates 2019-11-26 02:00:22 -03:00
James Agnew ca620d652f
Add tests (#1606)
* Support chained HAS

* Add some tests

* Add some cleanup

* Work on intermittent tests
2019-11-24 10:11:49 +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
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 b90f285218 Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-30 08:41:14 -04:00
James Agnew 9c852283e9
Correctly handle "special" search params in CS (#1569)
* Correctly handle "special" search params in CS

* Add another test
2019-10-30 05:31:25 -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 6580c98ed7 Work on extractor 2019-10-26 16:56:12 -04:00
James Agnew 74c03b5bb7 Add a test 2019-10-24 08:32:52 -04:00
James Agnew 385a885abf Add ability for resource source to be specified by header 2019-10-24 08:32:52 -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 a71d969ba1 Add line numbers to validation failures 2019-10-18 14:10:47 -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 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
jamesagnew 92c6b88964 Add test 2019-10-10 07:16:18 -04:00
James Agnew 1f1b94a566
Resolve XXE issue in validator (#1530)
* Resolve XXE issue in validator

* Ensure that we're blocking XXE events into validator XML parser

* A bit of cleanup

* Add an LGTM config

* Add one more fix
2019-10-08 13:06:03 -05:00
Ken Stevens 53f47fbb1e Merge remote-tracking branch 'remotes/origin/master' into ks-narrow-search-pointcut 2019-10-03 12:20:20 -04:00
Ken Stevens d1deedf247 pre-review cleanup 2019-10-03 12:14:11 -04:00
Ken Stevens 566443d0fe move BundleUtil back 2019-10-03 12:05:26 -04:00
Ken Stevens 98c76a4d49 Test passes 2019-10-03 12:03:38 -04:00
Ken Stevens 29e7cdc476 Added ability to modify URLs in BundleUtil 2019-10-03 09:46:32 -04:00
James Agnew db668d96b9 Add a few tests and remove some dead code 2019-10-03 09:00:14 -04:00
James Agnew 2193a30b45
CodeSystem Delta Uploader (#1520)
* Terminology Delta Uploading

* Add delta operations

* Fix up tests

* Improve test coverage a bit

* Improve test coverage reporting

* fix yaml

* A couple of test enhancements

* FIx intermittent test failure
2019-10-03 07:19:00 -04:00
Clayton Bodendein 08825a81d9 Add missing @Override annotations
Added missing @Override annotations so that if/when methods in superclasses change
there will be a compile-time error if subclasses haven't been changed accordingly.

This was done using IntelliJ IDEA's "Missing @Override annotation" inspection.
2019-10-02 05:45:59 -04:00
James Agnew fd16b9efca
Merge branch 'master' into oliveregger_#402 2019-09-30 20:19:25 -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 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
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 57377f5557 Fix #1483 - Don't let RP methods handle a request with includes if the
method doesn't understand them
2019-09-25 10:54:37 -04:00
James Agnew 58b7e3a923 Start splitting docs into separate project 2019-09-22 08:58:17 -04:00
James Agnew a989a746b0 Fix #1494 - Upgrade to new :recurse syntax for R4 include/revinclude
statements
2019-09-20 09:38:29 -04:00
James Agnew 20d33afb6f Credit for #1489 2019-09-19 20:48:17 -04:00
James Agnew 6f6cc960ad Add timing tests 2019-09-19 20:39:16 -04:00
James Agnew eddb98084d Move PreferReturnEnum back to original location to avoid regressions 2019-09-19 15:48:58 -04:00
James Agnew 5e74a6f3e8 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-17 16:01:53 -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 d3c8962ae6 Add some tests 2019-09-17 14:04:35 -04:00
James Agnew 08835c1615 FIx a failure in FhirTerser when visiting custom types 2019-09-13 09:11:47 -04:00
James Agnew 722c7a8211 Work on GraphQL updates 2019-09-06 14:56:17 -04:00
James Agnew 7d162c50db Don't guess content type for create/put 2019-09-05 14:47:04 -04:00
James Agnew ce879b3863 Fix versioned API incompatibility with GraphQL 2019-08-20 08:35:27 -04:00
James Agnew 74c83f6148 Test fixes 2019-08-17 12:01:04 -04:00
James Agnew afb682dfe9 Handle AuthorizationInterceptor rejection of by-type reads on the wrong type earlier in the process 2019-08-15 09:16:45 -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 b127867ef7 Fix responsehighlighterinterceptor to work with graphql 2019-08-13 18:00:30 -04:00
James Agnew 33767b5399 Test fix 2019-08-13 16:12:28 -04:00
James Agnew 94c498a744 A but more tweaking to the graphql interceptor 2019-08-13 16:05:33 -04:00
Stig Rohde Døssing bb20c2134b Issue-1387: Read version from resource meta when deciding whether to return 304 on read 2019-08-13 05:28:03 -04:00
James Agnew c04f1d15d8 Fix #1399 - Issue with DiagnosticReport R4 narrative generation template 2019-08-12 17:17:45 -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 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
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
James Agnew a4ca5374ec
Add terminology delta operations (#1401)
* Start work on delta operations

* Add changelog

* Some build fixes

* Move upload terminology command to CodeSystem resource

* Updates

* Some test fixes

* Add changelog

* Some test fixes

* More test fixes

* Test fix

* Add additional tests

* Transaction boundary fixes
2019-07-29 17:46:42 -04:00
jamesagnew 8158292665 Allow operations to better work across multiple versions of FHIR 2019-07-26 05:46:37 -04:00
James Agnew 7e3d062d15
Switch default client to JSON (#1392)
* Start work on changing over

* Update tests

* More test fixes

* Work on generalizing binary access provider a bit

* Add expunge capability to binary storage, and also support actual binary
resources

* Work on binary provider

* Get the DB bound binary storage service working

* Test fixes

* Compile fix

* Fix compile error

* Test fix

* Test tweak

* Trying to figure out an intermittent failure

* Work on tests

* More work on tests

* Another test fix
2019-07-22 21:27:10 -04:00
James Agnew 55c0d5b604
Add binary storage for Attachments (#1386)
* Have this working now

* Add utility method

* Build fixes

* Add changelog
2019-07-17 18:31:17 -04:00
James Agnew 7831e8a0ed Add support for $snapshot generation and validation based on snapshots 2019-07-14 16:15:56 -04:00
James Agnew 120b93f204
Use HL7 FHIR Core Structures (#1382)
* Ongoing work on core structures suport

* Ongoing work on this merge

* Ongoing work to clean up structures

* Credit for #1179

* Address compile issues

* Latest changes

* Work on parallel execution

* Work on getting tests passing

* Add H2 to migrator

* Test fix
2019-07-14 10:16:40 -04:00
James Agnew 75f0dc993c Try to prevent an intermittent test fix 2019-07-11 21:39:41 -04:00
James Agnew a352137938 Test fixes 2019-07-11 21:10:30 -04:00
James Agnew 34f7d4ddbd Refactor ServerConformanceProvider so that it no longer keeps any state 2019-07-07 12:57:31 -04:00
James Agnew 56aaef641c Add request ID 2019-07-02 21:32:28 -04:00
jamesagnew 742389642d Add tests for delete conflicts and authorizationinterceptor 2019-07-01 10:49:38 -04:00
jamesagnew 5c0e54fb86 Improve processing of deletes in AuthorizationInterceptor 2019-06-29 14:40:51 -04:00
James Agnew 1fd99dac63
Enable optional cascading deletes on JPA server (#1363)
* Start working on cascading deleets

* WOrk on cascading deletes

* Work on cascading deletes

* Enable cascading deletes

* Cascade deletes almost working

* FIx test

* Test fix
2019-06-28 17:32:39 -04:00
James Agnew 10d969c514
Add Consent Service (#1359)
* Initial consent svc

* Ongoing consent svc work

* Add docs

* Ongoing consent service work

* Work on consent service

* More work on consent svc

* License header updates

* Ongoing consent svc work

* Some test fixes

* Some test fixes

* More work on consent svc

* Tests working

* Test fix

* Propagate RequestDetails to everything in JPA server

* More interceptor tweaks

* Fix compile error

* One more tweak to captured SQL

* Ongoing interceptor tweaks

* Ongoing interceptor tweaks

* More interceptor tweaks

* Interceptor tweaks

* Tweaks to tests

* Fix tests

* Test fix

* Raise warnings when encoding extensions with missing values

* Consent service work

* More interceptor tweaks

* Consent interceptor tweaks

* Add logging to test
2019-06-27 16:35:29 -04:00
jamesagnew 3274693576 FIx a test 2019-06-22 16:31:55 -04:00
jamesagnew 95876ec3cb Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-06-22 16:24:07 -04:00
jamesagnew 638cb976fd Fix #1250 - Don't include Bundle.entry.response on search results 2019-06-22 16:23:32 -04:00
James Agnew 4ad1808da3
Propagate RequestDetails to everything in JPA server (#1358) 2019-06-22 15:18:06 -05:00
James Agnew 6724fd0348
Implement the $subsumes operation (#1344)
* Implement the $subsumes operation

* Fix #976
2019-06-17 17:31:24 -04:00
Stig Rohde Døssing b56f59542a Move JettyUtil to new module 2019-06-14 18:34:45 -04:00
Stig Rohde Døssing aab7bb6b64 Issue-1325: Let OS assign random ports to servers during testing, and let tests get the port of the running server once the OS has assigned a port. Delete PortUtil and similar utilities. 2019-06-14 18:34:45 -04:00
James Agnew 50a8c66bf5 Version bump to 4.0.0-SNAPSHOT 2019-05-30 17:13:03 -04:00
jamesagnew 73aa53be8f Release 3.8.0 2019-05-30 16:50:04 -04:00
Christian Ohr cd8b2feb2f Allow to set additional Http headers directly on the IClientExecutable 2019-05-29 21:17:52 -04:00
Oliver Egger 24c9c27abb overwritten section text in composition #402 2019-05-29 23:18:18 +02:00
James Agnew 6b37525f2d
Clean up redundant dependencies (#1306)
* Remove a bunch of unneedd deps

* Test fix

* Disable useless test
2019-05-09 12:51:13 -04:00
James Agnew 37b9e1a42c Improve validation of enableWhen questionnaires 2019-04-29 14:43:42 -04:00
patrick-werner 7f45660a15 changed toListOfResources to send IBaseResource as Type instead of null 2019-04-26 12:55:18 +02:00
James Agnew f3f5c570b1 A couple of compile glitches 2019-04-24 21:35:49 -04:00
James Agnew 738c2c1797
Interceptor framework refactoring (#1287)
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
James Agnew 210d99d121 Correct validation of questionnaire enableWhen 2019-04-17 16:50:37 -04:00
patrick-werner 15fda25771 added fetchValueSet to IValidationSupport and made it public to enable overwriting it in subclasses 2019-03-27 17:35:01 +01:00
James Agnew e85bec2858
Ja inline references (#1252)
* Use a single IN clause for OR reference searches

* Add changelog

* One more attempt at getting the free port util to actually work... sigh

* One more tweak to free ports

* Bundle fix
2019-03-26 10:42:42 +01:00
James Agnew 3433ecfd14 Test fixes 2019-03-11 16:14:34 -04:00
Ken Stevens dcfacfea49
Has param no in (#1232) 2019-03-10 20:50:24 -04:00
James Agnew 48c10bddc5
Narrative Generator refactoring (#1219)
* Starting work on this

* Working on narrative templates

* Work on new narrative system

* Account for some failing tests due to refactoring of narrative mode

* Another test fix

* More test fixes

* One more test fix

* Work on searches

* Address review comments
2019-02-27 14:59:57 -05:00
James Agnew 87ed00a002 Add ability to generate named parametrrs in a version independent way 2019-02-15 16:27:16 -05:00
James Agnew 10c348d44f Tweak to elements parametr support 2019-02-14 19:30:10 -05:00
James Agnew 810f1ad969 Improvements to elements parameter as well as adding attributes to
RequestDetails
2019-02-07 16:45:59 -05:00
James Agnew 0f8c8d18e2 Bump version to 3.8.0-SNAPSHOT 2019-02-06 20:02:28 -05:00
jamesagnew 207015c3af Version bump to 3.7.0 2019-02-05 21:36:38 -05:00
James Agnew 9a8e3245b8 Build fixes 2019-02-05 15:00:36 -05:00
James Agnew 4498335ae5 Elements query cleanup 2019-02-05 14:16:47 -05:00
jamesagnew d4af1ee2a3 Add tests and license headers 2019-02-04 16:34:39 -05:00
James Agnew e401ec86e4
Enhanced elements (#1192)
Squashed merge: Add elements exclude mode

* Start working on elements enhancement

* Work on elements projection

* Work on elements filter

* Feature is now working

* Just some cleanup

* Address compile issues
2019-02-03 16:41:33 -05:00
James Agnew b7ba529353
Merge pull request #1114 from zilin375/hapiFhir001
Fix NPE
2019-02-02 11:31:43 -05:00
bdenton 737ee9e97c add JSON-like tests for DSTU3 and R4 2019-01-30 17:32:06 -08:00
James Agnew 68fae08f20 Fix casing in base64Binary type 2019-01-23 08:34:09 -05:00
James Agnew 9cf64f78d0 Deprecate a bad setter on RetfulServer, fix a paging issue, and add a
disabled unit test to the subscription matcher
2019-01-21 14:46:17 -05:00
James Agnew 93bf2788ec Add subscription narrowing interceptor and refactor RuleBuilder to be a
bit cleaner
2019-01-12 14:23:26 -06:00
James Agnew fc09ed6966 Fix #1163 - Correctly handle invalid CapabilityStatement 2019-01-11 08:01:48 -07:00
James Agnew ee52d6fb31 Add SearchNarrowingInterceptor 2019-01-09 20:20:46 -06:00
jamesagnew b3c9b32db4 Credit for #1065 and forward-port fix to R4 provider 2019-01-09 07:19:55 -05:00
jamesagnew 39f2062802 FIx errorprone detected issues 2019-01-05 13:43:55 -05:00
James Agnew 5b8fee869e Add config options for default Prefer header and _total param on server 2019-01-04 16:12:45 -05:00
James Agnew 8c87c7c089 Correct an issue detected by ErrorProne 2019-01-04 14:28:38 -05:00
James Agnew 14a132a937 Squashed commit of the following:
commit 9659655830
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Dec 27 17:54:25 2018 -0500

    Finish sync

commit 70da25b76f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Dec 27 10:32:51 2018 -0500

    Work on RI4 sync
2018-12-27 17:58:47 -05:00
James Agnew 6eb4c28e7c More merging 2018-12-27 17:58:08 -05:00
James Agnew a0cb7edd08 Version bump a few dependencies 2018-12-22 20:13:03 -05:00
jamesagnew 6e0a9525a1 Remove dependency on public test server in unit test 2018-12-20 06:28:01 -05:00
James Agnew 19954fa252 Resolve failing test 2018-12-09 14:09:12 -05:00
James Agnew b442982310 Add media interceptor 2018-12-08 18:49:58 -05:00
James Agnew b41c222880 Require explicit declaration of authorizationinterceptor operation rules
on whether the response is authorized or not
2018-11-23 14:25:46 -05:00
James Agnew 719339fc14 One more test fix 2018-11-19 10:27:16 -05:00
James Agnew 2e1d5e4124 Fix an occasional NPE in the tests 2018-11-19 09:56:40 -05:00
James Agnew 58388bb614 Allow client to return methodoutcome instead of resdource for operation
call
2018-11-19 11:11:49 +01:00
James Agnew 67dbc802be Better detection of binary content in ResponseHighlighterInterceptor 2018-11-18 14:32:54 +01:00