Commit Graph

2210 Commits

Author SHA1 Message Date
Ken Stevens 6b019492fe
Merge pull request #1758 from jamesagnew/ks-20200312-json-annotation
moved common Json annotations out into an interface
2020-03-13 15:58:21 -04:00
James Agnew 1dc5d89013
Optmize forced ID resolution (#1754)
* Add forced ID caching

* Work on id optimization

* Test fixes

* More optimization work

* Add some docs

* Work on docs

* Test fixes

* Test fixes

* Test fixes

* Address review comments

* Compile fix
2020-03-12 17:12:50 -04:00
Ken Stevens ecf5284c87 moved common Json annotations out into an interface 2020-03-12 13:36:34 -04:00
Tadgh 828ddd5185 Update docs 2020-03-04 12:14:55 -08:00
James Agnew 4a160a2df3 Merge branch 'master' into ja_20200206_multitenancy 2020-03-03 09:25:19 -05:00
James Agnew ac9a371f18 Add test 2020-03-03 08:28:04 -05:00
James Agnew 5bc554949b
Remove deleted resources from cached search results (#1732)
* Remove deleted resources from cached search results

* Add changelog

* Add tests
2020-02-28 10:57:26 -05:00
Gary Graham b1d7072c42 Add precision checker for ordinal date returning on DateRangeParam 2020-02-26 22:22:42 -05:00
Gary Graham 165f5fd808 fix bugs in calculating ordinal date 2020-02-26 09:32:20 -05:00
Gary Graham 97c98254d0 Extract Common functionality out of CalculateHashesTask, build CalculateOrdinalDatesTask based on it 2020-02-25 16:09:08 -05:00
Gary Graham 3ec772b527 rework ResourceIndexedSearchParamDate constructor to support incoming string values 2020-02-25 14:06:36 -05:00
Gary Graham 34d5925393 Move common work to DateUtils. Rename function for clarity. 2020-02-25 09:37:57 -05:00
Gary Graham 7f5b3394e0 Hacky first-pass of adding ordinal date field to ResourceIndexedSearchParamDate and using it for search 2020-02-24 19:34:16 -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
Ken Stevens 2545fc6e3d Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml
2020-01-29 17:06:02 -05:00
dionmcm 00fdc978cc narrative gen removed old code and enhanced error message
I ran into an issue trying to use the old .class style property. The validation message was useful, but I spotted some unreachable code investigating which I've removed. I also enhanced the configuration exception to indicate what was wrong with a supplied key and expected extension types.
2020-01-29 05:58:22 -05:00
Ken Stevens f2e8037c90 Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search 2020-01-22 15:06:52 -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
Ken Stevens 9413e8f198 r4 works. But distance calculation still needs to be fixed. 2020-01-22 11:59:03 -05:00
James Agnew c0e929dacb
Copy identifiers to placeholder resources (#1675)
* Copy identifiers to placeholder resources

* Add tests

* Maven cleanup

* Still messing around with azure

* Adding to logging

* More azure work

* One more attempt

* More messing around with azure

* Test fix

* Another caching attempt

* More work on azure pipeline

* Fix pipeline file

* Keep working on pipeline

* More work on azure

* More azure

* More azure work

* More azure
2020-01-21 06:09:06 +09:00
jamesagnew 634458c447 License header update 2020-01-17 00:16:56 -05:00
James Agnew 0385c25aa3 Fix FHIR version defaults 2020-01-15 14:03:59 +08:00
James Agnew 1390ea3c06
Update FHIR R5 structures to 4.2.0 version (#1665)
* Work on upgrading core

* Work on R5 updates

* Work on core updates

* Test fix

* Update model version properties file for R5

* Bump core version

* Test fixes

* Add 4.2.0-SNAPSHOT version to versions page in docs
2020-01-14 10:27:01 +08:00
Petro Mykhaylyshyn 8ed3dcc9ac [(fixjsongenerationtomaster)] Remove unused import. 2020-01-13 13:37:54 +08:00
Petro Mykhaylyshyn fdab81361c [(fixjsongenerationtomaster)] When max cardinality in profile is changed to 1 output JSON contain an array. 2020-01-13 13:37:54 +08:00
Petro Mykhaylyshyn a234b1f8a9 [(fixjsongeneration)] When max cardinality in profile is changed to 1 output JSON should still contain an array. 2020-01-13 13:37:54 +08:00
jamesagnew 3ac4172bc4 License header versions 2020-01-11 23:23:02 -05:00
Diederik Muylwyk 8615d10730 Fix typo. 2019-12-31 09:27:26 -05:00
Diederik Muylwyk 48f7ee5afb Rolling back previous unnecessary changes. 2019-12-31 09:25:56 -05:00
Diederik Muylwyk 170b607992 Added some FIXMEs. 2019-12-30 18:43:15 -05:00
Diederik Muylwyk 856993edf8 Moved changelog entry, and added clarifying comments to DateRangeParam. 2019-12-30 15:29:35 -05:00
Diederik Muylwyk 4eaeb7ef9e Implemented isDateWithinRange() and supporting methods. 2019-12-30 14:35:51 -05:00
Diederik Muylwyk d8133487b2 Initial commits. 2019-12-23 17:14:47 -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
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 86bd9a28fe
Fix to valueset expansion logic (#1613)
* Fox to valueset expansion logic

* Work on docs

* Docs tweaks

* Docs tweaks

* Fix test

* Remove unused class

* Add changelog
2019-12-01 21:21:19 -05:00
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 74159dcb26
Work on refactoring how PIDs work (#1580)
* Start work on refactoring how PIDs work

* Some test fixes

* Test fixes

* Test fixes

* Restore accidentally deleted line

* One more tweak

* Rework resource link extraction

* Test fix

* Split out transaction processor

* Updates

* Test fix

* Test fixes

* Test fixes

* Clean up LGTM warning

* Fix compile failure

* One more test fix

* Fix LGTM issue

* Add spot for metadata

* Add test logging

* Remove testing code

* More test logging

* Add some test logging

* Attempty to fix intermittent test failure

* Improve exception tracking

* Work on simplifying search param registry

* Fix compile

* Fix compile errors

* Fix two test bugs
2019-11-17 14:35:19 -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
James Agnew 1a348abaf5 Try to fix 2 intermittent test failures 2019-11-08 08:45:08 -05:00
jamesagnew 7c8342dcc1 Add some test logging 2019-11-08 05:53:59 -05:00
James Agnew ebc52e6b48 Correctly handle below expansion with missing system 2019-11-07 09:28:24 -05:00
James Agnew 0b9f921c3e Fix NPE in xml parser 2019-11-04 09:49:49 -05:00
jamesagnew 9c93d5d7f7 Test fixes 2019-11-04 07:04:26 -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
James Agnew 48930de31c Attempt to resolve #1356 2019-11-02 16:15:37 -04:00
Ken Stevens 1fd3948b12
Merge pull request #1572 from jamesagnew/ks-source-subscriptions
fixed in-memory search by _source for Dstu3
2019-10-30 16:20:14 -04:00
James Agnew e96500d54f Add a test 2019-10-30 15:51:46 -04:00
Ken Stevens 97f4de553a fix test. this is better 2019-10-30 15:24:43 -04:00
Ken Stevens 3ceb4085cb fix test (not super happy about this fix, but I think it's the right thing to do) 2019-10-30 15:21:21 -04:00
Ken Stevens 21c591eaf2 ready for review 2019-10-30 13:49:10 -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 007cfaf00e
Don't error out on missing CS (#1570)
* Don't error out on mi9ssing CS

* Add tests

* Add a bit of test coverage

* One more test
2019-10-30 08:38:39 -04:00
jamesagnew 8b227a59fc Add some tests 2019-10-28 06:02:19 -04:00
jamesagnew ac4d108126 Merge branch 'ja_20190928_rationalize_search_param_extractor' of github.com:jamesagnew/hapi-fhir into ja_20190928_rationalize_search_param_extractor 2019-10-27 18:17:29 -04:00
James Agnew d18550b96f Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-27 18:00:31 -04:00
James Agnew a82da8de1c Override enum factory interfaces 2019-10-27 17:51:57 -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 2b3c775b77 Some cleanup and fix a test 2019-10-26 12:45:57 -04:00
jamesagnew 5a300d2d8e Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-10-26 10:32:16 -04:00
James Agnew 9cc945b5bd Merge branch 'osgi-server-work' of https://github.com/bdenton/hapi-fhir into bdenton-osgi-server-work 2019-10-25 17:05:09 -04:00
jamesagnew fd73a593ea Work on merge 2019-10-25 08:50:34 -04:00
jamesagnew cd84af30b1 Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-25 05:56:39 -04:00
jamesagnew 935ec9ebc2 License headers 2019-10-25 05:44:51 -04:00
Ken Stevens f19100cbb3 final cleanup 2019-10-24 20:29:45 -04:00
Ken Stevens 4a2ed62357 review feedback 2019-10-24 20:25:16 -04:00
Ken Stevens 08472c1e3f ready to merge 2019-10-24 17:56:15 -04:00
Ken Stevens 5379ab8c2c implement in-memory match 2019-10-24 17:53:02 -04:00
Ken Stevens b7aa327118 pre-review cleanup 2019-10-24 16:47:43 -04:00
Ken Stevens 4fa849a3e5 pre-review cleanup 2019-10-24 16:43:47 -04:00
Ken Stevens 43f17534bb commiting with FIXMEs so James can review 2019-10-24 16:40:53 -04:00
James Agnew 74c03b5bb7 Add a test 2019-10-24 08:32:52 -04:00
James Agnew 91ec0a6922 Test fix 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 19247ffb46
Allow updating externalized binary (#1556)
* Add non working test

* Add a test

* FIx test

* Allow updating existing externalized binary data

* Add test

* Remove unneeded test

* Fix test
2019-10-22 18:10:03 -04:00
jelmer.terwal c337fdde14 Override breakes stuff here for Kotlin 2019-10-22 13:58:52 -04:00
jelmer.terwal 5002a087bb Some work on jamesagnew/hapi-fhir/#1297 2019-10-22 13:58:52 -04:00
James Agnew 73961072a6
Handle invalid chains on custom search params (#1553)
* Handle invalid chains on custom search params

* Add some more tests

* One more test fix
2019-10-21 21:21:33 -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 bfbc73caaf
Auto externalize binary contents (#1550)
* Auto externaliZe binary attachments

* Work on externalization

* Auto externalize binary content

* Work on tests

* Fix alert
2019-10-19 09:01:00 -04:00
James Agnew b51a93a2b5 Intermittent test fix 2019-10-18 15:46:02 -04:00
James Agnew a71d969ba1 Add line numbers to validation failures 2019-10-18 14:10:47 -04:00
James Agnew 9fff043892 Fix #1481 - Remove Jetty reference 2019-10-17 11:41:57 -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 9c23959b38 Licene header updates 2019-10-15 15:08:13 -04:00
James Agnew 9a050461a8 Make cache timeout configurable 2019-10-15 09:34:48 -04:00
James Agnew ff4fba15c9 Add a test 2019-10-15 07:34:44 -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
bdenton f81aaa7f00 refactor "split" packages; create osgi bundle for server framework 2019-10-12 14:08:41 -07:00
James Agnew 861ed36f00
Allow patches to be authorized for DSTU3 transactions (#1529)
* Allow patches to be authorized for DSTU3 transactions

* Add changelog
2019-10-08 14:29:27 -05:00
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
jamesagnew 150c865f68 License header updates 2019-10-03 21:20:08 -04:00
James Agnew 069db501ee
Fix _has parameter (#1525)
* Fix _has parameter

* Bug fixes

* Add a comment

* Test fixes
2019-10-03 21:19:31 -04:00
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
James Agnew a1bf50685d Work on cleanup 2019-09-30 21:40:41 -04:00
James Agnew eaaf2768c3 Fix #402 - Don't overwrite narrative sections 2019-09-30 20:14:36 -04:00
James Agnew 066c9a7fb7 Improvements to AutohrizationInterceptor create handling 2019-09-30 15:07:23 -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 3870c14a6c Remove unused contructors 2019-09-26 16:42:39 -04:00
James Agnew cc0df9850c Make sure the validator can get at codes defined in notpresent
codesystems
2019-09-26 14:44:09 -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
jamesagnew 473fa3456e Work on adding codecov 2019-09-25 14:12:42 -04:00
James Agnew dfe07e7a2b Avoid concurrency issue introduced by #1489 2019-09-25 13:45:02 -04:00
James Agnew 7b363c2c5c Some test fixes 2019-09-24 15:28:14 -04:00
James Agnew 9b2826f3c6
Handle searches with chained slash value (#1503)
* Work on test case for bug with searches

* Work on tests

* Fix issue with slashes in reference chain parameter for JPA server
2019-09-24 14:31:05 -04:00
jamesagnew 936587df6e Work on migrating docs 2019-09-22 15:52:49 -04:00
James Agnew 0a5eca0821 Work on docs 2019-09-22 13:25:50 -04:00
James Agnew a989a746b0 Fix #1494 - Upgrade to new :recurse syntax for R4 include/revinclude
statements
2019-09-20 09:38:29 -04:00
David Maplesden c2c07c95fc We can't short circuit traversal after all. 2019-09-19 20:38:30 -04:00
David Maplesden c8c8ab6881 Add modifier extensions to tha actual modifier extensions collection 2019-09-19 20:38:30 -04:00
David Maplesden 946f3a1732 Cut short traversal when finding top-level base references 2019-09-19 20:38:30 -04:00
David Maplesden 4021fccf3b We only need to extract the existing contained resources once 2019-09-19 20:38:30 -04:00
David Maplesden 1f253856cf Optimise for encoding String primitive data types
We typically have many more string primitives than anything else
2019-09-19 20:38:30 -04:00
David Maplesden 8b84b8ffea Cache the composite children that need encoding to improve performance 2019-09-19 20:38:30 -04:00
David Maplesden 5120fe795e Dramatically improve the performance of containResourcesForEncoding
We do this by avoiding the double processing of contained resources when
looking for resources to contain
2019-09-19 20:38:30 -04:00
jamesagnew 6475146bc9 Add license headers 2019-09-19 18:08:21 -04:00
James Agnew eddb98084d Move PreferReturnEnum back to original location to avoid regressions 2019-09-19 15:48:58 -04:00
James Agnew 2be63a1650 Test fixes 2019-09-19 09:45:07 -04:00
James Agnew 30dfde645b Upgrade to Fontawesdome 5 and prevent uploading resources with binary
storage extensions
2019-09-19 05:28:05 -04:00
James Agnew 6b21e8cd90 Add some testing to the bulk export service 2019-09-18 14:43:00 -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 08835c1615 FIx a failure in FhirTerser when visiting custom types 2019-09-13 09:11:47 -04:00
Ken Stevens abef4455eb done 2019-09-09 17:22:07 -04:00
Ken Stevens 7cfbf710fe Merge remote-tracking branch 'remotes/origin/master' into ks-in-memory-date-compare
# Conflicts:
#	src/changes/changes.xml
2019-09-09 14:46:25 -04:00
Ken Stevens 9e83f1d40a changelog 2019-09-09 14:22:42 -04:00
James Agnew 722c7a8211 Work on GraphQL updates 2019-09-06 14:56:17 -04:00
jamesagnew 1ef70a0fca Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-03 07:02:09 -04:00
jamesagnew 8b09b3f3eb Rename config enum for consistency 2019-09-03 07:01:36 -04:00
Diederik Muylwyk 9f7cf3923b
Merge pull request #1458 from jamesagnew/1457-valueset-pre-expansion-need-to-account-for-existing-valuesets-and-user-assigned-ids
Resolve "ValueSet pre-expansion - need to account for existing ValueSets and user-assigned IDs."
2019-08-30 10:48:39 -04:00
Diederik Muylwyk 8ef9c61b83 Address review comments; improve logging. 2019-08-30 10:47:21 -04:00
Diederik Muylwyk e03d6a5d47 Fixed handling of pre-expansion in light of pre-existing, non-pre-expanded ValueSets. 2019-08-29 18:09:30 -04:00
James Agnew c5a88444b6 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-08-29 14:00:37 -04:00
James Agnew 956bb39327 Resolve an inefficient regex expression 2019-08-29 13:59:31 -04:00
Diederik Muylwyk b41926307c Completed work on large ValueSet expansion support; ready for review. 2019-08-23 17:40:45 -04:00
Diederik Muylwyk 890555a77d Incremental work on large ValueSet expansion support; transaction boundaries need to be broken up. 2019-08-23 11:46:32 -04:00
Diederik Muylwyk 97a235ddfc Merging master into working branch.
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
2019-08-22 14:02:56 -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
James Agnew ce44115152
Handle cascading deletes correctly with circular references (#1435)
* Handle cascading deletes correctly with circular references

* A bit of cleanup

* Address review comments

* FIx some javadocs

* Fix an incorrect message
2019-08-20 10:08:34 -04:00
Diederik Muylwyk 8590e0ca4d Merging master into working branch.
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
2019-08-19 02:28:30 -04:00
Diederik Muylwyk dfd098c374 Incremental work on large ValueSet expansion support; added use of terminology tables when expanding. 2019-08-19 02:26:12 -04:00
James Agnew 57c6064d89 Another test fix 2019-08-17 12:21:08 -04:00
James Agnew 74c83f6148 Test fixes 2019-08-17 12:01:04 -04:00
James Agnew 1e07fcd2b3
Fix an unintended regression in #1357 (#1429)
* Start working on a tweak to #1357 - Not yet complete

* Tweaks to avoid an unintended regression from #1357
2019-08-15 08:35:50 -04:00
Ken Stevens f29c37a654 added IBaseReference constructor to TokenParam 2019-08-14 15:33:50 -04:00
jamesagnew 2d35db877e Add version constant 2019-08-14 15:03:05 -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 01a6aa8f5b Test fix 2019-08-13 14:54:35 -04:00
James Agnew b4fece0ae9 Add interceptor hook for graphql calls 2019-08-13 14:46:50 -04:00
James Agnew ef7182228f One more fix for #1399 2019-08-12 18:07:09 -04:00
James Agnew c04f1d15d8 Fix #1399 - Issue with DiagnosticReport R4 narrative generation template 2019-08-12 17:17:45 -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
James Agnew bfaf617142 Add some more chars to the sanitizer function 2019-08-12 08:16:38 -04:00
James Agnew 4f5a2b3c0c Add fhirType() to IBase to bring it in line with what the core structures do 2019-08-09 09:44:20 -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
Ken Stevens 1b17097f62 a couple more int -> long 2019-08-07 13:35:27 -04:00
James Agnew 6aa7916ba7
Merge pull request #1415 from jamesagnew/ks-inmemory-id-match
in-memory id match
2019-08-07 08:31:38 -04:00
James Agnew b0eb19cf2f A few fixes resulting from the R5 merge 2019-08-06 17:55:51 -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
Ken Stevens c11d719957 Fix bug when in-memory matcher compares long id to string id 2019-08-06 15:17:09 -04:00
Ken Stevens 48c8497086 Changed migration test from derby to h2
Added a new test from 340 to latest version.
2019-08-02 16:00:43 -04:00
jamesagnew 46c8c61932 Restore build - May need to roll back the RDF changes 2019-08-01 10:14:56 -04:00
James Agnew 0f4738c1b5
Merge branch 'master' into rdf_parser 2019-08-01 09:25:40 -04:00
Ken Stevens f1d3fc2307 Changed Stopwatch getThroughput param from int to long
Added FhirVersion accessor to AnyListResource
2019-08-01 06:32:09 -04:00
James Agnew 04ce9cfc1a Add support for uploading custom terminology using the
$upload-external-code-system operation
2019-07-30 17:30:18 -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
Ken Stevens 84f5c7d467 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-24 21:54:05 -04:00
Ken Stevens e05387da02 Recover from failed merge again. This time with feeling! 2019-07-24 13:46:20 -04:00
James Agnew ddb8e385bf Test fix 2019-07-24 13:24:48 -04:00
James Agnew e8cf2738f0 Handle oversized payload request 2019-07-24 13:18:30 -04:00
Ken Stevens 64e83fa3df Revert "Recovering Pointcut from a failed merge"
This reverts commit 19c0b4fd
2019-07-24 13:00:49 -04:00
Ken Stevens 19c0b4fdd2 Recovering Pointcut from a failed merge 2019-07-24 11:30:36 -04:00
Ken Stevens 0efe69f891 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
2019-07-24 10:41:37 -04:00
Ken Stevens 8d86e34bcf Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
2019-07-23 09:12:08 -04:00
jamesagnew 60ea922e8d Add license headers 2019-07-23 05:38:10 -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
Ken Stevens 7ba3ceec90 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-19 10:54:56 -04:00