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376 Commits

Author SHA1 Message Date
James Agnew eb0a657b62 Fix intermittent test failure 2019-10-08 20:45:12 -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
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 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
James Agnew 004f42cdcc Clean up docs 2019-09-23 15:56:02 -04:00
James Agnew 2cfa08f179 Add test case 2019-09-17 11:13:57 -04:00
James Agnew 38cf830384 Accurately reflect codesystem URL 2019-09-16 15:55:32 -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
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 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 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
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
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 6e20b53979 Fix a crash in R4 validation 2019-07-04 16:27:04 -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
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
James Agnew c2d4891434 Test fix 2019-05-29 21:13:52 -04:00
James Agnew 772d31dc6c
Merge pull request #1228 from eevaturkka/enablewhen_master 
QuestionnaireResponses should be able to have Items without Answers in disabled Questions
 2019-05-29 20:47:31 -04:00
Matti Uusitalo 225916a4b6 Changes requested in Pull Request review 2019-05-23 16:48:49 +03:00
James Agnew d4d3178621 A couple of test fixes 2019-05-11 15:04:44 -04:00
James Agnew 444730373b Fix an NPE in validation 2019-05-10 12:49:34 -04:00
James Agnew 92bd2c7173 Fix regression in validator when validating codesystems explicitly 
defined in the JPA database
 2019-05-10 12:08:40 -04:00
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 61902da527 Tweak to validator 2019-05-06 10:18:55 -04:00
James Agnew 7753ba2e5c Several test fixes 2019-05-04 14:38:37 -04:00
James Agnew 5132f1f4ed COnfirm validation support comntains codesystem 2019-05-02 07:50:59 -04:00
James Agnew 37b9e1a42c Improve validation of enableWhen questionnaires 2019-04-29 14:43:42 -04:00
Matti Uusitalo b95b4cf110 Merge with master 2019-04-25 10:44:07 +03:00
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 41a032ae9f added more missing methods 2019-03-30 15:36:06 +01:00
patrick-werner 2f3ac9d734 added missing method 2019-03-30 15:21:01 +01:00
Matti Uusitalo 5e0996d8ff Better method comment 2019-03-05 12:00:56 +02:00
Matti Uusitalo 9549a1615c Merge with origin/master 2019-03-05 11:44:30 +02:00
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 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 47123196a0 Merge branch 'master' of https://github.com/eevaturkka/hapi-fhir into eevaturkka-master 2019-02-05 14:26:41 -05:00
Eeva Turkka be746854e5 version number for release 2019-01-31 15:42:37 +02:00
Eeva Turkka 1c9f7f7ca9 Version number changed for build 2019-01-31 13:26:13 +02:00
Eeva Turkka 7e7d4d8879 Allowing items without answers even if item is disabled. 2019-01-31 13:00:41 +02:00
Eeva Turkka e6df4a21e4 Merge branch 'enablewhen_fix' of https://github.com/eevaturkka/hapi-fhir into enablewhen_fix 2019-01-28 10:31:44 +02:00
James Agnew 4f16fea580 Fix compile error 2018-12-28 12:11:19 -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 a0cb7edd08 Version bump a few dependencies 2018-12-22 20:13:03 -05:00
Ken Stevens 84a34eb3c9
Subscription module support (#1147) 
* Reorganizing packages and dependencies to support standalone subscription running within a CDR container where all hapi modules are on the classpath.

Moved Subscription registry out of interceptor and introduced SubscriptionLoader

* Created ActiveSubscription and moved cache bits into it

* Moved ExecutorQueue stuff out into its own class

* Add test and supporting code to validate SubscriptionConstants.EXT_SUBSCRIPTION_RESTHOOK_DELIVER_LATEST_VERSION behaviour

* Added SubscriptionCheckingSubscriber

* Moved a few beans to @ComponentScan

* Replaced use of beanFactory with concrete factory classes

* Switched test to use subscribablechannel

* Added SubscriptionLoaderFhirClientTest

* Confirm that our SubscriptionProviderFhirClient works with a live fhir client

* Register interceptors with DaoConfig instead of RestServer.
Also, Rename @VisibleForTesting methods with ForUnitTest

* Fix triggering service so it uses new subscriptionmatcherinterceptor

* Renamed "Database" classes to "Dao"

* processing -> matching naming change
 2018-12-18 13:09:06 -05:00
Matti Uusitalo a3e7f5b18f Corrected group ids back to ca.uhn.hapi.fhir 2018-12-18 11:21:29 +02:00
Matti Uusitalo 01eb7faf66 Deleted unnecessary Inteface class 2018-12-18 10:15:47 +02:00
Matti Uusitalo 98f929997b Sync with upstream/master 2018-12-17 15:38:05 +02:00
Matti Uusitalo 7ad45308e0 Make this configurable 2018-12-17 14:10:15 +02:00
Matti Uusitalo 89e3cac0e2 Corrected problems caused by merge 2018-12-17 13:55:15 +02:00
Matti Uusitalo 8183c18406 Corrected project dependency version numberts 2018-12-17 13:54:43 +02:00
Matti Uusitalo 58959eec48 Do not force enableWhen to have system 2018-12-17 13:31:07 +02:00
Matti Uusitalo dd8e027ff4 Don't evaluate Extensions when determining type of answer 2018-12-17 13:31:07 +02:00
Matti Uusitalo a1f79a2063 Filter Extensions from enablewhen evaluation 2018-12-17 13:31:07 +02:00
Matti Uusitalo 755eaa5f25 bumped version n. for release 2018-12-17 13:31:07 +02:00
Matti Uusitalo c2b3d48afe Support required questionnaireitem groups 2018-12-17 13:31:07 +02:00
Matti Uusitalo a0db7e20b6 temporarily set hard coded error when no profile found 2018-12-17 13:30:36 +02:00
Matti Uusitalo cefacdc18c Returned to original state as the experiment failed 2018-12-17 13:30:36 +02:00
Matti Uusitalo 24ebe6cf03 Temporarily set isNoTerminologyServer() return true to avoid errors about loinc codes 2018-12-17 13:30:36 +02:00
Matti Uusitalo 311d92f276 Added more information to the error message about misplaced QuestionnaireResponseItem 2018-12-17 13:30:36 +02:00
Eeva Turkka 076d18977d Added support for Quantity in the default enable when evaluator 2018-12-17 13:30:36 +02:00
Matti Uusitalo b29e8d987c Avoid infinite loop when validating misaligned questionnaireresponseitems 2018-12-17 13:27:27 +02:00
Matti Uusitalo a9c625365d Added missing propagation of QuestionnaireResponse root element 2018-12-17 13:27:27 +02:00
Matti Uusitalo ab484c9819 Thread questionnaireResponse root element through questionnaire validation so implementations of enablewhen may validate against the complete resource 2018-12-17 13:27:27 +02:00
Matti Uusitalo 10fe878540 Changed versions to use fi.kela.kanta.phr parent 2018-12-17 13:27:27 +02:00
Matti Uusitalo e84689b167 Way to inject custom enablewhen evaluator added 2018-12-17 13:27:27 +02:00
Matti Uusitalo 507c78320c Added check for answering questions which are not enabled 2018-12-17 13:27:27 +02:00
Matti Uusitalo d2c6a98c24 Removed unused HapiWorkerContext 2018-12-17 13:27:27 +02:00
Okko Kauhanen a12f5892e2 Added operator evaluation for R4 enableWhen 2018-12-17 13:26:31 +02:00
Eeva Turkka 69d9e5d2b2 Unit tests up to date and maybe we need to use r4 path 2018-12-17 13:15:43 +02:00
Eeva Turkka 84c02d2e79 Cherry picked changes from master to 3.5.0 branch 2018-12-17 13:13:38 +02:00
Matti Uusitalo 3c56640d57 Do not force enableWhen to have system 2018-12-17 12:48:53 +02:00
Matti Uusitalo 73e85ce668 Don't evaluate Extensions when determining type of answer 2018-12-17 12:48:53 +02:00
Matti Uusitalo 14b5d88530 Filter Extensions from enablewhen evaluation 2018-12-17 12:48:53 +02:00
Matti Uusitalo 4956c9c7e0 bumped version n. for release 2018-12-17 12:48:53 +02:00
Matti Uusitalo c04a172fcd Support required questionnaireitem groups 2018-12-17 12:48:53 +02:00
Matti Uusitalo e13bc28b42 temporarily set hard coded error when no profile found 2018-12-17 12:45:51 +02:00
Matti Uusitalo 3f21bfb560 Returned to original state as the experiment failed 2018-12-17 12:45:51 +02:00
Matti Uusitalo 154a1d92e0 Temporarily set isNoTerminologyServer() return true to avoid errors about loinc codes 2018-12-17 12:45:51 +02:00
Matti Uusitalo c86ae90c4d Added more information to the error message about misplaced QuestionnaireResponseItem 2018-12-17 12:45:51 +02:00
Eeva Turkka 074e812162 Added support for Quantity in the default enable when evaluator 2018-12-17 12:45:51 +02:00
Matti Uusitalo 94f0520982 Avoid infinite loop when validating misaligned questionnaireresponseitems 2018-12-17 12:43:43 +02:00
Matti Uusitalo a6b0cb2a6e Added missing propagation of QuestionnaireResponse root element 2018-12-17 12:43:43 +02:00
Matti Uusitalo fa0b61d9b8 Thread questionnaireResponse root element through questionnaire validation so implementations of enablewhen may validate against the complete resource 2018-12-17 12:43:43 +02:00
Matti Uusitalo a981452957 Reverted to original version 2018-12-17 12:43:43 +02:00
Matti Uusitalo b7843498dc Changed versions to use fi.kela.kanta.phr parent 2018-12-17 12:43:43 +02:00
Matti Uusitalo 76eb85308c Way to inject custom enablewhen evaluator added 2018-12-17 12:43:43 +02:00
Matti Uusitalo 78ab112204 Added check for answering questions which are not enabled 2018-12-17 12:43:43 +02:00
Matti Uusitalo 16a4004f02 Removed unused HapiWorkerContext 2018-12-17 12:43:43 +02:00
Matti Uusitalo e7e039a851 Added default enablewhen behaviour to STU3 resources converted to R4 2018-12-17 12:43:43 +02:00
Okko Kauhanen 8f338c1b63 Remove unnecessary throw 2018-12-17 12:43:43 +02:00
Okko Kauhanen 4fff5ee27a Fixed bug in finding QuestionnaireResponse child items 2018-12-17 12:43:43 +02:00
Okko Kauhanen cddb6b993c Added operator evaluation for R4 enableWhen 2018-12-17 12:43:43 +02:00
Okko Kauhanen 6a83a3fb59 fix enablewhen result 2018-12-17 12:42:29 +02:00
Okko Kauhanen 275cc9556f Missing file 2018-12-17 12:42:29 +02:00
Okko Kauhanen 48db1d8770 First implementation of enableWhen evaluator 2018-12-17 12:42:29 +02:00
Eeva Turkka ad11409705 Unit tests up to date and maybe we need to use r4 path 2018-12-17 12:42:29 +02:00
Eeva Turkka 7097526f81 Cherry picked changes from master to 3.5.0 branch 2018-12-17 12:41:05 +02:00
James Agnew 46f5c18adc Prepare for 3.6.0 release 2018-12-17 12:32:33 +02:00
Matti Uusitalo b262985e21 Do not force enableWhen to have system 2018-12-13 13:29:17 +02:00
hdconradi 89ede0e524 Extension domains configuration for the fhr instance validator (#917) 
* Fix the url of the StructureDefinition extensions

http://hl7.org/fhir/tools/StructureDefinition/ -> http://hl7.org/fhir/StructureDefinition/
That makes the entry for the structuredefinition-expression superfluous.

The url behind IG_DEPENDSON_PACKAGE_EXTENSION does not point is not (yet?) valid too.

* Add ability to configure custom extension domains.

* Testing the extension domains configuration

* Fix obvious bug when determining resource name

The for loop was completely superfluous beforehand.
Either fix it as e.g. in this patch or remove it.

* small improvements and TODO's for possible NPE's

- javadoc see
- use diamond operator for generics
- remove throws clause when exception is not thrown
- add TODO's for some cases a NPE might occur.
  My knowledge of the context is not sufficient to suggest the proper
  way to solve this.
 2018-12-13 05:32:47 -05:00
Matti Uusitalo c85f4b8362 Don't evaluate Extensions when determining type of answer 2018-12-13 12:12:56 +02:00
Matti Uusitalo 82387e6902 Filter Extensions from enablewhen evaluation 2018-12-12 14:22:38 +02:00
Matti Uusitalo 3df4004539 bumped version n. for release 2018-12-11 11:17:40 +02:00
Matti Uusitalo 64f378ae78 Support required questionnaireitem groups 2018-12-10 13:58:14 +02:00
Matti Uusitalo b2e20b5c31 temporarily set hard coded error when no profile found 2018-12-10 13:57:04 +02:00
Matti Uusitalo 5a508f45b9 Returned to original state as the experiment failed 2018-12-10 13:52:38 +02:00
Matti Uusitalo f72fbbe402 Temporarily set isNoTerminologyServer() return true to avoid errors about loinc codes 2018-12-10 13:52:38 +02:00
Matti Uusitalo b922670d97 Added more information to the error message about misplaced QuestionnaireResponseItem 2018-12-10 13:52:38 +02:00
Eeva Turkka efbff93247 Added support for Quantity in the default enable when evaluator 2018-12-10 13:52:38 +02:00
Matti Uusitalo d2a1be82f8 Avoid infinite loop when validating misaligned questionnaireresponseitems 2018-12-10 13:51:12 +02:00
Matti Uusitalo 55287f126c Added missing propagation of QuestionnaireResponse root element 2018-12-10 13:51:12 +02:00
Matti Uusitalo 2941e7067a Thread questionnaireResponse root element through questionnaire validation so implementations of enablewhen may validate against the complete resource 2018-12-10 13:51:12 +02:00
Matti Uusitalo 606d901523 Reverted to original version 2018-12-10 13:48:23 +02:00
Matti Uusitalo addc44b5f4 Changed versions to use fi.kela.kanta.phr parent 2018-12-10 13:48:23 +02:00
Matti Uusitalo 11b1114fe8 Way to inject custom enablewhen evaluator added 2018-12-10 13:48:23 +02:00
Matti Uusitalo deb8de8705 Added check for answering questions which are not enabled 2018-12-10 13:48:23 +02:00
Matti Uusitalo e2cdb7bbe6 Removed unused HapiWorkerContext 2018-12-10 13:48:23 +02:00
Matti Uusitalo 98cf1becb1 Added default enablewhen behaviour to STU3 resources converted to R4 2018-12-10 13:46:45 +02:00
Okko Kauhanen 360e8d2d8f Remove unnecessary throw 2018-12-10 13:45:12 +02:00
Okko Kauhanen 430e8c89e8 Fixed bug in finding QuestionnaireResponse child items 2018-12-10 13:45:12 +02:00
Okko Kauhanen 0540efa49b Added operator evaluation for R4 enableWhen 2018-12-10 13:45:12 +02:00
Okko Kauhanen f56ad302dd fix enablewhen result 2018-12-10 13:45:12 +02:00
Okko Kauhanen 44b24a65cb Missing file 2018-12-10 13:45:12 +02:00
Okko Kauhanen e4db83ce41 First implementation of enableWhen evaluator 2018-12-10 13:45:12 +02:00
Eeva Turkka c67554e5aa Unit tests up to date and maybe we need to use r4 path 2018-12-10 13:45:12 +02:00
Eeva Turkka b0635a91cd Fixed unit test asserts 2018-12-10 13:33:55 +02:00
Eeva Turkka 4dbef9a799 Cherry picked changes from master to 3.5.0 branch 2018-12-10 13:33:55 +02:00
Matti Uusitalo b76fe1e6be Sync our fork with Hapi master. Merge remote-tracking branch 'upstream/master' 2018-12-10 13:20:27 +02:00
jamesagnew cc57bacab8 Version bump to 3.7.0-SNAPSHOT 2018-11-12 10:07:28 -05:00
James Agnew 63af04a7b4 Prepare for 3.6.0 release 2018-11-12 05:40:55 -05:00
Matti Uusitalo 130fc3a90e Removed unused HapiWorkerContext 2018-11-07 11:46:24 +02:00
Matti Uusitalo b140351650 Added default enablewhen behaviour to STU3 resources converted to R4 2018-11-06 13:11:12 +02:00
Okko Kauhanen 139ec6503f Remove unnecessary throw 2018-11-05 18:39:13 +02:00
Okko Kauhanen c099fcda0a Fixed bug in finding QuestionnaireResponse child items 2018-11-05 17:49:12 +02:00
Okko Kauhanen 4c4c8ba87a Added operator evaluation for R4 enableWhen 2018-11-05 17:03:50 +02:00
Okko Kauhanen 38a2b17a5e fix enablewhen result 2018-11-05 13:00:32 +02:00
Okko Kauhanen 91bf3b61f6 Missing file 2018-11-05 12:55:02 +02:00
Okko Kauhanen 0dcc4fa189 First implementation of enableWhen evaluator 2018-11-05 12:01:25 +02:00