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1792 Commits

Author SHA1 Message Date
James Agnew ee52d6fb31 Add SearchNarrowingInterceptor 2019-01-09 20:20:46 -06:00
James Agnew 8beccab9ab Merge branch 'master' into test-openjdk-11 2019-01-09 10:48:57 -05:00
jpoth 1bd63f4454 Add JKD11 support for Karaf 2019-01-09 11:18:42 +01:00
jamesagnew 3d94761bcb Improve response for transactions 2019-01-06 18:08:32 -05:00
jamesagnew 98d93df12a License header updates 2019-01-04 16:22:15 -05:00
James Agnew a1275874f8 Correct subscription delivery metadata 2019-01-04 10:56:21 -05:00
James Agnew 1bfa29bbcc Site updates 2018-12-28 11:42:21 -05:00
jamesagnew 4599a10180 Merge branch 'master' into test-openjdk-11 2018-12-23 14:19:59 -05:00
James Agnew a0cb7edd08 Version bump a few dependencies 2018-12-22 20:13:03 -05:00
James Agnew 11b8304cb4 Fix case sensitivity issue 2018-12-13 08:31:35 -05:00
James Agnew b442982310 Add media interceptor 2018-12-08 18:49:58 -05:00
jamesagnew 3109a269b3 Attempting to get ErrorProne working on JDK11 2018-12-08 18:22:17 -05:00
jamesagnew 3a3b81a6a8 Preparing things for OpenJDK 11 2018-12-08 17:52:48 -05:00
James Agnew c484c69664 Better error message for unqualified search parameter types 2018-12-03 13:14:10 -05:00
Ken Stevens 6baee4dc3f
Standalone subscription (#1125) 2018-11-30 17:19:16 -05:00
Ken Stevens 03ebcafdf5
In-memory matcher (#1116) 
* Initial refactoring to move database matcher out into its own class

* MAJOR REFACTOR: Pulled indexing code out of BaseHapiFhirDao into a new class ResourceIndexedSearchParams

* Moved calculateHashes

* Replaced @Bean definitions in BaseConfig.java with @ComponentScan

Annotated bean classes with either @Service (if it's stateless) or @Component (if it's stateful).  It doesn't really matter which annotation is used, but it's helpful to see at a glance whether a bean is stateful or stateless.

* Move services out of BaseHapiFhirDao

Moved services required by ResourceIndexedSearchParams out of BaseHapiFhirDao and into new classes called LogicalReferenceHelper, IdHelperService, MatchUrlService, and DaoProvider.

Converted SearchBuilder into Prototype Bean

Mark Spring components that depend on daos and entitymanagers with @Lazy so they aren't picked up by hapi-fhir-spring-boot-autoconfigure.

* Added SubscriptionMatcherInMemory

Moved static data out of BaseHapiFhirDao into ResourceMetaParams

Moved translateMatchUrl methods out of BaseHapiFhirDao into MatchUrlService bean

Simplified SubscriptionMatcherInMemory to not depend on entity or dao

Turned all subscribers into prototype beans

* Moved searchParam method out to mySearchParamProvider

Also removed dao and contest parameters from of myMatchUrlService methods

Moved code out of SearchBuilder into SearchParameterMap.clean() so it can be used by inMemoryMatcher

Introduced a new composite subscription matcher that tries to match in memory and if it finds a parameter in the criteria it doesn't support, it falls back to the database matcher.

* Added support for references

Also fixed a small bug in SearchParameterMap that was missing the ";" after "_has" when creating a normalized query from search params.

* Finished implementing all tests from FhirResourceDaoR4SearchNoFtTest

* Make in-memory matcher configurable, disabled by default

* Validate Subscription criteria when they're submitted

Send HTTP 422 UnprocessableEntityException if the criteria fail validation.

* fixed Sonar "Blocker" issues.

*  Don't reload the resource before sending it out

Since we can always force a reload using restHookDetails.isDeliverLatestVersion

* Added tests to cover Custom Search param.

* Split ResourceIndexedSearchParam into separate state and service classes

* Cleaned up SearchBuilder.

Removed uses of myCallingDao as an injection mechanism.
Left // FIXME KHS cookie crumbs to clean up

* Reduced dependencies on BaseHapiFhirDao

Removed methods from IDao interface that were used for injection

* Updated change log
 2018-11-19 16:19:52 -05:00
jamesagnew bf8f26bc5f Work on bugfixes 2018-11-19 05:49:05 -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 6a6451f694 Reduce number of queries on some DB operations 2018-11-16 12:41:50 +01:00
James Agnew e4f6b3e9a2 Add a warning if an invalid class is scanned 2018-11-16 10:42:21 +01:00
James Agnew 4b099cf057 Fix #944 - NPE when using a custom resource class that has a @Block 
child
 2018-11-15 16:11:55 +01:00
James Agnew 75210d614b Bump to 3.7.0-SNAPSHOT 2018-11-12 22:37:52 -05:00
James Agnew 63af04a7b4 Prepare for 3.6.0 release 2018-11-12 05:40:55 -05:00
James Agnew 023877e09f
Merge pull request #1047 from hdconradi/null-pointer-in-date-range-param 
Fix NullPointerExceptions in DateRangeRaram
 2018-11-11 17:02:27 -05:00
jamesagnew 3942f1bb29 License header updates 2018-11-09 14:41:57 -05:00
James Agnew f61df5c3fe Use FHIRPath expression parser for custom SP validation 2018-11-09 14:41:20 -05:00
James Agnew b32e232eb2 A bit of client tweaking 2018-11-08 17:10:39 -05:00
James Agnew 82ec721c99 Allow client defined parameter style for _format param 2018-11-08 15:27:35 -05:00
James Agnew 80b0f14c4b
Merge pull request #1103 from RuthAlk/own_message_resolver_3.6.6 
Allow slotting in own IMessageResolver
 2018-11-08 13:22:48 -05:00
James Agnew 76cd3f6b47 Allow client assigned IDs to be purely numeric in JPA server if 
configured to do so
 2018-11-07 18:25:50 -05:00
jamesagnew 8c2d868f16 License updates 2018-11-01 16:13:34 -04:00
James Agnew bb59e2d73a Fix broken test 2018-11-01 10:25:13 -04:00
jamesagnew bbce2c69cf Fix typo 2018-11-01 05:51:26 -04:00
jamesagnew 3f6960d82b Add multithreaded migrator tool 2018-11-01 05:42:51 -04:00
jamesagnew 31ef4c68e1 Merge branch 'philips-3.6.0' of github.com:jamesagnew/hapi-fhir into philips-3.6.0 2018-10-31 05:51:13 -04:00
jamesagnew 8955a9e54d Add threading to migrator 2018-10-31 05:50:50 -04:00
James Agnew 4cd86596f2
Merge branch 'master' into fhirterser-getvalues-enhancements 2018-10-29 09:55:34 -05:00
James Agnew b66e01ce65 Allow plain server @Operation methods to declare a wildcard so that any 
opeeration invocations will be direected to them
 2018-10-29 10:36:32 -04:00
Ruth Alkema 729bbe04d0 Allow slotting in own IMessageResolver 
This is useful in case we want to define our own way of translating
the codes in the thymeleaf templates.
 2018-10-26 12:13:58 +02:00
James Agnew 794d9145e9 Move query count tests to consolidate them, and avoid an accidental 
rewrite of existing indexes in some conditions
 2018-10-24 17:54:58 -03:00
Diederik Muylwyk 21a0390e6e Even more additional work on FhirTerser.getValues(...) enhancements. Almost ready for review. 2018-10-24 11:43:19 -04:00
Diederik Muylwyk 688e159493 Additional work on FhirTerser.getValues(...) enhancements. 2018-10-22 18:22:03 -04:00
Diederik Muylwyk 225007d681 Completed work on FhirTerser.getValues(...) enhancements. 2018-10-19 18:24:26 -04:00
Diederik Muylwyk cd6d4302c3 Incremental work on FhirTerser.getValues(...) enhancements. 2018-10-19 15:13:51 -04:00
James Agnew da2763d8c8 Merge branch 'master' into philips-3.6.0 2018-10-17 22:38:27 -04:00
James Agnew 99cd4ce5f7 Allow for _total parameter 2018-10-17 09:47:35 -04:00
jamesagnew 1c1f601332 License header updates 2018-10-16 19:56:52 -04:00
James Agnew 755060f91e Allow subscription triggering on a block of resources 2018-10-16 15:29:41 -04:00
James Agnew 34bb70af65 Add validator test and allow migrator to be used for 3_3_0 2018-10-08 21:04:17 -04:00
jamesagnew 970c48ec37 A bit more test cleanup 2018-10-04 13:29:09 -04:00
James Agnew 95f00e1c94 Fix NPE in tests 2018-10-04 08:33:40 -04:00
James Agnew b265c0281b Expand search range when searching by date 2018-10-03 21:31:01 -04:00
James Agnew 5d5ee78873 API cleanup following JPA search performance enhancements 2018-10-03 07:43:01 -04:00
James Agnew 62d6771814 Use a select count query for summary count searches in JPA server 2018-09-29 21:58:14 -04:00
James Agnew 3e445faf47 Squashed commit of the following: 
commit df641506885e09e63f80efc6c658d01a1a3a8142
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sat Sep 29 13:47:22 2018 -0400

    Shrink validation resources

commit 4c1550eafa26f4235b4b8804741aecc03276b5c6
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Sep 28 22:45:28 2018 -0400

    Updates to get R4 working

commit 8332f15291006691ed9b07ead3e3524b0fc85510
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Fri Sep 28 09:02:13 2018 -0400

    Ongoing work on gettign R4 working

commit f7146cab7aed937bb625a8aec95744d76db00041
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Sep 28 05:21:01 2018 -0400

    More work on sync

commit f48de4a10b1bab2584fee813017d9b27b237bfa9
Merge: 9e4f3cc722 aacb78b779
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:11:29 2018 -0400

    Merge branch 'sync_r4' of github.com:jamesagnew/hapi-fhir into sync_r4

commit 9e4f3cc722668aae31a77b19bf9b032af3ae01b0
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:11:19 2018 -0400

    Fix compile error

commit 7ec29e0ceda8f9013cbabb95767cbe15b4b81303
Merge: 23f7517325 002c4b3ff7
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:04:23 2018 -0400

    Merge branch 'master' into sync_r4

commit aacb78b7793ab2c71e0a2a774240ee2b5d3f9e7f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:01:42 2018 -0400

    Keep working on getting R4 building

commit 4950de46d99897e74d41dfdb10d3d8a3435cb0c9
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Sep 25 13:11:27 2018 -0400

    Ongoing work to get R4 working

commit 819d69c20e112dd3c72569ec50114ddb8263c300
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Sep 20 08:15:36 2018 -0400

    Work on getting build working

commit 2c61b6cd1205ced5d7b822cf10942c69272ea078
Merge: 16b5bb06c8 dfb4de86f1
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Sep 20 05:16:53 2018 -0400

    Merge branch 'master' into sync_r4

commit 16b5bb06c8cdaf8d67c3b80f5aa9be9fccd99aef
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Sep 17 05:30:39 2018 -0400

    Work on R4 sync

commit 23f7517325a14dd2ca1eb5641296ead2776634ae
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Sep 16 10:19:00 2018 -0400

    Work on sync

commit 6cc413c1f1dea538295aa4c16c21a5677494ac4c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Sep 14 17:28:28 2018 -0400

    Work on R$ sync

commit df6f6ad2ce783b07ccc383134705d874bc5d2cf1
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Fri Sep 14 08:33:07 2018 -0400

    Work on R4
 2018-09-29 13:48:35 -04:00
Heinz-Dieter Conradi ea5cf9f956 Fix the null pointer problems in the DataRangeParam class 2018-09-27 11:25:56 +02:00
Heinz-Dieter Conradi 734835de96 Add some test demonstrating null pointer problems in the DateRangeParam class 2018-09-27 11:25:56 +02:00
James Agnew c0051f309b Avoid NPE on parser 2018-09-21 09:48:18 -04:00
jamesagnew dfb4de86f1 License updates 2018-09-20 05:16:15 -04:00
James Agnew 706e004b9d Bump to 3.6.0-SNAPSHOT 2018-09-19 10:24:48 -04:00
jamesagnew 321e88c811 License header updates 2018-09-14 05:25:07 -04:00
James Agnew ce6a9dbc36 Fix regression from new jetty version 2018-09-11 08:27:34 -04:00
James Agnew daef975734 Version bump to 3.5.0 2018-09-08 07:22:21 +08:00
James Agnew f5d567cd00 Work on migrator 2018-09-08 03:30:35 +08:00
James Agnew 0f7c4219cb Merge branch 'master' into jpa_migration 2018-09-02 06:05:11 +08:00
James Agnew f4a21eadda Fix this issue 2018-09-01 14:38:52 +08:00
James Agnew 07cfed14b8 Work on migrator 2018-08-27 08:21:20 -04:00
jamesagnew df651c830e Remove dynamic mode 2018-08-19 17:35:08 -04:00
James Agnew bc1ee1f9dc Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-08-13 11:54:36 -04:00
James Agnew ea1f17762e Don't apply last updated to includes 2018-08-11 12:20:07 -04:00
jamesagnew 64b3b64208 License header updates 2018-08-06 19:06:09 -04:00
James Agnew 4eb3281fa6 Merge branch 'client_enhancements' 2018-07-30 18:34:49 -04:00
James Agnew 709a5dbd0a
Merge pull request #965 from jbalbien/fixBundleUtilBug 
fix bundle util bug
 2018-07-30 09:45:09 -04:00
James Agnew d6293cf9b3 Merge branch 'client_enhancements' 2018-07-30 09:42:38 -04:00
James Agnew db0f082222
Merge pull request #996 from anamariaradu10/master 
Changes regarding behavior for Prefer header
 2018-07-30 09:16:20 -04:00
jamesagnew 0f1724ac0a Credit and a unit test for #912 2018-07-30 05:48:38 -04:00
James Agnew d50dda19ae
Merge pull request #912 from InfiniteLoop90/911-contains-modifier 
Fixes #911 - Adds support for :contains modifier
 2018-07-30 05:39:27 -04:00
jamesagnew fc9f2ec0fb FIx test issue 2018-07-29 18:20:09 -04:00
James Agnew 518092cbd4 More updates 2018-07-29 17:10:26 -04:00
anamariaradu10 3a5556006b
Merge branch 'master' into master 2018-07-27 16:59:52 +03:00
Ana Maria Radu 9c39733aff Fixed issues 2018-07-27 16:48:44 +03:00
James Agnew 75a68a0332 Unit test fix 2018-07-26 18:58:23 +07:00
James Agnew a4e4111376 Fix a unit test 2018-07-26 18:08:59 +07:00
James Agnew 3c80238f0e Ongoing work on interceptors 2018-07-24 17:22:21 +07:00
James Agnew 23083a9283 Improvements to client and SP indexing in JPA server 2018-07-23 17:37:49 +09:00
James Agnew b4aa4c0e89 Add protection against HTML injection attacks 2018-07-19 08:56:22 -04:00
jamesagnew 401a4cd738 Clean up concept reindexing 2018-07-15 17:18:07 -04:00
jamesagnew 43ac912033 Clean up terminology uploading 2018-07-15 15:22:52 -04:00
jamesagnew 6d83edabb6 License header updates 2018-07-01 20:59:04 -04:00
patrick-werner a2d6435597 adding contentType matching independent of Charset to non-strict method 2018-06-25 10:51:05 +02:00
Patrick Werner b1e09fcdf7
Merge pull request #1007 from jamesagnew/1006-Writing-structured-Binary 
1006 writing structured binary
 2018-06-21 18:03:14 +02:00
Patrick Werner 8bd1313492
removed unused import 2018-06-21 14:56:38 +02:00
patrick-werner f470653ba4 fixing tests 2018-06-21 11:50:58 +02:00
patrick-werner ef9f97a576 fixes #1006 2018-06-20 17:26:23 +02:00
James Agnew ed0b5f54a5 More authorizationinterceptor tweaks for better security 2018-06-12 21:52:01 +08:00
Ana Maria Radu dc476aeeea In my opinion these changes should be made in order to have the behavior 
for the Prefer header values as the one explained in the official
documentation from https://www.hl7.org/fhir/http.html
 2018-06-12 14:04:05 +03:00
patrick-werner 9498247082 Allows the Cache-Control Header in CORS header for jpa-example-server & CLI 2018-06-04 16:12:31 +02:00
James Agnew d819d685ee Test fix 2018-05-30 09:57:41 -04:00
Diederik Muylwyk 0e2c57fa60 Bumping version. 2018-05-28 17:44:38 -04:00
Diederik Muylwyk 2871920734 Preparing release. 2018-05-28 10:45:47 -04:00