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291 Commits

Author SHA1 Message Date
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
James Agnew 0d0f67b299 Add GraphQL support to public server 2018-11-16 11:41:39 +01:00
axdad 952dc7dd01 Fix NPE 2018-11-14 09:24:27 +01:00
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
James Agnew b32e232eb2 A bit of client tweaking 2018-11-08 17:10:39 -05:00
James Agnew 01c7618867 Failing test cleanup 2018-11-08 15:46:49 -05:00
James Agnew 82ec721c99 Allow client defined parameter style for _format param 2018-11-08 15:27:35 -05:00
jamesagnew bbce2c69cf Fix typo 2018-11-01 05:51:26 -04:00
James Agnew 6b1ea5b989 Add tests for operation method binding 2018-10-30 15:22:39 -04:00
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
James Agnew aa177c1421 Authorize batch operation in AuthorizationInterceptor 2018-10-19 09:45:56 -04:00
James Agnew c8db7fe035 Add a test 2018-10-18 15:12:22 -04:00
James Agnew 4e252063b8 Allow transactions and batches with transaction permission in 
AuthorizationInterceptor
 2018-10-16 19:54:55 -04:00
James Agnew b44e96a5cd Merge branch 'philips-3.6.0' 2018-10-15 08:37:00 -04:00
James Agnew 51a69f0dc9 Fixes to migrator and count logic 2018-10-13 12:02:19 -04:00
Patrick Werner 90a3ead24f
Merge pull request #1089 from srdo/issue-545 
Issue-545: Base resource profile links should point to http://hl7.org…
 2018-10-09 12:05:47 +02:00
James Agnew c64567be68 More redundant test cleanup 2018-10-04 09:15:12 -04:00
James Agnew 597c8dbafe Remove redundant tests 2018-10-04 08:57:37 -04:00
James Agnew 95f00e1c94 Fix NPE in tests 2018-10-04 08:33:40 -04:00
Stig Rohde Døssing 2050355e1e Issue-545: Base resource profile links should point to http://hl7.org/fhir/StructureDefinition (invariant sdf-7 in spec) 2018-10-03 13:36:34 +02:00
James Agnew 12b23fbf23 Make JPA searches more efficient by prefetching a much smaller number of 
resources
 2018-10-01 21:36:10 -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
James Agnew 002c4b3ff7 Add retrigger subscription operation 2018-09-27 20:03:01 -04:00
James Agnew 706e004b9d Bump to 3.6.0-SNAPSHOT 2018-09-19 10:24:48 -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 77305eb570 Work on migrator 2018-09-04 10:32:08 +08:00
James Agnew f4a21eadda Fix this issue 2018-09-01 14:38:52 +08:00
James Agnew fee0166800 Work on removing validstion cache 2018-08-28 05:26:06 -04:00
James Agnew 54c07263b6 Increase code lengths 2018-08-26 12:32:35 -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 78a7d64d2c
Merge pull request #1022 from alinleonard/master 
Patch operation on OperationsWhichAllowPreferHeader
 2018-08-12 17:55:16 -04:00