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483 Commits

Author SHA1 Message Date
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
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
James Agnew 4eb3281fa6 Merge branch 'client_enhancements' 2018-07-30 18:34:49 -04:00
James Agnew 4fcaf37729 Test cleanup 2018-07-30 18:34:28 -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
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 a9291b4e4b Add security test 2018-07-19 08:09:07 -04:00
James Agnew e6ca408f67 Permissions for operations 2018-07-12 18:40:15 -04:00
James Agnew 03e7b018a6 Add skeleton for the $process-message operation in JPA erver 2018-07-12 17:52:24 -04:00
Alin 62c7c0fa55 fixed the AuthorizationInterceptorR4Test return code based on fhir doc 2018-07-09 16:43:31 +03:00
James Agnew b929864873 Merge branch 'improve_jpa_indexes' 2018-07-01 12:08:03 -04:00
James Agnew 495fd9f68e Add support for patch in AuthorizationInterceptor 2018-07-01 11:46:11 -04:00
jamesagnew e5cb609f4d Performance improvements 2018-06-24 20:02:27 -04:00
James Agnew e9fffd3cdc Allow indexing in custom search params to descend into contained 
resources
 2018-06-22 11:22:07 -04:00
James Agnew ed0b5f54a5 More authorizationinterceptor tweaks for better security 2018-06-12 21:52:01 +08:00
James Agnew cc0e836680
Auth interceptor early checks (#995) 
* Validator fix

* Enhance AuthorizationInterceptor so that it tries to deny access earlier
for compartment searches that are outside the allowable compartment.

* FIx DSTU2 test that wasn't updated

* More test fixes
 2018-06-10 17:48:20 -04:00
James Agnew 6feb23896f Hopefully fix #983 2018-06-06 15:51:23 -04:00
jamesagnew 987679483a Version bumps 2018-06-03 15:29:10 -04:00
jamesagnew 9db3be8536 Include implementation URL in generated capabilitystatement 2018-06-03 14:22:15 -04:00
jamesagnew d127a89047 Some test fixes 2018-05-30 11:01:43 -04:00
James Agnew a52805e504 Work on JDK9 support 2018-05-30 05:45:08 -04:00
James Agnew 7951d883d0 Merge branch 'master' into java9 2018-05-29 08:43:21 -04:00
Diederik Muylwyk 0e2c57fa60 Bumping version. 2018-05-28 17:44:38 -04:00
James Agnew 27d0d4d7af Fix build failure 2018-05-28 11:51:26 -04:00
Diederik Muylwyk 2871920734 Preparing release. 2018-05-28 10:45:47 -04:00
jamesagnew 67f21426cb Disable content header on response for non-create operations 2018-05-25 07:28:01 -04:00
James Agnew a3687e446e Correctly handle missing search params with new indexing infrastructure 2018-05-23 11:42:38 -04:00
James Agnew 2f2900e837 Improve indexing on JPA server in anticipation of a new indexing 
strategy in HAPI FHIR 3.5.0
 2018-05-23 08:09:57 -04:00
jamesagnew 98d997c620 Add changelog and credit for #867 2018-05-23 06:21:00 -04:00
James Agnew 4d93b78c24 Credit for #836 2018-05-22 08:44:17 -04:00
patrick-werner 07d0cc7876 Merge branch 'master' into bpCheckValFix 2018-05-17 09:53:41 +02:00
patrick-werner 78f9d6333a temp. fixed: "Attempt to read a single element when there is more than one present" #949 
Will be overwritten by next RI import!
 2018-05-17 09:43:35 +02:00
patrick-werner 730d02b7c6 added R4 core-extension validation support 2018-05-16 18:51:55 -04:00
James Agnew d29a9a7f96 AutohrizationInterceptor should correctly recognize type-level operation 
invocations
 2018-05-15 16:14:10 -04:00
jamesagnew 4d62120a18 Fix issues reported by errorprone 2018-05-15 08:44:15 -04:00
James Agnew a3ff08d9ec
Replace phloc with ph for #775 (#930) 
* Replace phloc with ph

* Enable schematron tests

* Make HAPI-FHIR ph-schematron on OSGI

* Work on getting tests passing

* Another test fix

* Fix up transaction handling for DSTU2

* Add changelog

* Avoid double transaction

* Dont use readonly

* One more test fix

* Update to snapshow build

* Resolve a circular dependency

* Try to fix tests

* Solve recurring NPE in DSTU2 tests

* Fix one more test

* Test fix

* More test threading fixes

* One more attempt to get tests passing

* Refactoring for tests

* Refactoring for tests
 2018-05-14 17:38:40 -04:00
jamesagnew 3d762b984b Sync to R4 definitions 2018-05-12 19:35:42 -04:00
James Agnew b17eebd8d2 Squashed commit of the following: 
commit 2be11651c2
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 11:50:53 2018 -0400

    Update changelog

commit b3bb5f9052
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 11:19:28 2018 -0400

    Parameter updates

commit f6b1082ba4
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 07:24:30 2018 -0400

    More test fixes

commit 81a69c265f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:26:48 2018 -0400

    Fix compile error

commit 935938e92c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:25:18 2018 -0400

    Another test fix

commit 43568a1f8d
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:18:06 2018 -0400

    Fix compile error

commit e95894e643
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:13:50 2018 -0400

    More work on tests

commit 9393fb8f4f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 05:36:27 2018 -0400

    One more fix

commit 437f5051e4
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 21:32:10 2018 -0400

    Work on validator

commit 20c51add4f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 19:34:10 2018 -0400

    Validator fix

commit 7bf2b0a0e9
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 18:44:04 2018 -0400

    Fix test

commit adc73e75c9
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 17:22:34 2018 -0400

    Merge validator
 2018-05-10 11:53:32 -04:00
James Agnew 7688be1231 Work on getting java9 building 2018-05-03 18:34:29 -04:00
James Agnew 593a705365 Performance enhancements on the CapabilityStatement generator for JPA 
server
 2018-04-28 11:06:42 -04:00
James Agnew 09b1f547d0 Add expunge 2018-04-24 15:11:00 -04:00
James Agnew 07e7af746f Work on expunge operation 2018-04-22 22:03:23 -04:00
James Agnew a21d0a7752 Add auth tester methods 2018-04-22 19:30:09 -04:00
James Agnew 591539cf13 Add expunge method 2018-04-22 18:34:56 -04:00
jamesagnew 8c889267e5 One more parser fix 2018-04-18 06:20:11 -04:00
James Agnew 162069776a Correctly handle encoding contained resources where some have user 
assigned IDs and some do not
 2018-04-17 18:26:06 -04:00
jamesagnew c5b286921e Tests all passing 2018-03-30 15:18:57 -04:00
jamesagnew 180336e076 Sync to master 2018-03-29 06:54:24 -04:00
jamesagnew 53c2d8a38d Merge branch 'master' into loinc_loader_update 2018-03-29 06:21:55 -04:00
jamesagnew 418e82032f Prep for 3.3.0 2018-03-29 05:48:13 -04:00
James Agnew d9c167455e Make sure we correctly clean up resources 2018-03-27 15:20:22 -04:00
James Agnew b56d65ef5b
Merge pull request #871 from johnpoth/hapi-fhir-osgi 
Implement #826 - add OSGI support and Apache Karaf features with inte…
 2018-03-27 06:06:34 -04:00
James Agnew 29c09e40f0
Merge pull request #858 from patrick-werner/master 
added Test for #11 to Dstu3 and R4, fixed #853
 2018-03-24 06:31:24 -04:00
James Agnew 308ac63a77 Merge branch 'master' into loinc_loader_update 2018-03-20 07:53:41 -04:00
James Agnew 6359f7f8a1 More work on loinc 2018-03-19 08:51:02 -04:00
patrick-werner ff04ab3358 ${argLine} -> [at]{argLine} 
see:
http://maven.apache.org/surefire/maven-surefire-plugin/faq.html#late-property-evaluation
 2018-03-19 10:45:33 +01:00
patrick-werner 0cee57392a Merge remote-tracking branch 'upstream/master' 
# Conflicts:
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
 2018-03-07 11:45:31 -03:00
jamesagnew e201091e3a Update licenses for changed files 2018-03-04 13:53:04 -05:00
jamesagnew d22670ddb5 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-03-04 12:21:07 -05:00
James Agnew 2f7751a079 Move stopwatch into hapi-fhir-base and add timing into to client 
LoggingInterceptor
 2018-03-04 12:13:18 -05:00
jamesagnew 8bdca012d6 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-03-04 11:04:07 -05:00
jamesagnew 07290ae8a0 Sync to latest R4 code 2018-03-04 11:02:47 -05:00
jamesagnew b2ceb87a70 Work on #873 2018-03-03 17:50:29 -05:00
James Agnew 0c0b9bd74b Fix #814 - Don't create duplicate contained resources 2018-03-02 09:46:29 -05:00
jpoth 66ebfa0ed3 Implement #826 - add OSGI support and Apache Karaf features with integration tests 2018-02-28 11:32:53 +01:00
James Agnew 458401864b Handle deletes properly in HashMapResourceProvider 2018-02-25 14:20:04 -05:00
James Agnew 84c72203b7 Add HashMapResourcePrvider 2018-02-25 13:16:02 -05:00
patrick-werner a8f3c2efb6 added Test for #11 to Dstu3 and R4 2018-02-21 16:03:31 +01:00
James Agnew 84dcd51091 Add tests for #814 2018-02-12 09:25:59 -05:00
James Agnew e4785b17b5 Add test 2018-02-08 17:50:45 -05:00
jamesagnew a395e48cd4 Don't crash when a multitenant server has a request for / 2018-02-04 18:44:37 -05:00
jamesagnew 371be03b0f Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-02-02 13:20:09 -05:00
James Agnew 0e2d55081f Fix a crash when no count parameter supplied 2018-02-02 12:31:59 -05:00
jamesagnew 351a2fc2f1 Fix #837 - Use non-legacy content-type for plain json and xml accept 
header
 2018-02-02 06:43:19 -05:00
James Agnew b61887e841 Improve performance of base64 validation 2018-01-30 17:37:12 -06:00
jamesagnew f7f69f6148 Ad some tests for #837 2018-01-26 08:39:46 -05:00
jamesagnew 5750cfd03c Prevent double calling server interceptor methods under certain 
conditions
 2018-01-26 07:44:13 -05:00
James Agnew 0677f35847 Implement tenant ID checking in authorizationinterceptor 2018-01-23 11:32:35 -05:00
James Agnew 16038ece26 Version bump to 3.3.0-SNAPSHOT 2018-01-23 10:31:01 -05:00
James Agnew 3644151a69 Fix crash in JSON parser when parsing extensions on primitive elements 2018-01-18 09:07:23 +07:00
James Agnew 6468ca474a Verion bump to 3.2.0 2018-01-13 02:14:33 -05:00
James Agnew 01186ec8cb Squashed commit of the following: 
commit ab876ef864005b6758d3e00a1bb1ef2dad5d2161
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Jan 12 18:59:15 2018 -0500

    Tests all passing

commit 4f8a5d98307da1bb5ca7602e34b1d3b791f73d25
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Fri Jan 12 08:21:58 2018 -0500

    Almost compiling
 2018-01-12 18:59:43 -05:00
James Agnew f6c9e3d0fe Add multitenancy support for server 2018-01-11 11:14:54 -05:00
James Agnew 9a72927dbc Fix #808 - Use version from meta if not found in the resource ID 2018-01-08 14:07:27 -05:00
James Agnew 377bae8c16 Allow interceptors to modify request contents 2018-01-06 14:27:32 -05:00
James Agnew 19863de012 Update javadocs on IdType 2017-12-19 15:57:22 -05:00
James Agnew 44ec091b35 Still more test tweaks 2017-12-13 13:29:24 -05:00
James Agnew 3e296f9d1b Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2017-11-25 17:53:01 -05:00
James Agnew 6afe6804db Fix #796 - Correctly escape spaces in generated URLs 2017-11-25 17:52:12 -05:00
jamesagnew 5b909b4746 Version bump to 3.2.0-SNAPSHOT 2017-11-24 13:32:47 -05:00
jamesagnew 42dd34252d Version bump to 3.1.0 2017-11-23 13:27:21 -05:00
James Agnew 4887f18bb3 Further refine #762 2017-11-23 11:05:11 -05:00
jamesagnew db1d2d77cd Updated tests 2017-11-23 10:40:44 -05:00
jamesagnew ffac599a30 Credit and tests for #762 2017-11-23 06:42:10 -05:00
jamesagnew 059265a041 Test cleanup 2017-11-22 19:15:27 -05:00
James Agnew 4042a3a353 Prevent accidental deletion of deeply nested resources in JPA server 2017-11-22 18:17:35 -05:00
James Agnew a87323fa08 Add tests 2017-11-17 09:53:44 +01:00
James Agnew 59f4177a59 Fix #750 - Elements are not preserved in page requests 2017-11-06 19:49:50 -05:00
James Agnew 675d7981bf Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2017-11-05 18:53:09 -05:00
James Agnew 37c8e6c645 Add test for #751 2017-11-05 18:52:28 -05:00