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937 Commits

Author SHA1 Message Date
James Agnew c09e26e28f Clean up calls in JPA server for ID 2017-04-22 06:31:55 -04:00
James 716fa56b8f Merge branch 'jpa_perf_enhancements' 2017-04-21 06:30:22 -04:00
James cbc652d226 Version bump to 2.5-SNAPSHOT 2017-04-20 16:13:15 -04:00
James Agnew 282f90d174 Perf work 2017-04-20 05:59:10 -04:00
James 9d3d15ce6f Version bump to 2.4 2017-04-19 21:38:36 -04:00
James Agnew 552bd90d59 More perf work 2017-04-19 18:08:38 -04:00
James cc526f6d99 Upgrade to STU3 2017-04-18 21:58:23 -04:00
James Agnew 61a61cddee More perf work 2017-04-18 21:02:25 -04:00
James 077676fd03 Bring DSTU3 structs up to FHIR R3 
Squashed commit of the following:

commit 65b70d30c9
Author: James <jamesagnew@gmail.com>
Date:   Tue Apr 18 07:44:08 2017 -0400

    More work on bringing structs up to date

commit 1df2de0667
Author: James <jamesagnew@gmail.com>
Date:   Tue Apr 18 07:12:45 2017 -0400

    Working

commit 9a51323e03
Author: James <jamesagnew@gmail.com>
Date:   Mon Apr 17 22:18:24 2017 -0400

    Updates to STU3

commit 40aebba0a7
Author: James <jamesagnew@gmail.com>
Date:   Mon Apr 17 18:30:26 2017 -0400

    Fix regression caused by #610
 2017-04-18 07:48:38 -04:00
James 4bf97e836a Fix memory leak 2017-04-18 06:13:48 -04:00
James 7f2cf17f9f Fix perf issue 2017-04-17 17:29:32 -04:00
James 5adc09ad56 perf enhancements finally working 2017-04-17 16:56:53 -04:00
James Agnew fbbe792726 Perf work 2017-04-17 14:00:36 -04:00
James Agnew 08ec97e78a More work on perf 2017-04-16 15:57:58 -04:00
James Agnew 217d9f8176 More perf work 2017-04-16 14:46:15 -04:00
James Agnew 62ece72e6f More perf work 2017-04-16 12:08:23 -04:00
James Agnew 913fd422a1 Merge branch 'master' into jpa_perf_enhancements 2017-04-14 11:30:19 -04:00
James Agnew f6acb5633b Work on perf 2017-04-14 09:50:05 -04:00
James Agnew 54055f5bfb Support extensions pointing to references for JPA custom search params 2017-04-14 07:26:49 -04:00
James 1039bbec97 More perf work 2017-04-14 07:25:01 -04:00
James Agnew 23b7de5dd8 More perf work 2017-04-12 18:28:10 -04:00
James 81aae2b672 More perf work 2017-04-11 06:56:17 -04:00
James Agnew cba5aeb47b More perf work 2017-04-10 17:55:50 -04:00
James Agnew 0a8900ee78 Perf updates possibly working? 2017-04-10 16:29:24 -04:00
James aa02dd5037 More perf work 2017-04-10 08:05:25 -04:00
James Agnew 04468c8352 More perf work 2017-04-09 21:52:55 -04:00
James e32d6bb56e More perf work 2017-04-09 20:06:56 -04:00
James bf0f1421b3 Work on perf 2017-04-09 19:13:55 -04:00
James fa435fb8b2 More perf work 2017-04-09 11:48:56 -04:00
James Agnew c5c154346e More work on perf 2017-04-08 22:21:57 -04:00
James Agnew 801ae7cb75 NOFT test passing 2017-04-08 21:19:10 -04:00
James 90a4e2def2 More work on perf improvements 2017-04-08 19:46:51 -04:00
James Agnew 08e5681d8b Work on perf 2017-04-08 15:12:10 -04:00
James Agnew dd84fced5e Merge branch 'master' into jpa_perf_enhancements 2017-04-08 06:54:13 -04:00
James Agnew 0a61096f6f Add JPA utility method 2017-04-07 11:14:48 -04:00
James 8284fcab1b More work on performance 2017-04-07 08:37:48 -04:00
James Agnew 660c2bde72 More work on perf 2017-04-06 22:23:20 -04:00
James Agnew f48d0d677b More work on performance 2017-04-06 12:50:36 -04:00
James 1581cdf9a8 Work on perf 2017-04-04 08:26:04 -04:00
James Agnew 233eb54710 Work on perf 2017-04-03 22:05:53 -04:00
James Agnew 9b1366734a Merge branch 'master' into jpa_perf_enhancements 2017-04-03 15:20:55 -04:00
James Agnew 6ab1cb4c2e Fix compile issues from new version of errorprone 2017-04-03 14:43:59 -04:00
James Agnew efaa7a74cb Work on perf enhancements to JPA 2017-03-30 19:58:32 +08:00
James Agnew ce73e89715 For bit of work on JPA perf enhancements 2017-03-30 06:28:34 +08:00
James Agnew 2c9a6e65e7 Fix #534: Add setting for logical references to DAOConfig 
Merge branch 'master' into issue534
 2017-03-30 03:21:50 +08:00
James Agnew 14d861992c Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2017-03-29 15:29:10 +08:00
James Agnew c6555ddd4f DaoConfig#setAllowInlineMatchUrlReferences now defaults to true 2017-03-29 15:23:23 +08:00
James Agnew d9749b652d Work on issue 534 2017-03-29 15:19:52 +08:00
Diederik Muylwyk 4748c8ba74 New DSTU2 FhirInstanceValidator bean exposed. (#611) 
Merging with master, issue #609 will be closed.
 2017-03-28 23:19:20 -04:00
James Agnew 3ecfbf098f Work on #534 2017-03-27 08:37:31 +08:00
James Agnew 72f682d81e Refactor search param registry 2017-03-18 19:36:10 -04:00
James 40848b1beb Version bump to 2.4-SNAPSHOT 2017-03-18 12:24:39 -04:00
James d009e836bb Fix tests for 2.3 2017-03-18 08:06:18 -04:00
James e18ab206d7 Version bump to 2.3 2017-03-17 21:21:59 -04:00
James 8758b6f3da Updating to 1.9.0 structures 
Squashed commit of the following:

commit 81edf46fe02a88851693f958e60855edfe69c04c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Mar 17 21:05:22 2017 -0400

    Work on converter

commit 3342d987008892dd3a75dddd251fe599c31c5a6c
Author: James <jamesagnew@gmail.com>
Date:   Fri Mar 17 08:40:37 2017 -0400

    Site updates

commit 7dcb63904ece1fcb59a09dc268e8382ac0b75535
Author: James <jamesagnew@gmail.com>
Date:   Fri Mar 17 08:36:39 2017 -0400

    STU3 structs working!

commit c5aec809e3f19f3fedf0aaaeab8cdd7924c144a2
Author: James <jamesagnew@gmail.com>
Date:   Fri Mar 17 07:05:54 2017 -0400

    Format test

commit 5033090010e8c93644505bccaa5e41ccbd756485
Author: James <jamesagnew@gmail.com>
Date:   Fri Mar 17 07:03:39 2017 -0400

    Merge tests for STU3

commit de40a516bfa4d2ab7f5e28e2d95815fde68bd10a
Merge: d5a5a60 899ed25
Author: James <jamesagnew@gmail.com>
Date:   Fri Mar 17 06:59:20 2017 -0400

    Merge branch 'master' into dstu3_latest_structs

commit d5a5a601b53d8be6712f0bfe37ba7e6eb4d3ce58
Author: James <jamesagnew@gmail.com>
Date:   Tue Mar 14 12:04:37 2017 -0400

    Latest fixes

commit ae46ad53d2075e66e3c58c1e626652b4e144f20c
Author: James <jamesagnew@gmail.com>
Date:   Tue Mar 14 06:51:59 2017 -0400

    STU3 structs passing

commit ec3b62d31131d303001f8574c58fb7a8b8194f68
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Mar 12 22:20:05 2017 -0400

    Fix some tests

commit 933f9b08c32dd8671638f406a0966c5ee07d86a1
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Mar 12 21:18:03 2017 -0400

    Fix test

commit 2a3ad0b422f58cfffea966a7005c6a3d86d189da
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Mar 12 21:07:33 2017 -0400

    Resolve compile issues in STU3

commit fe04eba312a42c74b10a3971e4d61d58ba003bf9
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Mar 12 20:51:35 2017 -0400

    FIx compilation error

commit 6c63a558c97cf176105967a84a0b32472c6c0fcb
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Mar 12 20:48:13 2017 -0400

    Another STU3 struct fix

commit 6acd25458aad89aaff94768c824d4d1fcdac97ba
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Mar 12 20:41:16 2017 -0400

    Work on STU3 structs

commit 90a476dba2665a129572ad5cbbd8dd29afd9d4c8
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Mar 12 20:28:32 2017 -0400

    Resolve JDK8 dependencies

commit 783bc1519971e977fe7139aa1d3a2e7f37940a63
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Mar 12 20:20:57 2017 -0400

    Fix some tests

commit 60c379175b689495e65278bb6a237af3de379aa8
Author: James <jamesagnew@gmail.com>
Date:   Sun Mar 12 19:56:29 2017 -0400

    Work on STU3 structs

commit e98c2eed6601f7009e199aca3b82399a3377077c
Author: James <jamesagnew@gmail.com>
Date:   Sun Mar 12 19:41:48 2017 -0400

    Work on DSTU3 structures

commit 3ce909212bf0f11561b8342d406cffcf957afeb3
Author: James <jamesagnew@gmail.com>
Date:   Tue Mar 7 21:03:14 2017 -0500

    Work up upgrading structs
 2017-03-17 21:06:12 -04:00
James Agnew 899ed2567f Merge pull request #575 from joelsch/large-codesystem-persistence-fix 
Revise saveConcept method to use save() instead of saveAndFlush()
 2017-03-17 06:52:57 -04:00
James Agnew 0be818c31c Add validation results to oo (#595) 
* Add interceptor

* Add changelog entry

* Update changes.xml

Corrected reference to issue 586 (was 585). Corrected order of actions for issues 586 and 595 (was reversed).

* Update changes.xml

Should have been 585 after all. Whoops!

* Update changes.xml

Adding an item for pull request 565 that was previously approved and merged.

* Fixed test with English String in assertion.
 2017-03-16 13:31:25 -04:00
James 95ef644612 Missed a param type for updated 2017-03-12 18:50:49 -04:00
James 0e3cc29c50 Add update time to search parameters 2017-03-12 12:13:31 -04:00
James 120227da2f License headers 2017-03-11 14:57:43 -05:00
James 0c6679ac44 JPA server interceptor methods for create/update/delete provided the wrong version ID to the interceptors 2017-03-11 07:57:33 -05:00
James Agnew bcff22c769 Add an interface for the stale search deleter 2017-03-01 19:50:17 -05:00
James Agnew d1d208c6c7 Rename a few reindexing methods to make their names more intuitive 2017-03-01 16:44:48 -05:00
Joel Schneider (NMDP) 2f1662b59f Revise saveConcept method to use myConceptDao.save instead of myConceptDao.saveAndFlush (to avoid overloading CPU with flush computations when persisting large codesystems, e.g. one with 399837 concepts). 2017-02-28 22:43:00 -06:00
James 7ea7bd45cf Make preDelete consistent with postCreate 2017-02-14 21:28:23 -05:00
James Agnew f7187fbc0a Fix another test 2017-02-11 19:39:01 -05:00
James Agnew 79e336025c Fix test 2017-02-11 19:31:00 -05:00
James Agnew 82ac69d86c Throw correct HTTP status when validation fails because of missing ID 2017-02-11 19:22:25 -05:00
James 53f6effd56 Clean up custom seach param code 2017-02-11 18:37:21 -05:00
James f1828d1ca8 Fix handling of filters on valueset expansions 2017-02-10 11:05:59 -05:00
James Agnew 0dd6364fe5 Improve paging in JPA server for _history operation 2017-02-08 21:42:17 -05:00
James ef23b45d25 Custom extension params working now 2017-02-08 19:17:12 -05:00
James Agnew d28122ff3e Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2017-02-07 12:24:35 -05:00
James Agnew ad781334d8 Fix conditional creates updating resource body 2017-02-07 11:36:24 -05:00
James 21ea5a070f Fix test 2017-02-07 08:46:22 -05:00
James d5fbcf8e82 Return an OperationOutcome in the response for a delete in JPA 2017-02-07 07:44:57 -05:00
James 116cb1c8f7 Work on repopulating 2017-02-06 21:57:23 -05:00
James Agnew a760f1df7c Work on custom params 2017-02-05 21:27:07 -05:00
James Agnew 30df29c083 Work on custom params 2017-02-05 21:04:19 -05:00
James 73924199a9 Work on custom search params 2017-02-05 20:34:12 -05:00
James d4dda1dace headers 2017-02-04 18:21:09 -05:00
James 7149d2e053 Merge branch 'custom_jpa_search_params' 2017-02-04 16:34:05 -05:00
James dd0e47afc3 Make projects import cleanly into eclipse 2017-02-04 16:31:18 -05:00
James Agnew 3f8a8cd8aa Merge pull request #548 from sekaijin/cleanup 
Cleanup
 2017-02-04 16:02:50 -05:00
James 54ac780cd5 Custom params works! 2017-02-04 16:02:00 -05:00
James Agnew c85c2269a1 Work on custom params 2017-02-04 14:41:11 -05:00
James 12dc4d1c11 Work on custom params 2017-02-04 07:14:21 -05:00
James Agnew aa5588826e Work on custom search params 2017-02-02 22:31:34 -05:00
James 97ff79d730 Work on custom params 2017-02-02 20:37:58 -05:00
James Agnew 3191c907a3 Work on JPA 2017-02-02 06:23:28 -05:00
James b4a362b8ee Work in progress 2017-02-01 05:55:35 -05:00
James e5b9aa4536 Bump some dependency versions 2017-01-30 17:59:01 -05:00
James ad324174bd Try to get travis working again 2017-01-30 08:06:31 -05:00
James ce80007f8d Bump spring version and refactor examples 2017-01-29 22:55:22 -05:00
James Agnew 4963f8908b Merge pull request #533 from Robbert1/spring-4.3-compat 
correct ordering of codesystem dao types
 2017-01-29 17:58:56 -05:00
sekaijin a150a96089 dependencies convergence 
correct dependencies convergence
correct version use ${project.version}
 2017-01-29 19:22:28 +01:00
sekaijin 23784c1619 remove .settings .project .classpath file of eclipse 2017-01-28 17:13:47 +01:00
James 12598b4e3b Correctly handle declared extensions with multiple possible types 
Squashed commit of the following:

commit d6ea0552b7
Author: James <jamesagnew@gmail.com>
Date:   Thu Jan 26 09:04:58 2017 -0500

    FIx test

commit e5876f7d86
Author: James <jamesagnew@gmail.com>
Date:   Thu Jan 26 08:35:38 2017 -0500

    Work on extensison

commit 7e573c2299
Author: James <jamesagnew@gmail.com>
Date:   Thu Jan 26 07:27:25 2017 -0500

    Work on extensions

commit 234b4a0c1c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Jan 26 06:25:47 2017 -0500

    More work on these extensison

commit 2eb780a690
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed Jan 25 22:35:57 2017 -0500

    Work on multitype extensions
 2017-01-26 11:07:52 -05:00
James 8e0a904997 Add adapter for IServerOperationInterceptor 2017-01-24 13:34:30 -05:00
James Agnew 344e324929 Fix #544 
Squashed commit of the following:

commit 1ab9b58e9f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Tue Jan 24 10:46:56 2017 -0500

    Changes working now

commit 5c752cdace
Author: James <jamesagnew@gmail.com>
Date:   Tue Jan 24 08:43:04 2017 -0500

    Get JPA working with new uuid: logic

commit 127b76884a
Author: James Agnew <jamesagnew@gmail.com>
Date:   Mon Jan 23 21:11:18 2017 -0500

    Fix test

commit 599bbe236c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Mon Jan 23 18:42:46 2017 -0500

    Work on #544
 2017-01-24 10:47:24 -05:00
James Agnew a63b42d08f Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2017-01-23 17:59:11 -05:00
James Agnew 222333059d Add test 2017-01-21 13:09:33 -05:00
James Agnew bde8aebc5a Merge pull request #467 from Robbert1/transaction-index-links 
fix resources links being correctly indexed when linking eachother as part of a single transaction bundle
 2017-01-20 19:12:18 -05:00
James Agnew d1542e98c5 JPA server was not correctly validating and expanding SCT codes 2017-01-19 17:37:43 -05:00
James Agnew 64e3435a8e Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2017-01-19 15:50:48 -05:00
James Agnew e342d211d1 Add some logging and a test 2017-01-19 15:50:41 -05:00
James 56a25dc3c6 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2017-01-18 22:18:50 -05:00
James f59ac8cf83 Version bump license header 2017-01-18 22:18:37 -05:00
James Agnew 495e57b4ec Allow processing of transactions without a servlet in context 2017-01-18 22:18:03 -05:00
James Agnew 837b12a690 Docs updates 2017-01-14 11:40:05 -06:00
James Agnew 322051a383 Fix failing tests 2017-01-14 07:55:42 -06:00
James Agnew fa1ad5ba85 Fix #519 - Issues with JPA capabilitystatement related to the _id param 2017-01-13 21:19:19 -06:00
James Agnew 37c40c4f9e Fix #503 - Checking authorization again patient compartment fails with delete operation 2017-01-13 11:06:00 -05:00
James af32c4b7e9 Websockets working once more on the public server 2017-01-12 08:59:51 -05:00
James Agnew a8eb4a1967 More websocket work 2017-01-11 22:12:41 -05:00
James Agnew 47a81ebd8f More websocket work 2017-01-11 21:23:39 -05:00
James Agnew d7c4016896 Websocket work 2017-01-11 21:10:10 -05:00
James 3b41d85952 Server interceptor methods were being called twice unnecessarily by the JPA server, and the DaoConfig interceptor registration framework was not actually useful. Thanks to GitHub user @mattiuusitalo for reporting! Fixes #532 2017-01-11 20:57:39 -05:00
James Agnew 5b7abf15dc Properly purge subscriptions 2017-01-11 18:19:46 -05:00
James Agnew fe24841350 Work on #532 2017-01-09 19:00:56 -05:00
James Agnew c7767937fc License version bumps 2017-01-09 17:48:42 -05:00
James e05b0e5d8a Add test for localizer and add some docs 2016-12-30 08:53:42 -05:00
Waveren, Robbert van 07525db83f correct ordering of codesystem dao types 2016-12-29 12:16:32 +01:00
James b448e13edd Version bump to 2.3 2016-12-20 19:01:31 -05:00
James 0ec61533a8 Publish 2.2 2016-12-20 19:00:37 -05:00
James Agnew 750d6d4655 Switch public server to use CapabilityStatement for metadata return type 2016-12-20 15:35:54 -05:00
James 7838d511d0 Fix typo in IHttpResponse 2016-12-19 11:29:05 -05:00
James Agnew 74a73e74c5 Dependency version bumps 2016-12-14 09:21:00 -05:00
jamesagnew a77c4270ae Generate schemas directly into class folder 2016-12-11 21:33:33 -05:00
James 901a85880c Update STU3 definitions and being in STU2.1 defs too 2016-12-10 19:51:25 -05:00
James ee63bbea74 Fix #516 - Handle STU3 invalid enum values with an appropriate exception 2016-12-10 14:14:22 -05:00
James 5149e581db Fix #521 - Wrong or missing ID body in update should be an error 2016-12-08 08:31:52 -05:00
James 2457dfd693 Bring back generated creation SQL 2016-12-08 07:07:29 -05:00
James Agnew ffefb79bf1 Fix crash in JPA when _include points to external reference 2016-12-01 12:43:31 -05:00
James Agnew f984ca723b Add unit test 2016-12-01 12:31:19 -05:00
James Agnew 888f42a032 Introduce new CORS interceptor and switch examples to use it 2016-11-21 18:30:51 +01:00
James Agnew 03935be97f Work on common FluentPath interface 2016-11-21 15:52:17 +01:00
James Agnew 5846ce4518 Make the parser configurable so that when parsing an invalid empty value (e.g. {"status":""} parser will either throw a meaningful exception or log a warning depending on the configured error handler. 2016-11-21 14:48:44 +01:00
James Agnew 4ed17457dd Work on CORS 2016-11-17 17:10:52 +01:00
James Agnew ca9223fb70 Add ability to disable stale search expiry 2016-11-17 10:01:23 +01:00
James 6314f5efb3 Fix structuredefinition regression 2016-11-14 12:04:56 -05:00
James 2d7592f7a8 Version bump to 2.2-SNAPSHOT 2016-11-11 22:39:45 -05:00
James 42295caa61 Site changes 2016-11-11 22:30:19 -05:00
James 2dd26b6367 Version bump to 2.1 2016-11-11 15:16:53 -05:00
James Agnew 846aecfe89 Merging #470 2016-11-11 10:45:53 -05:00
James Agnew 01afc49863 Documentation 2016-11-11 10:43:03 -05:00
James ef9f0bc35b Fix unneccesary database flush operation 2016-11-08 22:48:04 -05:00
James a5d5d3e031 Bump FHR version 2016-11-06 17:34:13 -05:00
James Agnew 9f37646518 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2016-11-03 11:28:24 -04:00
James Agnew 1a24ac2af2 Fix examples 2016-11-03 11:27:51 -04:00