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690 Commits

Author SHA1 Message Date
Stig Rohde Døssing d25e882d9a Issue-1351: Add a BOM POM for HAPI FHIR 2019-06-28 15:18:06 -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
James Agnew c14f5c1520 Credit for #1361 2019-06-25 18:31:25 -04:00
jvi 8b4ceb8d5f changed json patch framework to slightly more maintained fork 2019-06-17 16:45:17 -04:00
Stig Rohde Døssing b56f59542a Move JettyUtil to new module 2019-06-14 18:34:45 -04:00
admin 3b35e6add4 Test Classes 2019-06-14 05:24:11 -05:00
Ken Stevens 2bf680509b
DeleteConflict hook, SearchableHashMapResourceProvider, and in-memory searching (#1341) 
* Make IBundle list interface more flexible

* Make matchResourceLinks visible

* Make matchResourceLinks visible

* Pull in-memory matching functionality out of subscription module into dedicated classes in searchparam module

* Added more accessors to version independent resource classes

* improved forcedid matching (needs to be verified by James)
filter out nulls from HashMapProvider.searchAll() (hopefully no tests depend on this)

* add AnyComposition

* cleanup of Any classes

* create searchparam config so people can use that module without using subscriptions

* create searchparam config so people can use that module without using subscriptions

* fix broken test

* added derivedFrom

* renamed daoRegistry.getResourceDaoIfExists to getResourceDaoOrNull
also added method to add a new dao to the registry and retrieve registered types

* TokenParam.equals

* add error check to searchable hashmap resource provider

* added support for R4

* add successor to measure

* delete conflict hook
start with failing test

* test passes.
hook is called.

* added delete conflict hook
all delete conflict tests pass

* added javadoc

* Performance test

* test bad interceptor case

* typo

* rename criteria matcher

* added support for multiple topics

* fix method name

* add effective period

* Temporarily excluding StressTest from build to try to get Travis under time limit

* change log

* review feedback

* review feedback

* review feedback
 2019-06-13 13:59:51 -04:00
Ken Stevens dd203ae28f Credit for #1337 2019-06-10 11:14:52 -04:00
jamesagnew a952663dc3 Disable OSGI mdule for now# 2019-06-09 23:51:41 -04:00
James Agnew c2aec5c1a9 Respect the _total parameter for all JPA searches 2019-06-09 05:44:49 -04:00
James Agnew 9500f6e6fe Roll back derby version for now 2019-06-07 16:27:19 -04:00
James Agnew 517b68882c Fix derby dependencies for tests 2019-06-07 11:11:25 -04:00
James Agnew cab44e9626 One more version bump for dependencies 2019-06-07 09:17:07 -04:00
James Agnew a0fa752eac A number of dependency updates 2019-06-07 09:06:30 -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 13f3c02b2b Credit for #1244 2019-05-29 21:44:30 -04:00
James Agnew 83616bb53d Upgrade to newer checkstyle 2019-05-29 21:25:20 -04:00
James Agnew 96c70f6093 Credit for #1213 2019-05-29 21:22:54 -04:00
jpoth 43a8499bf6 Bump Karaf version 2019-05-29 09:31:00 +02:00
James Agnew f17fc4ce82 Credit for #1305 2019-05-23 09:09:44 -04:00
James Agnew 5f858066da Bump jackson version 2019-05-23 08:49:05 -04:00
jamesagnew aa88816d9a Credit for #1311 2019-05-22 17:13:33 -04:00
jamesagnew f5a7333c4c Bump greenmail version 2019-05-11 15:47:06 -04:00
James Agnew 37b9e1a42c Improve validation of enableWhen questionnaires 2019-04-29 14:43:42 -04:00
James Agnew 685adf7754 Revert Jetty upgrade, and improve patch error messages 2019-04-26 11:23:22 -04:00
James Agnew da962b8c10 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-24 14:33:28 -04:00
James Agnew 738c2c1797
Interceptor framework refactoring (#1287) 
Interceptor framework overhaul
 2019-04-24 14:32:30 -04:00
James Agnew f2e382a132 Swap JSON Patch provider 2019-04-24 14:10:21 -04:00
James Agnew 2ed9b39ff4 Remove useless test case 2019-04-15 16:55:54 -04:00
James Agnew c8f2e4bbc9 Return HTTP 400 for missing body on POST and PUT 2019-04-14 12:32:09 -04:00
jamesagnew 835b89f449 Build fixes 2019-04-01 18:55:55 -04:00
James Agnew e6a6c22783 Bump a few project dependencies 2019-03-31 13:57:02 -04:00
James Agnew 08c7afb804 Reduce logging in JPA server 2019-03-14 17:42:13 -04:00
James Agnew f934f76c96
Several JPA search fixes (#1231) 
* Search fixes

* Add some tests

* CHangelog

* Some cleanup of the query tracker

* FIx XML issue in changelog

* Test fixes

* SOme test fixes

* Address review comments

* Fix test breakage
 2019-03-11 15:49:34 -04:00
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
jamesagnew 86a12bcf2a Credit for #1114 2019-02-02 11:33:08 -05:00
jamesagnew ea84f2c377 Version bump hibernate search 2019-02-02 11:26:19 -05:00
Ken Stevens 9280cde491
Subscription only registers active (#1189) 
* Fixed a bug in standalone subscription subscriber:  It was adding REQUESTED subscriptions to the active subscription registry.  (Only ACTIVE subscriptions should be added.)
 2019-02-01 10:14:46 -05:00
jamesagnew b46b60798a Credit for #1130 2019-01-31 05:26:14 -05:00
jamesagnew db42609ca7 Credit for #1135 2019-01-31 05:20:43 -05:00
jamesagnew 5d540d9208 Query optimization in JPA 2019-01-27 20:03:48 -05:00
jamesagnew afaa1b065f Hivernate back to 5.4.0 2019-01-23 09:38:49 -05:00
jamesagnew eee4c75300 Version bump hibernate 2019-01-23 05:57:20 -05:00
James Agnew 4367e340ae Log the version number and commit on startup 2019-01-17 16:05:54 -05:00
James Agnew 38bade0429 Credit for #1118 2019-01-13 17:22:29 -06:00
James Agnew 3c260e5ef2 Ignore unfinished test 2019-01-10 07:36:37 -07:00
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
jamesagnew b3c9b32db4 Credit for #1065 and forward-port fix to R4 provider 2019-01-09 07:19:55 -05:00
James Agnew 1bfa29bbcc Site updates 2018-12-28 11:42:21 -05:00
James Agnew c462b5ba3e Prep new site version 2018-12-28 09:16:48 -05:00
jamesagnew 49e418edf0 Adjust migrator to handle updated Hibernate version 2018-12-23 15:11:44 -05:00
jamesagnew 4599a10180 Merge branch 'master' into test-openjdk-11 2018-12-23 14:19:59 -05:00
James Agnew 9d3904ef3e Fix #1142 - Upgrade Spring Boot to latest version 2018-12-23 13:10:03 -05:00
James Agnew a0cb7edd08 Version bump a few dependencies 2018-12-22 20:13:03 -05:00
jamesagnew 226e31b0d9 Reenable karaf 2018-12-22 15:07:26 -05:00
jpoth cda84c4b3a Karaf related fixes for jdk11 2018-12-22 13:25:09 -05:00
jamesagnew ea80d03a74 Credit for #1051 2018-12-21 05:42:39 -05:00
James Agnew 11b8304cb4 Fix case sensitivity issue 2018-12-13 08:31:35 -05:00
jamesagnew 3109a269b3 Attempting to get ErrorProne working on JDK11 2018-12-08 18:22:17 -05:00
jamesagnew 9a97d21660 Bump compiler plugin 2018-12-08 18:06:39 -05:00
jamesagnew 3a3b81a6a8 Preparing things for OpenJDK 11 2018-12-08 17:52:48 -05:00
Ken Stevens 6baee4dc3f
Standalone subscription (#1125) 2018-11-30 17:19:16 -05:00
James Agnew 14c0a52831 Fix xml typo 2018-11-16 09:21:53 +01:00
James Agnew e75d2e1f10 Credit for #1117 2018-11-15 13:37:32 +01:00
James Agnew 84acafe3af Streamline expunge operation 2018-11-15 11:37:16 +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 e5b04710ea Version bump a few dependencies 2018-11-11 17:06:40 -05:00
James Agnew 7e2e53a354 Credit for #1071 2018-11-08 13:33:25 -05:00
James Agnew 9fee827398 Credit for #1103 2018-11-08 13:24:24 -05:00
jamesagnew 692bdb5fdd FIx bad merge 2018-11-07 18:29:37 -05:00
jamesagnew 3121334bfd Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-11-07 18:28:28 -05:00
jamesagnew ca9268970e Site updates 2018-11-07 18:27:08 -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
James Agnew bc72093555 Add reindexing support based on table instead of column 2018-11-04 20:00:27 +01:00
jamesagnew 8955a9e54d Add threading to migrator 2018-10-31 05:50:50 -04:00
jpoth 4edb9c32f8 Upgrade Apache Karaf to 4.1.6 2018-10-15 12:36:42 +02:00
James Agnew 706e004b9d Bump to 3.6.0-SNAPSHOT 2018-09-19 10:24:48 -04:00
jamesagnew 3bfce11d2c Add OSGI dependency for commons-text 2018-09-17 16:06:11 -04:00
jamesagnew 6cfa452d8c Bump PGSQL version 2018-09-17 14:35:54 -04:00
James Agnew daef975734 Version bump to 3.5.0 2018-09-08 07:22:21 +08:00
James Agnew 4852b0b60f Work on migration 2018-09-08 07:14:43 +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 67fede9eda Start work on migrator 2018-08-23 05:24:13 -04:00
jamesagnew 080559027b Credit for #1022 2018-08-12 17:56:42 -04:00
jamesagnew 4f15027df3 Merge branch 'subscription_cleanup' of github.com:jamesagnew/hapi-fhir into subscription_cleanup 2018-08-12 13:43:48 -04:00
James Agnew 52cfdb7b8b Add some test logging 2018-08-12 13:43:31 -04:00
jamesagnew bf68adfdba Restore working POM for Karaf version 2018-08-11 16:56:46 -04:00
James Agnew 321e71e9a9 Merge branch 'master' into subscription_cleanup 2018-08-10 09:16:32 -04:00
jamesagnew 64b3b64208 License header updates 2018-08-06 19:06:09 -04:00
jamesagnew d07fd76d60 Dont keep resource bodies in the queue for JPA subscription delivery 2018-08-03 10:44:15 -04:00
James Agnew 4eb3281fa6 Merge branch 'client_enhancements' 2018-07-30 18:34:49 -04:00
jamesagnew 79d43e45b1 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-07-30 18:33:39 -04:00
jamesagnew f639ebf595 Build fixes 2018-07-30 18:33:26 -04:00
James Agnew e32bc9bae4 Credit for #996 2018-07-30 11:12:53 -04:00
James Agnew bf63caf3fb Credit for #965 2018-07-30 09:47:28 -04:00
James Agnew e670fe2644 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-07-30 09:41:19 -04:00
James Agnew 78b2cf1d26 Merge branch 'master' of https://github.com/c-schuler/hapi-fhir into c-schuler-master 2018-07-30 09:40:14 -04:00
jamesagnew 17a976369b Credit for #996 2018-07-30 09:15:28 -04:00
jamesagnew fc9f2ec0fb FIx test issue 2018-07-29 18:20:09 -04:00
jamesagnew 47633214e0 Credit for #1010 2018-06-24 15:12:47 -04:00
patrick-werner eb1742f44a added oss.sonatype as pluginRepository, fixes #958 2018-06-06 12:11:17 +02:00
jamesagnew 6788eb992d Bump datasource proxy plugin version 2018-06-03 16:24:41 -04:00
jamesagnew fafa86a80d Lucene version bump 2018-06-03 16:23:34 -04:00
jamesagnew 3583dfd503 Correctly include project description in capabilitystatement 2018-06-03 16:19:33 -04:00
jamesagnew 6d09f5025f Credit for #974 2018-06-03 15:31:40 -04:00
jamesagnew 987679483a Version bumps 2018-06-03 15:29:10 -04:00
Roman Doboni 8f1effe5e3
Merge branch 'master' into master 2018-06-02 09:37:56 +02:00
James Agnew 44c6292a45 Merge branch 'java9' 2018-05-31 21:56:58 -04:00
jamesagnew 543c9a0a19 Bump the failsafe plugin version 2018-05-31 12:20:55 -04:00
Romanow a336f33b4b Update Spring Data 1.11.6.RELEASE to 2.0.7.RELEASE 2018-05-31 14:42:15 +02:00
jamesagnew d127a89047 Some test fixes 2018-05-30 11:01:43 -04:00
jamesagnew be74312955 Update errorprone 2018-05-30 09:07:50 -04:00
jamesagnew 833a46d07e Work on test compilation 2018-05-30 08:27:09 -04:00
James Agnew a52805e504 Work on JDK9 support 2018-05-30 05:45:08 -04:00
jamesagnew 5be11b53b9 Fix java9 support 2018-05-29 09:08:00 -04:00
James Agnew 7951d883d0 Merge branch 'master' into java9 2018-05-29 08:43:21 -04:00
jamesagnew 674005bab8 Site updates 2018-05-29 06:14:28 -04:00
Diederik Muylwyk 0e2c57fa60 Bumping version. 2018-05-28 17:44:38 -04:00
Diederik Muylwyk f440acd847 Fixed project description. 2018-05-28 13:09:44 -04:00
Diederik Muylwyk 2b8c918a22 Added project description. 2018-05-28 12:57:51 -04:00
Diederik Muylwyk 05f05b5147 Fix distribution management repo. 2018-05-28 10:52:46 -04:00
Diederik Muylwyk 2871920734 Preparing release. 2018-05-28 10:45:47 -04:00
jamesagnew d74023925b Credit for #910 2018-05-28 06:04:04 -04:00
jamesagnew 8139178fcc Move example project to example-projects directory 2018-05-28 06:01:13 -04:00
James Agnew ed6609e414 One more test fix 2018-05-23 16:28:13 -04:00
James Agnew 0c5c347db7 FIx broken reindex process 2018-05-23 10:48:07 -04:00
jamesagnew be86eb196b Credit for #874 2018-05-23 06:32:52 -04:00
jamesagnew 98d997c620 Add changelog and credit for #867 2018-05-23 06:21:00 -04:00
jamesagnew 39163304ee Credit for #857 2018-05-23 06:07:32 -04:00
James Agnew 4d93b78c24 Credit for #836 2018-05-22 08:44:17 -04:00
James Agnew 33c4e3276d Drop maven version requirement 2018-05-15 11:48:04 -04:00
jamesagnew f9946fee61 Fixes to get the build passing once more 2018-05-15 07:34:44 -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
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 a0c40cf98a Move a few more constants around 2018-05-05 12:21:56 -04:00
James Agnew 127a8389ac Credit for #903 2018-05-04 08:55:41 -04:00
James Agnew 7688be1231 Work on getting java9 building 2018-05-03 18:34:29 -04:00
patrick-werner a62718692f added credit for t4deon 2018-05-03 10:50:33 +02:00
jamesagnew ac8be4493e Restore external repos 2018-04-30 15:59:24 -04:00
James Agnew 392feb7082 Refactor CLI to extract commands 2018-04-30 15:04:35 -04:00
James Agnew d85efbaa5b Refactor CLI to merge both CLI command frameworks 2018-04-30 08:29:38 -04:00
jamesagnew 92dc0d42ee Switch Maven deploy to use new recommended method 2018-04-29 08:02:05 -04:00
jamesagnew 83a5eedb29 Fix performance regression in DSTU3 validation 2018-04-28 11:42:59 -04:00