Commit Graph

1988 Commits

Author SHA1 Message Date
James Agnew 301a8f8432
Merge #1146 - Filter implementation (#1220)
* Initial commit of _filter keyword implementation.

* - Completed all search parameter types for _filter.
- Implemented handling for _has, _id, _security, language, _profile, _security, and _tag.

* - Changes to support "ne" matching on resource ID for _filter

* Implemented language

* Commit/push before creation of pull request

* Ongoing merge work

* Ongoing merge work

* Merge master in

* Test fix
2019-08-12 11:59:33 -04:00
James Agnew bfaf617142 Add some more chars to the sanitizer function 2019-08-12 08:16:38 -04:00
James Agnew 4f5a2b3c0c Add fhirType() to IBase to bring it in line with what the core structures do 2019-08-09 09:44:20 -04:00
jamesagnew 4e1bbe681a Bump supported PGSQL driver 2019-08-08 15:12:29 -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* Ignore outdated DSTU2 validation test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
Ken Stevens 1b17097f62 a couple more int -> long 2019-08-07 13:35:27 -04:00
James Agnew 6aa7916ba7
Merge pull request #1415 from jamesagnew/ks-inmemory-id-match
in-memory id match
2019-08-07 08:31:38 -04:00
James Agnew b0eb19cf2f A few fixes resulting from the R5 merge 2019-08-06 17:55:51 -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
Ken Stevens c11d719957 Fix bug when in-memory matcher compares long id to string id 2019-08-06 15:17:09 -04:00
Ken Stevens 48c8497086 Changed migration test from derby to h2
Added a new test from 340 to latest version.
2019-08-02 16:00:43 -04:00
jamesagnew 46c8c61932 Restore build - May need to roll back the RDF changes 2019-08-01 10:14:56 -04:00
James Agnew 0f4738c1b5
Merge branch 'master' into rdf_parser 2019-08-01 09:25:40 -04:00
Ken Stevens f1d3fc2307 Changed Stopwatch getThroughput param from int to long
Added FhirVersion accessor to AnyListResource
2019-08-01 06:32:09 -04:00
James Agnew 04ce9cfc1a Add support for uploading custom terminology using the
$upload-external-code-system operation
2019-07-30 17:30:18 -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
Ken Stevens 84f5c7d467 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-24 21:54:05 -04:00
Ken Stevens e05387da02 Recover from failed merge again. This time with feeling! 2019-07-24 13:46:20 -04:00
James Agnew ddb8e385bf Test fix 2019-07-24 13:24:48 -04:00
James Agnew e8cf2738f0 Handle oversized payload request 2019-07-24 13:18:30 -04:00
Ken Stevens 64e83fa3df Revert "Recovering Pointcut from a failed merge"
This reverts commit 19c0b4fd
2019-07-24 13:00:49 -04:00
Ken Stevens 19c0b4fdd2 Recovering Pointcut from a failed merge 2019-07-24 11:30:36 -04:00
Ken Stevens 0efe69f891 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
2019-07-24 10:41:37 -04:00
Ken Stevens 8d86e34bcf Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
2019-07-23 09:12:08 -04:00
jamesagnew 60ea922e8d Add license headers 2019-07-23 05:38:10 -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
Ken Stevens 7ba3ceec90 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-19 10:54:56 -04:00
jamesagnew 13dae527d1 Fix #1390 - DiagnosticReport template correction 2019-07-19 05:44:08 -04:00
Ken Stevens e634aa6d10 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-18 22:06:10 -04:00
James Agnew 5bf4fa22e7 Allow patching in tranactions 2019-07-18 16:41:07 -04:00
Ken Stevens 72aa4932d6 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-18 10:12:15 -04:00
jamesagnew 7488047686 Add license headers 2019-07-17 18:53:23 -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
Ken Stevens fe21dba4a6 Added Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE.
Also added a couple of tests.
2019-07-17 13:26:50 -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 ba4bb005bc
Switch JPA unit tests to use H2 (#1381)
* Start working on this

* Ongoing fixes to H2 branch

* Work on fixing tests

* Updated fixes

* Some test fixes

* More work on H2 migration

* Fixes to try and get the H2 migration building

* Test seem to be passing!

* Tweaks to locale randomization

* Add changelog
2019-07-13 17:22:43 -04:00
Ken Stevens 26ab115ff5 changes.xml 2019-07-12 13:34:32 -04:00
Ken Stevens 8d817b364c Merge remote-tracking branch 'remotes/origin/master' into expunge-hooks
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
2019-07-12 13:27:11 -04:00
James Agnew a352137938 Test fixes 2019-07-11 21:10:30 -04:00
James Agnew 1db019b6df Test fix and try to get Travis building again 2019-07-11 20:20:27 -04:00
James Agnew dca55d054b Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-07-11 18:17:09 -04:00
Diederik Muylwyk 0729e38e6e
Resolve "experimental implementation for storing expanded ValueSets in terminology tables" (#1369)
* Added experimental implementation for storing expanded ValueSets in terminology tables.

* Minor tweak to log message for consistency.

* Another minor tweak to log message for consistency.

* Renamed test.

* Addressing review comments.

* Added migration tasks.
2019-07-11 16:52:19 -04:00
James Agnew 32a8e1aead Omit extensions when encoding in summary mode (except for
CapabilityStatement)
2019-07-11 16:28:50 -04:00
Ken Stevens b445df3e05 Merge remote-tracking branch 'remotes/origin/master' into expunge-hooks 2019-07-10 10:09:55 -04:00
Ken Stevens 7aaa75c255 fixed pointcut 2019-07-10 10:09:43 -04:00
James Agnew 0fb8db11a2 Add new pointcut: PROCESSING_COMPLETED 2019-07-09 14:32:11 -04:00
Ken Stevens 5e05703c1a Add expunge-everything hook. Also add RequestDetails to all expunge operations 2019-07-09 10:58:57 -04:00
James Agnew cc20893018 Add hardcoded keys to localizer 2019-07-08 08:58:06 -04:00
jamesagnew dff2fdd3cf GET RID OF TRAILING LICENSE HEADER SPACES ONCE AND FOR ALL
YESSSSSSSSSSSSS
2019-07-05 11:19:51 -04:00
jamesagnew aff88d3ebb License header updates 2019-07-05 07:27:18 -04:00
James Agnew f1848fb1ad Include version ID in response for deleted resource 2019-07-03 14:44:12 -04:00
James Agnew 56aaef641c Add request ID 2019-07-02 21:32:28 -04:00
James Agnew 1faf7785c4 Dont filter constraints from the event broadcast - this was not needed
after all
2019-07-02 09:21:15 -04:00
jamesagnew 742389642d Add tests for delete conflicts and authorizationinterceptor 2019-07-01 10:49:38 -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
jamesagnew 5910131319 License header updates 2019-06-27 18:23:45 -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 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
jamesagnew 989e26fdb4 Fix #1355 - Failed to call access method: java.lang.NullPointerException in case of bundle entry without resource 2019-06-22 15:51:56 -04:00
James Agnew 36ff58a320 Add docs 2019-06-17 17:46:28 -04:00
James Agnew b2e99cf035
Add support for conditional patch (#1348)
* Add support for conditional patch

* Add changelog

* Test fix
2019-06-17 16:12:05 -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
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
admin e58224e63b Adding multiformat 2019-06-06 12:22:32 -05:00
James Agnew f2be9f47a0 Add 4.0.0 version enum 2019-05-30 20:59:23 -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 7863393c2c
Merge pull request #1303 from jasmdk/BaseParserFix
Removing not needed "super." when calling preProcessValues()
2019-05-29 21:46:33 -04:00
James Agnew c7a224c99d
Merge branch 'master' into upgrade-25-to-33 2019-05-29 21:33:02 -04:00
Christian Ohr cd8b2feb2f Allow to set additional Http headers directly on the IClientExecutable 2019-05-29 21:17:52 -04:00
admin 69089b81b3 Typo in pom.xml 2019-05-28 10:40:21 -05:00
admin fc27325dbc RDF XML Parser 2019-05-28 10:37:01 -05:00
admin a15c90be6d RDF Parser 0.1 2019-05-24 05:00:29 -05:00
James Agnew b4eecdef38 Test fix 2019-05-22 17:27:49 -04:00
basecade 3bb3c3a383 Preserve contained resource meta when encoding to dao (#1311)
* Preserve contained resource meta when encoding with: parser.setDontEncodeElements(ResourceMetaParams.EXCLUDE_ELEMENTS_IN_ENCODED)

* - Correct so security, lastUpdated and versionId is not encoded
- Added test
2019-05-22 17:11:03 -04:00
James Agnew 9353ea5b06 Enable websockets on public HAPI server 2019-05-04 10:06:10 -04:00
jamesagnew 150a84d52f CLeanup 2019-04-29 21:54:34 -04:00
James Agnew 828df1528f Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-26 11:24:00 -04:00
James Agnew 685adf7754 Revert Jetty upgrade, and improve patch error messages 2019-04-26 11:23:22 -04:00
patrick-werner 7f45660a15 changed toListOfResources to send IBaseResource as Type instead of null 2019-04-26 12:55:18 +02:00
patrick-werner a5e7ea16ae added all fetchValueSet Implementations 2019-04-26 10:47:58 +02:00
Jacob Stampe Mikkelsen 1e640718c0 Merge branch 'master' of https://github.com/jasmdk/hapi-fhir into BaseParserFix 2019-04-26 08:33:40 +02:00
jamesagnew abd53c0cbe License header updates 2019-04-24 21:20:11 -04:00
James Agnew 738c2c1797
Interceptor framework refactoring (#1287)
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
jamesagnew a9cfce3615 Header updates 2019-04-15 12:31:11 -04:00
James Agnew cff79e6aef PortUtil fixes from my working branch to avoid test failures 2019-04-15 10:34:27 -04:00
James Agnew c8f2e4bbc9 Return HTTP 400 for missing body on POST and PUT 2019-04-14 12:32:09 -04:00
ahn 3f15100a45 Removing irrelevant super call to preProcessValues 2019-04-10 12:03:32 +02:00
jamesagnew 8b5143f436 License header updates 2019-04-02 10:44:41 -04:00
jamesagnew 835b89f449 Build fixes 2019-04-01 18:55:55 -04:00
James Agnew 81de6cca32 Add a bit of documentation 2019-04-01 10:28:26 -04:00
James Agnew 3eeca4a8fd Merge branch 'master' into ja_interceptor_jpa_queries 2019-04-01 09:59:03 -04:00
James Agnew 3c18275b3d Make port delays configurable 2019-03-29 17:19:22 -04:00
jamesagnew 8791ed5793 Test tweaks 2019-03-29 17:13:41 -04:00
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 3e98c3a87d Fix a param issue 2019-03-22 01:18:16 +01:00
James Agnew c701de2861 Create a performance interceptor framework for HAPI FHIR 2019-03-22 01:06:03 +01:00
James Agnew d1667487c2 Clean up unique composite search params 2019-03-21 21:57:38 +01:00
James Agnew 715b451d94 Add some javadocs to PortUtil 2019-03-18 15:27:04 +01:00
James Agnew c81c5c2497 One more tweak to the port test 2019-03-17 17:54:48 -04:00
James Agnew 50a8d2fbc8 More updates to port tests 2019-03-17 17:51:54 -04:00
jamesagnew 8818a2479c Try to prevent build failure 2019-03-17 16:14:19 -04:00
jamesagnew 7cbd7a0d50 License header update 2019-03-17 14:22:29 -04:00
jamesagnew 3e57fdb491 Improvements to PortUtil to avoid reusing ports 2019-03-17 14:09:21 -04:00
jamesagnew c482d22cff Improvements to PortUtil 2019-03-17 13:23:48 -04:00
James Agnew e15afbc4f0 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-03-14 13:32:03 -04:00
James Agnew a8c76450e5 Re-enable contains searches on the public HAPI FHIR server and improve
message formatting in HapiLocalizer
2019-03-14 13:19:26 -04:00
jamesagnew 7b1950aeed License headers 2019-03-12 17:45:51 -04:00
James Agnew e3ecf21fa9 One more test fix 2019-03-12 13:24:18 -04:00
James Agnew 00a8f8c759 Fix broken build 2019-03-12 13:13:13 -04:00
James Agnew 71a07c0239 Refactor the way that contexts are used in narrative generator 2019-03-11 16:05:25 -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
Ken Stevens dcfacfea49
Has param no in (#1232) 2019-03-10 20:50:24 -04:00
jamesagnew 64facdab0a Disabling test logging 2019-03-06 16:14:32 -05:00
James Agnew 9bc0f6784d
Search paging timeout with 1500 < n < 2000 results (#1221)
* Avoid paging links when offset is artificially set very high

* Ongoing fixes

* Adding logging and clean up transaction processing

* Add changelog

* More work on queries

* Keep working on getting tests passing

* More test fixes

* More work on tests

* More test works

* One more test attempt

* Ongoing fixes

* One more change

* FIxes to search algorithm

* Add changelog

* Clean up for review

* Fixed NPE in token matcher when system is not null and value is null

* test opposite (null system not null value)

* added null protection to all matchers

* Address review comments

* Address broken test

* Trying to resolve DB ordering issues
2019-03-06 05:45:05 -05:00
James Agnew 4138832071 Add a test 2019-03-01 14:03:14 -05:00
James Agnew 3972e17e62 Add "is trusted" property to server exceptions 2019-03-01 13:58:13 -05:00
jamesagnew 6e41f90bf9 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-02-27 16:49:20 -05:00
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
jamesagnew aef5989477 Header updates 2019-02-25 20:47:30 -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 485335e975 Allow terminology service to work without having Lucene enabled for
simple ValueSet expansions
2019-02-14 20:47:28 -05:00
James Agnew 10c348d44f Tweak to elements parametr support 2019-02-14 19:30:10 -05:00
James Agnew 00636276d3 Add missing version constant 2019-02-07 17:02:42 -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
jamesagnew c7d857df98 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-02-04 16:34:55 -05:00
jamesagnew d4af1ee2a3 Add tests and license headers 2019-02-04 16:34:39 -05:00
James Agnew edb79b8c6a Updates to parser dont encode elements functionality 2019-02-04 16:34:05 -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
jamesagnew 5f29e4fbf3 Fix #1174 - Prevent serialization exception 2019-01-30 05:49:45 -05:00
Ken Stevens 10c59fceeb
Subscription strategy tag (#1178)
tests pass
2019-01-25 13:01:04 -05:00
jamesagnew cd1e0e881c Add headers 2019-01-19 18:31:17 -05:00
jamesagnew b0cbd52ae9 Interceptor cleanup 2019-01-19 18:01:00 -05:00
James Agnew 3e84173180 Merge branch 'master' into ja-subscription-interceptors 2019-01-18 17:52:23 -05:00
James Agnew 5ce9d444e9 Work on interceptors 2019-01-18 09:04:45 -05:00
James Agnew 4367e340ae Log the version number and commit on startup 2019-01-17 16:05:54 -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 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