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2473 Commits

Author SHA1 Message Date
jamesagnew 8a2b799df0 Test fixes 2020-04-22 08:43:00 -04:00
jamesagnew 009d6443f5 Compile fx 2020-04-21 21:34:15 -04:00
jamesagnew 7efd8a9f6e Merge branch 'ja_20200206_multitenancy' of github.com:jamesagnew/hapi-fhir into ja_20200206_multitenancy 2020-04-21 20:55:09 -04:00
jamesagnew 6226381595 Merge branch 'master' into ja_20200206_multitenancy 2020-04-21 20:54:56 -04:00
jamesagnew 1f37cdd8cf Address review comments 2020-04-21 20:53:10 -04:00
James Agnew cc2b7452be
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java 
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
 2020-04-21 20:36:19 -04:00
jamesagnew c7de85339c Work on review comments 2020-04-21 20:18:06 -04:00
Maciej Kucharek f69fb1a39b
Set ES username and password only if they're not blank (#1806) 
This is important for AWS-hosted ES, as it does not accept HTTP requests with Basic authentication (even if the username/passwords are blank). Skipping those settings in case they're blank solves the issue.

Co-authored-by: Maciej Kucharek <maciej@oraoncology.com>
 2020-04-21 15:32:12 -04:00
Ibrohim Kholilul Islam 3225075f9e
Fix GraphQL Error (#1791) 
* add debug log

* add debug log to value iteration

* fix _filter issue on /$graphql, fix dash and underscore issue on /$graphql, and give helpful error message on wrong argument.

* remove debug logging

* implement JpaStorageServicesTest
 2020-04-21 15:28:28 -04:00
James Agnew c716216b34
Adjust return type for fluent delete() operation (#1805) 
* Add cascading delete to client

* Add changelog

* Client delete should return MethodOutcome

* Rerturn more appropriate type for delete operations

* Refactor cascade detection to be reusable
 2020-04-21 15:23:11 -04:00
jamesagnew 998c1f7751 Work on docs 2020-04-21 14:32:41 -04:00
jamesagnew e6c806283e Merge branch 'ja_20200206_multitenancy' of github.com:jamesagnew/hapi-fhir into ja_20200206_multitenancy 2020-04-20 16:58:59 -04:00
jamesagnew 544d9fbc6c Add migration tasks 2020-04-20 16:58:48 -04:00
jamesagnew bbab016ca6 Rename config 2020-04-20 12:38:04 -04:00
jamesagnew 7248b4e18e Finish docs 2020-04-20 11:02:27 -04:00
jamesagnew cd3e1c5e72 Tenancy docs 2020-04-19 10:15:51 -04:00
jamesagnew 48057b9d8e Merge branch 'master' into ja_20200206_multitenancy 2020-04-17 17:59:48 -04:00
ianmarshall 540375a7eb Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-04-17 17:39:27 -04:00
ianmarshall 4a89860f9b Additional tests and cleanup. 2020-04-17 17:38:42 -04:00
jamesagnew e0b419354f Bump up hamcrest version and force the use of the latest version 2020-04-17 13:59:22 -04:00
James Agnew 497757501b
Improve search method binding priority (#1802) 
* Work on search method binding priority

* Work on method priority

* Work on binding priority

* Test fixes

* Add changelog

* Test fixes

* compile fix

* One more comple fix

* Test cleanup

* Test fix
 2020-04-17 09:28:33 -04:00
jamesagnew 81723c30d8 Work on multitenancy 2020-04-16 15:52:15 -04:00
jamesagnew 25cdbb15c2 Work on multitenancy 2020-04-16 15:33:48 -04:00
jamesagnew 8873749d9c Add license headers 2020-04-16 10:06:56 -04:00
jamesagnew cd06137745 Work on multitenancy 2020-04-15 22:12:28 -04:00
jamesagnew d822867a4a Merge branch 'master' into ja_20200206_multitenancy 2020-04-15 22:12:20 -04:00
James Agnew f95f619bdc
Correct two JPA processing bugs (#1801) 
* Work on search params on contained

* Add workaround for stored decimals with leading decimal point

* Add changelog

* Cleanup

* Test fix

* Test fix

* One more test fix
 2020-04-15 14:22:47 -04:00
ianmarshall d03ce6533e Fixed conflicts after merging latest from Master. 2020-04-13 20:01:34 -04:00
ianmarshall 925bbbbcdc Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java
#	hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
#	pom.xml
 2020-04-13 18:35:15 -04:00
ianmarshall 0f9bdbd3af Undid previous re-factoring and fixed a bug introduced in last commit. 2020-04-13 16:14:38 -04:00
jamesagnew 982b54df57 Work on multitenancy 2020-04-13 11:50:49 -04:00
jamesagnew f2fa8659c4 Test fix 2020-04-13 09:35:51 -04:00
ianmarshall af11763dee Fixes to command line tool, clean-up and minor re-factoring. 2020-04-13 08:56:56 -04:00
jamesagnew c26a5553e9 Multitenancy work 2020-04-12 20:47:32 -04:00
jamesagnew e55ccf88fc Work on multitenancy 2020-04-10 20:01:59 -04:00
ianmarshall e64d67f429 Consolidate changes to Command Line Tool and add/improve tests. 2020-04-10 16:58:00 -04:00
jamesagnew 8d8c657ce2 More work on multitenancy 2020-04-10 13:05:17 -04:00
jamesagnew 219332e9e3 Work on multitenancy 2020-04-10 11:11:29 -04:00
jamesagnew e0fcbe1df2 Merge branch 'master' into ja_20200206_multitenancy 2020-04-09 11:52:27 -04:00
James Agnew 8cdc3a72ce
Fix #1794 - Client ID and Server ID mode clash (#1795) 
* Fix #1794 - Client ID and Server ID mode clash

* Try to track down intermittent test failure
 2020-04-09 09:31:13 -04:00
jamesagnew 96a4eff38e Test fix 2020-04-08 19:54:54 -04:00
James Agnew 1c738b903d
Decouple subscription submission / matching (#1790) 
* Start work on subscription cleanup

* Work on subscription cleanup

* Work on subscriptions

* Subscription cleanup

* More work on subscriptions

* Queue factory cleanup

* Work on subscription cleanup

* Subscription cleanup

* Work on subscription cleanup

* Work on subscription cleanup

* Work on subscription cleanup

* Ongoing cleanup

* Subscription work

* Tests passing

* Move resource provider factory

* Test fixes

* Address review changes

* One more change

* Test fixes
 2020-04-08 18:08:27 -04:00
jamesagnew edc30568f2 Address review changes 2020-04-07 19:07:07 -04:00
jamesagnew 35e1dbae32 One more bugfix on #1772 2020-04-07 15:22:59 -04:00
jamesagnew c2e00bb73b Bugfix on #1772 2020-04-07 14:21:42 -04:00
jamesagnew 47786660d5 Test fixes 2020-04-07 13:58:24 -04:00
jamesagnew 2205d2306c Move resource provider factory 2020-04-07 10:56:05 -04:00
jamesagnew 347ecc7d51 Tests passing 2020-04-07 09:39:14 -04:00
jamesagnew 826ba6458a Subscription work 2020-04-06 20:15:41 -04:00
jamesagnew b78205c218 Ongoing cleanup 2020-04-06 17:00:45 -04:00
jamesagnew 40d0c27ae3 Work on subscription cleanup 2020-04-05 18:43:27 -04:00
jamesagnew 0a28c0c060 Work on subscription cleanup 2020-04-05 07:21:05 -04:00
jamesagnew 79da1578cb Subscription cleanup 2020-04-04 20:04:32 -04:00
jamesagnew fef447afee Work on subscription cleanup 2020-04-04 16:07:01 -04:00
ianmarshall 83e673e725 Consolidate changes to Command Line Tool and add/improve tests. 2020-04-03 17:12:04 -04:00
jamesagnew 7c6024fa14 More work on subscriptions 2020-04-03 07:43:21 -04:00
jamesagnew 43b4d8e0e3 Work on subscriptions 2020-04-02 21:15:07 -04:00
jamesagnew 6baf1995c9 Work on subscription cleanup 2020-04-02 20:30:19 -04:00
jamesagnew e1142f4043 Start work on subscription cleanup 2020-04-02 05:31:12 -04:00
ianmarshall f819c91530 Initial implementation of lastn operation. 2020-03-31 21:55:57 -04:00
ianmarshall f891634341 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-03-31 13:30:28 -04:00
jamesagnew ea1f35beaa Work on multitenancy 2020-03-31 10:33:47 -04:00
jamesagnew c4bd1a97fd Add test 2020-03-30 11:54:27 -04:00
jamesagnew 2e43c57032 Work on multitenancy 2020-03-30 09:49:17 -04:00
jamesagnew 8e714b6b14 Work on uniques 2020-03-30 05:36:24 -04:00
jamesagnew 62d867902f Work on multitenancy 2020-03-29 18:16:04 -04:00
jamesagnew 691f2c4e9a Work on muiltitenancy 2020-03-29 13:35:20 -04:00
jamesagnew 9df4c58122 Work on multitenancy 2020-03-27 09:22:00 -04:00
jamesagnew ec6fe70acb Merge branch 'master' into ja_20200206_multitenancy 2020-03-27 05:50:08 -04:00
ianmarshall 83fde61846 Initial commit of changes to support $lastn operation. 2020-03-25 18:02:57 -04:00
ianmarshall 4e4c8dbd9a Initial commit of changes to support $lastn operation. 2020-03-25 18:02:13 -04:00
jamesagnew 718c248c69 Test fix 2020-03-24 07:55:25 -04:00
jamesagnew 13f0e5384b Address review comments 2020-03-24 06:02:55 -04:00
jamesagnew 0ac434ea5d Add chain on _type parameter 2020-03-23 17:53:30 -04:00
jamesagnew 14316147c5 Resolve some docs issues 2020-03-23 10:34:12 -04:00
jamesagnew 3f20f7b67f Make SubscriptionDeliveryHandlerFactory not abstract 2020-03-22 21:01:19 -04:00
jamesagnew a5257f0fa8 Add new indexing extractor method 2020-03-19 20:22:30 -04:00
James Agnew bde7c356fe
Implement Jackson parser/serializer (#1733) 
* [dev] Integration of a Jackson serializer and deserializer - first stage

* [fix] Fixed some serializing issues
[improve] Improved the processing, removed the loggers

* [clean] Removed the JacksonSerializer class, replaced all the Gson classes with Jackson classes

* [clean] Small cleanup

* [improve] Throw a ConfigurationException if the JsonGenerator cannot be created

* [improve] Use the ObjectMapper's `readTree` instead of `readValue`

* [dev] Latest fixes and improvements

* [dev] Use the Jackson serializer

* [clean] Removed the ObjectMapper configuration, for now

* [fix] Use the GsonStructure also for the parsing of a FHIR resource

* [clean] Removed the LinkedList usage

* Work on preparing for merge of #1673

* Resolve build errors

* Work on parser integration

* Tests passing

* Resolve fixme

* CLeanup

* Fix dependency

Co-authored-by: Bogdan Solga <bogdan.solga@gmail.com>
 2020-03-17 17:27:26 -04:00
Tadgh 4583cb9939
Merge pull request #1760 from jamesagnew/bugfix/1752-support-chained-parameters-inside-reverse-chained-parameter 
Bugfix/1752 support chained parameters inside reverse chained parameter
 2020-03-17 13:27:20 -07:00
jamesagnew 4c1bbd01cb Intermittent test fix 2020-03-17 14:19:36 -04:00
Tadgh 3eb09b15f0 Merge branch 'master' into bugfix/1752-support-chained-parameters-inside-reverse-chained-parameter 2020-03-17 10:32:43 -07:00
James Agnew 22413911bf
Validation api changes (#1719) 
* Validation enhancements

* Work on validation api reworking

* Keep working on validation API

* Keep working on new term API

* Work on validation api

* Ongoing work on validation

* Work on integrating validation

* Work on validation API

* Add to validation API

* Work on validation

* Work on API

* Work on validation

* Work on validation API

* Work on validation API

* Work on validation api

* Work on validation API

* Work on validation api

* Validation API changes

* Work on API

* More work on validationo API

* Work on validation API

* FIxes

* WOrk on validation api

* Work on validation API

* Tests passing!

* More cleanup

* More validation API changes

* Fix intermittent test failure

* Package reorg

* Validation API work

* Work on doocumentation

* Work on API

* More work on new validation API

* Fix errorprone-reported error

* Test fixes

* Documentation updates

* Documentation tweaks

* Work on API

* Bean name adjustments

* Build fixes

* Some test fixes
 2020-03-17 13:28:59 -04:00
James Agnew 9305bef4ef
Remove useless migrator task generics (#1687) 
* Remove useless migrator task generics

* Clean a couple of compile errors

* Try to fix intermittent
 2020-03-17 13:28:43 -04:00
James Agnew 288abe4504
Improve efficiency in search deleting (#1759) 
* Improve efficiency in search deleting

* Changelog

* Address review comments
 2020-03-17 12:33:38 -04:00
James Agnew 5867d62d62
Avoid duplicate predicate in _id queries (#1761) 
* Avoid duplicate predicate in _id queries

* Add changelog

* Change to trigger CI

* Address review comments
 2020-03-17 11:12:58 -04:00
Tadgh 6f872ffb51 Minor refactor 2020-03-13 19:15:46 -07:00
Tadgh a39ac886af Fix error while resolving rebase 2020-03-13 18:43:43 -07:00
Tadgh 4777d75e6b Merge branch 'master' into bugfix/1752-support-chained-parameters-inside-reverse-chained-parameter 2020-03-13 18:40:11 -07:00
Tadgh b80e71773d Tidy, fix up tests 2020-03-13 18:36:43 -07:00
Tadgh d91cb7524c Fix up whitespace 2020-03-13 15:30:49 -07:00
Tadgh 03567c5831 Add perftrace. Remove regex 2020-03-13 15:29:48 -07:00
Ken Stevens 6b019492fe
Merge pull request #1758 from jamesagnew/ks-20200312-json-annotation 
moved common Json annotations out into an interface
 2020-03-13 15:58:21 -04:00
Tadgh 74fd2c1519 wip 2020-03-13 11:28:44 -07:00
jamesagnew 72b9d9a350 FIx spelling mistake 2020-03-13 09:19:45 -04:00
James Agnew 1dc5d89013
Optmize forced ID resolution (#1754) 
* Add forced ID caching

* Work on id optimization

* Test fixes

* More optimization work

* Add some docs

* Work on docs

* Test fixes

* Test fixes

* Test fixes

* Address review comments

* Compile fix
 2020-03-12 17:12:50 -04:00
Ken Stevens ecf5284c87 moved common Json annotations out into an interface 2020-03-12 13:36:34 -04:00
Tadgh c3ceffbd72 wip 2020-03-09 16:05:41 -07:00
Tadgh e38ec3e3dd Fix typo 2020-03-09 14:57:53 -07:00
Tadgh 12412a7be9 Add query capturing to query 2020-03-09 13:58:59 -07:00
Tadgh 59d1603597 Some variable renaming. Adds some questions. 2020-03-09 13:51:47 -07:00
Tadgh aca4bcfaad Minor refactoring for readability 2020-03-06 14:22:31 -08:00
Tadgh b299d0b63f Fix Typos, reduce code duplication 
* Change Two streams into one.
* Fix typos.
* Begin Writing docstrings
* Rename variables for clarity
 2020-03-06 11:39:39 -08:00
Tadgh 0acfc51082 Split test into two tests, one of which passes, one of which fails, showing the missing functionality 2020-03-05 16:38:42 -08:00
James Agnew 58ee76549c Merge branch 'master' into ja_20200206_multitenancy 2020-03-04 08:19:22 -05:00
Ken Stevens 9b37ba35d0
Merge pull request #1747 from jamesagnew/ks-20200303-bulk-export-filter 
fixed a copy/paste error in bulk export with test
 2020-03-03 19:54:26 -05:00
Ken Stevens e819d40414 fix near searching for R4 2020-03-03 18:33:19 -05:00
Tadgh a510543933 Fix log conditional 2020-03-03 14:03:55 -08:00
Tadgh df7a9916c3 Swap from trace to info logging 2020-03-03 14:01:12 -08:00
Ken Stevens d104fbdf7d fixed a copy/paste error in bulk export with test 2020-03-03 16:40:31 -05:00
Ken Stevens 705735b9c0 review feedback: javadoc 2020-03-03 13:29:10 -05:00
Ken Stevens 5b5ef08500 Merge remote-tracking branch 'remotes/origin/master' into ks-20200302-near-chain 2020-03-03 09:44:52 -05:00
James Agnew 4a160a2df3 Merge branch 'master' into ja_20200206_multitenancy 2020-03-03 09:25:19 -05:00
James Agnew 58b5bd9664
Limit type on _has query (#1743) 
* Limit type on _has query

* Add changelog
 2020-03-03 08:28:38 -05:00
James Agnew 3c2c1dab2e
Error on missing profile validation (#1742) 
* Error on missing profile validation

* Add changelog

* Test fixes
 2020-03-03 08:28:26 -05:00
Ken Stevens a56df03055 restrict near-distance extraction to DSTU3 2020-03-02 21:50:57 -05:00
Ken Stevens 4e1be80525 fixme 2020-03-02 21:39:28 -05:00
Ken Stevens d1b54a9668 pre-review cleanup 2020-03-02 21:32:27 -05:00
Ken Stevens 27dcafe4f2 all but unit tests 2020-03-02 21:27:50 -05:00
Ken Stevens 24acb57f3b began with failing test. 
test now passes.
 2020-03-02 17:56:25 -05:00
Tadgh 8d9119faef Rework span name 2020-03-02 14:37:09 -08:00
Gary Graham 6123e4b189 rework based on PR comments 2020-02-28 16:31:16 -05:00
Gary Graham ed7b9fc6b6 Initial attempt at integrating elastic APM for search performance 2020-02-28 16:09:16 -05:00
James Agnew 8c78e465b1
Defer large term delta adds (#1736) 
* Defer large term delta adds

* Add changelog
 2020-02-28 14:41:15 -05:00
James Agnew 5bc554949b
Remove deleted resources from cached search results (#1732) 
* Remove deleted resources from cached search results

* Add changelog

* Add tests
 2020-02-28 10:57:26 -05:00
Gary Graham f86a4c9fa1 Add date ordinals to subscription matching checker 2020-02-26 17:05:23 -05:00
Gary Graham 2dc94de6bb roll back change to inmemory matcher test 2020-02-26 14:31:35 -05:00
Gary Graham 077f9df814 I keep finding more tests 2020-02-26 12:04:33 -05:00
Gary Graham a97443b1ed Fix test failures. One caused by invalid test. One caused by granularity need LT not LTE 2020-02-26 11:12:27 -05:00
James Agnew cb9906580e
Index canonical references (#1728) 
* Index canonical references

* Add changelog

* Fix compile error

* Add whitespace
 2020-02-25 21:45:46 -05:00
Gary Graham df9e86ec66 Merge branch 'master' into date-match-bug 2020-02-25 17:26:53 -05:00
James Agnew b2b0ff22b4
Collapse date joins (#1726) 
* Collapse date joins

* Add changelog

* Address review comments

* Add whitespace

* fix test

Co-authored-by: Ken Stevens <ken.stevens@sympatico.ca>
 2020-02-25 17:17:13 -05:00
Gary Graham 2204fbeabd Adding some comments 2020-02-25 17:08:11 -05:00
Gary Graham 1e833af5f0 Variable reuse 2020-02-25 17:06:38 -05:00
Gary Graham f56e38148b Add flag to DaoConfig controlling behaviour 2020-02-25 16:43:17 -05:00
Gary Graham 512af5b87d Add changelog entry 2020-02-25 14:09:51 -05:00
Gary Graham da7224ff89 update broken test to reflect new reality of business logic of ordinal date comparison 2020-02-25 14:07:03 -05:00
Gary Graham 3ec772b527 rework ResourceIndexedSearchParamDate constructor to support incoming string values 2020-02-25 14:06:36 -05:00
Gary Graham 3b41b5b960 Type migration to boxed integer to avoid int defaulting to 0 2020-02-25 11:18:39 -05:00
Gary Graham 34d5925393 Move common work to DateUtils. Rename function for clarity. 2020-02-25 09:37:57 -05:00
Gary Graham 7f5b3394e0 Hacky first-pass of adding ordinal date field to ResourceIndexedSearchParamDate and using it for search 2020-02-24 19:34:16 -05:00
Ken Stevens b33ad73d46 switch subscriptionchannelfactory to autowire 2020-02-24 14:28:14 -05:00
Ken Stevens 18d859281e Merge remote-tracking branch 'remotes/origin/master' into date-match-bug 2020-02-24 11:47:43 -05:00
Ken Stevens 41b5eb2484 Switching cdrsubscribablefactory from @ComponentScan to @Bean 2020-02-23 15:43:30 -05:00
j-chan c0811376b7
Moved TranslateRawParameters method from BaseHapiFhirResourceDao to BaseStorageDao (#1722) 2020-02-20 10:52:43 -05:00
James Agnew 6200cd2ddc Add test asserts 2020-02-19 21:21:22 -05:00
James Agnew 79ad0aebb5 Add a test 2020-02-19 18:01:35 -05:00
James Agnew a05c4ce9eb
Don't thrash delta links (#1721) 
* Don't thrash delta links

* Add changelog

* Remove commented out code
 2020-02-19 17:46:54 -05:00
James Agnew ab8dfa5a03
Avoid multi-term for ElasticSearch (#1717) 
* Avoid multi-term for ElasticSearch

* Add changelog

* Remove redundant code
 2020-02-18 16:40:44 -05:00
IanMMarshall fba28950ec
Merge pull request #1693 from jamesagnew/im_20200131_remove_circular_dependency_forcedid 
Changes to schema to loosen dependencies involving Forced ID table
 2020-02-18 14:16:09 -05:00
James Agnew 64f07e4dc0
Includes performance enhancement (#1702) 
* Includes performance enhancement

* Add changelog

* Test fix

* Fix typo

* A few coverage cleanups

* Test fix

* Fix changelog
 2020-02-18 14:11:48 -05:00