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265 Commits

Author SHA1 Message Date
jamesagnew fe0e07a313 Bump to 5.0.1 2020-05-15 05:47:01 -04:00
James Agnew 79a064dfd9
Optimize chain sql paths (#1844) 
* Start cleanup

* Almost workinf

* Possibly working!!

* Fixes

* Test fix

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Add changelog

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-05-15 05:36:12 -04:00
ianmarshall 529e1e1f5e Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-14 12:09:24 -04:00
jamesagnew 1d13e29ac0 Version bump to 5.1.0-SNAPSHOT 2020-05-12 20:04:20 -04:00
jamesagnew d631ecff4a Prepare for 5.0.0 2020-05-12 11:49:18 -04:00
ianmarshall e56cb049f7 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-08 09:19:44 -04:00
ianmarshall c290fa3493 Fixes to enable $lastn to return more than 32K records. 2020-05-08 09:19:14 -04:00
James Agnew 6cc07b6689
Make binary storage work for bulk export (#1836) 
* Make binary storage work for bulk export

* Add changelog

* Build fixes

* Test fix

* Test fix

* Test fix
 2020-05-07 19:20:22 -04:00
James Agnew b67509d7ff
Transaction write performance fix (#1832) 
* Performance fix for transactions

* Test fix

* Fixes

* Add docs

* Test fixes
 2020-05-07 10:56:41 -04:00
ianmarshall 1e882d640d Merging with latest from Master. 2020-05-05 17:35:22 -04:00
ianmarshall 4cced40b54 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
 2020-05-05 17:19:32 -04:00
ianmarshall 4db5beeabf Additional changes to enable processing of lastn operations with large numbers of parameters. 2020-05-05 16:53:47 -04:00
James Agnew a77aa6a28e
Multitenancy Ticket 2 - #1813 (#1821) 
* Work on multitenancy

* Second ticket started

* More multitenancy work

* Work on tenancy security

* Work on multitenancy

* Test fixes

* Add docs

* cs tweak

* Multitenancy fixes

* Add debug log

* Fix build

* Add headers

* Add partition selection interceptor hook

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Account for review comments

* Resolve FIXMES

* Work on tests

* Test fixes

* A bit more cleanup

* Work on multitenancy

* Update hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientExamples.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Allow disabling text modifier indexing

* Add changelog

* Docs fixes

* Address review comment

* Resolve merge conflicts

* Merge master

* Compile fix

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-05-05 15:12:15 -04:00
James Agnew 35c2b7a2c1
Allow disabling text modifier indexing (#1831) 
* Allow disabling text modifier indexing

* Add changelog

* Address review comment

* Resolve merge conflicts
 2020-05-05 12:16:55 -04:00
James Agnew dada217966
Clean up hash code calculation (#1830) 
* Clean up hash code calculation

* Test fixes

* Test fix

* Test fixes

* Compile fix

* Test fix
 2020-05-05 11:11:24 -04:00
Tadgh 8f8a8a3dc2 Merge branch 'master' into date-match-bug 2020-04-29 16:17:50 -07:00
ianmarshall 3e49e5615f Fixing merge conflicts after merge from Master. 2020-04-25 22:14:55 -04:00
ianmarshall dd749791db Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
 2020-04-24 16:55:45 -04:00
ianmarshall 0e45db0ba9 More cleanup and test fixes. 2020-04-24 16:23:59 -04:00
ianmarshall 197bf2b6a8 Further refinements and test fixes. 2020-04-23 23:21:45 -04:00
jamesagnew c7de85339c Work on review comments 2020-04-21 20:18:06 -04:00
jamesagnew bbab016ca6 Rename config 2020-04-20 12:38:04 -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
jamesagnew 25cdbb15c2 Work on multitenancy 2020-04-16 15:33:48 -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 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
jamesagnew 982b54df57 Work on multitenancy 2020-04-13 11:50:49 -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
jamesagnew 7c6024fa14 More work on subscriptions 2020-04-03 07:43:21 -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
jamesagnew a5257f0fa8 Add new indexing extractor method 2020-03-19 20:22:30 -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
Tadgh 4777d75e6b Merge branch 'master' into bugfix/1752-support-chained-parameters-inside-reverse-chained-parameter 2020-03-13 18:40:11 -07:00
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
Tadgh 59d1603597 Some variable renaming. Adds some questions. 2020-03-09 13:51:47 -07:00
jamesagnew 202b9c9a51 License header 2020-03-08 07:23:57 -04:00
Tadgh aca4bcfaad Minor refactoring for readability 2020-03-06 14:22:31 -08:00
Ken Stevens ccd983ab42 review feedback: code improvement 2020-03-03 13:46:23 -05:00
Ken Stevens 705735b9c0 review feedback: javadoc 2020-03-03 13:29:10 -05:00
Ken Stevens 4e1be80525 fixme 2020-03-02 21:39:28 -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
Gary Graham b1d7072c42 Add precision checker for ordinal date returning on DateRangeParam 2020-02-26 22:22:42 -05:00
Gary Graham f86a4c9fa1 Add date ordinals to subscription matching checker 2020-02-26 17:05:23 -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 a1b6e37395 Fix bug with Period bounds not counting as first value 2020-02-25 17:03:50 -05:00
Gary Graham 3ec772b527 rework ResourceIndexedSearchParamDate constructor to support incoming string values 2020-02-25 14:06:36 -05:00
James Agnew 60f16dd91d
Update to 4.3.x core JAR (#1715) 
* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Start working on converter

* Account for compile errors

* Test fix

* Work no validator

* Work on getting core working

* Add some test coverage

* Many test fixes

Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
 2020-02-17 14:28:29 -05:00
jamesagnew ddc7b601ee Version bump to 4.3.0-SNAPSHOT 2020-02-16 19:23:22 -05:00
jamesagnew 4fd80cfca7 Bump to 4.2.0 2020-02-16 19:00:15 -05:00
Ken Stevens 63f2f38689 reinstate near param count validation 2020-02-02 21:21:37 -05:00
Ken Stevens c10d44327c fix in-memory matcher 2020-02-02 17:52:09 -05:00
Ken Stevens decb47dfc2 remove unused block 2020-02-02 16:56:25 -05:00
Ken Stevens 74948737a7 pre-review cleanup 2020-02-01 20:18:42 -05:00
Ken Stevens fb1eb7ca8f parking wip 2020-02-01 13:58:27 -05:00
Ken Stevens 2bc3181218 ensure in-memory matching location search for Dstu3 falls back to a db search 2020-01-25 13:30:26 -05:00
Ken Stevens 2c53468177 fix test 2020-01-24 21:11:37 -05:00
Ken Stevens c87f8e0f4a tested near anti-meridian 2020-01-24 18:55:32 -05:00
Ken Stevens 72ccd76ed0 prepping for antimeridian test 2020-01-24 14:37:28 -05:00
Ken Stevens 39c7642d8c fix test 2020-01-24 09:27:20 -05:00
Ken Stevens b465a7b781 final cleanup 2020-01-23 19:20:51 -05:00
Ken Stevens 01bc941f5f Optimize imports 2020-01-23 19:15:30 -05:00
Ken Stevens e6f5af01ed convert degrees to kilometers for near calculation 2020-01-22 16:55:19 -05:00
Ken Stevens 9413e8f198 r4 works. But distance calculation still needs to be fixed. 2020-01-22 11:59:03 -05:00
Ken Stevens 6cebb56f13 testing complete. Now just need pre-review cleanup. 2020-01-21 17:06:19 -05:00
Ken Stevens 3cb9a9f4a2 added asserts 2020-01-21 15:45:41 -05:00
Ken Stevens b463929c28 parse nearDistance into a special search parameter field so it's available when we're adding the near parameter 2020-01-21 15:38:25 -05:00
Ken Stevens 299e1e35e1 removed coordextractor and moved to token (looks cleaner and more in line with how the other ones are parsed) 2020-01-21 11:06:40 -05:00
Ken Stevens dd137a0a30 Coord extraction implemented 2020-01-21 10:17:49 -05:00
James Agnew c0e929dacb
Copy identifiers to placeholder resources (#1675) 
* Copy identifiers to placeholder resources

* Add tests

* Maven cleanup

* Still messing around with azure

* Adding to logging

* More azure work

* One more attempt

* More messing around with azure

* Test fix

* Another caching attempt

* More work on azure pipeline

* Fix pipeline file

* Keep working on pipeline

* More work on azure

* More azure

* More azure work

* More azure
 2020-01-21 06:09:06 +09:00
James Agnew 1390ea3c06
Update FHIR R5 structures to 4.2.0 version (#1665) 
* Work on upgrading core

* Work on R5 updates

* Work on core updates

* Test fix

* Update model version properties file for R5

* Bump core version

* Test fixes

* Add 4.2.0-SNAPSHOT version to versions page in docs
 2020-01-14 10:27:01 +08:00
jamesagnew 9c7f5e1b9b License header updates 2020-01-12 10:15:08 -05:00
Ken Stevens 2d0c30f7a2 fix test 2019-12-20 15:46:55 -05:00
Ken Stevens 625f967688 ready for review 2019-12-20 14:56:44 -05:00
James Agnew 0a21ab6941 Use datasource for migrator 2019-12-18 14:23:46 -05:00
Ken Stevens 993d8220d1 review feedback 2019-12-02 11:18:52 -05:00
Ken Stevens f92c2bb5f9 ensure only one @PostConstruct method to make order explicit 2019-11-29 11:46:03 -05:00
Ken Stevens 37eef4e3e4 rename schedule interface methods 2019-11-29 11:04:35 -05:00
Ken Stevens 8c4ffc024d Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-11-25 16:40:40 -05:00
James Agnew 27749f4e23
Support chained HAS (#1605) 2019-11-24 06:29:56 +01:00
James Agnew 51b608188b
Some CI surefire improvements (#1602) 
* Some CI surefire improvements

* Build tweak

* More tweak

* Update azure-pipelines.yml for Azure Pipelines

* Update azure-pipelines.yml for Azure Pipelines

* One more CI attempt

* Update azure-pipelines.yml for Azure Pipelines

* Tweak command line

* Another build test fixc

* More build cleanup
 2019-11-23 19:51:02 +01:00
James Agnew a2f77b23d2
Fix #1583 - Index local refs in canonical types (#1593) 
* Fix #1583 - Index local refs in canonical types

* Add fix to pre-expansion

* Test fix

* Rework ID handling

* Test fixes

* Fix test
 2019-11-23 16:32:37 +01:00
Ken Stevens 6f9cd56c81 moved scheduler up to hapi-server 2019-11-20 14:30:24 -05:00
Ken Stevens 8fca468e1f remove boolean from scheduling API 2019-11-19 10:13:22 -05:00
James Agnew 74159dcb26
Work on refactoring how PIDs work (#1580) 
* Start work on refactoring how PIDs work

* Some test fixes

* Test fixes

* Test fixes

* Restore accidentally deleted line

* One more tweak

* Rework resource link extraction

* Test fix

* Split out transaction processor

* Updates

* Test fix

* Test fixes

* Test fixes

* Clean up LGTM warning

* Fix compile failure

* One more test fix

* Fix LGTM issue

* Add spot for metadata

* Add test logging

* Remove testing code

* More test logging

* Add some test logging

* Attempty to fix intermittent test failure

* Improve exception tracking

* Work on simplifying search param registry

* Fix compile

* Fix compile errors

* Fix two test bugs
 2019-11-17 14:35:19 -05:00
Ken Stevens f11d939131 oops 2019-11-14 14:55:02 -05:00
Ken Stevens 25c094e38a skip trying to populate resources in search result bundle if no resources were found 2019-11-14 14:55:02 -05:00
James Agnew 497a96ae68 Version bump for next round of development 2019-11-12 22:09:21 -05:00
jamesagnew f99ad981b5 Version bump to 4.1.0 2019-11-12 16:08:20 -05:00
jamesagnew 9c93d5d7f7 Test fixes 2019-11-04 07:04:26 -05:00
James Agnew 78a323f105 Test fixes 2019-11-03 21:20:22 -05:00
James Agnew 9672dac827 Fir build 2019-11-03 19:15:53 -05:00
James Agnew f481e11ad5 Update migration tasks 2019-11-03 18:49:47 -05:00
James Agnew c3c67966fd Test fix 2019-11-03 14:37:14 -05:00
James Agnew d937889878 Resolve startup issue 2019-11-03 14:08:59 -05:00