2210 Commits

Author SHA1 Message Date
Frank Tao
ce1caee9fa
Feature 2020 10 28 reverse chain (#2160)
* Added test cases for multiple '_has'

* Fixed composite search for the new SearchBuilder

* Added more test cases
2020-11-05 05:27:11 -05:00
jamesagnew
53c23b8d9b Add method to stringutil 2020-10-27 11:29:16 -04:00
James Agnew
72294fc0a0
Suport typeFilter parameter for bulk export (#2147)
* Cleanup

* Fix tests

* Work on bulk export

* Work on export

* Test fixes

* Add changelog

* Address review comments

* Address review comments
2020-10-26 12:28:07 -04:00
James Agnew
8000d2d0cf
SQL Join Rework (#2086)
* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* added the other six index links

* trying different annotations

* Start testing

* Update resources on package install

* Add changelog

* Join rework

* CLean up SQL builder

* Add docs

* SP rework

* Join work

* Work on params

* Work on refactor

* Work on chains

* Work on joins

* Rework queries

* Work on queries

* Many more tests passing

* Refs test

* Work on sorting

* Work on tests

* More joins work

* Work on tests

* Work on queries

* Tests passing

* More test fixes

* Test fixes

* Work on SQL

* Tests passing

* Add some tests

* Add some tests

* License headers

* Use entity manager to get datasourcd

* One more fix

* Model cleanup

* Ongoing work

* Fixes

* Fixes

* Work on joins

* Ongoing fixes

* Merge conflict

* Cleanup

* clean up unused fields

* Work on join

* COmpile fix

* Rework querying

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java

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

* Address review comments

* Resolve fixmes

* Test fix

* Test fixes

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-10-26 05:24:26 -04:00
Ken Stevens
3b91873b7c
delete expunge (#2131)
Added delete _expunge=true
2020-10-20 17:21:50 -04:00
jamesagnew
3738297354 Test fix 2020-10-19 20:13:31 -04:00
jamesagnew
a25aa37e6a Update to #1607 2020-10-16 14:52:40 -04:00
jamesagnew
7903b2b577 License headers 2020-10-13 11:43:09 -04:00
Tuomo Ala-Vannesluoma
1435540320
Improve synchronous searching by providing offset & limit support (#2059)
* Improve synchronous searching by providing offset & limit support

Add support for offset querying which leverages paging at the query level
Add configuration for search default page size and search maximum page size
If using offset, always use synchronous searching to avoid extra database insert/update etc.
When using offset, only calculate count if it's wanted
Validate params closer to provider and handle size if search returned "all" (or last)

* Review and test fixes

Comment _offset as nonstandard parameter
Make synchronous search always count the total value (for now)
Fix issue with FulltextSearchSvcImpl mutating param map
Dirty fix for BaseJpaTest (not sure how to fix the including resources issue)

* Remove temporary count querying fix for synchronous loads

* Fix offsetting of everything operations, do not drop zero offset

* Fix jpa test default and maximum page size, add some fixmes to tests before resolved

* Ignore one failing test, fix others

* Fix Dereferenced variable may be null

* Fix everything paging in R4 by adding DISTINCT if synchronous load is used

Also fix assertion of size when hitting fetchSizeDefaultMaximum

* Add documentation about offset annotation and paging

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-10-12 17:42:03 -04:00
Josh Collins
844624b6dd
RDF Support in HAPI FHIR (#2118)
* RDF Support in HAPI FHIR

* Ability to read/write FHIR resources as RDF (turtle serialization)
* Test suite to test roundtrip-ability of RDF parser

* Add null checks to appease LGTM

* Correct null check logic
2020-10-12 17:16:00 -04:00
Oliver Egger
8294b8ddb6
add namespace, prefix for attributes (xml:lang) (#2112) 2020-10-11 15:25:37 -04:00
abrsystematic
cad3ba5a66
Fix gettimezone performanceissue (#1607)
* [(release_3_7_SSE)] cache timezone since timezone.gettimezone is static synchronized and performs poorly

* [(fixgettimezoneperformanceissue)] fiximport
2020-10-09 11:51:50 -04:00
James Agnew
2134d40f1c
Account for timezones in lastUpdated search (#2113)
* Add test

* Fix

* Add changelog

* Test fixes

* Test fix

* Test fixes

* Resolve fixme

* Test fixes

* Remove debug logs

* Try to get CI tests passing again
2020-10-09 07:52:46 -04:00
ianmarshall
8e7b4e8437 Changes per code review. 2020-09-29 21:05:28 -04:00
IanMMarshall
26688aac65
Update hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-09-29 12:11:56 -04:00
ianmarshall
47244c54dc Merge remote-tracking branch 'origin/feature_2020_09_02_term_multi_version_support' into im_20200728_term_multi_version_support
# Conflicts:
#	hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
2020-09-25 09:10:07 -04:00
ianmarshall
6f9874468a Merge remote-tracking branch 'origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-25 08:54:17 -04:00
ianmarshall
ceb5ec6384 Use canonical identifiers for code systems rather than specifying version separately. 2020-09-23 16:42:29 -04:00
ianmarshall
4216cee8c6 Added and enhanced tests plus fixes arising from tests. 2020-09-22 14:44:32 -04:00
ianmarshall
f9f8bf6515 Merge remote-tracking branch 'origin/master' into im_20200728_term_multi_version_support 2020-09-20 22:02:08 -04:00
ianmarshall
302bbca8fd Changes to support multi-versioning in ValueSet $expand operation. 2020-09-20 22:01:21 -04:00
Tadgh
74bba9dbcc Rename to ResourceOperationMessage 2020-09-15 18:57:55 -04:00
ianmarshall
3add1320b7 Merge remote-tracking branch 'remotes/origin/im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:52:02 -04:00
ianmarshall
539ef63fc0 Merge branch 'im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:24:47 -04:00
Tadgh
ea64bea1b0 Refactor to use concrete class instead of parent 2020-09-15 15:27:21 -04:00
ianmarshall
7b15f85fa1 Merge remote-tracking branch 'remotes/origin/feature_20200830_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:35:31 -04:00
ianmarshall
087c9e3c3b Merge remote-tracking branch 'remotes/origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:34:11 -04:00
Tadgh
28a9a53917 Rework to keep several things in subscription 2020-09-10 16:05:56 -04:00
ianmarshall
d00db11586 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-09-09 17:38:24 -04:00
Frank Tao
5410042643 Multi-version supported for ConceptMap $translate operation 2020-09-07 10:43:58 -04:00
Frank Tao
1ecec0abc9 Fixed duplicate ConceptMap URL only 2020-09-06 15:23:26 -04:00
jamesagnew
2d7c808326 Localizer refactor 2020-09-05 15:47:10 -04:00
ianmarshall
5f005120c9 Initial changes to support multi-version ValueSets 2020-09-03 22:36:15 -04:00
ianmarshall
1c55d87b10 Problem found in LOINC loader. 2020-08-30 17:11:48 -04:00
ianmarshall
dc786eaff9 Refine model for storing multiple code versions. 2020-08-21 10:16:10 -04:00
ianmarshall
2126c5c556 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-18 11:15:09 -04:00
James Agnew
eab828f47a
Add transactionbuilder (#2041)
* Add transactionbuilder

* Add changelog

* Add creates
2020-08-17 07:47:40 -04:00
ianmarshall
bd94ff96cc Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-16 21:38:41 -04:00
jamesagnew
92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew
5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
jamesagnew
90ebaf8549 Add one more test for #2023 2020-08-11 08:54:03 -04:00
James Agnew
e61b39fc30
Force a flush of the SearchParameter cache sooner when SPs change (#2030)
* Force a flush of the SearchParameter cache sooner when SPs change

* Add changelog

* Test fixes
2020-08-09 19:30:59 -04:00
ianmarshall
d39348d7bd Initial changes to support multiple versions for code system. 2020-08-09 11:49:04 -04:00
James Agnew
0de0b88aa0
Fix TestpageOverlay XSS Vulnerability (#2027)
* Resolve XSS vulnerability

* Add changelog
2020-08-09 07:06:11 -04:00
James Agnew
5d9d4070fb
Fix an issue with binary storage not updating correctly if a retry (#2014)
interceptor is present
2020-08-05 09:14:40 -04:00
jamesagnew
a35c97e13d Add utility method to XmlUtil 2020-07-26 17:54:45 -04:00
christian ohr
1c27726055
#1817: fix problem with missing resource references when extensions are used (#1848)
Co-authored-by: Christian Ohr <christian.ohr@icw.de>
2020-07-21 05:36:25 -04:00
James Agnew
5db90d3e6e
Address issues when importing US Core (#1986)
* Work on US Core import

* Work on US Core

* Resolve issues with US Core import

* Test fix
2020-07-17 15:28:16 -04:00
Ken Stevens
ebd6ca4b64
Empi 3 ruleset version (#1978)
* add rule version

* add rule version

* Rough in model for Golden Record.

* Test Link Rule Version

* add eid match boolean

* added new fields to EmpiLink to provide more information about how the link was created

* add logging to check an edge case

* all tests pass

* wip with failing tests

* tests pass

* FIXME

* optimize imports

* test score in provider output

* FIXME

* FIXME

* Fix jpa test app context

* fix migration string length

* review feedback param name

* review feedback javadoc

* review feedback javadoc

* bean config reorganization for cdr

* add more tests
2020-07-17 08:31:15 -04:00
jamesagnew
f5222f3105 License headeer update 2020-07-17 08:27:10 -04:00