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3052 Commits

Author SHA1 Message Date
Kevin Hartmann 26a385a595 Merge remote-tracking branch 'origin/master' into kh-20200222-search-list 2021-02-24 10:29:38 -05:00
Kevin Hartmann 1eab2caf9f Added _list as a valid parameter in MatchUrlService 
Wrote tests for and/or/both processing in FhirResourceDaoSearchListTest.
 2021-02-24 10:27:22 -05:00
Patrick Werner cf1f2f27db
added nullchecks to prevent NPE (#2417) 
* added nullchecks to prevent NPE
fixes #2171

* Add test from #2171 and changelog

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-02-24 10:09:04 -05:00
Kevin Hartmann 62bfa2cdbc Merge remote-tracking branch 'origin/master' into kh-20200222-search-list 2021-02-24 09:20:07 -05:00
Ken Stevens fb884f9f15 test infrastructure 2021-02-23 11:32:02 -05:00
Ken Stevens 330cafa83e initial implementation 2021-02-23 11:25:56 -05:00
James Agnew b108e43600
Allow partition date for non-partitionable resources (#2407) 
* Allow partition date for searchparam resources

* Cleanup

* Test fix

* Documentation update

* Docs tweak
 2021-02-22 20:49:09 -05:00
Ken Stevens 24efa97b17 begin with failing test 2021-02-22 11:37:32 -05:00
James Agnew 3eda19c65a
Version bump (#2400) 
* Version bump

* Docs changes

* Docs tweaks

* Docs tweak

* Spelling fixes

* Docs tweaks
 2021-02-18 11:07:49 -05:00
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
James Agnew 65ac0e80fb
Add CapabilityStatement customizer (#2387) 
* Add CapabilityStatement customizer

* Fix javadocs
 2021-02-15 14:58:34 -05:00
ianmarshall 88d820bf38 Make LOINC Top2000* files optional in terminology loader. 2021-02-11 09:12:08 -05:00
ianmarshall a383cb94fc Make LOINC Top2000* files optional in terminology loader. 2021-02-10 22:30:19 -05:00
Tadgh 2759db2a31
Merge pull request #2371 from hapifhir/config-error-on-url-protocol 
Throw ConfigurationError if you attempt to provide a Rest URL that contains a protocol.
 2021-02-09 20:25:14 -05:00
Tadgh 64878c23d3 Update text, add changelog 2021-02-09 19:03:09 -05:00
Tadgh 2e3712357f Throw configueration error when somebody tries to put a protocol in the rest URL 2021-02-09 18:59:11 -05:00
Ken Stevens 7f127f75f9
validate that Terminology beans are proxied so that @Transactional annotated methods are run within transactions (#2362) 2021-02-08 13:11:29 -05:00
Hanan Awwad 6384067e50
Customize concept display in value set expansion (#2282) 
* fix issue #2280

* revert the indentation back.

* revert-back untouched changes.
 2021-02-07 12:29:05 -05:00
James Agnew 92669b29da
Add elastic test (#2348) 
* Add elastic test

* Rework

* Add test
 2021-02-04 11:04:27 -05:00
James Agnew 0f31d106e5
Allow empty request details in JPA (#2343) 
* Allow empty request details in JPA

* Test fixes
 2021-02-02 11:00:14 -05:00
Mike G f61cb163ae refactor and modify for prefix and suffix 2021-02-01 12:11:11 -05:00
Frank Tao 1d835d82d6
Fixed Ucum Conversion NullPointerException issue (#2331) 
* Fixed Ucum Conversion NullPointerException issue

* Revoke:save value to the original table if it can't be normalized
 2021-01-30 19:30:12 -05:00
Ken Stevens ba63f65115
changed $expand filter matching from left-match to contains match (#2327) 
* changed $expand filter matching from left-match to contains match

* changelog

* pure substring match is too generous (a regression test checked for that).  Tightened the match up to word boundaries.

* CLean up to avoid intermittent test failure

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-01-29 12:37:54 -05:00
jamesagnew 8854f344b3 Add test 2021-01-28 16:22:36 -05:00
Nick Goupinets 3be480c9f0 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-27 16:47:40 -05:00
James Agnew 909d9f742c
Enable Auto-reference versions in JPA (#2323) 
* Automatic reference versions

* Auto reference versions

* resolve fixmes

* Add changelog

* Test fixes

* Test fixes

* Resolve fixmes

* Work on versioning

* Add support for _includes

* Update headers

* Change visibility

* One more tweak

* One more API tweak

* Fixes

* Account for review comments

* Fix errorprone reported issue

* Test fix

* Test fixes

* Test fixes
 2021-01-27 14:49:10 -05:00
Nick Goupinets 04db4ed229 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-26 09:18:20 -05:00
Ken Stevens 86ea0d60ef
reduce _count to the maximum page size rather than throwing an error. (#2319) 
* reduce _count to the maximum page size rather than throwing an error.

Also when setting the paging provider on a restful server, automatically set the default page size and max page sized of the restful server from the paging provider.

* reword log message

* fixing this paging issue has uncovered all sorts of interesting things, including this long hidden bug!

* fix tests in sub-optimal way

* fix NPE

* fix test

* fixed a couple of bugs in SearchCoordinatorSvcImpl that surfaced when i added a default page size to RestfulServer
 2021-01-25 08:19:29 -05:00
Frank Tao 1d1ebcf5e8
Improved DateQuery and removed 'OR' in the SQL (#2302) 
* improved DateQuery and removed 'OR' in the SQL

* improved DateQuery and removed 'OR' in the SQL

* Date handling cleanup (#2316)

* Date handling cleanup

* Fix codecov

* One more fix

* Fix tests

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2021-01-23 17:53:18 -05:00
Ken Stevens 749934d5f1
fixed name text indexing (#2309) 
* fixed name text indexing

* fixed name text indexing
 2021-01-22 15:39:26 -05:00
dependabot[bot] feff734736
Bump jaxb-runtime from 2.3.1 to 3.0.0 (#2289) 
* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

Signed-off-by: dependabot[bot] <support@github.com>

* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

Signed-off-by: dependabot[bot] <support@github.com>

* Add jakarta bindings

* Dependency cleanup

* More depndency cleanup

* Work on deps

* Replace transaction annotation

* Cleanup

* Another fix

* Build fix

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-01-22 11:24:23 -05:00
Nick cfc798cb2b Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-22 09:45:04 -05:00
Frank Tao 341eb404e6
Improved the performance for multiple _has by exclude previous pids (#2304) 
* Improved the performance for multiple _has by exclude prev pids

* Removed extra import

* Added test case for SQL contains RES_ID NOT IN ()
 2021-01-21 14:42:10 -05:00
Nick ed5727d795 Fixed missing imports 2021-01-21 10:04:16 -05:00
jamesagnew 7cf41a7e85 One more build fix (grrrrrr) 2021-01-21 09:24:42 -05:00
Nick 82e52750e7 Merge branch 'master' into ng_20201218_survivorship_poc 2021-01-21 09:00:28 -05:00
jamesagnew 078a94f1a6 Fix nonnull annotations 2021-01-21 08:47:44 -05:00
James Agnew 14b0688f69
Bump core version to 5.2.16 (#2308) 
* Bump core library version

* Test fix

* Build fixes

* Some test fixes

* One more bit of docs

* Build fix

* Test fix

* Test fix

* Docs fix
 2021-01-21 05:30:23 -05:00
Tadgh 3d5255d88c Bump ES version running in tests 2021-01-20 11:34:51 -05:00
Nick f5e2086cfd Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-19 09:35:31 -05:00
Tadgh edbc789a93 Add annotation to skip test classes which require docker if it is not found on the host 2021-01-18 21:49:43 -05:00
Tadgh 7c6c64bfb7 Remove dead import 2021-01-18 15:53:49 -05:00
Tadgh 5b2530a948 Remove dead beans 2021-01-18 14:55:33 -05:00
Tadgh 8f72970063 Add bean to config 2021-01-18 14:09:38 -05:00
Nick b00f47ef81 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-18 09:25:58 -05:00
James Agnew 66e1a51e01
Add validation options to RepositoryValidingInterceptor (#2294) 
* Add repository validating interceptor outcome to response

* Add a doc

* Add a test and some docs

* Rework validation
 2021-01-17 16:40:32 -05:00
dependabot[bot] 391a6d1a3f
Bump ph-schematron from 5.2.0 to 5.6.5 (#2184) 
* Bump ph-schematron from 5.2.0 to 5.6.5

Bumps [ph-schematron](https://github.com/phax/ph-schematron) from 5.2.0 to 5.6.5.
- [Release notes](https://github.com/phax/ph-schematron/releases)
- [Commits](https://github.com/phax/ph-schematron/compare/ph-schematron-parent-pom-5.2.0...ph-schematron-parent-pom-5.6.5)

Signed-off-by: dependabot[bot] <support@github.com>

* Fix compile error

* Build fix

* Add test logging

* Test fix

* Resolve classpath duplicates

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-01-17 14:27:26 -05:00
James Agnew 29cf20aac3
Add repo validation outcome to response (#2293) 
* Add repository validating interceptor outcome to response

* Add a doc

* Add a test and some docs
 2021-01-17 12:50:13 -05:00
vedion 99b646eed7
Mapping noExtensibleWarnings and noBindingMsgSuppressed between FhirInstanceValidator and InstanceValidator (#2054) 
Co-authored-by: ahn <anders.havn@systematic.com>
 2021-01-17 09:21:08 -05:00
James Agnew 1dc4fb2206
Make quantity indexes use double datatype (#2290) 
* Make quantity indexes use double datatype

* Add changelog

* Test fixes

* Test fixes

* Disable test
 2021-01-16 18:44:15 -05:00