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626 Commits

Author SHA1 Message Date
jamesagnew 1576227fc8 Credit for #2194 2021-03-26 09:19:02 -04:00
Nick Goupinets 644885e91a Fixed typo in the docs 2021-03-25 18:32:08 -04:00
Nick Goupinets 05c3ca2512 Merge branch 'master' into 2478_add_extension_mdm_matcher 2021-03-25 12:22:23 -04:00
James Agnew 8352bc9c01
Correct the path to the select2 library in the testpage overlay (#2505) 
* Correct the path to the select2 library in the testpage overlay

* Add changelog
 2021-03-25 10:52:15 -04:00
long 6aab327612 modified documentation wording 2021-03-23 14:27:17 -06:00
Nick Goupinets de0399da23 Merge branch 'master' into 2478_add_extension_mdm_matcher 2021-03-22 09:34:32 -04:00
James Agnew dc41d5ad61
Add terminology mapping and display population interceptors (#2488) 
* Start work on code mapping interceptors

* Work on generation

* Add terminology mapping and display population interceptors

* Add changelog

* License header updates

* Test fixes

* Fix typo

* Interceptor fixes

* License header update

* Test fixes

* Mapping fixes

* Version bump

* License header updates

* Add null tests

* Add null guard

* Intermittent fix
 2021-03-21 12:03:57 -04:00
long 989e9e7903 refactored terserUtil, added equals function in ExtensionUtil 2021-03-17 13:02:59 -06:00
James Agnew d857048207
Preserve meta values in stored resources (#2481) 
* Fix #1731

* Test fix

* Test fixes

* Avoid intermittent failure
 2021-03-17 09:23:22 -04:00
Kunjan Patel bdee1f1269
Update points.json for adding a point in atlas (#2482) 2021-03-17 05:50:07 -04:00
Tadgh b191f1da2b
Merge pull request #2480 from hapifhir/issue-2479-bad-packages 
Have CreatePackageCommand automatically add fhirVersions based on --fhir-version flag
 2021-03-16 18:00:27 -04:00
michelgleeson 0a6c61372c
Parameterize term valueset concept view dao (#2477) 
* Generic the list type to accomidate different substring queries

* special subquery for Oracle

* change the conceptview dao depending on dialect

* address review comments

* remove generics

* no longer inherits

* copy paste from non Oracle version

* dang copy pasters

* changelog

Co-authored-by: Mike G <michel.gleeson@gmail.com>
 2021-03-16 16:26:19 -04:00
Tadgh c3e6de3aff Add changelog 2021-03-16 13:47:29 -04:00
Nick Goupinets 744adb2d08 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-15 10:32:04 -04:00
James Agnew 2e7eb972ff
Avoid NPE in ResourceVersionConflictResolutionStrategy for system request (#2471) 
* Avoid NPE in ResourceVersionConflictResolutionStrategy for system
request

* Add changelog
 2021-03-12 19:23:49 -05:00
Nick Goupinets e188a95d66 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-12 16:17:25 -05:00
James Agnew 0ad57c51bb
Fix resource reindexing on partitioned seerver (#2468) 
* Fix resource reindexing on partitioned seerver

* Add changelog

* Test fix

* Test fix

* Tets fix

* Test fix
 2021-03-12 14:14:39 -05:00
Nick Goupinets f9f0b2705d Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-12 10:30:36 -05:00
Nick Goupinets 8b8bbcc91f Refactored based on the code review 2021-03-11 17:14:01 -05:00
James Agnew 2633cbd141
Improve error message for invalid date param (#2466) 
* Improve error message for invalid date param

* Add changelog

* Test fixes
 2021-03-11 14:23:02 -05:00
Nick Goupinets 8c77882da0 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-11 09:48:39 -05:00
Tadgh 75f756b49f Add changelog 2021-03-10 15:00:54 -05:00
Tadgh b7398cb6f2 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-10 10:33:24 -05:00
Tadgh e26d757ba3 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-09 22:54:24 -05:00
James Agnew 807d9d53f0
Improve performance for large transactions (#2462) 
* Performance tweaks

* Work on processing speed

* Disable no longer relevant tests

* Work on performance

* Work on tests

* Work on large transaction performance

* Add changelog

* Perf tweaks

* Test fixes

* Resolve FIXME

* Fixes

* Test cleanup

* Fix broken changelog entry
 2021-03-09 18:16:02 -05:00
Nick Goupinets 9056c95865 Updated docs 2021-03-09 16:41:50 -05:00
Nick Goupinets 02eae95c85 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-09 14:06:33 -05:00
James Agnew be50a46d76
Tweaks to contained searches (#2461) 
* Tweaks to contained searches

* Add changelog

* Build fix
 2021-03-09 11:51:30 -05:00
Frank Tao bf8e890a0c
Supported contained resource search (#2441) 
* POC for indexing on contained resource - test case may failed

* Test contained url

* Add a spt to handle contained flag

* Added search option for contained resource

* Impl contained resource search

* fixed typo

* Reworked on creating index based on the review comments

* Added changelog

* Added more test cases

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-03-09 06:50:23 -05:00
Diederik Muylwyk 6cc8a5ce4d
Fix HasParam#doGetQueryParameterQualifier() (#2460) 
* Fix HasParam#doGetQueryParameterQualifier(); add changelog entry

* Fix bad test in SearchParameterMapTest
 2021-03-09 06:28:40 -05:00
Nick Goupinets ab4f02b2bd Added changelog 2021-03-08 18:02:40 -05:00
James Agnew 62df320ceb
Avoid a crash reading an unknown ID on partitioned server (#2451) 
* Avoid a crash reading an unknown ID on partitioned server. Fix #1953.

* Attempt 2 at fixing #1953
 2021-03-07 10:16:30 -05:00
Diederik Muylwyk 11ee6dedd3 Address CVE-2020-27223; bumped minor version of Jetty in root POM 2021-03-06 16:33:05 -05:00
Diederik Muylwyk 6035f78ddf Fix typos 2021-03-05 18:46:42 -05:00
Diederik Muylwyk 35645999d7 Add changelog entries. 2021-03-04 19:55:39 -05:00
Tadgh f5372c9f07 Fix typo 2021-03-04 16:53:52 -05:00
Tadgh 6129194353 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-04 16:53:20 -05:00
Tadgh 2f1518344b Add changelogs, add patientbulkredaer implementation 2021-03-04 16:53:05 -05:00
Diederik Muylwyk 8dcac3e8b7
Improved generic client docs to remind of client.search.byUrl for params like _has. (#2440) 2021-03-03 18:34:18 -05:00
James Agnew db44244405
Fix #2426 - Include modifiers in generic search URLs for map (#2428) 2021-02-28 10:33:43 -05:00
Tadgh 74066a81b6
Merge pull request #2420 from hapifhir/issue-2401-add-support-for-group-id-export 
Issue 2401 add support for group id export
 2021-02-26 10:23:42 -05:00
Ken Stevens 7d769e3b05
Issue 2332 create via put for implementationguide that references some placeholders (#2423) 
* begin with failing test

* fixed.  test passes.

* documentation and changelog

* added ConceptMap

* review feedback
 2021-02-26 09:44:48 -05:00
Tadgh 1663e367a6 Address review comments 2021-02-25 16:23:36 -05:00
Tadgh 3937d2ef01 Remove some dead code 2021-02-24 15:57:55 -05:00
Tadgh 8e45a84927 Add changelog 2021-02-24 15:28:52 -05:00
Kevin Hartmann 3b60034a08 Added Changelog entry 2021-02-24 15:25:36 -05:00
michaelabuckley ad6431b24c
Merge pull request #2418 from hapifhir/add-changelog-for-mdm-update 
Add MDM FHIRPath Changelog
 2021-02-24 13:52:22 -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
Ken Stevens 30905aeba7 Merge remote-tracking branch 'origin/master' into issue-2401-add-support-for-group-id-export 2021-02-24 09:38:59 -05:00
Tadgh 66b59ae327 Update issue number 2021-02-24 09:22:10 -05:00
Tadgh 5ee7793ac4 Add MDM Changelog 2021-02-24 09:20:45 -05:00
Tadgh 29eabbd4f0 Add skeleton 2021-02-23 18:42:41 -05:00
Tadgh ecacef0498 Add bulk export md file 2021-02-23 18:39:25 -05:00
Tadgh c92f302d41
Merge pull request #2410 from hapifhir/2409-support-fhirpath-in-field-matchers 
Support FHIRPath in field matchers if present
 2021-02-23 09:48:14 -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
Tadgh 18b61f21d0 re-add only relevant code 2021-02-22 18:23:03 -05:00
Jens Kristian Villadsen 65c9f5fbf8
Update repository_validating_interceptor.md (#2368) 
Refined the wording on the repo interceptor
 2021-02-22 07:28:49 -05:00
Nick Goupinets 3541249a5e
Fixed docs (#2405) 2021-02-22 05:42:59 -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
Kevin Dougan SmileCDR aa05667761
Clarified partitioning docs. (#2396) 
* Clarified partitioning docs.

* Added some more ResourceTypes to the list of non-partitioned ones according to the authoritative list found in RequestPartitionHelperSvc.java.
 2021-02-17 08:32:37 -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 7413584bff Make LOINC Top2000* files optional in terminology loader. 2021-02-10 22:35:15 -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
James Agnew dd7a156d19
Call startOperation for paging requests (#2370) 2021-02-09 15:47:11 -05:00
jamesagnew 028ef1b088 Credit for #2365 2021-02-08 09:15:04 -05:00
jamesagnew da847ad08a Credit for #2282 2021-02-07 12:32:41 -05:00
James Agnew c69d741b43
Add CapbilityStatement customizing hook (#2364) 
* Add CapbilityStatement customizing hook

* Add additional method

* Interceptor service tweak
 2021-02-07 09:12:09 -05:00
Michael Buckley 42afcebd11 Merge in ca.uhn.fhir.rest.param.DateParamTest and add changelog. 2021-02-05 09:57:10 -05:00
Kevin Dougan SmileCDR dd13827290
Added changelog entry for -measure operation. (#2347) 2021-02-03 14:01:20 -05:00
jamesagnew c0142a67b1 Credit for #2340 2021-02-02 14:27:42 -05:00
jamesagnew 8c5b54bf54 Fix broken changelog 2021-01-30 19:26:58 -05:00
jamesagnew 5961fde2dd Docs tweak 2021-01-29 16:12:06 -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 589eb3158e Credit for #2310 2021-01-29 11:02:51 -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
jamesagnew c55410e6b6 Add changelog for #2302 2021-01-23 17:54:51 -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
Nick d783229406 updated docs 2021-01-22 13:28:24 -05:00
Nick cfc798cb2b Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-22 09:45:04 -05:00
Tadgh edd9769686 Add documentation fixes for MDM-match 2021-01-22 09:17:51 -05:00
Nick 82e52750e7 Merge branch 'master' into ng_20201218_survivorship_poc 2021-01-21 09:00:28 -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
Nick 4b53ef3920 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-20 14:59:38 -05:00
Tadgh 159128109b Add versionenum value 2021-01-20 10:49:08 -05:00
Nick ae9d4a191f Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-19 11:34:01 -05:00
James Agnew 874b16207f
Bundle.entry.resource.id should not be stripped on POST from client #2297 (#2303) 2021-01-19 11:12:42 -05:00
Nick f5e2086cfd Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-19 09:35:31 -05:00
Tadgh 17d74648de
Merge pull request #2300 from hapifhir/2299-bug-with-bulk-export-bean 
Add bean to config
 2021-01-18 16:53:36 -05:00
Tadgh 141cd14918 Add changelog 2021-01-18 15:04:03 -05:00
ianmarshall 26491f3bc8 Ensure that table indexes are not deleted during DB migration dry-run. 2021-01-18 14:09:06 -05:00
Nick b00f47ef81 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-18 09:25:58 -05:00
jamesagnew 6ff7d579a3 Update changelog 2021-01-17 17:43:42 -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
jamesagnew ae3930f204 Update changelog 2021-01-17 13:30:19 -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