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525 Commits

Author SHA1 Message Date
James Agnew dc627dc019
Add bulk export authorization layer (#2712) 
* Add bulk export authorization layer

* Add docs

* Version bump

* Authorize any

* Add bulk export - all

* Address lgtm issue
 2021-06-06 20:47:43 -04:00
James Agnew a2950324ef
Avoid SQL based transaction dupe check (#2688) 
* Avoid SQL based transaction dupe check

* Add changelog

* Test fixes

* Test fixes
 2021-05-30 20:26:36 -04:00
jamesagnew 8636e4f155 Test fix 2021-05-27 07:30:09 -04:00
Nick Goupinets 2acb3501a5 Removed sout 2021-05-20 16:15:15 -04:00
Nick Goupinets 8a7fc58e91 Fixed primitive field merging 2021-05-20 15:48:00 -04:00
jamesagnew 926bf393d3 Merge branch 'rel_5_4' 2021-05-17 09:10:58 -04:00
Tadgh 424ec2118b Add implementation. Add test. Add changelog 2021-05-11 10:31:29 -04:00
jamesagnew 2068372998 Version bump 2021-05-07 17:43:54 -04:00
jamesagnew 63c4b22cd3 Undo bump 2021-05-07 17:42:50 -04:00
jamesagnew 17e41520a4 Version bump 2021-05-07 17:41:39 -04:00
jamesagnew 5db01f3139 Build fixes 2021-05-03 05:57:45 -04:00
James Agnew 0cea403800
Fix vulnerability warning on maven plugin (#2621) 
* Fix vulnerability warning on maven plugin

* Compile fixes

* Fix bootstrap dep

* Test fix

* Fix tests

* FIx deps
 2021-05-02 12:14:32 -04:00
James Agnew 970a9884f0
Avoid tag definition constraint (#2620) 
* Avoid tag definition constraint failure

* Version bumps

* Add changelog

* Avoid guava issue

* Test fix

* Test fix

* Bump pom
 2021-05-01 17:16:15 -04:00
Nick Goupinets 896c8fbd4f Code review 2021-04-29 17:25:06 -04:00
Nick Goupinets d67537231c Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-29 13:55:48 -04:00
Nick Goupinets d45972abed Added geo accuracy code 2021-04-29 11:46:09 -04:00
Nick Goupinets 4050c42bf4 Treating C addresses as valid 2021-04-28 15:31:34 -04:00
James Agnew 95d7ba6fa8
Streamline Search SQLs (#2576) 
* Streamline SQL queries

* SQL query tidying

* Add changelog

* Test fixes

* Tests passing

* Ongoing work

* Test fixes

* Test fixes

* Build fix

* Cleanup

* Fixes
 2021-04-28 10:29:09 -04:00
Nick Goupinets 21d8cdfefc Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-28 10:16:27 -04:00
Nick Goupinets 418c1aa2c6 Added avc code to the interceptors 2021-04-28 10:15:38 -04:00
Nick Goupinets 7cef07b0c1 Improved test coverage 2021-04-27 11:47:57 -04:00
Nick Goupinets 29722ad8ec Fixed exception handling 2021-04-27 10:14:30 -04:00
Nick Goupinets 024f553fc9 Merge branch 'master' into 2566_update_s13n_and_validation_handling 2021-04-27 09:31:42 -04:00
Tadgh a5e734fec8 Handle sorting entries which contain no resources 2021-04-26 22:24:47 -04:00
Nick Goupinets 08934d2364 Updated standardization logic and removed obsolete validator 2021-04-26 16:27:44 -04:00
Nick Goupinets f6ed93b343 Updated validation logic 2021-04-26 14:17:05 -04:00
Tadgh b007fecb1d Add comment 2021-04-26 13:40:40 -04:00
Tadgh 9ecb390dae Move tests to proper class. Fix issue with version referencing 2021-04-26 13:40:11 -04:00
James Agnew 2ba1005762
OpenAPI Support (#2560) 
* Start work on OpenAPI

* Fixes

* Work on OpenAPI

* Cleanup

* Cleanup

* More swagger work

* Build fix

* More work

* More work

* Add documentation

* Docs fixes

* Add changelog

* License updates

* Add API

* Cleanup

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md

Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>

* Work on scripts

* Add docs

* Compile fix

* Work on fixes

* Fix tests

* Test fix

* Test fix

* Build fix

* Tests

* Build fix

* Work on pipeline

* Version bump

* Test fix

* Version bump

* Test fix attempts

* Test fix

* Test fix

* Remove accidentally committed files

* Fixes

* Tets fixes

* Test fix

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fixes

* License header updates

* test fix

* Test fixes

* Test fix

* Test fixes

* Test fix

* Checkstyle bump

Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
 2021-04-25 15:40:50 -04:00
Nick Goupinets ac2aac4342 Updated address validation handling 2021-04-23 18:55:51 -04:00
Nick Goupinets 902cd94ca2 Updated address and field validation handling 2021-04-22 16:55:34 -04:00
Nick Goupinets 961f16a1be Initial commit 2021-04-22 09:48:40 -04:00
Tadgh e711dfb07c enhance bundlebuilder to support deletes 2021-04-21 16:44:22 -04:00
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -04:00
Nick Goupinets 1f10a15c35 Merge branch 'master' into 2515_MDM_survivorship_rules 2021-04-19 17:33:53 -04:00
Nick Goupinets 536ca0e73d Code review updates 2021-04-19 16:27:31 -04:00
James Agnew ca2088f3ad
Add framework for Bulk Import (#2538) 
* Start work on bul;k import

* Work on bulk import

* Have batch working

* Working

* Working

* More work

* More work on bulk export

* Address fixmes

* License header updates

* Test fixes

* License header updates

* Test fix

* Test fix

* Version bumps

* Work on config

* Test cleanup

* One more version bump

* Version bump

* CLeanup

* A few additions

* Test fixes

* Test fix

* Test fix

* Migration fix

* Test fix

* Test fix
 2021-04-14 17:41:32 -04:00
James Agnew bc4266d3d2
Improve narrative templates for custom structures (#2537) 
* Improve narrative templates for custom structures

* Add changelog

* Test fix
 2021-04-12 06:00:31 -04:00
James Agnew a6cbf7eebd
Add support for hierarchycal valueset expansion (#2525) 
* Add support for hierarchycal valueset expansion

* Add changelog

* Add tests

* Cleanup

* Test fix

* Test fixes
 2021-04-06 17:36:54 -04:00
James Agnew b617c7690d
Search Parameter Infrastructure Cleanup (#2522) 
* Search param service cleanup

* Work on collapsing search param

* Search param cleanup

* Work on build

* Test fix

* Test fixes

* Ongoing work

* Test fix

* Compile fix

* Test fixes

* Test fix

* Test fix

* License header updates

* Remove fixme

* Cleanup

* Cleanup
 2021-04-05 17:40:10 -04:00
Nick Goupinets d366558749 Merge branch 'master' into 2515_MDM_survivorship_rules 2021-04-05 09:17:42 -04:00
James Agnew 0bf746f23b
Add support for revincludes to CapabilityStatement generator (#2521) 
* Add support for revincludes to CapabilotyStatement generator

* Add changelog

* Fixes

* Test fix

* Test fixes

* Test fix

* Test fix

* More fixes to CS cache

* Test fix

* Test fix

* Test fix
 2021-04-05 08:29:04 -04:00
Nick Goupinets 9629aceff0 Removed obsolete test and added more control to replace fields in TU 2021-04-01 15:52:52 -04:00
jamesagnew 06bdefa16c Improve error handling 2021-03-30 07:36:08 -04:00
James Agnew 049097e5b4
Improve CapabilityStatement Generation (#2511) 
* Start work

* Work on testing

* Version bump

* Test fix

* Compile fix

* Test Fixes

* Test fix

* Test fix

* Compile fix

* Tst fix

* Test fix

* Test fix

* Test fix
 2021-03-30 05:48:03 -04:00
Eric Prud'hommeaux 939a57960d
+ informative header in structures-r4 RDFParserTest (#2474) 2021-03-30 05:37:02 -04:00
Diederik Muylwyk b720c32c1d Version bump 2021-03-29 18:23:16 -04:00
Nick Goupinets 8ead3c5f22 Code review fixes 2021-03-23 15:01:22 -04:00
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
Nick Goupinets 9b94718cab Added ext util test 2021-03-20 21:22:21 -04:00
Nick Goupinets 4928e726cf Added tests for teser utils 2021-03-20 21:14:51 -04:00
Nick Goupinets 5f2c0a55b7 Merge branch '2478_add_extension_mdm_matcher' of github.com:hapifhir/hapi-fhir into 2478_add_extension_mdm_matcher 2021-03-19 18:15:43 -04:00
Nick Goupinets 5747d5d841 Initial commit 2021-03-19 09:58:15 -04:00
long 6c41ded507 fixed based on pull request comments, added tests 2021-03-18 13:59:07 -06:00
Eric Prud'hommeaux d92a6787c5
- remove-JSON-round-trip-guard (#2472) 
hapi-fhir-structures-r4/.../RDFParserTest.java included a guard to NOT
report round-trip errors if JSON didn't round-trip due to changed
ordering of contained resources (and entries in Bundles). be50a46
appears to have fixed these issues so the guard is no longer
necessary.
 2021-03-17 05:51:29 -04:00
Nick Goupinets d80a9ed848 Fixed test bug 2021-03-16 11:37:49 -04:00
Nick Goupinets f9f703abe2 Added support for additional types 2021-03-16 11:14:40 -04:00
Nick Goupinets 83acb66675 Touch for a rebuild 2021-03-15 16:16:59 -04:00
Nick Goupinets 04a0ecfc2b Added tests 2021-03-15 10:31:38 -04:00
Nick Goupinets 8c80e0838d Fixing line break problem 2021-03-12 17:48:17 -05:00
Nick Goupinets d68ee68b5d Added test 2021-03-12 10:30:12 -05:00
Nick Goupinets efae1b5e5f Added test 2021-03-11 17:44:34 -05:00
Nick Goupinets 8b8bbcc91f Refactored based on the code review 2021-03-11 17:14:01 -05:00
Nick Goupinets 23f3cc1f42 Code review 2021-03-11 14:51:13 -05:00
Nick Goupinets 8c77882da0 Merge branch 'master' into ng_validation_s13n_interceptors 2021-03-11 09:48:39 -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 052919eb33 Finished tests 2021-03-09 16:17:13 -05:00
Nick Goupinets dd47c71f44 Fixed test failures 2021-03-09 13:17:48 -05:00
Nick Goupinets ccb5b1aaad Addresses #2449 2021-03-08 17:40:16 -05:00
Tadgh 11b413ee9b Rework tests which relied on old behaviour 2021-03-01 14:19:20 -05:00
Tadgh 9dd42fa605 Remove duplicate constant 2021-03-01 14:00:20 -05:00
Tadgh 27cac16de6 Add custom mimetypes to capability statement 2021-03-01 13:54:21 -05:00
James Agnew db44244405
Fix #2426 - Include modifiers in generic search URLs for map (#2428) 2021-02-28 10:33:43 -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
James Agnew dd7a156d19
Call startOperation for paging requests (#2370) 2021-02-09 15:47:11 -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
James Agnew 273a5bbbd7
Add BundleUtil utility method (#2356) 2021-02-04 13:13:25 -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 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
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
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
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
Eric Prud'hommeaux 8b338cd168
rework r4 RDF tests to skip fewer examples (#2159) 
+ relative URL resolution in RDFParser
+ test non-DomainResources in RDFParserTest
~ factor/organize RDFParserTest
~ avoid EXTERNAL shapes (for now) in shex-java
- disable the bundle-response.json example as it is apparently malformed
+ added urn:-guard to PreResourceStateHl7Org.wereBack ID update
 2021-01-16 19:15:39 -05:00
Ken Stevens 520400d6ea
added IPagingProvider.canSearchByOffset() (#2281) 
* init rev

* added IPagingProvider.canSearchByOffset()
consolidated parameters in bundle link methods

* fix refactoring error

* add @Nonnull to BundleLinks parameter

* null check

* fix test

* cleanup

* fix refactoring

* final cleanup

* review feedback

* review feedback

* review feedback
 2021-01-11 20:42:41 -05:00
James Agnew 8f8c5c31f1
Add validation rules interceptor (#2264) 
* Start work on validation rules interceptor

* Work on interceptor

* Add tests

* Work on validation interceptor

* Work on interceptor

* Test fix

* Documentation tweaks
 2021-01-01 14:29:10 -05:00
Bill Denton 84d9854e24
OSGi manifest maintenance (#2217) 
* manifest cleanup and delete Fragment-Host

* make hapi-fhir-server-empi into an OSGi bundle
 2020-12-18 16:48:44 -05:00
James Agnew f228b4a167
Fix an error parsing extensions with a value type of UUID (#2258) 2020-12-18 10:57:31 -05:00
jamesagnew 5dc12b8787 Add test for custom field parsing 2020-12-18 08:49:20 -05:00
Tadgh e79114e2ec
Un-revert the MDM changes, now that issues have been addressed (#2226) 
* Backward compatibility changes

* Revert "Revert "Remove all references to Person from EMPI.""

* Updated docs

* Removed mdm channel references

* Initial implementation

* fix coarseness bug. Fix tests. reinitialize silly bean

* Add forgotten json file

* Generic provider PoC

* Refactored provider to use BundleBuilder

* Removed version-specific MDM providers

* Addressed code review comments

* Fixed after merge

* Fixed docs

* MDM SVG for Update Use Cases

* Removed obsolete docs

Co-authored-by: Nick <nick.goupinets@smilecdr.com>
Co-authored-by: Nick Goupinets <73255752+nvg-smile@users.noreply.github.com>
 2020-12-17 10:12:53 -05:00
James Agnew 81f6fe9106
Support IBaseBundle as parameetr type for @Transaction method (#2237) 
* Support IBaseBundle as parameetr type for @Transaction method

* Add changelog

* Add bundle setter
 2020-12-11 18:33:00 -05:00
James Agnew 1e5def260c
Bump woodstox version (#2199) 2020-11-27 19:49:06 -05:00
jamesagnew 0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew 4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -05:00
jamesagnew 7903b2b577 License headers 2020-10-13 11:43:09 -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
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