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907 Commits

Author SHA1 Message Date
JasonRoberts-smile b5e31abf9b
add authorization check to inline matches (#3048) 
* add authorization check to inline matches

* code review feedback: cached results case

* Add query count test

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3047-inline-match-security.yaml

Accept code review suggestion

Co-authored-by: James Agnew <jamesagnew@gmail.com>

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2021-10-18 12:21:26 +00:00
Tadgh b427135b04
Patient/$everything _id parameter (#3077) 
* Add tests. Add implementation in R4. Add changelog

* Wip partial fixup of other STU versions

* Updated usages of new patient type everything api

* Partial commit of incomplete documentation

* Remove docs

* Cut to token instead of string

* Bump hapi version due to breaking api changes
 2021-10-17 14:34:33 +00:00
jamesagnew f6c8ecdc43 Credit for #3022 2021-10-17 09:09:22 -04:00
Thomas Vitale 721b1817a7
Add Systematic (Columna Cura) to HAPI FHIR Global Atlas (#3052) 2021-10-17 09:03:38 -04:00
jamesagnew 1c8f364f0e Credit for #3043 2021-10-14 16:37:13 -04:00
Tadgh d2ea4655a7
Rel 5 5 2 (#3060) 
* Add versionenum, bump maven version

* failing tests

* more logs

* Add more test cases, not passing

* fixed the double chain with contained resource second case

* clean up a bit

* add tests for qualifiers

* force the resource table to be the root of the query if we might be traversing a contained reference

* tidy up

* tests for longer chains

* changelog

* code review feedback

* backport changelog

* Add version.yaml

* [2935] Escape "%" in like expression

* Add backport to changelog

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
 2021-10-12 14:25:03 +00:00
James Agnew 310a4cdb58
Migrate CLOB columns to LOB (SMILE-3072) (#3016) 
* Migration finished

* Work on LOBS

* Add to ClobMigrated annotation

* Deal with lobs

* Work on new approach

* HAPI FHIR version bump

* Add changelog

* Add license header

* Fix intermittent

* CLeanup

* Cleanup
 2021-10-11 16:47:37 -04:00
James Agnew 756b0fdc7b
Fix transaction scoping (#2799) 
* Work on transaction boundaries

* Test fixes

* Test fixes

* Test fix

* Resolve FIXME

* Test fix

* Test fix

* Test fix

* Test fixes

* Test fix

* Adjust changelog

* Remove unneeded changelog

* Test fix

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fixes

* Test fix
 2021-10-11 16:45:22 -04:00
James Agnew aed718bd6f
Avoid redundant PID lookups in transaction processing (#3061) 
* Avoid redundant PID lookups in transaction processing

* Add changelog

* Test fix
 2021-10-11 13:45:57 -04:00
TipzCM 6ad0dffd00
build fix (#3058) 
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
 2021-10-07 16:38:42 -04:00
Tadgh 383f76982a Fix broken link in yaml 2021-10-07 15:12:18 -04:00
katiesmilecdr 3c80dba90e
[3040] finish implementation (#3049) 
* [3040] finish implementation

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* [3040] throw exception if link exists

* [3040] add matchResult parameter/update documentation

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2021-10-07 17:42:21 +00:00
TipzCM a474e88ed4
issue-2397 implementing the mdm expansion on everything and searches (#3044) 
* issue-2397 implementing the mdm expansion on everything and searches

* issue-2397 code cleanup and removal of test code

* issue-2397 some tests

* issue-2397 changelog added

* issue-2397 review fixes

* issue-2397 updated change log with example and fixed failing tests

* issue-2397 test fixing

* issue-2397 fixing test

* issue-2397 review fix

* issue 2397 fixing changelog file

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2021-10-07 10:46:23 -04:00
Tadgh 59afbe086c
Allow canonical references to support treating given base URLs as local. (#3050) 
* Add failling test, works on #2843

* Partial hack to get this working

* Move implementation into pre-processing

* Add changelog

* Move implementation

* Minify Test

* Remove fixmes

* Tidying

* Ensure this only operates on STU versions which support canonical
 2021-10-05 11:09:49 -04:00
James Agnew d320b78ae1
Improve synthea ingest performance (#3033) 
* Improve synthea ingest performance

* Tweaks

* Fix param splitting

* Update to test

* Add changelog

* Test fix

* Add some runtime checks

* Remove useless test

* Test fix
 2021-10-04 05:46:06 -04:00
James Agnew eca725afa4
Improve versioned URL support for ValueSet expansion (#2994) 
* Add test

* Test fixes

* Work on expansion errors

* Fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fixes

* Work on fix

* Test fixes

* Test fixes

* Test fix

* Cleanup

* Test fixes

* Remove accidental commit

* Test fixes

* Version bump

* Add changelog

* Fixes

* Test fix

* Fix conflicts
 2021-10-03 19:47:23 -04:00
James Agnew 95e853bdf7
Improve parallel model scanning (#3046) 
* Improve parallel model scanning

* Add changelog

* Resolve fixme

* Test fix
 2021-10-03 19:40:24 -04:00
Tadgh 6f36a0aab3
Merge branch 'master' into remove-parallel-non-gets 2021-09-28 10:17:38 -04:00
Tadgh ad05a5ec09
Merge branch 'master' into remove-parallel-non-gets 2021-09-28 09:43:01 -04:00
Jason Roberts 58a2f23c0d Merge branch 'master' into jr-20210922-narrowing-interceptor 2021-09-28 07:41:39 -04:00
Tadgh 591286a9cc Add changelog 2021-09-27 15:37:59 -04:00
katie_smilecdr d121f6eff1 Merge branch 'master' into 3020_Add_documentation_for_$partition-management-create-partition 2021-09-27 15:10:19 -04:00
katie_smilecdr b86f596c80 [3020] add sample response in documentation 2021-09-27 15:09:44 -04:00
katie_smilecdr c5cacacb23 [3020] fix changelog 2021-09-24 16:55:03 -04:00
katie_smilecdr d067586607 [3020] add documentation/changelog 2021-09-24 14:49:07 -04:00
Jason Roberts 4a53d10c78 Merge branch 'master' into jr-20210922-narrowing-interceptor 2021-09-24 14:39:10 -04:00
katie_smilecdr 8c145d1212 Merge branch 'master' into 3020_Add_documentation_for_$partition-management-create-partition 2021-09-24 13:01:38 -04:00
jmarchionatto a40a27bd46
Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology 2021-09-24 12:58:44 -04:00
Jason Roberts 4c28b1b552 fix npe 2021-09-24 09:46:48 -04:00
jmarchionatto 4ab60e2f9b
Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology 2021-09-24 08:59:15 -04:00
Ken Stevens 53c7476dae
hapi storage (#3024) 
* first pass moving core storage classes to storage-api

* move term service apis

* nearly done

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* create new SearchConstants class to store platform independent search constants

* move a couple of subscription services

* move transaction processor adapter to storage

* version bump

* move searchparam

* fix test

* fix compile includes

* fix text

* fix docs
 2021-09-23 22:04:46 -04:00
juan.marchionatto 91d9101785 Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology 2021-09-23 13:45:28 -04:00
juan.marchionatto d1e9c23c13 Remove loinc.xml file from application. Now it required as input for loinc upload. 2021-09-23 13:43:27 -04:00
Jason Roberts 4f00b88512 Merge branch 'master' into jr-20210922-narrowing-interceptor 2021-09-23 12:28:16 -04:00
Jason Roberts 712a6a798f clean up 2021-09-23 12:27:32 -04:00
juan.marchionatto 9c8fd26692 Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning 2021-09-23 11:56:44 -04:00
juan.marchionatto 751c5d0d05 Implement revision suggestions. Add changelog. 2021-09-23 11:55:50 -04:00
Tadgh ad9e0f1c9a
Merge branch 'master' into 3014-prevent-delete-expunge-cascade 2021-09-23 09:33:04 -04:00
katie_smilecdr 2489702ab9 [3020] add documentation for $partition-management-read-partition 2021-09-22 16:08:11 -04:00
Jason Roberts e52d11b5ba search narrowing interceptor responds with 403 Forbidden instead of creating an impossible query 2021-09-22 14:00:12 -04:00
Jimmy Deng 26ac649946 changelog 2021-09-22 11:11:10 -04:00
Jimmy Deng 9a18422173 fix review 2021-09-22 11:09:50 -04:00
Tadgh b8ef2f6763 Add changes 2021-09-21 15:25:46 -04:00
James Agnew 7379dee3d8
Merge branch 'master' into add-device-to-patient-compartment 2021-09-21 14:38:39 -04:00
JasonRoberts-smile 645386c999
Apply suggestions from code review 
Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2021-09-21 12:26:21 -04:00
Jason Roberts fa96c5b8be Merge branch 'master' into jr-20210921-mssql-data-migration 2021-09-21 12:22:56 -04:00
Ken Stevens 060791aeb4
hapi-fhir-storage-api (#3006) 
* rename hapi-fhir-jpaserver-migrate to hapi-fhir-sql-migrate and move hapi-tasks into jpaserver-persistence

* rename hapi-fhir-jpaserver-api to hapi-fhir-storage-api

* move bulk import apis

* create hapi-fhir-jpa

* create hapi-fhir-jpa

* move CircularQueueCaptureQueriesListener to japi-fhir-jpa

* move mdm logs to storage-api

* move gziputil to storage-api

* move quartz scheduling to hapi-fhir-jpa

* move default subscription channel factory to storage-api

* consolidated batch constants

* correct accidental Logs change

* remove dependency of cdr-api on cdr-persistence

* fix javadoc

* pom descriptions

* review feedback
 2021-09-21 15:36:08 +00:00
Jason Roberts b6c8658f8c Fix MS SQLServer database migration 2021-09-21 10:42:59 -04:00
Johnson Lu f1f9c672ad
3110 zh disallow unknown extensions (#3009) 
* Added allowKnownExtensionsOnly() method such which calls setAnyExtensionsAllowed() to set myAnyExtensionsAllowed to false and modified changelogs to add entry for this ticket.

* Modified docs to remove description for .allowAnyExtensions() and included it within a description for .allowKnownExtensionsOnly() and also added test for .allowKnownExtensionsOnly()

* refactored allowKnownExtensionsOnly() to rejectUnknownExtensions()
 2021-09-20 15:40:56 -04:00
JasonRoberts-smile 624ad3fcab
Merge branch 'master' into jr-20210914-oidc-support-in-swagger 2021-09-17 17:09:19 -04:00