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7521 Commits

Author SHA1 Message Date
Tadgh 141cd14918 Add changelog 2021-01-18 15:04:03 -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
ianmarshall 26491f3bc8 Ensure that table indexes are not deleted during DB migration dry-run. 2021-01-18 14:09:06 -05:00
ianmarshall 1972838249 Ensure that table indexes are not deleted during DB migration dry-run. 2021-01-18 14:03:50 -05:00
Nick b00f47ef81 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-18 09:25:58 -05:00
jamesagnew a08392e6b2 Add license header 2021-01-17 19:10:34 -05:00
jamesagnew 6ff7d579a3 Update changelog 2021-01-17 17:43:42 -05:00
dependabot[bot] 2db35f4dcb
Bump spring_version from 5.3.2 to 5.3.3 (#2295) 
Bumps `spring_version` from 5.3.2 to 5.3.3.

Updates `spring-beans` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-context` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-context-support` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-core` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-jdbc` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-messaging` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-orm` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-test` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-tx` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-web` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-webmvc` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

Updates `spring-websocket` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases)
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3)

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2021-01-17 17:43:11 -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
dependabot[bot] cc2a1c16c8
Bump commons-collections4 from 4.3 to 4.4 (#2292) 
Bumps commons-collections4 from 4.3 to 4.4.

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2021-01-17 13:27:48 -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
jamesagnew 9d8bbaf868 Add credit for #2054 2021-01-17 09:44:18 -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
jamesagnew 57bebe50e8 One more test fix 2021-01-17 08:52:40 -05:00
jamesagnew 4913c33fdf Test fix 2021-01-17 07:24:00 -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
dependabot[bot] 8a0b0885f2
Bump jersey_version from 2.25.1 to 3.0.0 (#2245) 
Bumps `jersey_version` from 2.25.1 to 3.0.0.

Updates `jersey-server` from 2.25.1 to 3.0.0

Updates `jersey-container-servlet-core` from 2.25.1 to 3.0.0

Updates `jersey-container-jetty-http` from 2.25.1 to 3.0.0

Updates `jersey-media-moxy` from 2.25.1 to 3.0.0

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2021-01-16 19:13:54 -05:00
jamesagnew a7c9b9d2f3 Changelog 2021-01-16 19:08:55 -05:00
dependabot[bot] 472eba040a
Bump jansi from 1.18 to 2.1.1 (#2253) 
Bumps [jansi](https://github.com/fusesource/jansi) from 1.18 to 2.1.1.
- [Release notes](https://github.com/fusesource/jansi/releases)
- [Changelog](https://github.com/fusesource/jansi/blob/master/changelog.md)
- [Commits](https://github.com/fusesource/jansi/compare/jansi-project-1.18...jansi-2.1.1)

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2021-01-16 19:05:31 -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
dependabot[bot] 24ac055b50
Bump jackson_version from 2.11.2 to 2.12.1 (#2287) 
Bumps `jackson_version` from 2.11.2 to 2.12.1.

Updates `jackson-annotations` from 2.11.2 to 2.12.1
- [Release notes](https://github.com/FasterXML/jackson/releases)
- [Commits](https://github.com/FasterXML/jackson/commits)

Updates `jackson-core` from 2.11.2 to 2.12.1
- [Release notes](https://github.com/FasterXML/jackson-core/releases)
- [Commits](https://github.com/FasterXML/jackson-core/compare/jackson-core-2.11.2...jackson-core-2.12.1)

Updates `jackson-datatype-jsr310` from 2.11.2 to 2.12.1

Updates `jackson-dataformat-yaml` from 2.11.2 to 2.12.1
- [Release notes](https://github.com/FasterXML/jackson-dataformats-text/releases)
- [Commits](https://github.com/FasterXML/jackson-dataformats-text/compare/jackson-dataformats-text-2.11.2...jackson-dataformats-text-2.12.1)

Updates `jackson-module-jaxb-annotations` from 2.11.2 to 2.12.1
- [Release notes](https://github.com/FasterXML/jackson-modules-base/releases)
- [Commits](https://github.com/FasterXML/jackson-modules-base/compare/jackson-modules-base-2.11.2...jackson-modules-base-2.12.1)

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2021-01-16 13:47:30 -05:00
Nick 1d7ec3cc13 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-15 14:18:27 -05:00
Nick f10785ed43 Code review updates 2021-01-15 14:07:14 -05:00
jamesagnew 4791c81aec Improve package loading logs 2021-01-15 06:19:57 -05:00
Nick 6cc40b134e Pre-review commit 2021-01-14 20:35:09 -05:00
Nick 759f06ce48 Added optional manual override to link update 2021-01-14 14:24:59 -05:00
Nick 8a5651093b Renamed method param 2021-01-14 11:16:17 -05:00
Nick 07be675484 Reverted active flag check on golden resource 2021-01-14 11:10:34 -05:00
Nick e6f484cefd Added tests 2021-01-14 10:52:28 -05:00
Nick 24204f4425 Merge branch 'ng_20201218_survivorship_poc' of github.com:jamesagnew/hapi-fhir into ng_20201218_survivorship_poc 2021-01-12 19:09:33 -05:00
Nick 6781718702 Survivorship 7 2021-01-12 19:08:54 -05:00
Nick a2e1bb57fa Survivorship 7 2021-01-12 14:15:04 -05:00
Nick 57662eedb3 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-12 09:22:38 -05:00
jamesagnew ef407d85bf Add logging 2021-01-12 08:56:12 -05:00
jamesagnew 5b5023e6ac License headers 2021-01-11 21:00:12 -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
Frank Tao ee7b19fe3c
Fixed the migration scripts (#2283) 2021-01-11 20:36:54 -05:00
Nick 5aa85c7e17 Survivorship 6 2021-01-11 17:22:06 -05:00
Nick 684b77d396 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-11 09:21:29 -05:00
Frank Tao f6d4a40388
UCUM Service Support (#2261) 
* Added UcumServiceUtil

* Removed ucum-essense.xml

* Added ucum service existing test cases passed

* Added more test cases

* Merge branch 'master' into ft-ucum-support

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

* Added back extractReferenceParamsAsQueryTokens

* Added changelog and migration script

* Added length for the string type

* Moved UCUM util to hapi-fhir-jpaserver-model

* Renamed UCUM support to Normalized Quantity Search Support

* Moved setNormalizedQuantitySearchNotSupported to AfterEach

* Changed migrate task to 530

* Removed comments

* Fixed in memory search issue and added more test cases

* Fixed the version order

* License header updates

* Updated based on review comments

* Updated the migration task based on review comments

* Fixed RES_TYPE with type String and length 100

* Changed myParamsQuantityNormalizedPopulated type to Boolean class
 2021-01-10 21:05:24 -05:00
Frank Tao 88b01a3bb4
Changed the minGramSize back to 3 (#2279) 2021-01-10 09:02:59 -05:00
Nick 9338a4e73e Survivorship 5 2021-01-08 19:25:25 -05:00
jamesagnew 0b6e8e3f4d Add license header 2021-01-08 16:35:42 -05:00
Nick 30ba5822bd Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-08 11:54:33 -05:00
Nick bec056cf9d Survivorship 4 2021-01-07 17:36:04 -05:00
IanMMarshall 4b310f0a3c
Merge pull request #2271 from hapifhir/im_2021_01_04_package_load_with_partitioning 
Fixed package loading when partitioning is enabled
 2021-01-07 13:25:44 -05:00
Nick ebefb141f3 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-07 11:15:54 -05:00