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7370 Commits

Author SHA1 Message Date
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
Tadgh e7bc2f0e2d
Merge pull request #2311 from hapifhir/cve-fix-2021-20190 
bump databind version for CVE
 2021-01-21 10:48:24 -05:00
Tadgh 7159d65902 bump databind version for CVE 2021-01-21 10:03:16 -05:00
jamesagnew 7cf41a7e85 One more build fix (grrrrrr) 2021-01-21 09:24:42 -05:00
jamesagnew 656dd33ba8 FIx javadoc build 2021-01-21 08:58:23 -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 a538ed571a
Merge pull request #2306 from hapifhir/bump-es-version-for-cve 
Minor version bump for CVE-2021-22132
 2021-01-20 22:54:51 -05:00
Tadgh f99733244e
Merge pull request #2305 from hapifhir/add-backport-information 
Prepare for backporting
 2021-01-20 14:45:14 -05:00
Tadgh 3d5255d88c Bump ES version running in tests 2021-01-20 11:34:51 -05:00
Tadgh fa17ea35cd Minor version bump for CVE-2021-22132 2021-01-20 11:31:00 -05:00
Tadgh 159128109b Add versionenum value 2021-01-20 10:49:08 -05:00
jamesagnew 063f4b7700 Add license headers 2021-01-19 14:18:46 -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
Kevin Dougan SmileCDR 240decc210
Added an extra check for an IS NOT NULL Constraint when checking an Oracle DB Column for Nullability (#2288) 
* Added an extra check for an IS NOT NULL Constraint when checking an Oracle DB Column for Nullability.
 2021-01-19 08:44:41 -05:00
Tadgh 649032681d
Merge pull request #2301 from hapifhir/disable-docker-tests-in-non-docker 
Disable docker tests in non docker
 2021-01-18 23:11:54 -05:00
Tadgh ceb0155ab7 Fix hamcrest inclusion via compile scope 2021-01-18 22:07:12 -05:00
Tadgh 8d87f0f92b Simplify check 2021-01-18 21:53:14 -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 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 7c6c64bfb7 Remove dead import 2021-01-18 15:53:49 -05:00
IanMMarshall 292d7751b3
Merge pull request #2298 from hapifhir/im_20210118_db_migrate_dryrun_issue 
Ensure that table indexes are not deleted during DB migration dry-run.
 2021-01-18 15:14:22 -05:00
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
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
jamesagnew 4791c81aec Improve package loading logs 2021-01-15 06:19:57 -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