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7380 Commits

Author SHA1 Message Date
Frank Tao 1d1ebcf5e8
Improved DateQuery and removed 'OR' in the SQL (#2302) 
* improved DateQuery and removed 'OR' in the SQL

* improved DateQuery and removed 'OR' in the SQL

* Date handling cleanup (#2316)

* Date handling cleanup

* Fix codecov

* One more fix

* Fix tests

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2021-01-23 17:53:18 -05:00
James Agnew 522efc87d9
Reusable interceptor service (#2318) 
* Reusable interceptor service

* Azure fix
 2021-01-22 19:17:08 -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
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
Tadgh 71c76e3ea1
Merge pull request #2314 from hapifhir/2313/error-in-mdm-docs 
Add documentation fixes for MDM-match
 2021-01-22 09:26:20 -05:00
Tadgh edd9769686 Add documentation fixes for MDM-match 2021-01-22 09:17:51 -05:00
Mark Iantorno d5250e6f1a Adding back in test runs. 2021-01-21 16:40:17 -05:00
Mark Iantorno c09b1394fc Variable name fix. 2021-01-21 16:01:36 -05:00
Mark Iantorno 560d960ec9 I am a dummy who puts typos everywhere in his code. 2021-01-21 15:53:29 -05:00
Mark Iantorno 7f3e0726c8 Initial setup for snapshot pipeline 
Still have to enable tests. They are only disabled now so I can run this multiple times quickly to test deployment. [skip ci]
 2021-01-21 15:39:26 -05:00
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