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368 Commits

Author SHA1 Message Date
Nick Goupinets d63c580e82 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-01 13:18:42 -05:00
James Agnew c309737166
Allow reading from multiple partitions (#2198) 
* Partitioning rework

* Work on partition improvements

* Partition updates

* Work on partitiong

* Test fixes

* Add docs

* Add changelog

* Resolve FIXME

* Test fixes

* Test fixes

* Test fixes

* Compile fix

* Fix compile error

* Test fix

* Test fixes
 2020-11-30 17:59:52 -05:00
Nick Goupinets 5f97428d38 Added schema migration steps for MDM 2020-11-24 15:50:56 -05:00
Tadgh 953b662827 Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references 2020-11-19 14:24:51 -05:00
Tadgh 75c0c25d7b remove references to EMPI 2020-11-18 19:50:00 -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
James Agnew 63b7b379c2
Improve ValueSet filtering (#2162) 
* Improve filter search

* Filter improvements

* Tests passing

* Test fixes

* Fix transaction filter

* Add changelog

* Test fix

* Update hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Resolve FIXME

* Test fix

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-11-10 11:01:13 -05:00
IanMMarshall 38a975f09d
Im 20201028 fix versioned valueset expansions (#2151) 
* Fixes to ValueSet expansion for cases where CodeSystem is versioned.

* Fixes to ValueSet expansion for case where URL and filter parameters specified.

* Restore maven-wrapper.properties file inadvertently deleted from GitHub.

* Fix JUnit tests and ValueSet exclude.

Co-authored-by: ianmarshall <ian@simpatico.ai>
 2020-11-04 16:36:43 -05:00
ianmarshall 1dc4a533d6 Fixes to terminology loader. 2020-09-25 21:43:15 -04:00
ianmarshall 47244c54dc Merge remote-tracking branch 'origin/feature_2020_09_02_term_multi_version_support' into im_20200728_term_multi_version_support 
# Conflicts:
#	hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
 2020-09-25 09:10:07 -04:00
ianmarshall e5daea17b7 Additional cleanup and migration tasks. 2020-09-23 17:17:07 -04:00
ianmarshall 302bbca8fd Changes to support multi-versioning in ValueSet $expand operation. 2020-09-20 22:01:21 -04:00
ianmarshall 087c9e3c3b Merge remote-tracking branch 'remotes/origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:34:11 -04:00
Frank Tao 448caa3f93 Changed the ConceptMap.VER to nullable 2020-09-11 09:02:46 -04:00
Frank Tao 16a5f57ae9 Added for ConceptMap DB migration 2020-09-10 21:41:06 -04:00
jamesagnew 0e34f16890 Make PID column name configurable in migrator 2020-09-07 20:46:53 -04:00
Mike G 8167a0c509 use new getters 2020-09-03 10:15:55 -04:00
Mike G 1de1ebb794 rename getters 2020-09-03 10:15:07 -04:00
Mike G faab567095 replace fetching of query strings with running of tasks 2020-09-03 00:58:49 -04:00
Mike G 60c03c429b add constraint dropping when dropping index in case of unique 2020-09-03 00:57:32 -04:00
Mike G 6012bc4c56 add getters and modify some setters to return a reference to itself 2020-09-03 00:56:12 -04:00
jamesagnew a0710d4f47 Add constructor 2020-08-19 06:05:23 -04:00
jamesagnew 92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew 5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
Tadgh 2cf48eb9b9 Move field length into constants 2020-08-01 13:11:33 -07:00
Tadgh 0e88f359f5 Merge remote-tracking branch 'remotes/origin/master' into batch-empi-job 2020-07-29 09:42:12 -07:00
jamesagnew 20d1ab2fac Mark renameTask as deprecated 2020-07-28 08:38:28 -04:00
jamesagnew a6213fe1e0 One more tweak for #2002 on Oracle 2020-07-28 08:27:13 -04:00
Tadgh 82dcc395ec Merge branch 'master' into batch-empi-job 2020-07-27 14:59:27 -07:00
James Agnew 06fd306898
Allow constraints to be deleted by the migrator on H2 (#2002) 2020-07-27 10:20:27 -04:00
Mike G b67f30a03b fix oracle and derby default 2020-07-24 10:03:21 -04:00
Tadgh 9236cdc211 Add length to migration to string type 2020-07-22 14:02:03 -07:00
Tadgh 16c6071062 Fix migration 2020-07-22 12:43:36 -07:00
Tadgh bbe6d5600e Address review comments 2020-07-22 11:58:08 -07:00
Mike G 92312537a6 Modify drop index syntax for mssql 2020-07-22 12:22:08 -04:00
Mike G 6f1d46dc68 modify add index logic to behave like the other jdbc databases 2020-07-22 12:21:58 -04:00
Mike G f285318185 Add mssql to drop FK constraints when column is dropped 2020-07-22 12:21:50 -04:00
Tadgh 1e12c740f6 Merge branch 'master' into batch-empi-job 2020-07-17 09:28:10 -07:00
Ken Stevens ebd6ca4b64
Empi 3 ruleset version (#1978) 
* add rule version

* add rule version

* Rough in model for Golden Record.

* Test Link Rule Version

* add eid match boolean

* added new fields to EmpiLink to provide more information about how the link was created

* add logging to check an edge case

* all tests pass

* wip with failing tests

* tests pass

* FIXME

* optimize imports

* test score in provider output

* FIXME

* FIXME

* Fix jpa test app context

* fix migration string length

* review feedback param name

* review feedback javadoc

* review feedback javadoc

* bean config reorganization for cdr

* add more tests
 2020-07-17 08:31:15 -04:00
Tadgh 6bb92717f5 Merge branch 'master' into batch-empi-job 2020-07-16 11:00:32 -07:00
Ken Stevens 50ae07acaa
stub out all migrations if an empty schema was initialized (#1975) 2020-07-09 20:18:54 -04:00
Tadgh 57f5c10bca Add migration for MPI Score/TargetType 2020-07-07 07:56:43 -07:00
Ken Stevens 1e2505e548
change migration to correct table. (#1970) 
* change migration to correct table.

QUESTION: Do we need to stub this migration and add new ones?

* fix variable name
 2020-07-07 05:45:39 -04:00
Ken Stevens 79862c449a
add migration cutpoint (#1968) 2020-07-06 16:12:44 -04:00
James Agnew 6fb6675b1e
Resolve validation errors to ValueSet with UCUM (#1948) 
* Add tests for validation errors

* Work on validation errors

* Bump core version

* Fix validation errors

* Test fixes

* Add changelog

* Test fix

* Test fix

* Test fix
 2020-07-05 19:59:21 -04:00
James Agnew f356c7c385
Migrate to JUnit5 (#1952) 
* Work on junit

* Work on junit 5

* Work on junit 5

* Bump errorprone vcersion

* Work on tests

* Junit 5 tweaks

* Fixes

* Work on tests

* Work on junit5

* Work on tests

* Test fixes

* Work on junit5

* Test work

* Get junit5 working

* Test fix

* Work on tests

* WOrk on tests

* Work on tests

* fixes

* Compile fix

* One more tweak

* Compile fix

* Add changelog

* Fix compile error

* Compile fix
 2020-07-04 18:28:16 -04:00
dependabot[bot] ef4b79da7e
Bump mysql-connector-java in /hapi-fhir-jpaserver-migrate (#1955) 
Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 6.0.5 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/6.0.5...8.0.16)

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-07-01 18:29:57 -04:00
Tadgh e365e643ba
Merge pull request #1906 from jamesagnew/spring-batch-integration 
Spring batch integration
 2020-06-28 16:10:43 -07:00
ianmarshall 053094f2a6 Apply recent fixes for MySQL migration tasks to MariaDB as well. 2020-06-24 17:42:46 -04:00