Commit Graph

7322 Commits

Author SHA1 Message Date
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
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
jamesagnew 0b6e8e3f4d Add license header 2021-01-08 16:35:42 -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
ianmarshall 14270e8aa4 Remove the now redundant PackageSystemRequestDetails class. 2021-01-07 10:18:39 -05:00
jamesagnew 128d384153 Credit for #2273 2021-01-07 06:03:31 -05:00
Alejandro Medina f55cb96c8f
Update tmpl-head.html (#2273)
wrong path in library select2
2021-01-07 06:01:33 -05:00
ianmarshall e23e3c660c Merge remote-tracking branch 'origin/master' into im_2021_01_04_package_load_with_partitioning 2021-01-06 12:23:21 -05:00
ianmarshall 634f7a8026 Fix typo. 2021-01-06 10:33:47 -05:00
ianmarshall a4980ad845 Improve wording in documentation. 2021-01-06 10:32:05 -05:00
ianmarshall 659e83f451 Address use case where packages include non-conformance resources. Update documentation as well. 2021-01-06 10:29:10 -05:00
jamesagnew b79d154d81 Dependency version bumps 2021-01-06 10:21:25 -05:00
jamesagnew 6ea36e79a4 Fix migration task 2021-01-05 20:42:21 -05:00
jamesagnew 496a8bd3cd Test fix 2021-01-05 18:41:43 -05:00
James Agnew 0bb878e4a8
Repository validation enhancements (#2270) 2021-01-05 18:22:34 -05:00
jamesagnew 12d366c86e License header updates 2021-01-05 18:13:14 -05:00
ianmarshall d01c775b99 Fixed package loading to enable loading of binary package files into the default partition when partitioning is enabled. 2021-01-05 18:12:11 -05:00
Tadgh efc6809ea6
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190)
* Beginning work on converting to hibernate search 6
* replace all out of date properties
* replace all POM references to old versions
* remove the shaded ES jars as HS6 supports 7.9
* Convert "Bridges" to RoutingBinder and RoutingBridge
* Modernize all indexing annotations
* Begin refactoring of search queries (wip)

* Fix spatial API changes, work on BaseTermReadSvcImpl

* Most of the way through the various filter property conversions

* Finished i think with BaseTermReadSvcImpl

* Compiling, but definitely broken

* Start test compilation failures

* All tests compiling (i think)

* remove suggest keywords operation

* Fix bootstrap errors, still have to deal with transient fields

* Rollback CR

* More refactoring, got IDs baked back into docs

* Fix coord util, fix a few more fields which require projection

* merge fixes

* begin refactor of valuesetexpansion tests

* fix another test

* Update tests

* remove todos, add TestContainers

* Fix descendant in

* Add testcontainers, fix another test

* fix more tests, replace embedded es

* Rip out embedded elastic, replace with TestContainer

* merge conflicts for new analyzers

* Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs

* Remove dead deps, update testcontainer

* Remove java-hamcrest

* Pull asserts up, refactor tests to pass in RP tests

* Update V2 check

* Remove suggest keyword tests

* Split line for testing

* Fix perhaps one of the dumbest programming mistakes in my career so far

* Refactor tests which no longer rely on a strict known order

* Fix up test config, disable log test temporarily

* Remove log4j from being transitively pulled in. re-enable test

* Update log4j exclusions with new bridge. Update test to check for core class

* Move dependency to root pom in dep management section

* Update changelog, add changelog for HS6 with ES requirements. Remove dead comment

* update testst, remove todos

* Add hibernate props provider method, add elastic regexp query

* Add todo for high level client builder

* Modify ElasticsearchRestClientFactory to support HTTPS hosts

* Remove protocol extraction from rest url

* do we even need to index this...?

* remove purge of non-indexed resources

* Add longer timeout to testcontainers

* Add task to add docker CLI to azure pipeline via task, for testcontainers

* WIP remove this

* Dont update version

* Add test for duplicate termconcepts

* Use real hibernate ORM methods

* merge issues

* Add partitionsettigns bean to match master

* Trying to debug testcontainers on azure...

* Trying to debug testcontainers on azure...

* Run even on previous failure

* Fix testcontainer port binds

* Add full text logs attaching, and test reporting

* I love yaml

* Remove comment

* Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue

* Modify TX beheaviour

* wip

* Rework to use config and mocked beans for partition-aware lastN

* rework to not use beans and just inject vars i need for test, keps test envs cleaner

* update azure pipeline to only copy test results

* Remove erroneous publish

* Always get test logs

* Make it so indexing works,

* Add todos

* revert deleteByPid

* Work on test fixes

* Test fixes

* Test fixes

* Another test fix

* Test fix

* Work on tests

* Test fixes

* All tests passing locally

* Fix test failure

* FIx build error

* Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider

* Update ngram of token filters

* Tidying

* subvert the purpose of hibernate elastic props builder to inject template

* dead space

* Rename changed class

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-05 17:56:59 -05:00
ianmarshall 446dd5c782 Fixed package loading to enable loading of binary package files into the default partition when partitioning is enabled. 2021-01-05 17:51:04 -05:00
James Agnew d943260927
Rework valueset index for MySQL (#2269)
* Rework valueset index for MySQL

* Add changelog
2021-01-05 10:03:33 -05:00
IanMMarshall 14fc8f2598
Merge pull request #2262 from hapifhir/2260-fix-sorting-for-mysql
Fix order by clause in search query for MySQL, MSSQL and MariaDB
2021-01-04 21:19:04 -05:00
ianmarshall 1f0ea21cde Changes per code review plus test fixes. 2021-01-04 19:09:04 -05:00
ianmarshall bac47dbbf6 Changes per code review plus test fixes. 2021-01-04 19:06:39 -05:00
dependabot[bot] 86f254cd66
Bump datasource-proxy from 1.5.1 to 1.7 (#2267)
* Bump datasource-proxy from 1.5.1 to 1.7

Bumps [datasource-proxy](https://github.com/ttddyy/datasource-proxy) from 1.5.1 to 1.7.
- [Release notes](https://github.com/ttddyy/datasource-proxy/releases)
- [Changelog](https://github.com/ttddyy/datasource-proxy/blob/1.x/CHANGELOG.md)
- [Commits](https://github.com/ttddyy/datasource-proxy/compare/datasource-proxy-1.5.1...datasource-proxy-1.7)

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

* Add changelog

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-04 10:32:52 -05:00
ianmarshall 8a2dfe86fd Merge remote-tracking branch 'origin/master' into 2260-fix-sorting-for-mysql 2021-01-04 09:00:21 -05:00
dependabot[bot] aa584d5b2d
Bump maven-dependency-plugin from 3.0.2 to 3.1.2 (#2266)
Bumps [maven-dependency-plugin](https://github.com/apache/maven-dependency-plugin) from 3.0.2 to 3.1.2.
- [Release notes](https://github.com/apache/maven-dependency-plugin/releases)
- [Commits](https://github.com/apache/maven-dependency-plugin/compare/maven-dependency-plugin-3.0.2...maven-dependency-plugin-3.1.2)

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-04 06:49:12 -05:00
dependabot[bot] 0ac9ea643a
Bump plexus_compiler_api_version from 2.8.5 to 2.8.8 (#2243)
Bumps `plexus_compiler_api_version` from 2.8.5 to 2.8.8.

Updates `plexus-compiler-api` from 2.8.5 to 2.8.8
- [Release notes](https://github.com/codehaus-plexus/plexus-compiler/releases)
- [Commits](https://github.com/codehaus-plexus/plexus-compiler/compare/plexus-compiler-2.8.5...plexus-compiler-2.8.8)

Updates `plexus-compiler-javac` from 2.8.5 to 2.8.8

Updates `plexus-compiler-javac-errorprone` from 2.8.5 to 2.8.8

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-04 06:18:36 -05:00
jamesagnew 8df8ed7838 Bump hibernate version 2021-01-03 16:56:02 -05:00
James Agnew 3e6d80bdc2
Fix SQL Server paging with new querybuilder (#2265)
* Fix SQL Server paging with new querybuilder

* Add changelog
2021-01-02 11:13:51 -05:00
jamesagnew a255044774 Test fixes 2021-01-01 16:50:06 -05:00
jamesagnew 5a8fb5dd01 Drop redundant tests 2021-01-01 16:43:03 -05:00
jamesagnew cbb16ce3af License header updates 2021-01-01 16:40:46 -05:00
jamesagnew 57347ddb63 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2021-01-01 15:52:06 -05:00
jamesagnew d20b07c78e Update license headers 2021-01-01 15:50:24 -05:00
jamesagnew ec712e086c Version bump mockito 2021-01-01 15:50:00 -05:00
jamesagnew ed4d7d7eb6 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2021-01-01 15:07:37 -05:00
jamesagnew f30999b053 License header updates 2021-01-01 15:07:23 -05:00
jamesagnew 4373b47207 Library version bumps 2021-01-01 15:06:55 -05:00
James Agnew 8f8c5c31f1
Add validation rules interceptor (#2264)
* Start work on validation rules interceptor

* Work on interceptor

* Add tests

* Work on validation interceptor

* Work on interceptor

* Test fix

* Documentation tweaks
2021-01-01 14:29:10 -05:00
ianmarshall eb59da3f03 Added changelog. 2020-12-24 15:23:50 -05:00
ianmarshall 63e0c90023 Change order by clause in search query to support MySQL, MSSQL and MariaDB. 2020-12-24 13:54:37 -05:00
Bill Denton 84d9854e24
OSGi manifest maintenance (#2217)
* manifest cleanup and delete Fragment-Host

* make hapi-fhir-server-empi into an OSGi bundle
2020-12-18 16:48:44 -05:00
James Agnew f228b4a167
Fix an error parsing extensions with a value type of UUID (#2258) 2020-12-18 10:57:31 -05:00
jamesagnew c745fb2561 Avoid deprecated method 2020-12-18 08:49:20 -05:00
jamesagnew 5dc12b8787 Add test for custom field parsing 2020-12-18 08:49:20 -05:00
Frank Tao 89cf6e6293
Fixed the pre-expansion with filter issue (#2257)
* Fixed the pre-expansion with filter issue

* Changed minGramSize to 3 instead of 2
2020-12-17 23:31:33 -05:00
Tadgh e79114e2ec
Un-revert the MDM changes, now that issues have been addressed (#2226)
* Backward compatibility changes

* Revert "Revert "Remove all references to Person from EMPI.""

* Updated docs

* Removed mdm channel references

* Initial implementation

* fix coarseness bug. Fix tests. reinitialize silly bean

* Add forgotten json file

* Generic provider PoC

* Refactored provider to use BundleBuilder

* Removed version-specific MDM providers

* Addressed code review comments

* Fixed after merge

* Fixed docs

* MDM SVG for Update Use Cases

* Removed obsolete docs

Co-authored-by: Nick <nick.goupinets@smilecdr.com>
Co-authored-by: Nick Goupinets <73255752+nvg-smile@users.noreply.github.com>
2020-12-17 10:12:53 -05:00
Frank Tao effbd19924
Merge pull request #2240 from hapifhir/ft_support_composite_sort
Add support for composite sorting
2020-12-16 16:54:56 -05:00