Commit Graph

9145 Commits

Author SHA1 Message Date
michaelabuckley 96cadbba3e
Run online index operations non-transactionally on Postgres (#3413)
* Run online index operations non-transactionally on Postgres

* narrow non-transactional
2022-02-23 02:49:53 +00:00
Tadgh fcada39044
add online deferred invalidation keyword for oracle (#3409)
* add online deferred invalidation keyword for oracle

* test

* remove online option from sql server drop index - it can only apply to clustered indices

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
2022-02-22 16:44:28 -05:00
James Agnew cc44deee1a
GraphQL Introspection Support (#3348)
* Start working on graphql Schema

* Start testing

* Work on introspection

* Work on introspection

* Use integers for date ordinals

* Add changelog

* GraphQL updates

* Ongoing wrk

* Cleanup

* Bump core lib

* Add changelog

* Clean up dependencies

* CLeanup

* Add missing message

* Test fix

* Change to force CI
2022-02-22 09:48:57 -05:00
James Agnew 1e2e17784a
Fix parameter count limitation on MSSQL/Oracle large transactions (#3075)
* Fix parameter count limitation on MSSQL/Oracle large transactions

* Changelog fix

* Move changelog

* Force a change to trigger CI

* Test refactoring
2022-02-20 11:52:42 -05:00
Olivia You e55f9d510a
3400 bulk export rules incorrectly applied to group and patient exports (#3403)
* export rules are applied now

* add changelog and test

* add changelog

* Delete 2797-bulk-export-getting-incorrect-group-data.yml

* update test

* add test

Co-authored-by: olivia-you <olivia.you@smilecdr.com>
2022-02-20 11:39:21 -05:00
James Agnew 058e53616f
Use integers for date ordinals (#3346)
* Use integers for date ordinals

* Add changelog

* Adjust changelog
2022-02-19 18:50:18 -05:00
Tadgh c6122bcb1b Add license files 2022-02-18 19:11:29 -08:00
Tadgh 3561672fe7
Rel 5 7 mergeback (#3401)
* fix handling of common search parameters

* Revert "fix handling of common search parameters"

This reverts commit 89c45eebdc.

* Fix implementation, add test (#3378)

* Fix implementation, add test

* Tighten test

* Rip out dead modules

* Add changelog

* Jr 20220210 handle common search params in contained searches (#3377)

* fix handling of common search parameters

* add support for reference search parameters with multiple paths

* Issue 3357

* Version bump

* Fixed null pointer exception for re-loading subscription on cdr restart and when there's no partition id in the request, and added tests

* added changelogs for this fix

* Fix broken changelog file

* Can't specify specific resource type permissions for bulk export (#3376)

* deny user from exporting without perms

* add unit tests

* add changelog

Co-authored-by: olivia-you <olivia.you@smilecdr.com>

* Make migration donothing as it was added in error

* Remove ehcache

* Add version.yaml:

* Add to sources/javadocs for dist

* Fix typo

* fix up pom

* wip test removing checkstyle plugin from deployable pom

* remove test pom changes, instead just dont deploy to sonatype

* typo

* Remove ehcache

Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
2022-02-18 19:22:44 +00:00
Patrick Werner 0c5d868f44
encode narratives of contained resources (#3402)
* encode narratives of contained resources
fixes #1466

* encode narratives of contained resources
fixes #1466
2022-02-17 18:54:03 +00:00
Ken Stevens 631391819b
remove hapi jpa spring config hierarchy (#3390)
* initial refactor to remove hapi jpa spring config hierarchy

* fix poms

* fix batch config

* dependency rearrangement arising from further testing

* fix searchDao bean name

* fixed dstu2 tests

* consolidate validation config

* dstu2 validation regression (man dstu2 support is expensive)

* fix test (with WIP comment)

* restore poms

* fix demo projects

* fix build

* bumping version

* rename generated config class
2022-02-16 20:44:03 -05:00
michaelabuckley 1c82d0933c
Mb new date search index (#3368)
* New date index definitions.
* Dropped unused indexes.
* Add online option to drop index and add index
* Push sp->resource FK down to control name
* Update annotations to match and redefine FK
* Continue to allow the legacy hibernate names while we update the indexing.
2022-02-16 22:12:20 +00:00
michaelabuckley ae33cf825b
Handle token search by partial code, and various nulls (#3399) 2022-02-16 08:23:16 -07:00
Ken Stevens fb342cc2a6
2825 ks smile startup (#3388)
* bump flyway

* update thymeleaf template from html5 to html

* add UNKNOWN to batch status test
2022-02-14 15:06:26 -05:00
StevenXLi 69a614d823
fixed ticket number to the correct issue number in hapi-fhir (#3393)
Co-authored-by: Steven Li <steven@smilecdr.com>
2022-02-14 18:46:37 +00:00
Tadgh 700221ad07
return concretions (#3373) 2022-02-10 21:07:47 -05:00
Tadgh 38912423c1
Remove dead modules (#3380)
* fix handling of common search parameters

* Revert "fix handling of common search parameters"

This reverts commit 89c45eebdc.

* Fix implementation, add test (#3378)

* Fix implementation, add test

* Tighten test

* Rip out dead modules

* Add changelog

Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
2022-02-10 16:44:26 -05:00
Jaison B ecdb8c2ce6
Fix datesearch issue to resolve CI build failures (#3375) 2022-02-10 19:55:31 +00:00
StevenXLi 7841e578ab
2789 nullpointerexception rest hook subscription is not being triggered when cross partition is (#3370)
* Fixed null pointer exception for re-loading subscription on cdr restart and when there's no partition id in the request, and added tests

* added changelogs for this fix

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-02-10 14:14:41 -05:00
Tadgh 43f570259e Merge branch 'rel_5_7' 2022-02-10 08:44:07 -08:00
Jaison B 7794113455
2838 lastn refactor to use extended lucene index (#3339)
* Change token and reference search params to 'keyword' field type

* remove normalizer for keyword field

* WIP - refactor lastN operation to use hibernate search generated ES index.

* Add ES native aggregation builder for lastN

* added date search param support for searching resourcetable ES index

* * Added DateSearch parameterized tests to ElasticSearch test suite

* Added more tests cases for Date searches

* WIP refactor LastN test data to central generator class and use it for both hibernate-search and elastic search implementations.

* WIP fix lastNDataGenerator to avoid assertion errors.

* Fixed tests to run test suite on both existing lastN search implementation and newer extended lucene index based search.

* Cleanup json string to avoid carriage return noise

* Fix checkstyle issues

* Fix checkstyle Msg code issues

* Fix checkstyle Msg code issues

* Add more test case for GT, SA precision modifier

* Fix date precision test cases

* Fix Msg Code conflicts

* Add more logging

* Add way more loggging

* even more logging

* fix msg code conflicts

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-02-10 11:05:31 +00:00
michaelabuckley 3531d9b4fc
Fix exception when contained indexing met hibernate search. (#3372)
* Fix exception when contained indexing met hibernate search.
2022-02-09 20:27:40 -05:00
James Agnew 0f2fc7a882
Allow search narrowing and auth interceptor by `token:in` (#3360)
* Optmize valueset expansion

* Working

* Version bump

* Add documentation

* Add test

* Checkstyle message cleanup

* Add reverse rule

* Test ficx

* Test fix

* Test fix

* Test fixes

* Test fixes

* Test fix

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/security/search_narrowing_interceptor.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/security/search_narrowing_interceptor.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Test fixes

* Fix conflict

* Add setter

* Test fixes

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-02-09 14:27:14 -05:00
Ken Stevens 6ae6d69254 review feedback 2022-02-07 20:25:25 -05:00
Tadgh 0ccf1bfa52 Merge branch 'rel_5_7' 2022-02-07 12:11:35 -08:00
Tadgh a9348b6c51
Bump dependencies for CVES (#3359)
* Bump dependencies for CVES

* Add to cchangesyaml

* Bump java agent
2022-02-07 07:56:25 -05:00
Patrick Werner 2531e6e57d
feat: added support for package.tgz uri in the "file:/" format (#3347)
* feat: added support for package.zgz uri in the "file:/" format

* added changelog entry

* add error code to thrown message

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-02-05 13:25:50 -05:00
Tadgh 1af4912603 Merge branch 'rel_5_7' 2022-02-04 22:22:02 -08:00
James Agnew 1d5714aec2
Fix #3261 - Incorrect revinclude selector (#3358) 2022-02-04 07:50:13 -05:00
TipzCM f6181fb6ff
3354 fixing flakey tests (#3355)
* 3354 fixing flakey tests

* must fix code

* updating number again

* fixing test

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-02-03 18:30:58 -05:00
michaelabuckley 6b15754b4a
Mb auto complete code (#3330)
New autocomplete extension to ValueSet $expand with contextDirection=existing
2022-02-02 21:03:53 +00:00
Tadgh 6982c4d680
bump version to 6.0.0-PRE1-SNAPSHOT (#3353)
* bump version

* Add new version enum

* Bumped to 6.0.0
2022-02-02 12:11:31 -08:00
michaelabuckley 717ff71695
Simplify JPA Elasticsearch Test Configuration (#3345)
* Delete TestR4WithLuceneDisabledConfig

* Split off the ES and ESClient test configs

* move hibernate search config out to add-ins

* Use addIn for all R4

* Finish R4

* Finish R3

* Finish dstu2

* R5

* Remove property override, and docs

* Apply error code to error

* Fix test to match new error code

* Lighten test

* Disabling broken test.
2022-02-02 16:09:19 +00:00
Johnson Lu c42ecc5c08
Add error codes to all exceptions (#3278)
* Initial design of adding exception codes to exceptions

* Initial design of adding exception codes to exceptions

* change int module name to string

* add comment

* shorten message

* shorten message

* added checkstyle

* developing checker

* completed checkstyle plugin and unit test for it

* fix NPE

* fix checker so it ignores throws on exceptions that aren't new

* change parameter order in InvalidResponseException

* accept Msg.code() in any parameter since some exceptions like MessageException have the message string as the second parameter

* exclude generated files

* BIG COMMIT added error codes to all exception throws

* example test fix

* Modified tests such that the assert statements would better match the message responses.

* Modified additional tests such that the assert statements would better match the message responses.

* fix test

* merge master

* merge master

* Fourth commit of modified tests such that the assert statements would better match the message response

* Changes made to modify assert statements such that they match the new errors which now use error codes. Also changed ResourceNotFoundException to include error codes in its messages.

* Modified assert messages to better match new error codes

* Time Zone changes DRAFT. Certain tests pass in intellij and fail during mvn install

* Modified assert messages to better match new error codes

* Added comments for time zone fixes. Previous commit comment on time zone fixes was incorrect. By invaliding caches, all tests on both intellij and mvn install passed.

* Reverted changes on azure-pipelines.yml

* updated hapi-fhir version for checkstyle module

* changes to azure-pipelines.yml

* changes to azure-pipelines.yml

* change to pom.xml to include hapi-fhir-checkstyle in ALLMODULES

* changes to azure-piplines (these changes are to be reverted after testing)

* reverted changes to azure-piplines

* reverted change where hapi-fhir-checkstyle was added to pom.xml (hapi-fhir)

* Attempted fix on checkstyle build error

* modified azure-piplines.yml to change maven repository for checkstyle build

* Attempted fix on checkstyle build error

* checkstyle config location change for hapi-depoloyable-pom. (will be reverted if it does not work)

* attempted dependency add for hapi-depoloyable-pom. (will be reverted if it does not work)

* reverted changes for hapi-deployable-pom

* add javadoc

* update last code

* Attempted fix on checkstyle build error

* Finished adding in missing error codes to pass Checkstyle checks

* Test pipelining

* Fixing errors and bumping version (as suggested by Gary)

* Merge

* Fixing Checkstyle error

* Attempted fix for date error

* Add error code onto assert statement

* Add in a couple more error codes

* Fixing assert statements

* Bump to static version for dependency

* Adding error code to message

* Adding error codes to exceptions

* Adding error codes to exceptions

* Change to work with cdr branch

* Update to faulty error message

* Merge changes

* allow checkstyle pom to deploy

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com>
Co-authored-by: Predap <simon.zuccherato@gmail.com>
Co-authored-by: Predap <46201929+Predap@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2022-01-31 13:10:15 -08:00
TipzCM 65398ca14f
3156 multiple tag race condition (#3297)
* 3156 fix race condition that results in multiple tags being created

* 3156 added changelog

* cleanup

* added smile jira ticket

* 3156 review fixes

* review fixes

* 3156 added an additional integratoin test

* cleanup

* review fix and master merge

* threadsafe stuff

* small change

* upping min threads for tests to pass

* changing test

* test check

* fix

* test testing

* one more update

* using threadpoolutil

* temporary measure

* git push

* all builds

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-01-31 08:49:12 -08:00
Tadgh ad3e282b8b Fix globbing pattern for log files 2022-01-28 10:46:57 -08:00
Jens Kristian Villadsen fc84fdc33e
Update instance_validator.md (#3328) 2022-01-28 13:16:44 +01:00
Tadgh 3d4a0d89cf
add needed dependendencies for mysql and mssql (#3343)
* add mssql and mysql flyway dependencies

* add exclusions to CQL to prevent duplicate classes on the classpath

* wip

* ad more databases

* finish test
2022-01-28 03:03:13 +00:00
Tadgh 0df332763e Add okhttp dep 2022-01-27 14:03:37 -08:00
TipzCM 41193c60db
3335 allow alternative character encoding length in searchparam (#3336)
* added fixme

* 2714 added support for specifying max code lengths for supported phonetic encoders

* 3335git status

* 3335 updated changelog

* 3335 review fixes

* review fixes

* fixing test

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-01-27 17:29:07 +00:00
Tadgh 6506527dd6
Fix mdm config for single application context environment. (#3338)
* wip

* remove beans

* Remove javax.mail from the classpath as we use simplemail instead, which uses jakarta.
2022-01-27 06:18:44 -05:00
James Agnew 3f42414287
Validate include statements for JPA (#3331)
* Validate include statements for JPA

* Add changelog

* Optmize test fix
2022-01-26 09:16:28 -05:00
Tadgh cd29d369b6
Add okhttp dep to r5 and indicate which deps need to be included (#3332) 2022-01-25 18:39:32 +00:00
James Agnew 31bb1d9e9a
Bump RestEasy to 5.0.2 (#3329)
* Bump deps

* Test fix

* Add test logging

* Add test logging

* Add logging
2022-01-24 20:15:41 -05:00
katiesmilecdr a11d72ba51
3322 graph ql searches cannot be executed when number of matching results exceeds default page size (#3323)
* fix NPE

* check if size is null
2022-01-24 11:53:21 -05:00
Patrick Werner 37e7d6eea5
populate ValueSet.url in $expand Operation (#3241) 2022-01-24 08:12:56 -08:00
James Agnew 715a4c4602
Fix resource version regression caused by Hibernate 5.6 (#3325)
* failing test

* failing test

* Fixes

* Updated note to self

* Improve pre-caching of resource IDs

* Work on tests

* Test fixes

* Add changelog

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-01-23 19:05:02 -05:00
Ken Stevens ed2ea91f56
concurrent validation performance improvement (#3327) 2022-01-23 15:55:31 -05:00
Tadgh 42ff607561
Rel 5 5 5 merge back (#3326)
* Add backport

* Add versions

* remove not real versions
2022-01-22 12:47:34 -05:00
dependabot[bot] 2b4ace3c78
Bump h2 from 2.0.206 to 2.1.210 (#3324)
* Bump h2 from 2.0.206 to 2.1.210

Bumps [h2](https://github.com/h2database/h2database) from 2.0.206 to 2.1.210.
- [Release notes](https://github.com/h2database/h2database/releases)
- [Commits](https://github.com/h2database/h2database/compare/version-2.0.206...version-2.1.210)

---
updated-dependencies:
- dependency-name: com.h2database:h2
  dependency-type: direct:production
...

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

* Add chasngelog

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2022-01-22 11:18:57 -05:00
James Agnew 3ab59f2e34
Avoid JsonParser load (just a test) (#3303)
* Fix #3268 - Avoid JsonParser load (just a test)

* Clean up tests

* Bump core version

* Test fix

* Bump
2022-01-21 19:24:20 -05:00