honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity
8,289 Commits 675 Branches 130 Tags 1.2 GiB
Commit Graph

434 Commits

Author SHA1 Message Date
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
Tadgh bb7a773f41 Merge branch 'master' into spring-batch-integration 2020-06-23 16:02:41 -07:00
ianmarshall 5b120ee71e Removed unused code and import statement. 2020-06-17 11:57:37 -04:00
ianmarshall 5d22af45bf Added tests for cases where a renamed column is used in a Foreign Key constraint. 2020-06-17 11:56:20 -04:00
ianmarshall eb990e9a68 Enhance added JUnit test. 2020-06-17 09:05:53 -04:00
ianmarshall cc7ed1b036 Cleanup JUnit test. 2020-06-16 17:21:17 -04:00
ianmarshall 2d857f484c Fix broken JUnit. 2020-06-16 17:13:00 -04:00
ianmarshall 0bd8084b5e Additional fixes to migration tasks for MySQL. 2020-06-16 16:05:10 -04:00
Tadgh 798fdb9cc2 Merge branch 'master' into spring-batch-integration 2020-06-15 09:10:41 -07:00
jamesagnew db4b749436 License updates 2020-06-14 15:44:33 -04:00
Tadgh 4270636d43 Merge branch 'master' into spring-batch-integration 2020-06-12 16:20:54 -07:00
Tadgh 0f469c1a56 Rework to allow for job creation inside of batch 2020-06-12 14:20:50 -07:00
ianmarshall 1ed65f2e03 Enable rename table column migration task for MySQL. 2020-06-12 09:01:46 -04:00
Tadgh a9c704c06e Merge branch 'master' into spring-batch-integration 2020-06-10 12:24:19 -07:00
jamesagnew 05df4f0827 Migration task updates 2020-06-10 09:56:49 -04:00
James Agnew b8da4f0140
Add package support (#1911) 
* Begin rework of package management

* Work on NPM

* Work on package management

* Work on NPM

* NPM rework

* Work on NPM

* NPM package rework

* Updates

* Updates

* Add license

* Work on package server

* Work on package importing

* Work on package management

* Package rework

* Work on packages

* Work on package manager

* Work on pkgs

* NPM work

* NPM rework

* Work on package cache

* Work on NPM

* Work on NPM

* Package fixes

* Add tests

* Tweaks

* Test fixes

* Add changelog

* Avoid snapshot dep
 2020-06-10 05:30:20 -04:00
Tadgh 9c153527dd remove dead imports 2020-06-09 09:03:56 -07:00
Tadgh 8b995f8be7 Remove dead test 2020-06-08 17:16:22 -07:00
Tadgh 278a1070ae :Merge branch 'master' into spring-batch-integration 2020-06-08 17:16:11 -07:00
Tadgh aa7d1cbcb7 Wip getting tasks built 2020-06-01 11:32:36 -07:00
Tadgh 81d5ff8f5a Add schema initialization 2020-05-27 17:06:52 -07:00
James Agnew 22af36ae7b
Conditional update on Partitioned Server fails (#1870) 
* Fix #1869

* Remove FIXME

* Test fix

* Test fix
 2020-05-27 10:40:29 -04:00
jamesagnew 5482367e37 Remove redundant index - Already covered by FK 2020-05-26 08:54:00 -04:00
jamesagnew 499f1ce672 Test order fix 2020-05-26 05:41:45 -04:00
jamesagnew 9192d41448 Credit for #1637 2020-05-23 17:16:19 -04:00
Jacob Stampe Mikkelsen 262a964a31
Add index on CONCEPT_PID on TRM_CONCEPT_PROPERTY to optimize a full-reindex of lucene index which can be needed when running in a docker container where the lucene files are discarded on redeploy. (#1637) 
Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-05-23 17:11:21 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857) 
EMPI Initial Implementation (still plenty of known gaps)
 2020-05-22 15:03:20 -04:00
jamesagnew 52c8e3551c Version bump to 5.1.0-SNAPSHOT 2020-05-15 14:43:32 -04:00
jamesagnew b46f4a993d One more fix for 5.0.1 2020-05-15 09:58:45 -04:00
jamesagnew fe0e07a313 Bump to 5.0.1 2020-05-15 05:47:01 -04:00
Tadgh 9fec726b0e
Add missing indexes on ResourceIndexedSearchParamDate (#1847) 
* Add migration tasks for new indexes. Add new indexes to ResourceIndexedSearchParamDate

* fix dates on task, remove redundant index

* Today is not the 20th

* Fix incorrectly named migration indexes

* out of order indexes
 2020-05-15 05:38:16 -04:00
jamesagnew 1d13e29ac0 Version bump to 5.1.0-SNAPSHOT 2020-05-12 20:04:20 -04:00
jamesagnew d631ecff4a Prepare for 5.0.0 2020-05-12 11:49:18 -04:00
jamesagnew 034e878a6f Add NOP tasks for 4.3.0 to avoid migrator issues 2020-05-10 12:09:47 -04:00
James Agnew a77aa6a28e
Multitenancy Ticket 2 - #1813 (#1821) 
* Work on multitenancy

* Second ticket started

* More multitenancy work

* Work on tenancy security

* Work on multitenancy

* Test fixes

* Add docs

* cs tweak

* Multitenancy fixes

* Add debug log

* Fix build

* Add headers

* Add partition selection interceptor hook

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

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

* Account for review comments

* Resolve FIXMES

* Work on tests

* Test fixes

* A bit more cleanup

* Work on multitenancy

* Update hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientExamples.java

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

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md

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

* Address review comments

* Allow disabling text modifier indexing

* Add changelog

* Docs fixes

* Address review comment

* Resolve merge conflicts

* Merge master

* Compile fix

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-05-05 15:12:15 -04:00
jamesagnew 8b49142b94 Clean up migrator tasks 2020-05-01 15:03:36 -04:00
James Agnew 3d5a8bb3f8
Add UCUM support (#1824) 
* Add UCUM support

* Add changelog

* Some cleanup

* Test fix

* Add flywayDB callback

* Add hooks to schema migrator
 2020-04-30 15:22:41 -04:00
Tadgh a5e1b3d159 Minor changes for merge conflicts 2020-04-29 16:18:02 -07:00
Tadgh 8f8a8a3dc2 Merge branch 'master' into date-match-bug 2020-04-29 16:17:50 -07:00
jamesagnew 0d8c42ee1a Migrator tweaks 2020-04-29 10:13:55 -04:00
jamesagnew 36a7e9c980 Test fixes 2020-04-22 14:56:13 -04:00
jamesagnew af43c4377a Roll back a change that was causing test failures 2020-04-22 14:11:01 -04:00
jamesagnew 465bce952e A couple more migration fixes 2020-04-20 18:32:48 -04:00
jamesagnew 9ed358f665 One more migration fix 2020-04-20 17:44:50 -04:00
jamesagnew e98bf2b0d3 Migration fix 2020-04-20 17:39:12 -04:00
jamesagnew 00b1912a67 Fix typo 2020-04-20 16:59:32 -04:00
jamesagnew e6c806283e Merge branch 'ja_20200206_multitenancy' of github.com:jamesagnew/hapi-fhir into ja_20200206_multitenancy 2020-04-20 16:58:59 -04:00
jamesagnew 544d9fbc6c Add migration tasks 2020-04-20 16:58:48 -04:00
jamesagnew bbab016ca6 Rename config 2020-04-20 12:38:04 -04:00
jamesagnew 982b54df57 Work on multitenancy 2020-04-13 11:50:49 -04:00
jamesagnew c26a5553e9 Multitenancy work 2020-04-12 20:47:32 -04:00
jamesagnew e55ccf88fc Work on multitenancy 2020-04-10 20:01:59 -04:00
jamesagnew e0fcbe1df2 Merge branch 'master' into ja_20200206_multitenancy 2020-04-09 11:52:27 -04:00
jamesagnew edc30568f2 Address review changes 2020-04-07 19:07:07 -04:00
jamesagnew 7f2605def1 Run migrator tests against DERBY and H2 2020-03-31 15:48:11 -04:00
jamesagnew 691f2c4e9a Work on muiltitenancy 2020-03-29 13:35:20 -04:00
jamesagnew 9df4c58122 Work on multitenancy 2020-03-27 09:22:00 -04:00
jamesagnew ec6fe70acb Merge branch 'master' into ja_20200206_multitenancy 2020-03-27 05:50:08 -04:00
jamesagnew 97ac551c87 Dont fail on shrink only task 2020-03-26 19:53:17 -04:00
jamesagnew 7bdb42d70f Restore accidentally removed method 2020-03-17 17:43:46 -04:00
James Agnew 22413911bf
Validation api changes (#1719) 
* Validation enhancements

* Work on validation api reworking

* Keep working on validation API

* Keep working on new term API

* Work on validation api

* Ongoing work on validation

* Work on integrating validation

* Work on validation API

* Add to validation API

* Work on validation

* Work on API

* Work on validation

* Work on validation API

* Work on validation API

* Work on validation api

* Work on validation API

* Work on validation api

* Validation API changes

* Work on API

* More work on validationo API

* Work on validation API

* FIxes

* WOrk on validation api

* Work on validation API

* Tests passing!

* More cleanup

* More validation API changes

* Fix intermittent test failure

* Package reorg

* Validation API work

* Work on doocumentation

* Work on API

* More work on new validation API

* Fix errorprone-reported error

* Test fixes

* Documentation updates

* Documentation tweaks

* Work on API

* Bean name adjustments

* Build fixes

* Some test fixes
 2020-03-17 13:28:59 -04:00
James Agnew 9305bef4ef
Remove useless migrator task generics (#1687) 
* Remove useless migrator task generics

* Clean a couple of compile errors

* Try to fix intermittent
 2020-03-17 13:28:43 -04:00
Tadgh 598bf56e87 Broken SQL Statement 2020-03-04 08:56:03 -08:00
Tadgh 14f671ec0b Fix SQL Typo 2020-03-03 22:31:37 -08:00
Tadgh 8b223a1fd9 Rework selection generation of calculator. Add null check for empty dates 2020-03-03 16:07:25 -08:00
James Agnew 4a160a2df3 Merge branch 'master' into ja_20200206_multitenancy 2020-03-03 09:25:19 -05:00
Gary Graham df9e86ec66 Merge branch 'master' into date-match-bug 2020-02-25 17:26:53 -05:00
James Agnew b2b0ff22b4
Collapse date joins (#1726) 
* Collapse date joins

* Add changelog

* Address review comments

* Add whitespace

* fix test

Co-authored-by: Ken Stevens <ken.stevens@sympatico.ca>
 2020-02-25 17:17:13 -05:00
Gary Graham f56e38148b Add flag to DaoConfig controlling behaviour 2020-02-25 16:43:17 -05:00
Gary Graham 97c98254d0 Extract Common functionality out of CalculateHashesTask, build CalculateOrdinalDatesTask based on it 2020-02-25 16:09:08 -05:00
Gary Graham 3ec772b527 rework ResourceIndexedSearchParamDate constructor to support incoming string values 2020-02-25 14:06:36 -05:00
Gary Graham 13cc8b69aa Add schema migration 2020-02-25 11:27:08 -05:00
Gary Graham 3b41b5b960 Type migration to boxed integer to avoid int defaulting to 0 2020-02-25 11:18:39 -05:00
Ken Stevens 38bae8866b quiet migration tasks during tests 
also add description to schema initialization tasks
 2020-02-25 09:43:34 -05:00
Ken Stevens 8d1d3cee75 Merge remote-tracking branch 'remotes/origin/master' into ks-20200204-quiet-migrate-in-test 2020-02-25 09:20:35 -05:00
jamesagnew d39b54e711 Add missing migration task 2020-02-20 05:39:56 -05:00
ianmarshall 96d00f633c Move new migration task to version 4.3.0. 2020-02-18 14:09:17 -05:00
ianmarshall f7db280099 Merge remote-tracking branch 'remotes/origin/master' into im_20200131_remove_circular_dependency_forcedid 
# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
 2020-02-18 12:13:00 -05:00
jamesagnew ddc7b601ee Version bump to 4.3.0-SNAPSHOT 2020-02-16 19:23:22 -05:00
jamesagnew 4fd80cfca7 Bump to 4.2.0 2020-02-16 19:00:15 -05:00
Ken Stevens da11d3d89e
remove distinct from search (#1712) 
* it works now

* oops

* add successful migration message

* add successful migration message

* Add fix for #1300

* Remove FIXME

* Test fix

* Test fix

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-02-15 12:45:59 -05:00
Ken Stevens 5e8eec8bf6 it works now 2020-02-09 18:29:55 -05:00
James Agnew b2d2346228 Work on multitenancy 2020-02-07 15:18:06 -05:00
Ken Stevens 5f30bdb27b not sure this is going to work yet 2020-02-04 17:00:56 -05:00
Ken Stevens 318b306020
fix migration (#1699) 2020-02-03 17:13:35 -05:00
Ken Stevens 3c46595e81 Merge remote-tracking branch 'remotes/origin/master' into ks-20200203-remove-search-lastused 2020-02-03 11:33:15 -05:00
Ken Stevens b4325199cf review feedback 2020-02-03 11:20:18 -05:00
James Agnew 709aeb4ae8
Drop unnecessary index (#1696) 2020-02-03 10:29:39 -05:00
Ken Stevens cda906d7b8 Column removed. Time to run tests. 2020-02-03 09:44:10 -05:00
ianmarshall 5d5b3d7639 Changes to schema to loosen dependencies between Forced ID table and the Resource and Resource History tables. 2020-01-31 11:16:01 -05:00
James Agnew 3edeb03edc
Rework hashcode generation (#1684) 
* Rework hashcode generation

* Compile fix

* Hashcoode refactoring

* FIx compile errors
 2020-01-26 22:23:06 -05:00
Jafer Khan 4a4fb0fd9d Remove transient fields from migration task 2020-01-24 08:28:01 -05:00
James Agnew 0718f6b52a
Allow schemalocation in XML validation (#1677) 
* Allow schemaLocation declaration in XML when validating

* Add fix for #1676
 2020-01-21 07:14:16 +09:00
James Agnew a19d246432 License header version bump, and add the ability for "add column" 
migration tasks to fail gracefully
 2020-01-12 11:01:21 +08:00
James Agnew a61527d4cb Allow multiple PK column in addTable migrator 2019-12-21 14:05:35 -05:00
James Agnew a94b684be5 Addres TODO 2019-12-18 14:43:57 -05:00
James Agnew 0a21ab6941 Use datasource for migrator 2019-12-18 14:23:46 -05:00
Ken Stevens 68a7613f9e Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseFlywayMigrateDatabaseCommand.java
 2019-12-16 08:58:26 -05:00
jamesagnew 4592decbfa Add license headers 2019-12-15 19:51:49 -05:00
Ken Stevens 9f422efd7a handle case where version list is quoted 2019-12-14 21:02:31 -05:00
Ken Stevens 7c3514fecc Skip versions tested 2019-12-14 19:00:58 -05:00
Ken Stevens 4946fffac2 pass test 2019-12-14 17:27:17 -05:00
Ken Stevens 11e55cebf5 begin with failing test 2019-12-14 17:26:56 -05:00
Ken Stevens 0dde239696 migration task don't compare length if no length is specified in the task 2019-12-13 15:12:59 -05:00
Ken Stevens 931a41938b added dry-run output to both Flyway and TaskOnly migrator 
dry-run only calls TaskOnly migrator now
 2019-12-12 14:42:43 -05:00
Ken Stevens 83106c92c1 move quartz stuff out 2019-12-11 17:00:31 -05:00
Ken Stevens 91f4e62148 Oracle works yay! 2019-12-11 15:15:47 -05:00
Ken Stevens 7cc690ffd3 Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-12-11 14:17:54 -05:00
Ken Stevens 7c1544d8f3 strip comments from sql before splitting ; (to avoid ; in comments) 2019-12-11 14:02:24 -05:00
Ken Stevens da5034959b start working on quartz fix 2019-12-11 13:41:27 -05:00
Ken Stevens ae5f00accc add support to stub out renameindex 2019-12-11 12:07:43 -05:00
Ken Stevens 176bf657a7 Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 
# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
 2019-12-10 10:10:41 -05:00
Ken Stevens 198779a25f fix MSSQL index rename 2019-12-09 18:36:41 -05:00
Ken Stevens 3657a3ad5a pre-review cleanup 2019-12-09 16:51:42 -05:00
Ken Stevens bd1b41ff82 change out-of-order-permitted from environment variablet to flag to work like dont-use-flyway 2019-12-09 16:44:24 -05:00
Ken Stevens 77373605bd add 420 migration 2019-12-09 15:58:08 -05:00
Ken Stevens b0b410384f add renameIndex task 2019-12-09 15:42:40 -05:00
Ken Stevens deb5fd40a7 Added stubbed tasks for add and drop index 2019-12-09 14:42:37 -05:00
Ken Stevens ec37138138 add environment variable to allow flyway out of order migration 2019-12-09 11:32:25 -05:00
Ken Stevens 0b30033b0a upgrade flyway to latest version 
automatically repair failed migrations
 2019-12-09 11:19:18 -05:00
Ken Stevens 45bab9879f migration failed when no-column-shrink was enabled. 2019-12-06 19:21:30 -05:00
Ken Stevens bfa89483e7 Merge remote-tracking branch 'origin/master' into ks-20191119-scheduler 2019-12-06 18:13:38 -05:00
James Agnew 438ef70fdb Reuse connections in brute force migrator 2019-12-06 16:52:26 -05:00
Ken Stevens 6c432733d5 Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-12-05 18:03:02 -05:00
James Agnew d91617e923
Account for review changes (#1623) 2019-12-05 18:01:45 -05:00
Ken Stevens 66cc83464f Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-12-05 13:06:44 -05:00
James Agnew 69a5266127 Allow non-flyway migration 2019-12-05 10:46:37 -05:00
Ken Stevens e0a2b9a179 support schema initialize naming in a backwards compatible way 2019-12-02 19:02:04 -05:00
Ken Stevens c27dfdff51 back out schema initialize naming. there may be migrated schemas in the wild this would interfere with. 2019-12-02 18:48:40 -05:00
Ken Stevens f29118fa9c move clustered quartz from cm db to pers db 2019-12-02 14:32:34 -05:00
Ken Stevens 63218e560d Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-12-02 08:59:17 -05:00
James Agnew 86bd9a28fe
Fix to valueset expansion logic (#1613) 
* Fox to valueset expansion logic

* Work on docs

* Docs tweaks

* Docs tweaks

* Fix test

* Remove unused class

* Add changelog
 2019-12-01 21:21:19 -05:00
Ken Stevens a58da3b535 name schema initializer to distinguish between different schemas 2019-11-28 12:10:34 -05:00
Ken Stevens bf003f0d16 cleaned up cleanup 2019-11-27 21:54:13 -05:00
Ken Stevens 9693b1736e fixed quartz sql with a hack. need a better fix. 2019-11-27 17:10:27 -05:00