Commit Graph

273 Commits

Author SHA1 Message Date
Tadgh b7398cb6f2 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-10 10:33:24 -05:00
Tadgh e26d757ba3 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-09 22:54:24 -05:00
James Agnew 807d9d53f0
Improve performance for large transactions (#2462)
* Performance tweaks

* Work on processing speed

* Disable no longer relevant tests

* Work on performance

* Work on tests

* Work on large transaction performance

* Add changelog

* Perf tweaks

* Test fixes

* Resolve FIXME

* Fixes

* Test cleanup

* Fix broken changelog entry
2021-03-09 18:16:02 -05:00
James Agnew be50a46d76
Tweaks to contained searches (#2461)
* Tweaks to contained searches

* Add changelog

* Build fix
2021-03-09 11:51:30 -05:00
Frank Tao bf8e890a0c
Supported contained resource search (#2441)
* POC for indexing on contained resource - test case may failed

* Test contained url

* Add a spt to handle contained flag

* Added search option for contained resource

* Impl contained resource search

* fixed typo

* Reworked on creating index based on the review comments

* Added changelog

* Added more test cases

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-03-09 06:50:23 -05:00
Tadgh 27952ab5e4 add patient export, partial rework for multiple _typeFilters 2021-03-09 00:56:49 -05:00
Tadgh ff1c6e4d27 Start with failling test and partial job config 2021-03-04 16:15:51 -05:00
Tadgh de09c7e2da Bit of logic tidying 2021-03-03 19:03:31 -05:00
Tadgh 7b663bfe99 Add constants, fix up some tests 2021-03-03 18:51:03 -05:00
Tadgh 74066a81b6
Merge pull request #2420 from hapifhir/issue-2401-add-support-for-group-id-export
Issue 2401 add support for group id export
2021-02-26 10:23:42 -05:00
Ken Stevens 7d769e3b05
Issue 2332 create via put for implementationguide that references some placeholders (#2423)
* begin with failing test

* fixed.  test passes.

* documentation and changelog

* added ConceptMap

* review feedback
2021-02-26 09:44:48 -05:00
Tadgh 1663e367a6 Address review comments 2021-02-25 16:23:36 -05:00
Ken Stevens 30905aeba7 Merge remote-tracking branch 'origin/master' into issue-2401-add-support-for-group-id-export 2021-02-24 09:38:59 -05:00
Ken Stevens 9bc051c193 added mdm flag 2021-02-19 20:47:43 -05:00
Nick Goupinets ddd7c0f267
Merge pull request #2397 from hapifhir/ng_codepoint_fix
UTF-16 characters might cause errors when calculating hash values
2021-02-19 17:22:20 -05:00
James Agnew 3eda19c65a
Version bump (#2400)
* Version bump

* Docs changes

* Docs tweaks

* Docs tweak

* Spelling fixes

* Docs tweaks
2021-02-18 11:07:49 -05:00
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
Nick Goupinets c4daefc9fb Initial implementation 2021-02-16 17:19:57 -05:00
James Agnew e195bdc065
Try to avoid codecov fluctuations (#2344)
* Try to avoid codecov fluctuations

* Less slowdown

* Another build tweak

* Build tweak

* Container bump

* Another build attempt

* One more test
2021-02-03 09:44:57 -05:00
James Agnew 0f31d106e5
Allow empty request details in JPA (#2343)
* Allow empty request details in JPA

* Test fixes
2021-02-02 11:00:14 -05:00
Frank Tao 1d835d82d6
Fixed Ucum Conversion NullPointerException issue (#2331)
* Fixed Ucum Conversion NullPointerException issue

* Revoke:save value to the original table if it can't be normalized
2021-01-30 19:30:12 -05:00
Kevin Dougan SmileCDR 2308d8f44b
Merge CQL Initial Implementation Into master (#2330)
* CQL initial implementation
2021-01-29 16:35:38 -05:00
James Agnew 909d9f742c
Enable Auto-reference versions in JPA (#2323)
* Automatic reference versions

* Auto reference versions

* resolve fixmes

* Add changelog

* Test fixes

* Test fixes

* Resolve fixmes

* Work on versioning

* Add support for _includes

* Update headers

* Change visibility

* One more tweak

* One more API tweak

* Fixes

* Account for review comments

* Fix errorprone reported issue

* Test fix

* Test fixes

* Test fixes
2021-01-27 14:49:10 -05:00
Frank Tao 66e6cab21f
Fixed xml.bind conflict between jakakax and javax (#2320) 2021-01-24 09:56:45 -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
James Agnew 1dc4fb2206
Make quantity indexes use double datatype (#2290)
* Make quantity indexes use double datatype

* Add changelog

* Test fixes

* Test fixes

* Disable test
2021-01-16 18:44:15 -05:00
jamesagnew 5b5023e6ac License headers 2021-01-11 21:00:12 -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
jamesagnew 12d366c86e License header updates 2021-01-05 18:13:14 -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
jamesagnew d20b07c78e Update license headers 2021-01-01 15:50:24 -05:00
jamesagnew f30999b053 License header updates 2021-01-01 15:07:23 -05:00
James Agnew 1eae5db374
autoCreatePlaceholderReferenceTargets true breaks multitenancy (#2215)
* Fix #2209 - autoCreatePlaceholderReferenceTargets true breaks multi-tenancy

* Add changelog

* Address fixme
2020-12-03 08:53:37 -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
James Agnew 8b65db0c98
Improve error message on unique constraint violation (#2182)
* Improve error message on unique constraint violation

* Add changelog

* Test fixes

* Test fix
2020-11-19 21:20:59 -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
IanMMarshall bf9e02bc16
Merge pull request #2164 from jamesagnew/im_20201029_ig_package_long_description
Truncate package descriptions that are longer than 200 characters.
2020-11-10 12:01:53 -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
ianmarshall 881193cf24 Truncate package descriptions that are longer than 200 characters. 2020-11-09 16:19:05 -05:00
jamesagnew 53c23b8d9b Add method to stringutil 2020-10-27 11:29:16 -04:00
James Agnew 8000d2d0cf
SQL Join Rework (#2086)
* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* added the other six index links

* trying different annotations

* Start testing

* Update resources on package install

* Add changelog

* Join rework

* CLean up SQL builder

* Add docs

* SP rework

* Join work

* Work on params

* Work on refactor

* Work on chains

* Work on joins

* Rework queries

* Work on queries

* Many more tests passing

* Refs test

* Work on sorting

* Work on tests

* More joins work

* Work on tests

* Work on queries

* Tests passing

* More test fixes

* Test fixes

* Work on SQL

* Tests passing

* Add some tests

* Add some tests

* License headers

* Use entity manager to get datasourcd

* One more fix

* Model cleanup

* Ongoing work

* Fixes

* Fixes

* Work on joins

* Ongoing fixes

* Merge conflict

* Cleanup

* clean up unused fields

* Work on join

* COmpile fix

* Rework querying

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java

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

* Address review comments

* Resolve fixmes

* Test fix

* Test fixes

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-10-26 05:24:26 -04:00
Ken Stevens 3b91873b7c
delete expunge (#2131)
Added delete _expunge=true
2020-10-20 17:21:50 -04:00
jamesagnew 3ba80de717 Add to date equals comparison 2020-10-11 15:35:28 -04:00
James Agnew 2134d40f1c
Account for timezones in lastUpdated search (#2113)
* Add test

* Fix

* Add changelog

* Test fixes

* Test fix

* Test fixes

* Resolve fixme

* Test fixes

* Remove debug logs

* Try to get CI tests passing again
2020-10-09 07:52:46 -04:00
James Agnew c6777578a8
Avoid DB binary storage deadlock (#2062)
* Avoid DB binary storage deadlock

* Add changelog

* Rework
2020-09-01 09:52:38 -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
James Agnew 3098affccb
Update path when updating resource links (#2007)
* fix resource link index reuse bug

* Resolve merge conflicts

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-07-28 21:40:56 -04:00
James Agnew baba4cc240
Avoid version conflicts on current writes (#1971)
* Add auto retry of transactions

* Experiment in Maven build

* Transaction autoretry

* Work on transaction retries

* Work on transaction retry

* Work on transaction retry

* Fix tests

* Avoid version conflicts

* Add changelog

* Resolve LGTM issue

* FIx transaction scope error

* Test fixes

* Test fix

* Test fixes

* Test fix

* Test fixes
2020-07-13 08:51:13 -04:00