2020-04-02 20:30:19 -04:00
|
|
|
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
|
|
|
|
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
|
|
|
<modelVersion>4.0.0</modelVersion>
|
|
|
|
|
|
|
|
<parent>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-deployable-pom</artifactId>
|
Rel 6 2 mergeback (#4257)
* jm wrong bundle entry url (#4213)
* Bug test
* here you go
* Generate relative URIs for bundle entry.request.url, as specified
* Point jira issue in changelog
* Adjust tests to fixes
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* improved logging (#4217)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Rel 6 1 3 mergeback (#4215)
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Revert offset mode change
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
* Updating version to: 6.1.1 post release.
* fix compile error
* Deploy to sonatype (#3934)
* adding sonatype profile to checkstyle module
* adding sonatype profile to tinder module
* adding sonatype profile to base pom
* adding final deployToSonatype profile
* wip
* Revert version enum
* Updating version to: 6.1.1 post release.
* Add test, changelog, and implementation
* Add backport info
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
* wip
* Add backport info
* Add info of new version
* Updating version to: 6.1.2 post release.
* bump info and backport for 6.1.2
* Bump for hapi
* Implement bug fixes, add new tests (#4022)
* Implement bug fixes, add new tests
* tidy
* Tidy
* refactor for cleaning
* More tidying
* Lower logging
* Split into nested tests, rename, add todos
* Typo
* Code review
* add backport info
* Updating version to: 6.1.3 post release.
* Updating version to: 6.1.3 post release.
* removed duplicate mention of ver 6.1.3 in versionEnum
* backport pr 4101
* mdm message key (#4111)
* begin with failing test
* fixed 2 tests
* fix tests
* fix tests
* change log
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* backport 6.1.3 docs changes
* fixed typo on doc backport message
* fix test breaking
* Updating version to: 6.1.4 post release.
* wip
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* pin okio-jvm for kotlin vuln (#4216)
* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)
* First commit: Failing unit test and a TODO with a vague idea of where the bug happens.
* Don't escape "+" in a URL GET parameter if it starts with "application".
* Remove unnecessary TODO.
* Add changelog.
* Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens.
* Ks 20221031 migration lock (#4224)
* started design
* complete with tests
* changelog
* cleanup
* tyop
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)
* Added test
* Added solution
* Changelog
* Changes made based on comments
* Fix bug with MDM submit
* fix
* Version bump
* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)
* Add constant for interceptor
* add test, changelog
* Allow Batch2 transition from ERRORED to COMPLETE (#4242)
* Allow Batch2 transition from ERRORED to COMPLETE
* Add changelog
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)
* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.
* Update test case.
* Cleaned up changelog.
* Added test case for multiple resource types.
* Added failing test case for not returning Binary resource.
* Refactor solution.
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add next version
* bulk export permanently reusing cached results (#4249)
* Add test, fix bug, add changelog
* minor refactor
* Fix
* Bump HAPI version
* Remove jetbrains
* Fix broken test
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2022-11-07 18:57:57 -05:00
|
|
|
<version>6.3.0-PRE3-SNAPSHOT</version>
|
2020-04-02 20:30:19 -04:00
|
|
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
|
|
|
</parent>
|
|
|
|
|
2021-09-23 22:04:46 -04:00
|
|
|
<artifactId>hapi-fhir-storage</artifactId>
|
2020-04-02 20:30:19 -04:00
|
|
|
<packaging>jar</packaging>
|
|
|
|
|
2021-09-21 11:36:08 -04:00
|
|
|
<name>HAPI FHIR Storage api</name>
|
|
|
|
<description>This project provides services useful for fhir repository storage. Actual repository storage services
|
|
|
|
are not in this project, just the api and helper libraries.
|
|
|
|
</description>
|
2020-04-02 20:30:19 -04:00
|
|
|
|
|
|
|
<dependencies>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-base</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
<exclusions>
|
|
|
|
<exclusion>
|
|
|
|
<artifactId>commons-logging</artifactId>
|
|
|
|
<groupId>commons-logging</groupId>
|
|
|
|
</exclusion>
|
|
|
|
</exclusions>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-server</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
2021-09-24 00:39:15 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-batch</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
2020-04-02 20:30:19 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-structures-dstu2</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-structures-dstu3</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-structures-r4</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-structures-r5</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
2021-11-24 01:05:13 -05:00
|
|
|
<!-- TODO KHS remove jpa stuff from here -->
|
2021-01-22 11:24:23 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-jpaserver-model</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-jpaserver-searchparam</artifactId>
|
|
|
|
<version>${project.version}</version>
|
2020-04-02 20:30:19 -04:00
|
|
|
</dependency>
|
2021-11-10 16:07:36 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-test-utilities</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
<scope>test</scope>
|
|
|
|
</dependency>
|
|
|
|
|
2020-04-02 20:30:19 -04:00
|
|
|
<dependency>
|
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
|
|
|
<groupId>org.hibernate.search</groupId>
|
|
|
|
<artifactId>hibernate-search-mapper-orm</artifactId>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.hibernate.search</groupId>
|
|
|
|
<artifactId>hibernate-search-backend-elasticsearch</artifactId>
|
2020-04-02 20:30:19 -04:00
|
|
|
</dependency>
|
|
|
|
|
|
|
|
<!-- Spring -->
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
<artifactId>spring-beans</artifactId>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
<artifactId>spring-context</artifactId>
|
|
|
|
<exclusions>
|
|
|
|
<exclusion>
|
|
|
|
<artifactId>xml-apis</artifactId>
|
|
|
|
<groupId>xml-apis</groupId>
|
|
|
|
</exclusion>
|
|
|
|
</exclusions>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>com.fasterxml.jackson.core</groupId>
|
|
|
|
<artifactId>jackson-annotations</artifactId>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.jscience</groupId>
|
|
|
|
<artifactId>jscience</artifactId>
|
|
|
|
</dependency>
|
|
|
|
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.quartz-scheduler</groupId>
|
|
|
|
<artifactId>quartz</artifactId>
|
|
|
|
</dependency>
|
|
|
|
|
|
|
|
<!-- Java -->
|
|
|
|
<dependency>
|
|
|
|
<groupId>javax.annotation</groupId>
|
|
|
|
<artifactId>javax.annotation-api</artifactId>
|
|
|
|
</dependency>
|
|
|
|
|
2021-01-22 11:24:23 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>javax.servlet</groupId>
|
|
|
|
<artifactId>javax.servlet-api</artifactId>
|
|
|
|
<scope>provided</scope>
|
|
|
|
</dependency>
|
2020-04-02 20:30:19 -04:00
|
|
|
|
2021-01-22 11:24:23 -05:00
|
|
|
<!-- test dependencies -->
|
2020-04-02 20:30:19 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ch.qos.logback</groupId>
|
|
|
|
<artifactId>logback-classic</artifactId>
|
|
|
|
<scope>test</scope>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
<artifactId>spring-test</artifactId>
|
|
|
|
<scope>test</scope>
|
|
|
|
</dependency>
|
2022-07-11 10:56:22 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>com.github.dnault</groupId>
|
|
|
|
<artifactId>xml-patch</artifactId>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>io.dogote</groupId>
|
|
|
|
<artifactId>json-patch</artifactId>
|
|
|
|
</dependency>
|
2022-07-29 11:12:53 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework.data</groupId>
|
|
|
|
<artifactId>spring-data-commons</artifactId>
|
|
|
|
</dependency>
|
2020-04-02 20:30:19 -04:00
|
|
|
|
2022-07-29 11:12:53 -04:00
|
|
|
</dependencies>
|
2020-04-02 20:30:19 -04:00
|
|
|
<build>
|
|
|
|
<pluginManagement>
|
|
|
|
<plugins>
|
|
|
|
<plugin>
|
|
|
|
<groupId>org.apache.maven.plugins</groupId>
|
|
|
|
<artifactId>maven-site-plugin</artifactId>
|
|
|
|
<configuration>
|
|
|
|
<skipDeploy>true</skipDeploy>
|
|
|
|
</configuration>
|
|
|
|
</plugin>
|
|
|
|
</plugins>
|
|
|
|
</pluginManagement>
|
|
|
|
</build>
|
|
|
|
</project>
|