Tadgh e7a4c49aac
Rel 6 1 mergeback (#3927)
* 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

* Bump Version for non-breaking purposes

* Fix broken test

* bump error code

* revert internal logic

* Revert offset mode change

* wip

* 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

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>
2022-08-18 17:21:27 -07:00

225 lines
7.1 KiB
XML

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 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>
<!-- Note: HAPI projects use the "hapi-fhir" POM as their base to provide easy management. You do not need to use this in your own projects, so the "parent" tag and it's contents below may be removed
if you are using this file as a basis for your own project. -->
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.2.0-PRE2-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>
<artifactId>hapi-fhir-cli-jpaserver</artifactId>
<packaging>war</packaging>
<name>HAPI FHIR - Command Line Client - Server WAR</name>
<dependencies>
<!-- This dependency includes the core HAPI-FHIR classes -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
<scope>provided</scope>
</dependency>
<!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency is used for the "FHIR Tester" web app overlay -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<type>war</type>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
</dependency>
<!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback
is used here, but log4j would also be fine. -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<scope>provided</scope>
</dependency>
<!-- Needed for JEE/Servlet support -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise the following can be omitted. -->
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
<scope>provided</scope>
</dependency>
<!-- Used for CORS support -->
<!-- Spring Web is used to deploy the server to a web container. -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<scope>provided</scope>
</dependency>
<!-- You may not need this if you are deploying to an application server which provides database connection pools itself. -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
</dependency>
<!-- This example uses H2 embedded database. If you are using another database such as Mysql or Oracle, you may omit the following dependencies and replace them with an appropriate database client
dependency for your database platform. -->
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
</dependency>
<!-- Hibernate search Lucene backend -->
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-lucene</artifactId>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analyzers-phonetic</artifactId>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-backward-codecs</artifactId>
</dependency>
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<exclusions>
<exclusion>
<artifactId>Saxon-HE</artifactId>
<groupId>net.sf.saxon</groupId>
</exclusion>
<exclusion>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-core</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<build>
<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver-example.war -->
<finalName>hapi-fhir-cli-jpaserver</finalName>
<!-- The following is not required for the application to build, but allows you to test it by issuing "mvn jetty:run" from the command line. -->
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<configuration>
<webApp>
<contextPath>/hapi-fhir-jpaserver-example</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifestEntries>
<Build-Time>${maven.build.timestamp}</Build-Time>
</manifestEntries>
</archive>
<overlays>
<overlay>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
</overlay>
</overlays>
<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
<attachClasses>true</attachClasses>
<packagingExcludes>
WEB-INF/lib/Saxon-HE-*,
WEB-INF/lib/hapi-*
</packagingExcludes>
</configuration>
</plugin>
<!-- This is to run the integration tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>