hapi-fhir/hapi-deployable-pom/pom.xml

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<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>
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<parent>
Convert delete expunge to use Spring Batch (#2697) * prepare to add $delete-expunge operation that will create a spring batch job * Add operation * Wire up jpa provider. Begin with failing test. * Copy/paste bulk import job as a starting point. FIXME with proposed design * delete expunge job parameter validation with test * implemented reader stubbed processor, writer * wip for master merge * started implementing reader * started implementing reader * working with stubs * happy path batch delete expunge is done * Provider done but test not passing. Guessing batch infrastructure not running in that test. * IT test works now * add reader test * Converted delete _expunge=true to use new batch job * DeleteExpungeDaoTest passes * Fix test * Change batch size to integer * rename search count to batch size * Make delete expunge partition aware * updated docs * pre-review cleanup * change log * add partition id to SystemRequestDetails * Make RequestPartitionId serializable * Change delete expunge provider to use partition id instead of tenant name * fix tests * test pointcut gets called * assert on pointcut calls * Add resource type to STORAGE_PARTITION_SELECTED pointcut * bump hapi-fhir version move expunge provider parameters from JpaConstants to ProviderConstants * bump hapi-fhir version * copyrights * restore deleteexpungeservice for mdm * restore deleteexpungeservice for mdm * fix test * public constants * convert instant to date * Moved expunge constants to ProviderConstants * final review * disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run * fix tests * fix tests * fix tests * fix tests * review feedback * review feedback * review feedback * review feedback * review feedback * review feedback * improve logging * bump version * version bump * recovering from failed merge * unzip RequestListJson per Gary's suggestion. I didn't want to do it at first, but as usual Gary was right. * fix serialization
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<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
GM1 Mergeback (#5203) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * Rename file to force IT mode * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * wip * Fix API usage * wip * Version bump --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@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: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
2023-08-15 15:32:10 -04:00
<version>6.9.3-SNAPSHOT</version>
Convert delete expunge to use Spring Batch (#2697) * prepare to add $delete-expunge operation that will create a spring batch job * Add operation * Wire up jpa provider. Begin with failing test. * Copy/paste bulk import job as a starting point. FIXME with proposed design * delete expunge job parameter validation with test * implemented reader stubbed processor, writer * wip for master merge * started implementing reader * started implementing reader * working with stubs * happy path batch delete expunge is done * Provider done but test not passing. Guessing batch infrastructure not running in that test. * IT test works now * add reader test * Converted delete _expunge=true to use new batch job * DeleteExpungeDaoTest passes * Fix test * Change batch size to integer * rename search count to batch size * Make delete expunge partition aware * updated docs * pre-review cleanup * change log * add partition id to SystemRequestDetails * Make RequestPartitionId serializable * Change delete expunge provider to use partition id instead of tenant name * fix tests * test pointcut gets called * assert on pointcut calls * Add resource type to STORAGE_PARTITION_SELECTED pointcut * bump hapi-fhir version move expunge provider parameters from JpaConstants to ProviderConstants * bump hapi-fhir version * copyrights * restore deleteexpungeservice for mdm * restore deleteexpungeservice for mdm * fix test * public constants * convert instant to date * Moved expunge constants to ProviderConstants * final review * disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run * fix tests * fix tests * fix tests * fix tests * review feedback * review feedback * review feedback * review feedback * review feedback * review feedback * improve logging * bump version * version bump * recovering from failed merge * unzip RequestListJson per Gary's suggestion. I didn't want to do it at first, but as usual Gary was right. * fix serialization
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<relativePath>../pom.xml</relativePath>
</parent>
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<artifactId>hapi-deployable-pom</artifactId>
<packaging>pom</packaging>
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<name>HAPI FHIR - Deployable Artifact Parent POM</name>
<build>
<plugins>
<!-- Anything deployable inherits the parent spotless configuration -->
<plugin>
<groupId>com.diffplug.spotless</groupId>
<artifactId>spotless-maven-plugin</artifactId>
<inherited>true</inherited>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
<executions>
<execution>
<id>default</id>
<phase>verify</phase>
<goals>
<goal>check</goal>
</goals>
<inherited>true</inherited>
</execution>
</executions>
<configuration>
<printEqualFiles>false</printEqualFiles>
<failBuildInCaseOfDifferentContentConflict>true</failBuildInCaseOfDifferentContentConflict>
<failBuildInCaseOfEqualContentConflict>true</failBuildInCaseOfEqualContentConflict>
<failBuildInCaseOfConflict>true</failBuildInCaseOfConflict>
<checkCompileClasspath>true</checkCompileClasspath>
<checkRuntimeClasspath>false</checkRuntimeClasspath>
<checkTestClasspath>false</checkTestClasspath>
<skip>false</skip>
<quiet>false</quiet>
<preferLocal>true</preferLocal>
<useResultFile>true</useResultFile>
<resultFileMinClasspathCount>2</resultFileMinClasspathCount>
<resultFile>${project.build.directory}/duplicate-finder-result.xml</resultFile>
<ignoredDependencies>
<dependency>
<groupId>javax.el</groupId>
<artifactId>javax.el-api</artifactId>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</dependency>
<dependency>
<groupId>org.jscience</groupId>
<artifactId>jscience</artifactId>
</dependency>
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<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</dependency>
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<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>annotations</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbynet</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
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<dependency>
<groupId>org.checkerframework</groupId>
<artifactId>checker-compat-qual</artifactId>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>ooxml-schemas</artifactId>
</dependency>
<dependency>
<groupId>net.bytebuddy</groupId>
<artifactId>byte-buddy</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
</dependency>
</ignoredDependencies>
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<ignoredResourcePatterns>
<ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>
<ignoredResourcePattern>.*\.html$</ignoredResourcePattern>
<ignoredResourcePattern>schemaorg_apache_xmlbeans.*</ignoredResourcePattern>
<ignoredResource>classpath.index</ignoredResource>
<ignoredResource>javac.bat</ignoredResource>
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<ignoredResource>about.html</ignoredResource>
<ignoredResource>changelog.xml</ignoredResource>
<ignoredResource>.*/favicon.ico$</ignoredResource>
<ignoredResource>Log4j-charsets.properties</ignoredResource>
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</ignoredResourcePatterns>
</configuration>
</plugin>
</plugins>
</build>
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<reporting>
<plugins>
<plugin>
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<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
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<configuration>
<skip>true</skip>
</configuration>
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</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<reportSets>
<reportSet>
<id>default</id>
<reports>
<report>javadoc</report>
</reports>
<configuration>
<links>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-base</link>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-dstu2</link>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-dstu3</link>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-r4</link>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-r5</link>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-client</link>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-server</link>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-jpaserver-base</link>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-converter</link>
<link>https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-structures-validation</link>
<link>https://docs.oracle.com/javaee/7/api/</link>
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</links>
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<additionalparam>-Xdoclint:none</additionalparam>
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<additionalJOption>-Xdoclint:none</additionalJOption>
<source>11</source>
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</configuration>
</reportSet>
</reportSets>
</plugin>
</plugins>
</reporting>
<profiles>
<profile>
<id>DIST</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<inherited>true</inherited>
<configuration>
<minmemory>128m</minmemory>
<maxmemory>1g</maxmemory>
<linksource>true</linksource>
<verbose>false</verbose>
<debug>false</debug>
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<additionalJOption>-Xdoclint:none</additionalJOption>
<source>11</source>
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</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
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<goal>jar</goal>
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</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
<executions>
<execution>
<id>first</id>
<goals>
<goal>update-file-header</goal>
</goals>
<phase>process-sources</phase>
<configuration>
<addJavaLicenseAfterPackage>false</addJavaLicenseAfterPackage>
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<licenseName>apache_v2</licenseName>
<canUpdateDescription>true</canUpdateDescription>
<canUpdateCopyright>true</canUpdateCopyright>
<trimHeaderLine>true</trimHeaderLine>
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<roots>
<root>src/main/java</root>
</roots>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>