hapi-fhir/hapi-fhir-sql-migrate/pom.xml

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<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">
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<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-deployable-pom</artifactId>
Rel 7 0 mb 2 (#5714) * pom bump to 7.0.0 (#5615) * pom bump to 7.0.0 * add version enum * fixed feb release name --------- Co-authored-by: Long Ma <long@smilecdr.com> * Check index existence on raw SQL creation (#5624) * Add conditional check on index existence before we try again * Add conditional check on index existence before we try again * Changelog * remit * remit * debug statements * 5621 deadlock on caffeine cache when creating a resource with conditional create (#5622) * Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback. * Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations. * adding changelog and spotless. * Fixing typo. * Addressing comments from code review. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614) * Failing test * fix * changelog * Avoiding Exception being thrown on @EventListener invocation (#5628) * replaced EventListener annotation with @PreDestroy * adding changelog --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * simple fix (#5630) Co-authored-by: Long Ma <long@smilecdr.com> * Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625) * Incorrect version from versioned_references.auto_at_paths for conditional update - implementation * Oracle: Ensure migrated database still takes large resource text updates (#5629) * First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration. * First stab at agreed upon solution. * Fix error with 4001 by removing unnecessary annotation. * Spotless and TODO. * Remove annotation for good and set length to LONG32. * Fix copyright year. * Finalize changelog. * Remove migration changes. Fix unit test. * Fix compile error. * Log output. * Refactor resource history code into new ResourceHistoryCalculator. * Spotless. * Convert record to POJO. * Restore pre-17 switch statement. * Finalize new resource history calculator code and tests. * Spotless. * Remove logging. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml Apply code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review feedback. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638) * When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases. * Minor change to fix test * Rename changelog file * Remove TODOs as they're replaced by reported issue * Revert accidental change added with TODO removal * $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637) * $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation * Fix Measure group id null pointer exception (#5620) * Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id * add changelog --------- Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> * Rule evaluation: Allow Bundles with PATCH Parameters (#5641) * Remove parameters clause. * Finalize changelog. Add tests. Finalize implementation. * Undo changes to this test. * Revert all changes to FhirQueryRuleImplTest. Add new RuleImplOpTest. Ensure that proper nested Bundle is created for test and other fixes. * Tweak test. * Use real rule applier in test and remove all mocks. * Prevent batch2 job execution to stop for empty chunk when last job st… (#5635) * Prevent batch2 job execution to stop for empty chunk when last job step is a reduction. Add output to bulk export result even when empty. * Fix test * Unimportant change to force fresh build * Implement review suggestions --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Index review fixes (#5649) * Don't hold locks while adding indices during upgrade. * concurrent indexing is non-transactional in PG. * Fix conditional creates without leading '?' (#5646) * First commit with failing test. * More tests and logs. * More logs * Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(). * Simplify solution. Add more tests. * Changelog. * javadoc * Searching for Bundles with read all Bundles permission returns 403 (#5644) * failing test * another failing test case * fix * changelog * fix bug * spotless * cr * Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660) * Bump json-path * Pin parrson * Bump elastic * Bump spring version * Exclude JDBC * Serializing changes for sensitive data (#5655) * Add new senstiive data serializer * Add new senstiive data serializer * Add new senstiive data serializer * Remove dead comments * Change up the test * review comments * wip * Tighten tests and push annotation down * Tighten tests and push annotation down * Changelog * Add test * 7.0.1-SNAPSHOT bump * Error code * Add method used by CDR * add version enum * Fix test * Revert change to other safe version to stop problem with deprecated field * Rel 7 0 CVE (#5663) * Bump json-path * Pin parrson * Bump elastic * Bump spring version * Exclude JDBC * Descendent fix (#5669) * Fix "is-a" ValueSet expansion, add "descendent-of" support * Fixed tests in DSTU3 and R5 * Trigger new build * Revert "Trigger new build" This reverts commit 46c672b338db1f85c4f438344bfa828bfc723a37. * fix default partition setting on resource (#5617) * fix default partition setting on resource * changelog * Handle DEFAULT partition in rule checker. * Fix spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> * pom bump, doc add, version enum add (#5616) Co-authored-by: Long Ma <long@smilecdr.com> * fix default partition setting on resource (#5618) * fix default partition setting on resource * Handle DEFAULT partition in rule checker. Co-authored-by: Ken Stevens <khstevens@gmail.com> * Add setting to make broker not use JacksonMessageConverter (#5611) * Add setting to make broker not use JacksonMessageConverter * Add changelog * Implement suggestions --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Fix version * add changelog, add attribution, remove accidental bring-overs * add changelog, add attribution, remove accidental bring-overs * Finish jira section --------- Co-authored-by: Ole Hedegaard <ohe@trifork.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * $poll-export-status operation with PatientIdPartitionInterceptor fails with NullPointerException (#5681) * Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. * Fix NPE on -export-status operation with PatientIdPartitionInterceptor * 5654 measurescorer bug for denominator exception (#5677) * update measure bundles and tests for enforced populationId specification on Measure group resources * bump CR version to PRE17 * fix bug in versionEnumTest * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5654-measurescorer-bug.yaml Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type. (#5698) * Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type. * Spotless fix * Address code review comments * version bump to 7.0.0 * pipeline fix * Update java home * Updating version to: 7.0.1 post release. * post mergeback cleanup * bump clinical-reasoning.version to pre17 * test fix * version bump to 7.1.5-snapshot --------- Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com> Co-authored-by: JP <jonathan.i.percival@gmail.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Ole Hedegaard <ohe@trifork.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: markiantorno <markiantorno@gmail.com>
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<version>7.1.5-SNAPSHOT</version>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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</parent>
<artifactId>hapi-fhir-sql-migrate</artifactId>
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<packaging>jar</packaging>
<name>HAPI FHIR Server - SQL Migration</name>
<description>Tooling for migrating SQL schemas.</description>
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<dependencies>
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<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
</dependency>
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<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
</dependency>
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<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
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<version>${project.version}</version>
</dependency>
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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<groupId>org.hibernate.orm</groupId>
<artifactId>hibernate-core</artifactId>
</dependency>
<dependency>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
</dependency>
<dependency>
<groupId>jakarta.transaction</groupId>
<artifactId>jakarta.transaction-api</artifactId>
</dependency>
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<!-- Test Database -->
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
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<scope>test</scope>
</dependency>
<dependency>
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<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
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<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbytools</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
<dependency>
<groupId>com.oracle.database.jdbc</groupId>
<artifactId>ojdbc11</artifactId>
</dependency>
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<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
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<scope>test</scope>
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</dependency>
<dependency>
<groupId>org.jetbrains</groupId>
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<artifactId>annotations</artifactId>
</dependency>
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<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
</dependency>
Ks 20220916 remove flyway (#4040) * removed flyway, started coding persistence * started wiring up new dao service * replace jpa with sqlbuilder * down to 16 failed tests * remove outOfOrder test. We no longer support validating order. * Removed noFlyway mode. It is no longer a thing. * merge migrator * down to 1 failing test * cleanup * removed unused noflyway cli arguments * cleanup * cleanup * cleanup * cleanup * create MigrationTaskList to replace the List<BaseTask> that gets passed around a lot. This allows us to add a bunch of behaviour to that as a first-order thing * fix test * fix test * improve migration table detection to use the catalogue * Msg.code() * cleanup * save version in same format as flyway * cleanup * add migration result to migration result class * failed migrations stay in the table and don't really affect anything. * change log * docs * ugh Flyway requires lower-case column names * integration test fixes * log * fix oracle issue * lowercase tablenames for postgres. fussy fussy! * Revert "lowercase tablenames for postgres. fussy fussy!" This reverts commit 92c9cb263b90cff2190cc327fab051dc3bb2f83f. * revert to capital table names. surround table name by quotes for Postgres. * added log message before executing find all query * changed log message from info to debug * javadoc * pom cleanup * review feedback * Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/MigrationTaskList.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * review feedback * review feedback. Use prepared statement. * Change installedOn insert from timestamp to date * Change installedOn column type from timestamp to date * bump hapi version * fix poms * fix poms and cdr compile * add exclusions to clean up build Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
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<!-- SQL Builder -->
<dependency>
Ks 20220916 remove flyway (#4040) * removed flyway, started coding persistence * started wiring up new dao service * replace jpa with sqlbuilder * down to 16 failed tests * remove outOfOrder test. We no longer support validating order. * Removed noFlyway mode. It is no longer a thing. * merge migrator * down to 1 failing test * cleanup * removed unused noflyway cli arguments * cleanup * cleanup * cleanup * cleanup * create MigrationTaskList to replace the List<BaseTask> that gets passed around a lot. This allows us to add a bunch of behaviour to that as a first-order thing * fix test * fix test * improve migration table detection to use the catalogue * Msg.code() * cleanup * save version in same format as flyway * cleanup * add migration result to migration result class * failed migrations stay in the table and don't really affect anything. * change log * docs * ugh Flyway requires lower-case column names * integration test fixes * log * fix oracle issue * lowercase tablenames for postgres. fussy fussy! * Revert "lowercase tablenames for postgres. fussy fussy!" This reverts commit 92c9cb263b90cff2190cc327fab051dc3bb2f83f. * revert to capital table names. surround table name by quotes for Postgres. * added log message before executing find all query * changed log message from info to debug * javadoc * pom cleanup * review feedback * Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/MigrationTaskList.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * review feedback * review feedback. Use prepared statement. * Change installedOn insert from timestamp to date * Change installedOn column type from timestamp to date * bump hapi version * fix poms * fix poms and cdr compile * add exclusions to clean up build Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
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<groupId>com.healthmarketscience.sqlbuilder</groupId>
<artifactId>sqlbuilder</artifactId>
</dependency>
<!-- test -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
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</dependencies>
<build>
<!-- The following is not required for the application to build, but allows you to test it by issuing "mvn jetty:run" from the command line. -->
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<configuration>
<webApp>
<contextPath>/hapi-fhir-jpaserver-example</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifestEntries>
<Build-Time>${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>
</configuration>
</plugin>
<!-- This is to run the integration tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>