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>
<version>7.7.9-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>
<version>10.16.1.1</version>
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</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbytools</artifactId>
<scope>test</scope>
<version>10.16.1.1</version>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
<dependency>
<groupId>com.oracle.database.jdbc</groupId>
<artifactId>ojdbc11</artifactId>
</dependency>
Mergeback 7_4 (#6158) * use SearchParamater validator in package installer (#6112) * Ensure ' ' is treated as '+' in timezones with offsets. (#6115) * Use lockless mode when adding index on Azure Sql server (#6100) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT (#6127) * fix hfj search migration task (#6143) * fix migration task * changelog * changelog * code review * spotless --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> * Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive (#6135) * MSSQL: Migrate HFJ_RESOURCE.FHIR_ID to new collation: SQL_Latin1_General_CP1_CS_AS * Spotless. * Enhance test. Fix case in ResourceSearchView to defend against future migration to case insensitive collation. * Remove TODOs. Add comment to ResourceSearchView explaining why all columns are uppercase. Changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml Code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Common API for FHIR Data Access (#6141) * Add initial interface for common FHIR API * Fix formatting * Update javadocs * Address code review comments --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: JP <jonathan.i.percival@gmail.com>
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<dependency>
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
<scope>test</scope>
</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>
Mergeback 7_4 (#6158) * use SearchParamater validator in package installer (#6112) * Ensure ' ' is treated as '+' in timezones with offsets. (#6115) * Use lockless mode when adding index on Azure Sql server (#6100) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT (#6127) * fix hfj search migration task (#6143) * fix migration task * changelog * changelog * code review * spotless --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> * Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive (#6135) * MSSQL: Migrate HFJ_RESOURCE.FHIR_ID to new collation: SQL_Latin1_General_CP1_CS_AS * Spotless. * Enhance test. Fix case in ResourceSearchView to defend against future migration to case insensitive collation. * Remove TODOs. Add comment to ResourceSearchView explaining why all columns are uppercase. Changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml Code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Common API for FHIR Data Access (#6141) * Add initial interface for common FHIR API * Fix formatting * Update javadocs * Address code review comments --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: JP <jonathan.i.percival@gmail.com>
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<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>junit-jupiter</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>postgresql</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>mssqlserver</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>oracle-xe</artifactId>
<scope>test</scope>
</dependency>
<!-- Stupid testcontainers has a runtime dep on junit4 -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
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<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>