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author
Anthony Cook
committed
Add support for Trino
1 parent 27021fa commit e9d368b

18 files changed

+199
-119
lines changed

‎.gitignore‎

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@@ -4,6 +4,7 @@ WebAPIConfig/
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.idea/
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.metadata/
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*.iml
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*.log
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sandbox/
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/target/
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.settings

‎code/arachne/arachne-commons-3.x-MDACA.jar‎

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‎code/sqlrender/SqlRender-1.19.2-MDACA.jar‎

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‎pom.xml‎

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@@ -20,17 +20,18 @@
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<hibernate.version>8.0.1.Final</hibernate.version>
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<postgresql.version>42.3.7</postgresql.version>
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<bouncycastle.version>1.78</bouncycastle.version>
23-
<shiro.version>2.0.1</shiro.version>
23+
<shiro.version>2.0.1</shiro.version>
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<dom4j.version>2.1.3</dom4j.version>
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<hydra.version>0.4.0</hydra.version>
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<featureExtraction.version>3.2.0</featureExtraction.version>
27-
<tomcat.embed.version>10.1.40</tomcat.embed.version>
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<tomcat.embed.version>10.1.34</tomcat.embed.version>
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<commons-fileupload.version>1.5</commons-fileupload.version>
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<circe.version>1.11.2</circe.version>
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<jersey.version>2.35</jersey.version>
33-
<SqlRender.version>1.16.1</SqlRender.version>
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<!-- <SqlRender.version>1.16.1</SqlRender.version> -->
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<SqlRender.version>1.19.2-MDACA</SqlRender.version>
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<hive-jdbc.version>3.1.2</hive-jdbc.version>
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<pac4j.version>6.0.3</pac4j.version>
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<jackson.version>2.14.3</jackson.version>
@@ -45,13 +46,13 @@
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<!-- default sql server - TODO How about making postgres the default (e.g. in line with open source tech)? -alexfranken -->
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<!-- datasource.driverClassName>com.microsoft.sqlserver.jdbc.SQLServerDriver</datasource.driverClassName>
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<datasource.url>jdbc:sqlserver://serverName;databaseName=databaseName</datasource.url -->
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<datasource.driverClassName>org.postgresql.Driver</datasource.driverClassName>
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<datasource.url>jdbc:postgresql://localhost:5432/OHDSI?currentSchema=webapi</datasource.url>
49+
<datasource.driverClassName>org.postgresql.Driver</datasource.driverClassName>
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<datasource.url>jdbc:postgresql://localhost:5432/OHDSI?currentSchema=webapi</datasource.url>
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<datasource.username>ohdsi_app_user</datasource.username>
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<datasource.password>app1</datasource.password>
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<!--<datasource.validationQuery>SELECT 1</datasource.validationQuery>-->
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<!-- datasource.dialect>sql server</datasource.dialect -->
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<datasource.dialect>postgresql</datasource.dialect>
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<datasource.dialect>postgresql</datasource.dialect>
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<datasource.ohdsi.schema>webapi</datasource.ohdsi.schema>
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<!-- datasource.dialect.source>sql server</datasource.dialect.source -->
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<datasource.dialect.source>postgresql</datasource.dialect.source>
@@ -64,13 +65,13 @@
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<flyway.datasource.username>ohdsi_admin_user</flyway.datasource.username>
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<flyway.datasource.password>admin1</flyway.datasource.password>
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<!-- flyway.locations>classpath:db/migration/sqlserver</flyway.locations -->
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<flyway.locations>classpath:db/migration/postgresql</flyway.locations>
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<flyway.locations>classpath:db/migration/postgresql</flyway.locations>
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<!-- Note: Schema name is case-sensitive. -->
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<flyway.schemas>${datasource.ohdsi.schema}</flyway.schemas>
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<flyway.placeholders.ohdsiSchema>${datasource.ohdsi.schema}</flyway.placeholders.ohdsiSchema>
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<flyway.validateOnMigrate>false</flyway.validateOnMigrate>
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73-
<hibernate.dialect>org.hibernate.dialect.PostgreSQLDialect</hibernate.dialect>
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<hibernate.dialect>org.hibernate.dialect.PostgreSQLDialect</hibernate.dialect>
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<!-- CDM properties -->
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<source.name>CDM_NAME</source.name>
@@ -88,10 +89,10 @@
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<spring.batch.repository.tableprefix>${datasource.ohdsi.schema}.BATCH_</spring.batch.repository.tableprefix>
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<spring.batch.repository.isolationLevelForCreate>ISOLATION_READ_COMMITTED</spring.batch.repository.isolationLevelForCreate>
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<!-- spring.profiles.active>default</spring.profiles.active -->
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<spring.profiles.active>webapi-postgresql</spring.profiles.active>
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<spring.profiles.active>webapi-postgresql</spring.profiles.active>
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<security.provider>AtlasRegularSecurity</security.provider>
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<!-- security.provider>DisabledSecurity</security.provider -->
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<security.provider>DisabledSecurity</security.provider>
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<!-- security.provider>AtlasRegularSecurity</security.provider -->
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<security.token.expiration>43200</security.token.expiration>
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<security.origin>http://localhost</security.origin>
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<security.ssl.enabled>false</security.ssl.enabled>
@@ -542,14 +543,24 @@
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<url>https://jitpack.io</url>
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</repository>
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<repository>
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<id>local-repo</id>
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<id>local-repo-arachne</id>
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<url>file:///code/arachne</url>
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<releases>
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<enabled>true</enabled>
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</releases>
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<snapshots>
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<enabled>true</enabled>
552-
</snapshots>
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<releases>
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<enabled>true</enabled>
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</releases>
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<snapshots>
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<enabled>true</enabled>
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</snapshots>
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</repository>
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<repository>
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<id>local-repo-sqlrender</id>
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<url>file:///code/sqlrender</url>
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<releases>
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<enabled>true</enabled>
560+
</releases>
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<snapshots>
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<enabled>true</enabled>
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</snapshots>
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</repository>
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<repository>
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<id>codeartifact</id>
@@ -581,17 +592,17 @@
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<artifactId>spring-core</artifactId>
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<version>6.1.14</version>
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</dependency>
584-
<dependency>
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<groupId>org.springframework</groupId>
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<artifactId>spring-context</artifactId>
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<version>6.1.14</version>
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</dependency>
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<dependency>
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<dependency>
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<groupId>org.springframework</groupId>
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<artifactId>spring-context</artifactId>
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<version>6.1.14</version>
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</dependency>
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<dependency>
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<groupId>org.springframework</groupId>
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<artifactId>spring-web</artifactId>
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<version>6.1.14</version>
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</dependency>
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<dependency>
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<dependency>
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<groupId>org.springframework</groupId>
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<artifactId>spring-webmvc</artifactId>
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<version>6.1.14</version>
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<scope>import</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.tomcat.embed</groupId>
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<artifactId>tomcat-embed-core</artifactId>
630-
<version>${tomcat.embed.version}</version>
631-
<scope>provided</scope>
632-
</dependency>
639+
<groupId>org.apache.tomcat.embed</groupId>
640+
<artifactId>tomcat-embed-core</artifactId>
641+
<version>${tomcat.embed.version}</version>
642+
<scope>provided</scope>
643+
</dependency>
633644
<dependency>
634-
<groupId>org.apache.tomcat.embed</groupId>
635-
<artifactId>tomcat-embed-websocket</artifactId>
636-
<version>${tomcat.embed.version}</version>
637-
<scope>provided</scope>
638-
</dependency>
645+
<groupId>org.apache.tomcat.embed</groupId>
646+
<artifactId>tomcat-embed-websocket</artifactId>
647+
<version>${tomcat.embed.version}</version>
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<scope>provided</scope>
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</dependency>
639650
<dependency>
640-
<groupId>org.apache.tomcat</groupId>
641-
<artifactId>tomcat-jdbc</artifactId>
642-
<version>${tomcat.embed.version}</version>
643-
<scope>provided</scope>
644-
</dependency>
651+
<groupId>org.apache.tomcat</groupId>
652+
<artifactId>tomcat-jdbc</artifactId>
653+
<version>${tomcat.embed.version}</version>
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<scope>provided</scope>
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</dependency>
645656
<dependency>
646-
<groupId>org.apache.tomcat</groupId>
647-
<artifactId>tomcat-juli</artifactId>
648-
<version>${tomcat.embed.version}</version>
649-
<scope>provided</scope>
650-
</dependency>
657+
<groupId>org.apache.tomcat</groupId>
658+
<artifactId>tomcat-juli</artifactId>
659+
<version>${tomcat.embed.version}</version>
660+
<scope>provided</scope>
661+
</dependency>
651662
<dependency>
652663
<groupId>commons-io</groupId>
653664
<artifactId>commons-io</artifactId>
654665
<version>2.14.0</version>
655666
</dependency>
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<dependency>
657-
<groupId>net.lingala.zip4j</groupId>
658-
<artifactId>zip4j</artifactId>
659-
<version>2.11.3</version>
660-
</dependency>
667+
<dependency>
668+
<groupId>net.lingala.zip4j</groupId>
669+
<artifactId>zip4j</artifactId>
670+
<version>2.11.3</version>
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</dependency>
661672
</dependencies>
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</dependencyManagement>
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<dependencies>
664-
<dependency>
665-
<groupId>org.apache.velocity</groupId>
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<artifactId>velocity-engine-core</artifactId>
667-
<version>2.4</version>
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<exclusions>
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<exclusion>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
675+
<dependency>
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<groupId>org.apache.velocity</groupId>
677+
<artifactId>velocity-engine-core</artifactId>
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<version>2.4</version>
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<exclusions>
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<exclusion>
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<groupId>commons-io</groupId>
682+
<artifactId>commons-io</artifactId>
683+
</exclusion>
684+
</exclusions>
685+
</dependency>
675686
<dependency>
676687
<groupId>org.codehaus.jettison</groupId>
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<artifactId>jettison</artifactId>
@@ -891,9 +902,9 @@
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<artifactId>flyway-core</artifactId>
892903
</dependency>
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<dependency>
894-
<groupId>org.apache.httpcomponents.client5</groupId>
895-
<artifactId>httpclient5</artifactId>
896-
</dependency>
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<groupId>org.apache.httpcomponents.client5</groupId>
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<artifactId>httpclient5</artifactId>
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</dependency>
897908
<!-- dependency>
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<groupId>org.springframework.batch</groupId>
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<artifactId>spring-batch-admin-manager</artifactId>
@@ -1061,19 +1072,19 @@
10611072
<artifactId>buji-pac4j</artifactId>
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<version>9.0.1</version>
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<exclusions>
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<exclusion>
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<groupId>org.pac4j</groupId>
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<artifactId>pac4j-javaee</artifactId>
1067-
</exclusion>
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<exclusion>
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<groupId>org.pac4j</groupId>
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<artifactId>pac4j-javaee</artifactId>
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</exclusion>
10681079
</exclusions>
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</dependency>
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<dependency>
1072-
<groupId>org.pac4j</groupId>
1073-
<artifactId>jakartaee-pac4j</artifactId>
1074-
<version>8.0.1</version>
1075-
</dependency>
1076-
1082+
<dependency>
1083+
<groupId>org.pac4j</groupId>
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<artifactId>jakartaee-pac4j</artifactId>
1085+
<version>8.0.1</version>
1086+
</dependency>
1087+
10771088
<dependency>
10781089
<groupId>org.pac4j</groupId>
10791090
<artifactId>pac4j-jakartaee</artifactId>
@@ -1130,16 +1141,16 @@
11301141
</exclusion>
11311142
</exclusions>
11321143
</dependency>
1133-
<dependency>
1134-
<groupId>org.pac4j</groupId>
1135-
<artifactId>pac4j-saml-opensamlv5</artifactId>
1136-
<version>5.7.7</version>
1137-
</dependency>
1138-
<dependency>
1139-
<groupId>org.apache.santuario</groupId>
1140-
<artifactId>xmlsec</artifactId>
1141-
<version>3.0.3</version>
1142-
</dependency>
1144+
<dependency>
1145+
<groupId>org.pac4j</groupId>
1146+
<artifactId>pac4j-saml-opensamlv5</artifactId>
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<version>5.7.7</version>
1148+
</dependency>
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<dependency>
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<groupId>org.apache.santuario</groupId>
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<artifactId>xmlsec</artifactId>
1152+
<version>3.0.3</version>
1153+
</dependency>
11431154
<dependency>
11441155
<groupId>org.ohdsi</groupId>
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<artifactId>circe</artifactId>
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13231334
<dependency>
13241335
<groupId>org.springframework.ldap</groupId>
13251336
<artifactId>spring-ldap-core</artifactId>
1326-
<version>3.2.8</version>
1337+
<version>3.2.8</version>
13271338
</dependency>
13281339
<dependency>
13291340
<groupId>com.odysseusinc</groupId>
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14471458
<version>1.1.7</version>
14481459
</dependency>
14491460
<dependency>
1450-
<groupId>org.springframework.boot</groupId>
1451-
<artifactId>spring-boot-configuration-processor</artifactId>
1452-
<optional>true</optional>
1461+
<groupId>org.springframework.boot</groupId>
1462+
<artifactId>spring-boot-configuration-processor</artifactId>
1463+
<optional>true</optional>
14531464
</dependency>
14541465
</dependencies>
14551466
<profiles>
@@ -1492,7 +1503,7 @@
14921503
<id>webapi-postgresql</id>
14931504
<properties>
14941505
<datasource.driverClassName>org.postgresql.Driver</datasource.driverClassName>
1495-
<datasource.url>jdbc:postgresql://localhost:5432/OHDSI?currentSchema=webapi</datasource.url>
1506+
<datasource.url>jdbc:postgresql://localhost:5432/OHDSI?currentSchema=webapi</datasource.url>
14961507
<datasource.username>ohdsi_app_user</datasource.username>
14971508
<datasource.password>app1</datasource.password>
14981509
<datasource.dialect>postgresql</datasource.dialect>
@@ -1516,10 +1527,9 @@
15161527
lower(email) = lower(?)</security.db.datasource.authenticationQuery>
15171528
</properties>
15181529
</profile>
1519-
<profile>
1530+
<profile>
15201531
<id>webapi-docker</id>
15211532
<properties>
1522-
<security.provider>AtlasRegularSecurity</security.provider>
15231533
<git.branch>unknown</git.branch>
15241534
<git.commit.id.abbrev>unknown</git.commit.id.abbrev>
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<maven.gitcommitid.skip>true</maven.gitcommitid.skip>
@@ -1554,17 +1564,17 @@
15541564
<security.oid.redirectUrl>${OID_REDIRECTURL}</security.oid.redirectUrl>
15551565
</properties>
15561566
<repositories>
1557-
<repository>
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<repository>
15581568
<id>ohdsi.snapshots</id>
15591569
<name>repo.ohdsi.org-snapshots</name>
15601570
<url>https://repo.ohdsi.org/nexus/content/repositories/snapshots</url>
15611571
<releases>
15621572
<enabled>false</enabled>
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</releases>
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<snapshots>
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<snapshots>
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<enabled>true</enabled>
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</snapshots>
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</repository>
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</snapshots>
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</repository>
15681578
</repositories>
15691579
</profile>
15701580
<!-- <profile> MDACA Spring Boot 3 migration
@@ -1637,7 +1647,7 @@
16371647
<impala.enabled>true</impala.enabled>
16381648
<impala.driver.version>2.6.15</impala.driver.version>
16391649
Impala JDBC driver path
1640-
<impala.classpath>...path/to/impala/jdbc/drivers...</impala.classpath>
1650+
<impala.classpath>...path/to/impala/jdbc/drivers...</impala.classpath>
16411651
</properties>
16421652
<dependencies>
16431653
<dependency>

‎src/main/java/org/ohdsi/webapi/DataAccessConfig.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -75,7 +75,7 @@ public DataSource primaryDataSource() {
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"org.postgresql.Driver", "com.microsoft.sqlserver.jdbc.SQLServerDriver", "oracle.jdbc.driver.OracleDriver",
7676
"com.amazon.redshift.jdbc.Driver", "com.cloudera.impala.jdbc.Driver", "net.starschema.clouddb.jdbc.BQDriver",
7777
"org.netezza.Driver", "com.simba.googlebigquery.jdbc42.Driver", "org.apache.hive.jdbc.HiveDriver",
78-
"com.simba.spark.jdbc.Driver", "net.snowflake.client.jdbc.SnowflakeDriver"
78+
"com.simba.spark.jdbc.Driver", "net.snowflake.client.jdbc.SnowflakeDriver", "io.trino.jdbc.TrinoDriver"
7979
};
8080

8181
for (String driverName : supportedDrivers) {

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