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switch to spring mvc (#2488)
* switch to spring mvc * cleanup * cleanup p2 * migreate auth provider * cleanup * fix build issues * fix * fix * fix * fix * fix * fix * fix * cleanup * fix * fix * cleanup * fix
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Lines changed: 3880 additions & 5016 deletions

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‎docker/auth-test/setup-test-users.sql‎

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-- Initial security data (roles required for the application to function)
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-- These must be created before WebAPI can properly handle authentication
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INSERT INTO webapi.sec_role (id, name, system_role) VALUES (1, 'public', true) ON CONFLICT (id) DO NOTHING;
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INSERT INTO webapi.sec_role (id, name, system_role) VALUES (2, 'admin', true) ON CONFLICT (id) DO NOTHING;
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INSERT INTO webapi.sec_role (id, name, system_role) VALUES (1001, 'Atlas users', true) ON CONFLICT (id) DO NOTHING;
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INSERT INTO webapi.sec_role (id, name, system_role) VALUES (1002, 'Moderator', true) ON CONFLICT (id) DO NOTHING;
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-- Anonymous user (required for public endpoints)
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INSERT INTO webapi.sec_user (id, login, name) VALUES (1, 'anonymous', 'anonymous') ON CONFLICT (id) DO NOTHING;
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INSERT INTO webapi.sec_user_role (id, user_id, role_id, origin) VALUES (1, 1, 1, 'SYSTEM') ON CONFLICT (id) DO NOTHING;
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-- Update sequences to avoid conflicts
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SELECT setval('webapi.sec_role_sequence', GREATEST((SELECT COALESCE(MAX(id), 0) + 1 FROM webapi.sec_role), nextval('webapi.sec_role_sequence')));
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SELECT setval('webapi.sec_user_sequence', GREATEST((SELECT COALESCE(MAX(id), 0) + 1 FROM webapi.sec_user), nextval('webapi.sec_user_sequence')));
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SELECT setval('webapi.sec_user_role_sequence', GREATEST((SELECT COALESCE(MAX(id), 0) + 1 FROM webapi.sec_user_role), nextval('webapi.sec_user_role_sequence')));
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-- Test users table for JDBC authentication
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CREATE TABLE IF NOT EXISTS webapi.users (
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id SERIAL PRIMARY KEY,
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email VARCHAR(255) UNIQUE NOT NULL,

‎docker/integration-test/postman/integration-tests.postman_collection.json‎

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"method": "GET",
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"header": [],
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"url": {
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"raw": "{{base_url}}/conceptset/",
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"raw": "{{base_url}}/conceptset",
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"host": ["{{base_url}}"],
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"path": ["conceptset", ""]
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"path": ["conceptset"]
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}
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}
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},
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"raw": "{\n \"name\": \"Test Concept Set\",\n \"description\": \"Integration test concept set\"\n}"
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},
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"url": {
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"raw": "{{base_url}}/conceptset/",
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"raw": "{{base_url}}/conceptset",
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"host": ["{{base_url}}"],
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"path": ["conceptset", ""]
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"path": ["conceptset"]
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}
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}
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},

‎pom.xml‎

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<shiro.version>2.0.2</shiro.version>
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<!-- tomcat.embed.version removed - using Spring Boot 3.5.6 managed version (10.1.48) -->
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<commons-fileupload.version>1.5</commons-fileupload.version>
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<circe.version>1.12.1</circe.version>
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<jersey.version>3.1.9</jersey.version>
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<SqlRender.version>1.19.1</SqlRender.version>
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<hive-jdbc.version>3.1.2</hive-jdbc.version>
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<pac4j.version>6.0.5</pac4j.version>
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<security.oid.extraScopes></security.oid.extraScopes>
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<security.oid.customParams>{:}</security.oid.customParams>
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<security.oid.redirectUrl>http://localhost/index.html#/welcome/</security.oid.redirectUrl>
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<security.oid.apiResource></security.oid.apiResource>
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<security.kerberos.spn></security.kerberos.spn>
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<security.kerberos.keytabPath></security.kerberos.keytabPath>
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<security.ldap.dn>cn={0},dc=example,dc=org</security.ldap.dn>
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<server.servlet.context-path>/WebAPI</server.servlet.context-path>
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<arachne.version>1.17.4</arachne.version>
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<jersey-media-multipart.version>3.1.9</jersey-media-multipart.version>
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<execution.invalidation.period>600000</execution.invalidation.period>
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<execution.invalidation.maxage.hours>12</execution.invalidation.maxage.hours>
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<execution.status.period>10000</execution.status.period>
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<artifactId>tomcat-juli</artifactId>
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<version>10.1.48</version><!-- Not managed by Spring Boot, must match tomcat-embed version -->
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</dependency>
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<dependency>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-starter-jersey</artifactId>
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<exclusions>
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<exclusion>
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<groupId>org.hibernate</groupId>
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<artifactId>hibernate-validator</artifactId>
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</exclusion>
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<exclusion>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-databind</artifactId>
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</exclusion>
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<exclusion>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-annotations</artifactId>
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</exclusion>
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<exclusion>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-core</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-starter-data-jpa</artifactId>
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<artifactId>cache-api</artifactId>
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<version>1.1.1</version>
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</dependency>
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<!-- JAXB dependencies for Java 11+ (ehcache still uses javax.xml.bind) -->
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<dependency>
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<groupId>javax.xml.bind</groupId>
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<artifactId>jaxb-api</artifactId>
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<version>2.3.1</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jaxb</groupId>
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<artifactId>jaxb-runtime</artifactId>
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<version>2.3.1</version>
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</dependency>
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<!-- javax.xml.bind dependencies removed - ehcache 3.11.0+ no longer requires them -->
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<dependency>
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<groupId>org.ohdsi.sql</groupId>
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<artifactId>SqlRender</artifactId>
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<version>9.1.6</version>
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</dependency>
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<!-- overriding commons-fileupload version from the plug-in above -->
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<dependency>
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<groupId>commons-fileupload</groupId>
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<artifactId>commons-fileupload</artifactId>
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<version>${commons-fileupload.version}</version>
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</dependency>
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<!-- commons-fileupload removed - not used in codebase -->
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<dependency>
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<groupId>org.postgresql</groupId>
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<artifactId>postgresql</artifactId>
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<artifactId>mssql-jdbc</artifactId>
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<version>12.8.1.jre11</version>
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</dependency>
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<dependency>
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<groupId>com.microsoft.azure</groupId>
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<artifactId>msal4j</artifactId>
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<version>1.9.0</version>
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</dependency>
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<!-- msal4j removed - not used in codebase -->
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<dependency>
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<groupId>com.opencsv</groupId>
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<artifactId>opencsv</artifactId>
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<artifactId>commons-csv</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.dom4j</groupId>
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<artifactId>dom4j</artifactId>
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<version>2.1.3</version>
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</dependency>
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<!-- dom4j removed - not used in codebase -->
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<dependency>
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<groupId>org.apache.shiro</groupId>
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<artifactId>shiro-core</artifactId>
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<artifactId>jasypt</artifactId>
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<version>1.9.3</version>
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</dependency>
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<!-- JAX-RS API removed - all Jersey code migrated to Spring MVC -->
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<!-- JAXB API - needed by some legacy code -->
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<dependency>
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<groupId>org.glassfish.jersey.media</groupId>
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<artifactId>jersey-media-multipart</artifactId>
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<version>${jersey-media-multipart.version}</version>
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<groupId>jakarta.xml.bind</groupId>
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<artifactId>jakarta.xml.bind-api</artifactId>
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<version>4.0.0</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish</groupId>
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<dependency>
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<groupId>org.ehcache</groupId>
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<artifactId>ehcache</artifactId>
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<version>3.9.11</version>
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<version>3.11.1</version>
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<classifier>jakarta</classifier><!-- Using Jakarta classifier to avoid javax.xml.bind dependency -->
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<exclusions>
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<exclusion>
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<groupId>org.glassfish.jaxb</groupId>
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<artifactId>jaxb-runtime</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<!-- Jakarta JAXB runtime for ehcache XML configuration -->
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<dependency>
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<groupId>org.glassfish.jaxb</groupId>
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<artifactId>jaxb-runtime</artifactId>
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<version>3.0.2</version><!-- Jakarta EE 9 compatible -->
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</dependency> <dependency>
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<groupId>com.opentable.components</groupId>
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<artifactId>otj-pg-embedded</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey</groupId>
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<artifactId>jersey-server</artifactId>
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<version>1.19.4</version>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey</groupId>
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<artifactId>jersey-core</artifactId>
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<version>1.19.4</version>
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<exclusions>
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<exclusion>
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<groupId>javax.ws.rs</groupId>
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<artifactId>jsr311-api</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey</groupId>
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<artifactId>jersey-client</artifactId>
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<version>1.19.4</version>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey</groupId>
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<artifactId>jersey-json</artifactId>
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<version>1.19.4</version>
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</dependency>
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</dependencies>
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</profile>
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<profile>

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

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

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

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@Value("${security.oauth.callback.api}")
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private String oauthApiCallback;
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@Value("${security.oid.apiResource:}")
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private String apiResource;
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public String getApiResource() {
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return apiResource;
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}
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/**
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* Returns the external OIDC URL for browser-facing endpoints.
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* If externalUrl is set, returns it; otherwise returns the discovery URL.

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