Merge branch 'rfc72'

cBioPortal · Aug 22, 2023 · 4f28eac · 4f28eac
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diff --git a/bin/SESSIONS.ser b/bin/SESSIONS.ser
diff --git a/bin/integration-tests/README.md b/bin/integration-tests/README.md
@@ -0,0 +1,7 @@
+# Integration tests
+
+This folder contains maven projects that test particular functionality of `cbioportal.war` started under different settings.
+
+These tests get called by `maven-invoker-plugin` that is declared in the `portal` maven module of the project.
+
+Keeping tests as separate maven projects liberate us from the application dependencies and unnecessary conflicts between them and test dependencies.
diff --git a/bin/integration-tests/saml-oauth2-setup/README.md b/bin/integration-tests/saml-oauth2-setup/README.md
@@ -0,0 +1,37 @@
+# saml-oauth2-setup
+
+Tests oauth2 security workflow of the API with SAML authentication method for the UI.
+
+- `OfflineTokenDownloadIntegrationTests` tests downloading an offline token to gain access to cbioportal API.
+- `Oauth2ResourceServerIntegrationTests` tests API access by different type of users (anonymous, non authorized and authorized).
+
+## Start mysql server for integration tests
+
+database name: cgds_test
+username: cbio_user
+password: somepassword
+port: 3306  
+
+## Start web container with cbioportal and saml IDP
+
+You can start tomcat to play with the setup with the following command (replace with your values):
+
+```$bash
+cd portal/src/integration-tests/saml-oauth2-setup
+CBIO_TEST_DB_USR=cbio_user \
+    CBIO_TEST_DB_PSW=somepassword \
+    CBIO_TEST_DB_HOST=127.0.0.1:3306 \
+    CBIO_TEST_DB_NAME=cgds_test \
+    CBIO_TEST_DB_CONNECTION_STRING=jdbc:mysql://127.0.0.1:3306/cgds_test?sessionVariables=default_storage_engine=InnoDB \
+    CBIO_WAR_LOCATION=../../../target/cbioportal.war \
+    mvn org.codehaus.cargo:cargo-maven2-plugin:run --non-recursive
+```
+
+## Run integration tests only
+
+After starting the tomcat server above, you can run all tests with:
+
+```$bash
+cd portal/src/integration-tests/saml-oauth2-setup
+mvn test failsafe:integration-test
+```
diff --git a/bin/integration-tests/saml-oauth2-setup/pom.xml b/bin/integration-tests/saml-oauth2-setup/pom.xml
@@ -0,0 +1,168 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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>
+    <groupId>org.mskcc.cbio</groupId>
+    <artifactId>saml-oauth2-setup</artifactId>
+    <version>0.0.1-SNAPSHOT</version>
+    <packaging>pom</packaging>
+
+    <modules>
+        <module>saml-idp</module>
+    </modules>
+
+    <dependencies>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.mock-server</groupId>
+            <artifactId>mockserver-netty</artifactId>
+            <version>5.8.0</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.mock-server</groupId>
+            <artifactId>mockserver-client-java</artifactId>
+            <version>5.8.0</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.5.1</version>
+                <configuration>
+                    <source>1.8</source>
+                    <target>1.8</target>
+                    <compilerArgs>
+                        <arg>-parameters</arg>
+                    </compilerArgs>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>testCompile</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.codehaus.cargo</groupId>
+                <artifactId>cargo-maven2-plugin</artifactId>
+                <version>1.7.8</version>
+                <configuration>
+                    <container>
+                        <containerId>tomcat8x</containerId>
+                        <type>embedded</type>
+                        <systemProperties>
+                            <authenticate>saml</authenticate>
+                            <dat.method>oauth2</dat.method>
+                            <!-- DB settings -->
+                            <db.user>${env.CBIO_TEST_DB_USR}</db.user>
+                            <db.password>${env.CBIO_TEST_DB_PSW}</db.password>
+                            <db.host>${env.CBIO_TEST_DB_HOST}</db.host>
+                            <db.portal_db_name>${env.CBIO_TEST_DB_NAME}</db.portal_db_name>
+                            <db.connection_string>${env.CBIO_TEST_DB_CONNECTION_STRING}</db.connection_string>
+                            <!-- SAML settings -->
+                            <saml.keystore.location>file://${project.basedir}/testSamlKeystore.jks
+                            </saml.keystore.location>
+                            <saml.keystore.password>123456</saml.keystore.password>
+                            <saml.keystore.private-key.key>secure-key</saml.keystore.private-key.key>
+                            <saml.keystore.private-key.password>654321</saml.keystore.private-key.password>
+                            <saml.keystore.default-key>secure-key</saml.keystore.default-key>
+
+                            <saml.idp.metadata.location>file://${project.basedir}/saml-idp-metadata.xml
+                            </saml.idp.metadata.location>
+                            <!--I had to use specificBinding because of this bug https://github.com/spring-projects/spring-security-saml/issues/460 -->
+                            <saml.idp.comm.binding.settings>specificBinding</saml.idp.comm.binding.settings>
+                            <saml.idp.comm.binding.type>bindings:HTTP-Redirect</saml.idp.comm.binding.type>
+                            <saml.sp.metadata.entitybaseurl>#{null}</saml.sp.metadata.entitybaseurl>
+                            <saml.sp.metadata.entityid>cbioportal</saml.sp.metadata.entityid>
+                            <saml.idp.metadata.entityid>spring.security.saml.idp.id</saml.idp.metadata.entityid>
+                            <saml.idp.metadata.attribute.email>User.email</saml.idp.metadata.attribute.email>
+                            <saml.custom.userservice.class>
+                                org.cbioportal.security.spring.authentication.saml.SAMLUserDetailsServiceImpl
+                            </saml.custom.userservice.class>
+                            <saml.logout.local>false</saml.logout.local>
+                            <!--FIXME Our test saml idp does not sign assertions for some reason-->
+                            <saml.sp.metadata.wantassertionsigned>false</saml.sp.metadata.wantassertionsigned>
+                            <saml.logout.url>/</saml.logout.url>
+                            <dat.oauth2.clientId>client_id</dat.oauth2.clientId>
+                            <dat.oauth2.clientSecret>client_secret</dat.oauth2.clientSecret>
+                            <dat.oauth2.issuer>token_issuer</dat.oauth2.issuer>
+                            <dat.oauth2.accessTokenUri>http://localhost:8443/auth/realms/cbio/token</dat.oauth2.accessTokenUri>
+                            <dat.oauth2.redirectUri>http://localhost:8080/api/data-access-token/oauth2</dat.oauth2.redirectUri>
+                            <dat.oauth2.userAuthorizationUri>http://localhost:8443/auth/realms/cbio/auth</dat.oauth2.userAuthorizationUri>
+                            <dat.oauth2.jwkUrl>http://localhost:8443/auth/realms/cbio/jwkUrl</dat.oauth2.jwkUrl>
+                            <dat.oauth2.jwtRolesPath>resource_access::cbioportal::roles</dat.oauth2.jwtRolesPath>
+                        </systemProperties>
+                    </container>
+                    <configuration>
+                        <properties>
+                            <cargo.servlet.port>8080</cargo.servlet.port>
+                            <cargo.start.jvmargs>
+                                -Xms2g
+                                -Xmx4g
+                            </cargo.start.jvmargs>
+                        </properties>
+                    </configuration>
+                    <wait>false</wait>
+                    <deployables>
+                        <deployable>
+                            <groupId>org.mskcc.cbio</groupId>
+                            <artifactId>cbioportal</artifactId>
+                            <type>war</type>
+                            <location>${env.CBIO_WAR_LOCATION}</location>
+                        </deployable>
+                        <deployable>
+                            <groupId>org.mskcc.cbio</groupId>
+                            <artifactId>saml-idp</artifactId>
+                            <type>war</type>
+                            <location>${project.basedir}/saml-idp/target/saml-idp.war</location>
+                        </deployable>
+                    </deployables>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>start-server</id>
+                        <phase>pre-integration-test</phase>
+                        <goals>
+                            <goal>start</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>stop-server</id>
+                        <phase>post-integration-test</phase>
+                        <goals>
+                            <goal>stop</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <artifactId>maven-failsafe-plugin</artifactId>
+                <version>3.0.0-M4</version>
+                <configuration>
+                    <includes>
+                        <include>**/*IntegrationTests</include>
+                    </includes>
+                    <trimStackTrace>false</trimStackTrace>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>integration-test</goal>
+                            <goal>verify</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>
diff --git a/bin/integration-tests/saml-oauth2-setup/saml-idp-metadata.xml b/bin/integration-tests/saml-oauth2-setup/saml-idp-metadata.xml
@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<md:EntityDescriptor ID="IDPM392d91fa-7520-4ab3-be02-a1876bb8d681" entityID="spring.security.saml.idp.id"
+                     xmlns:md="urn:oasis:names:tc:SAML:2.0:metadata">
+    <md:IDPSSODescriptor ID="RD4fac15fd-394b-4ef0-b896-7fb50dcce5b5" WantAuthnRequestsSigned="true"
+                         protocolSupportEnumeration="urn:oasis:names:tc:SAML:2.0:protocol">
+        <md:KeyDescriptor use="signing">
+            <ds:KeyInfo xmlns:ds="http://www.w3.org/2000/09/xmldsig#">
+                <ds:X509Data>
+                    <ds:X509Certificate>MIIChTCCAe4CCQDo0wjPUK8sMDANBgkqhkiG9w0BAQsFADCBhjELMAkGA1UEBhMCVVMxEzARBgNV
+                        BAgMCldhc2hpbmd0b24xEjAQBgNVBAcMCVZhbmNvdXZlcjEdMBsGA1UECgwUU3ByaW5nIFNlY3Vy
+                        aXR5IFNBTUwxDDAKBgNVBAsMA2lkcDEhMB8GA1UEAwwYaWRwLnNwcmluZy5zZWN1cml0eS5zYW1s
+                        MB4XDTE4MDUxNDE0NTUyMVoXDTI4MDUxMTE0NTUyMVowgYYxCzAJBgNVBAYTAlVTMRMwEQYDVQQI
+                        DApXYXNoaW5ndG9uMRIwEAYDVQQHDAlWYW5jb3V2ZXIxHTAbBgNVBAoMFFNwcmluZyBTZWN1cml0
+                        eSBTQU1MMQwwCgYDVQQLDANpZHAxITAfBgNVBAMMGGlkcC5zcHJpbmcuc2VjdXJpdHkuc2FtbDCB
+                        nzANBgkqhkiG9w0BAQEFAAOBjQAwgYkCgYEA2EuygAucRBWtYifgEH/ErVUive4dZdqo72Bze4Mb
+                        kPuTKLrMCLB6IXxt1p5lu+tr0JxOiRO3KFVOO3D0l+j9zOow4g+JdoMQsjSzA6HtL/D9ZjXP6iUx
+                        FCYx+qmnVl3X9ipBD/HVKOBlzIqeXTSa5D17uxPQVxK64UDOI3CyY4cCAwEAATANBgkqhkiG9w0B
+                        AQsFAAOBgQAj+6b6dlA6SitTfz44LdnFSW9mYaeimwPP8ZtU7/3EJCzLd5eq7N/0kYPNVclZvB45
+                        I0UMT77AHWrNyScm56MTcEpSuHhJHAqRAgJKbciCTNsFI928EqiWSmu//w0ASBN3bVa8nv8/rafu
+                        utCq3RskTkHVZnbT5Xa6ITEZxSncow==
+                    </ds:X509Certificate>
+                </ds:X509Data>
+            </ds:KeyInfo>
+        </md:KeyDescriptor>
+        <md:KeyDescriptor use="encryption">
+            <ds:KeyInfo xmlns:ds="http://www.w3.org/2000/09/xmldsig#">
+                <ds:X509Data>
+                    <ds:X509Certificate>MIIChTCCAe4CCQDo0wjPUK8sMDANBgkqhkiG9w0BAQsFADCBhjELMAkGA1UEBhMCVVMxEzARBgNV
+                        BAgMCldhc2hpbmd0b24xEjAQBgNVBAcMCVZhbmNvdXZlcjEdMBsGA1UECgwUU3ByaW5nIFNlY3Vy
+                        aXR5IFNBTUwxDDAKBgNVBAsMA2lkcDEhMB8GA1UEAwwYaWRwLnNwcmluZy5zZWN1cml0eS5zYW1s
+                        MB4XDTE4MDUxNDE0NTUyMVoXDTI4MDUxMTE0NTUyMVowgYYxCzAJBgNVBAYTAlVTMRMwEQYDVQQI
+                        DApXYXNoaW5ndG9uMRIwEAYDVQQHDAlWYW5jb3V2ZXIxHTAbBgNVBAoMFFNwcmluZyBTZWN1cml0
+                        eSBTQU1MMQwwCgYDVQQLDANpZHAxITAfBgNVBAMMGGlkcC5zcHJpbmcuc2VjdXJpdHkuc2FtbDCB
+                        nzANBgkqhkiG9w0BAQEFAAOBjQAwgYkCgYEA2EuygAucRBWtYifgEH/ErVUive4dZdqo72Bze4Mb
+                        kPuTKLrMCLB6IXxt1p5lu+tr0JxOiRO3KFVOO3D0l+j9zOow4g+JdoMQsjSzA6HtL/D9ZjXP6iUx
+                        FCYx+qmnVl3X9ipBD/HVKOBlzIqeXTSa5D17uxPQVxK64UDOI3CyY4cCAwEAATANBgkqhkiG9w0B
+                        AQsFAAOBgQAj+6b6dlA6SitTfz44LdnFSW9mYaeimwPP8ZtU7/3EJCzLd5eq7N/0kYPNVclZvB45
+                        I0UMT77AHWrNyScm56MTcEpSuHhJHAqRAgJKbciCTNsFI928EqiWSmu//w0ASBN3bVa8nv8/rafu
+                        utCq3RskTkHVZnbT5Xa6ITEZxSncow==
+                    </ds:X509Certificate>
+                </ds:X509Data>
+            </ds:KeyInfo>
+        </md:KeyDescriptor>
+        <md:NameIDFormat>urn:oasis:names:tc:SAML:1.1:nameid-format:emailAddress</md:NameIDFormat>
+        <md:SingleSignOnService Binding="urn:oasis:names:tc:SAML:2.0:bindings:HTTP-POST"
+                                Location="http://localhost:8080/saml-idp/saml/idp/SSO/alias/boot-sample-idp"/>
+        <md:SingleSignOnService Binding="urn:oasis:names:tc:SAML:2.0:bindings:HTTP-Redirect"
+                                Location="http://localhost:8080/saml-idp/saml/idp/SSO/alias/boot-sample-idp"/>
+    </md:IDPSSODescriptor>
+</md:EntityDescriptor>
diff --git a/bin/integration-tests/saml-oauth2-setup/saml-idp/README.md b/bin/integration-tests/saml-oauth2-setup/saml-idp/README.md
@@ -0,0 +1,18 @@
+# saml-idp
+
+A test SAML Identity Provider. It is used by cbioportal integration tests.
+It's modified version of [a saml IDP sample code](https://github.com/spring-projects/spring-security-saml/tree/develop/samples/boot/simple-identity-provider) of the spring security.
+`application.yml` specify a test user email that is added to assertions.
+
+## License
+
+The sample code is distributed under Apache License, Version 2.0.
+
+## Known limitations
+
+- The IDP does not sign assertions. That's why we had to set the following flag for the test cbioportal application: 
+
+```$xml
+    <!--FIXME Our test saml idp does not sing assertions for some reason-->
+    <saml.sp.metadata.wantassertionsigned>false</saml.sp.metadata.wantassertionsigned>
+```
diff --git a/bin/integration-tests/saml-oauth2-setup/saml-idp/pom.xml b/bin/integration-tests/saml-oauth2-setup/saml-idp/pom.xml
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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>
+    <groupId>org.mskcc.cbio</groupId>
+    <artifactId>saml-idp</artifactId>
+    <version>0.0.1-SNAPSHOT</version>
+    <packaging>war</packaging>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.springframework.security.extensions</groupId>
+            <artifactId>spring-security-saml2-core</artifactId>
+            <version>2.0.0.M31</version>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-web</artifactId>
+            <version>2.2.0.RELEASE</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>jul-to-slf4j</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-tomcat</artifactId>
+            <scope>provided</scope>
+            <version>2.2.0.RELEASE</version>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <finalName>saml-idp</finalName>
+        <plugins>
+            <plugin>
+                <artifactId>maven-war-plugin</artifactId>
+                <version>2.2</version>
+                <configuration>
+                    <failOnMissingWebXml>false</failOnMissingWebXml>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.5.1</version>
+                <configuration>
+                    <source>1.8</source>
+                    <target>1.8</target>
+                    <compilerArgs>
+                        <arg>-parameters</arg>
+                    </compilerArgs>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>