Enable integration tests

README.md

@@ -8,3 +8,39 @@ This repo contains:
 
 ## Inclusion in main codebase
 The `cbioportal-core` code is currently included in the final Docker image during the Docker build process: https://github.com/cBioPortal/cbioportal/blob/master/docker/web-and-data/Dockerfile#L48
+
+## How to run integration tests
+
+This section guides you through the process of running integration tests by setting up a cBioPortal MySQL database environment using Docker. Please follow these steps carefully to ensure your testing environment is configured correctly.
+
+### Preparing the cbioportal test database
+
+1. **Download the cBioPortal Database Schema**: To begin, you need to download the database schema for the version of cBioPortal you are interested in testing.
+Locate the pom.xml file in your project directory and check the values of `<db.version>` and `<cbioportal.version>` to determine the correct version.
+Replace `v6.0.3` in the command below with your desired cBioPortal version:
+```
+curl -o cgds.sql https://raw.githubusercontent.com/cBioPortal/cbioportal/v6.0.3/src/main/resources/db-scripts/cgds.sql
+```
+
+2. **Launch the MySQL Server Container**: Use Docker to start a MySQL server pre-loaded with the cBioPortal schema. Execute the following command from the root of your project directory.
+It is recommended to open a separate terminal tab or window for this operation as it will occupy the console until stopped:
+
+```
+docker run -p 3306:3306 \
+-v $(pwd)/src/test/resources/seed_mini.sql:/docker-entrypoint-initdb.d/seed.sql:ro \
+-v $(pwd)/cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro \
+-e MYSQL_ROOT_PASSWORD=root \
+-e MYSQL_USER=cbio_user \
+-e MYSQL_PASSWORD=somepassword \
+-e MYSQL_DATABASE=cgds_test \
+mysql:5.7
+```
+
+### Run integration tests
+
+With the database up and running, you are now ready to execute the integration tests.
+
+Use Maven to run the integration tests. Ensure you are in the root directory of your project and run the following command:
+```
+mvn integration-test
+```

pom.xml

@@ -247,7 +247,35 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
-				<version>2.12.4</version>
+				<version>2.21.0</version>
+				<executions>
+					<execution>
+						<id>default-test</id>
+						<phase>test</phase>
+						<goals>
+							<goal>test</goal>
+						</goals>
+						<configuration>
+							<excludes>
+								<exclude>**/integrationTest/**/*</exclude>
+							</excludes>
+						</configuration>
+					</execution>
+					<execution>
+						<id>integration-test</id>
+						<phase>integration-test</phase>
+						<goals>
+							<goal>test</goal>
+						</goals>
+						<configuration>
+							<includes>
+								<include>**/integrationTest/**/*</include>
+							</includes>
+							<forkCount>1</forkCount>
+							<reuseForks>false</reuseForks>
+						</configuration>
+					</execution>
+				</executions>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>

src/main/java/org/mskcc/cbio/portal/scripts/ImportGenesetData.java

@@ -278,7 +278,7 @@ public static int importData(File genesetFile,  boolean updateInfo, boolean newV
      * @param suppFile
      * @throws Exception 
      */
-    static void importSuppGenesetData(File suppFile) throws Exception {
+    public static void importSuppGenesetData(File suppFile) throws Exception {
 
         ProgressMonitor.setCurrentMessage("Reading data from: " + suppFile.getCanonicalPath());
 

src/main/java/org/mskcc/cbio/portal/util/ProgressMonitor.java

@@ -68,7 +68,10 @@ private ProgressMonitor() {
     }
 
     private static boolean isRunningOnServer() {
-        return ServerDetector.getServerId() != null;
+        // FXIME because we bring core as dependency into cbioportal-core, we have web server classes in classpath
+        // But we run loader as standalone java process atm, not from the web server.
+        // return ServerDetector.getServerId() != null;
+        return false;
     } 
     /**
      * Sets Console Flag.

src/test/java/org/mskcc/cbio/portal/dao/TestDaoCancerStudy.java → src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoCancerStudy.java

@@ -30,31 +30,34 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-package org.mskcc.cbio.portal.dao;
+package org.mskcc.cbio.portal.integrationTest.dao;
 
+import org.junit.Assert;
 import org.junit.Test;
-import org.junit.Ignore;
 import org.junit.runner.RunWith;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoTypeOfCancer;
 import org.mskcc.cbio.portal.model.CancerStudy;
-
-import java.io.IOException;
-import java.util.ArrayList;
-
 import org.mskcc.cbio.portal.model.ReferenceGenome;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 
 /**
  * JUnit Tests for DaoCancer Study.
  *
  * @author Arman Aksoy, Ethan Cerami, Arthur Goldberg, Ersin Ciftci.
  */
 @RunWith(SpringJUnit4ClassRunner.class)
-@Ignore
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
 @Rollback
 @Transactional
@@ -68,7 +71,7 @@ public class TestDaoCancerStudy {
 	@Test
     public void testDaoCancerStudy() throws DaoException, IOException {
 
-        assertEquals("Breast Invasive Carcinoma", DaoTypeOfCancer.getTypeOfCancerById("BRCA").getName());
+        Assert.assertEquals("Breast Invasive Carcinoma", DaoTypeOfCancer.getTypeOfCancerById("BRCA").getName());
 
         CancerStudy cancerStudy = new CancerStudy("GBM", "GBM Description", "gbm", "brca", false);
         cancerStudy.setReferenceGenome("hg19");

src/test/java/org/mskcc/cbio/portal/dao/TestDaoClinicalAttribute.java → src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoClinicalAttribute.java

@@ -30,21 +30,22 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-package org.mskcc.cbio.portal.dao;
+package org.mskcc.cbio.portal.integrationTest.dao;
 
-import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
+import org.mskcc.cbio.portal.dao.DaoClinicalAttributeMeta;
+import org.mskcc.cbio.portal.dao.DaoException;
 import org.mskcc.cbio.portal.model.ClinicalAttribute;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
 
 @RunWith(SpringJUnit4ClassRunner.class)
-@Ignore
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
 @Rollback
 @Transactional

src/test/java/org/mskcc/cbio/portal/dao/TestDaoGene.java → src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGene.java

@@ -30,11 +30,13 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-package org.mskcc.cbio.portal.dao;
+package org.mskcc.cbio.portal.integrationTest.dao;
 
-import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneOptimized;
+import org.mskcc.cbio.portal.dao.MySQLbulkLoader;
 import org.mskcc.cbio.portal.model.CanonicalGene;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
@@ -50,7 +52,6 @@
  * JUnit Tests for DaoGene and DaoGeneOptimized.
  */
 @RunWith(SpringJUnit4ClassRunner.class)
-@Ignore
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
 @Rollback
 @Transactional

src/test/java/org/mskcc/cbio/portal/dao/TestDaoGenePanel.java → src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGenePanel.java

@@ -30,30 +30,29 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-package org.mskcc.cbio.portal.dao;
+package org.mskcc.cbio.portal.integrationTest.dao;
 
-import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.dao.*;
-import org.mskcc.cbio.portal.model.*;
-
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneOptimized;
+import org.mskcc.cbio.portal.dao.DaoGenePanel;
+import org.mskcc.cbio.portal.model.CanonicalGene;
+import org.mskcc.cbio.portal.model.GenePanel;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import static org.junit.Assert.*;
+import java.util.HashSet;
 
-import java.util.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 /**
  * JUnit Tests for DaoGenePanel.
  */
 @RunWith(SpringJUnit4ClassRunner.class)
-@Ignore
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
 @Rollback
 @Transactional

src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticAlteration.java → src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticAlteration.java

@@ -30,27 +30,38 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-package org.mskcc.cbio.portal.dao;
+package org.mskcc.cbio.portal.integrationTest.dao;
 
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.model.*;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneticAlteration;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfile;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfileSamples;
+import org.mskcc.cbio.portal.dao.DaoPatient;
+import org.mskcc.cbio.portal.dao.DaoSample;
+import org.mskcc.cbio.portal.dao.MySQLbulkLoader;
+import org.mskcc.cbio.portal.model.CancerStudy;
+import org.mskcc.cbio.portal.model.CanonicalGene;
+import org.mskcc.cbio.portal.model.Patient;
+import org.mskcc.cbio.portal.model.Sample;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Set;
 
-import java.util.*;
+import static org.junit.Assert.assertEquals;
 
 /**
  * JUnit tests for DaoGeneticAlteration class.
  */
 @RunWith(SpringJUnit4ClassRunner.class)
-@Ignore
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
 @Rollback
 @Transactional

src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfile.java → src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfile.java

@@ -30,25 +30,30 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-package org.mskcc.cbio.portal.dao;
+package org.mskcc.cbio.portal.integrationTest.dao;
 
-import java.util.ArrayList;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.model.*;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfile;
+import org.mskcc.cbio.portal.model.GeneticAlterationType;
+import org.mskcc.cbio.portal.model.GeneticProfile;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
-import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 /**
  * JUnit tests for DaoGeneticProfile class.
  */
 @RunWith(SpringJUnit4ClassRunner.class)
-@Ignore
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
 @Rollback
 @Transactional

src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfileSamples.java → src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfileSamples.java

@@ -30,27 +30,33 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-package org.mskcc.cbio.portal.dao;
+package org.mskcc.cbio.portal.integrationTest.dao;
 
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.model.*;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfile;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfileSamples;
+import org.mskcc.cbio.portal.dao.DaoPatient;
+import org.mskcc.cbio.portal.dao.DaoSample;
+import org.mskcc.cbio.portal.model.CancerStudy;
+import org.mskcc.cbio.portal.model.Patient;
+import org.mskcc.cbio.portal.model.Sample;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 
-import static org.junit.Assert.*;
-
 import java.util.ArrayList;
 
+import static org.junit.Assert.assertEquals;
+
 /**
  * JUnit Tests for the Dao Genetic Profile Cases Class.
  *
  * @author Ethan Cerami.
  */
 @RunWith(SpringJUnit4ClassRunner.class)
-@Ignore
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
 public class TestDaoGeneticProfileSamples {
 

src/test/java/org/mskcc/cbio/portal/dao/TestDaoGistic.java → src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGistic.java

@@ -30,15 +30,12 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-package org.mskcc.cbio.portal.dao;
+package org.mskcc.cbio.portal.integrationTest.dao;
 
-import java.util.Arrays;
-
-import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.dao.DaoGeneOptimized;
 import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneOptimized;
 import org.mskcc.cbio.portal.dao.DaoGistic;
 import org.mskcc.cbio.portal.model.CanonicalGene;
 import org.mskcc.cbio.portal.model.Gistic;
@@ -48,13 +45,14 @@
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
-
 import java.sql.SQLException;
 import java.util.ArrayList;
+import java.util.Arrays;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 @RunWith(SpringJUnit4ClassRunner.class)
-@Ignore
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
 @Rollback
 @Transactional