Enable integration tests (#29)

* Make import clinical data tests to run * Fix testImportClinicalData_WithDuplInMixedAttrFormat Warning was not shown because process mistakenly thought it's running from a web server * Enable TestImportProfileData * Enable the rest of passing script tests They passing when run one by one. But fail when you run them in batch due dirty database state (created by other tests?). * Upgrade surefire version to insulate test executions better With the old version, db integration tests did not roll back inserted data properly * Run db tests at integration-test step * Un-ignore the rest of passing integration tests * Document how to run integration tests * Rename and move int.tests to integerationTest package Integrationt test class name does not have to follow any naming convention anymore as soon as it placed under integrationTest package. We renamed all integration tests from IT* to Test* for readability purpose. * Replace wildcard imports in integrationTest folder * Move TestImportGenesetData back to own class * Use static imports for asserts * Use asserts from org.junit.Assert class everywhere * Comment application context configuration that caused tests to fail --------- Co-authored-by: Ruslan Forostianov <[email protected]>
cBioPortal · Apr 8, 2024 · b83821c · b83821c
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diff --git a/README.md b/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
+```
diff --git a/pom.xml b/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>

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportGenesetData.java b/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());
 

diff --git a/src/main/java/org/mskcc/cbio/portal/util/ProgressMonitor.java b/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.

diff --git a/...c/cbio/portal/dao/TestDaoCancerStudy.java → ...tegrationTest/dao/TestDaoCancerStudy.java b/...c/cbio/portal/dao/TestDaoCancerStudy.java → ...tegrationTest/dao/TestDaoCancerStudy.java
@@ -30,31 +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.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

diff --git a/.../portal/dao/TestDaoClinicalAttribute.java → ...ionTest/dao/TestDaoClinicalAttribute.java b/.../portal/dao/TestDaoClinicalAttribute.java → ...ionTest/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

diff --git a/...rg/mskcc/cbio/portal/dao/TestDaoGene.java → ...rtal/integrationTest/dao/TestDaoGene.java b/...rg/mskcc/cbio/portal/dao/TestDaoGene.java → ...rtal/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

diff --git a/...kcc/cbio/portal/dao/TestDaoGenePanel.java → ...integrationTest/dao/TestDaoGenePanel.java b/...kcc/cbio/portal/dao/TestDaoGenePanel.java → ...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

diff --git a/.../portal/dao/TestDaoGeneticAlteration.java → ...ionTest/dao/TestDaoGeneticAlteration.java b/.../portal/dao/TestDaoGeneticAlteration.java → ...ionTest/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

diff --git a/...bio/portal/dao/TestDaoGeneticProfile.java → ...rationTest/dao/TestDaoGeneticProfile.java b/...bio/portal/dao/TestDaoGeneticProfile.java → ...rationTest/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

diff --git a/...tal/dao/TestDaoGeneticProfileSamples.java → ...est/dao/TestDaoGeneticProfileSamples.java b/...tal/dao/TestDaoGeneticProfileSamples.java → ...est/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 {
 

diff --git a/.../mskcc/cbio/portal/dao/TestDaoGistic.java → ...al/integrationTest/dao/TestDaoGistic.java b/.../mskcc/cbio/portal/dao/TestDaoGistic.java → ...al/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