From b83821cc3651b4ec5373123c592ee818d7cc0126 Mon Sep 17 00:00:00 2001 From: Ruslan Forostianov Date: Mon, 8 Apr 2024 22:40:00 +0200 Subject: [PATCH] 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 --- README.md | 36 +++++++++++ pom.xml | 30 ++++++++- .../portal/scripts/ImportGenesetData.java | 2 +- .../cbio/portal/util/ProgressMonitor.java | 5 +- .../dao/TestDaoCancerStudy.java | 18 +++--- .../dao/TestDaoClinicalAttribute.java | 9 +-- .../dao/TestDaoGene.java | 7 ++- .../dao/TestDaoGenePanel.java | 19 +++--- .../dao/TestDaoGeneticAlteration.java | 23 +++++-- .../dao/TestDaoGeneticProfile.java | 17 +++-- .../dao/TestDaoGeneticProfileSamples.java | 18 ++++-- .../dao/TestDaoGistic.java | 14 ++--- .../dao/TestDaoMutSig.java | 12 ++-- .../dao/TestDaoMutation.java | 48 ++++++++------ .../dao/TestDaoSampleList.java | 21 ++++--- .../dao/TestDaoSampleProfile.java | 31 +++++++--- .../dao/TestDaoUser.java | 18 +++--- .../dao/TestDaoUserAuthorities.java | 18 +++--- .../pancancer/LargeTestSetGenerator.java | 2 +- .../TestPanCancerStudySummaryImport.java | 17 +++-- .../scripts/TestGenerateMutationData.java | 10 +-- .../scripts/TestImportCaisesClinicalXML.java | 7 ++- .../scripts/TestImportClinicalData.java | 28 ++++++--- .../TestImportCnaDiscreteLongData.java | 33 +++++++--- .../TestImportCopyNumberSegmentData.java | 22 +++---- .../TestImportExtendedMutationData.java | 45 ++++++++++---- .../scripts/TestImportGeneData.java | 18 ++---- .../scripts/TestImportGenericAssayData.java | 25 ++++---- ...estImportGenericAssayPatientLevelData.java | 40 +++++++----- .../scripts/TestImportGenesetData.java | 39 +++++------- .../TestImportGenesetHierarchyData.java | 28 ++++----- .../scripts/TestImportProfileData.java | 31 +++++----- .../scripts/TestImportReferenceGenome.java | 15 ++--- .../TestImportStructuralVariantData.java | 34 ++++++---- .../scripts/TestImportTabDelimData.java | 39 ++++++++---- .../scripts/TestImportUsers.java | 15 ++--- .../scripts/TestIntegrationTest.java | 62 +++++++++---------- .../scripts/TestMutationFilter.java | 12 ++-- .../TestNormalizeExpressionLevels.java | 15 +++-- .../servlet/TestWebService.java | 40 ++++++++---- .../util/TestCancerStudyReader.java | 13 ++-- .../util/TestGenePanelUtil.java | 10 +-- .../util/TestGeneticProfileReader.java | 10 ++- .../util/TestMutSigReader.java | 20 +++--- .../util/TestTransactionalScripts.java | 6 +- .../web_api/TestGetGeneticProfiles.java | 8 +-- .../web_api/TestGetMutSig.java | 14 ++--- .../web_api/TestGetProfileData.java | 24 ++++--- .../web_api/TestGetSampleList.java | 8 +-- .../web_api/TestGetTypesOfCancer.java | 13 ++-- .../portal/scripts/TestCutInvalidCases.java | 5 +- .../cbio/portal/stats/TestOddsRatio.java | 2 +- src/test/resources/applicationContext-dao.xml | 35 +++-------- 53 files changed, 633 insertions(+), 458 deletions(-) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoCancerStudy.java (96%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoClinicalAttribute.java (90%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoGene.java (95%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoGenePanel.java (88%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoGeneticAlteration.java (86%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoGeneticProfile.java (94%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoGeneticProfileSamples.java (87%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoGistic.java (96%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoMutSig.java (92%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoMutation.java (87%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoSampleList.java (86%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoSampleProfile.java (85%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoUser.java (91%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/dao/TestDaoUserAuthorities.java (97%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/pancancer/LargeTestSetGenerator.java (99%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/pancancer/TestPanCancerStudySummaryImport.java (92%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestGenerateMutationData.java (94%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportCaisesClinicalXML.java (97%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportClinicalData.java (96%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportCnaDiscreteLongData.java (96%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportCopyNumberSegmentData.java (97%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportExtendedMutationData.java (93%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportGeneData.java (92%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportGenericAssayData.java (98%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportGenericAssayPatientLevelData.java (87%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportGenesetData.java (94%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportGenesetHierarchyData.java (96%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportProfileData.java (99%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportReferenceGenome.java (92%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportStructuralVariantData.java (90%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportTabDelimData.java (94%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestImportUsers.java (92%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestIntegrationTest.java (99%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestMutationFilter.java (98%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/scripts/TestNormalizeExpressionLevels.java (94%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/servlet/TestWebService.java (93%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/util/TestCancerStudyReader.java (93%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/util/TestGenePanelUtil.java (96%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/util/TestGeneticProfileReader.java (96%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/util/TestMutSigReader.java (85%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/util/TestTransactionalScripts.java (90%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/web_api/TestGetGeneticProfiles.java (94%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/web_api/TestGetMutSig.java (94%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/web_api/TestGetProfileData.java (88%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/web_api/TestGetSampleList.java (93%) rename src/test/java/org/mskcc/cbio/portal/{ => integrationTest}/web_api/TestGetTypesOfCancer.java (96%) diff --git a/README.md b/README.md index 34634d1f..1a04e860 100644 --- 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 `` and `` 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 index 802d5ce8..99339126 100644 --- a/pom.xml +++ b/pom.xml @@ -247,7 +247,35 @@ org.apache.maven.plugins maven-surefire-plugin - 2.12.4 + 2.21.0 + + + default-test + test + + test + + + + **/integrationTest/**/* + + + + + integration-test + integration-test + + test + + + + **/integrationTest/**/* + + 1 + false + + + org.apache.maven.plugins diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportGenesetData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportGenesetData.java index f912fa77..7c6ed3b7 100644 --- 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 index cd95a9ae..948d25d9 100644 --- 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/src/test/java/org/mskcc/cbio/portal/dao/TestDaoCancerStudy.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoCancerStudy.java similarity index 96% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoCancerStudy.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoCancerStudy.java index 5fa9ac4f..aec208b9 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoCancerStudy.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoCancerStudy.java @@ -30,23 +30,26 @@ * along with this program. If not, see . */ -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. @@ -54,7 +57,6 @@ * @author Arman Aksoy, Ethan Cerami, Arthur Goldberg, Ersin Ciftci. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoClinicalAttribute.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoClinicalAttribute.java similarity index 90% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoClinicalAttribute.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoClinicalAttribute.java index ecc83385..734a44db 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoClinicalAttribute.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoClinicalAttribute.java @@ -30,21 +30,22 @@ * along with this program. If not, see . */ -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/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGene.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGene.java similarity index 95% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoGene.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGene.java index 2d1180b8..9ba437c9 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGene.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGene.java @@ -30,11 +30,13 @@ * along with this program. If not, see . */ -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/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGenePanel.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGenePanel.java similarity index 88% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoGenePanel.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGenePanel.java index dc6f3bef..a0fbd5af 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGenePanel.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGenePanel.java @@ -30,30 +30,29 @@ * along with this program. If not, see . */ -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/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticAlteration.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticAlteration.java similarity index 86% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticAlteration.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticAlteration.java index f18f5cf8..000b90fa 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticAlteration.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticAlteration.java @@ -30,27 +30,38 @@ * along with this program. If not, see . */ -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/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfile.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfile.java similarity index 94% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfile.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfile.java index 20552257..8c1afdcc 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfile.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfile.java @@ -30,25 +30,30 @@ * along with this program. If not, see . */ -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/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfileSamples.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfileSamples.java similarity index 87% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfileSamples.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfileSamples.java index 0812aeb8..01d65388 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfileSamples.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfileSamples.java @@ -30,27 +30,33 @@ * along with this program. If not, see . */ -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/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGistic.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGistic.java similarity index 96% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoGistic.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGistic.java index b430e585..df152f7b 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGistic.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGistic.java @@ -30,15 +30,12 @@ * along with this program. If not, see . */ -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 diff --git a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutSig.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutSig.java similarity index 92% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutSig.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutSig.java index 1616f2e5..67714b6e 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutSig.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutSig.java @@ -30,11 +30,13 @@ * along with this program. If not, see . */ -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.DaoMutSig; import org.mskcc.cbio.portal.model.CanonicalGene; import org.mskcc.cbio.portal.model.MutSig; import org.springframework.test.annotation.Rollback; @@ -42,17 +44,17 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.transaction.annotation.Transactional; -import static org.junit.Assert.*; - import java.io.IOException; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + /** * @author Lennart Bastian */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutation.java similarity index 87% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutation.java index e31dc8c7..cd22ac6c 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutation.java @@ -30,32 +30,40 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.dao; +package org.mskcc.cbio.portal.integrationTest.dao; -import java.io.IOException; +import com.fasterxml.jackson.databind.ObjectMapper; 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.DaoGeneOptimized; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; +import org.mskcc.cbio.portal.dao.DaoMutation; +import org.mskcc.cbio.portal.dao.DaoSample; +import org.mskcc.cbio.portal.dao.MySQLbulkLoader; +import org.mskcc.cbio.portal.model.CanonicalGene; +import org.mskcc.cbio.portal.model.ExtendedMutation; +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.*; - -import com.fasterxml.jackson.databind.ObjectMapper; +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.Map; +import java.util.Set; -import org.junit.Assert; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; /** * JUnit tests for DaoMutation class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional @@ -215,23 +223,23 @@ private void validateMockAnnotationJson(ExtendedMutation mutation) { Map> expectedAnnotationJsonMap = makeMockExpectedAnnotationJsonMap(); // confirm expected sizes - Assert.assertTrue(annotationJsonMap.containsKey("namespace1")); - Assert.assertEquals(expectedAnnotationJsonMap.get("namespace1").size(), annotationJsonMap.get("namespace1").size()); - Assert.assertEquals(2, annotationJsonMap.get("namespace1").size()); - Assert.assertTrue(annotationJsonMap.containsKey("namespace2")); - Assert.assertEquals(1, annotationJsonMap.get("namespace2").size()); - Assert.assertEquals(expectedAnnotationJsonMap.get("namespace2").size(), annotationJsonMap.get("namespace2").size()); + assertTrue(annotationJsonMap.containsKey("namespace1")); + assertEquals(expectedAnnotationJsonMap.get("namespace1").size(), annotationJsonMap.get("namespace1").size()); + assertEquals(2, annotationJsonMap.get("namespace1").size()); + assertTrue(annotationJsonMap.containsKey("namespace2")); + assertEquals(1, annotationJsonMap.get("namespace2").size()); + assertEquals(expectedAnnotationJsonMap.get("namespace2").size(), annotationJsonMap.get("namespace2").size()); // compare namespace 1 annotation map values Map namespace1Map = annotationJsonMap.get("namespace1"); Map expectedNamespace1Map = expectedAnnotationJsonMap.get("namespace1"); - Assert.assertEquals(expectedNamespace1Map.get("header1"), namespace1Map.get("header1")); - Assert.assertEquals(expectedNamespace1Map.get("header2"), namespace1Map.get("header2")); + assertEquals(expectedNamespace1Map.get("header1"), namespace1Map.get("header1")); + assertEquals(expectedNamespace1Map.get("header2"), namespace1Map.get("header2")); // compare namespace 2 annotation map values Map namespace2Map = annotationJsonMap.get("namespace2"); Map expectedNamespace2Map = expectedAnnotationJsonMap.get("namespace2"); - Assert.assertEquals(expectedNamespace2Map.get("header1"), namespace2Map.get("header1")); + assertEquals(expectedNamespace2Map.get("header1"), namespace2Map.get("header1")); } private String makeMockAnnotationJsonString() { diff --git a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoSampleList.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleList.java similarity index 86% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoSampleList.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleList.java index 1b73db9e..83b807b3 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoSampleList.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleList.java @@ -30,27 +30,34 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.dao; - -import java.util.ArrayList; +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.DaoPatient; +import org.mskcc.cbio.portal.dao.DaoSample; +import org.mskcc.cbio.portal.dao.DaoSampleList; +import org.mskcc.cbio.portal.model.CancerStudy; +import org.mskcc.cbio.portal.model.Patient; +import org.mskcc.cbio.portal.model.Sample; +import org.mskcc.cbio.portal.model.SampleList; +import org.mskcc.cbio.portal.model.SampleListCategory; 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; /** * JUnit test for DaoCase List. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoSampleProfile.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleProfile.java similarity index 85% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoSampleProfile.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleProfile.java index f327facc..705f46b6 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoSampleProfile.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleProfile.java @@ -30,28 +30,39 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.dao; - -import org.junit.Ignore; -import org.mskcc.cbio.portal.model.*; +package org.mskcc.cbio.portal.integrationTest.dao; +import org.junit.Before; +import org.junit.Test; +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.DaoGeneOptimized; +import org.mskcc.cbio.portal.dao.DaoGenePanel; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; +import org.mskcc.cbio.portal.dao.DaoPatient; +import org.mskcc.cbio.portal.dao.DaoSample; +import org.mskcc.cbio.portal.dao.DaoSampleProfile; +import org.mskcc.cbio.portal.model.CancerStudy; +import org.mskcc.cbio.portal.model.CanonicalGene; +import org.mskcc.cbio.portal.model.GenePanel; +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 org.junit.Test; -import org.junit.Before; -import org.junit.runner.RunWith; -import static org.junit.Assert.*; +import java.util.ArrayList; +import java.util.HashSet; -import java.util.*; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; /** * JUnit test for DaoSample class */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoUser.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUser.java similarity index 91% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoUser.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUser.java index b6c2890e..2c6b78a0 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoUser.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUser.java @@ -30,13 +30,8 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.dao; +package org.mskcc.cbio.portal.integrationTest.dao; -import static org.junit.Assert.*; - -import java.util.ArrayList; - -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.dao.DaoUser; @@ -46,15 +41,20 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.transaction.annotation.Transactional; -import static org.junit.Assert.*; -import static org.hamcrest.CoreMatchers.*; +import java.util.ArrayList; + +import static org.hamcrest.CoreMatchers.is; +import static org.hamcrest.CoreMatchers.not; +import static org.hamcrest.CoreMatchers.notNullValue; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertThat; /** * JUnit test for DaoUser class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoUserAuthorities.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUserAuthorities.java similarity index 97% rename from src/test/java/org/mskcc/cbio/portal/dao/TestDaoUserAuthorities.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUserAuthorities.java index c90a8b3a..556a11dd 100644 --- a/src/test/java/org/mskcc/cbio/portal/dao/TestDaoUserAuthorities.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUserAuthorities.java @@ -30,19 +30,13 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.dao; +package org.mskcc.cbio.portal.integrationTest.dao; // imports -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; -import java.util.Arrays; - -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; +import org.mskcc.cbio.portal.dao.DaoUserAuthorities; import org.mskcc.cbio.portal.model.User; import org.mskcc.cbio.portal.model.UserAuthorities; import org.springframework.test.annotation.Rollback; @@ -50,11 +44,17 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.transaction.annotation.Transactional; +import java.util.Arrays; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; +import static org.junit.Assert.fail; + /** * JUnit test for DaoUserAuthorities class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/pancancer/LargeTestSetGenerator.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/pancancer/LargeTestSetGenerator.java similarity index 99% rename from src/test/java/org/mskcc/cbio/portal/pancancer/LargeTestSetGenerator.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/pancancer/LargeTestSetGenerator.java index 9ab181cd..f85d7f2b 100644 --- a/src/test/java/org/mskcc/cbio/portal/pancancer/LargeTestSetGenerator.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/pancancer/LargeTestSetGenerator.java @@ -1,4 +1,4 @@ -package org.mskcc.cbio.portal.pancancer; +package org.mskcc.cbio.portal.integrationTest.pancancer; import java.io.BufferedReader; import java.io.File; diff --git a/src/test/java/org/mskcc/cbio/portal/pancancer/TestPanCancerStudySummaryImport.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/pancancer/TestPanCancerStudySummaryImport.java similarity index 92% rename from src/test/java/org/mskcc/cbio/portal/pancancer/TestPanCancerStudySummaryImport.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/pancancer/TestPanCancerStudySummaryImport.java index 248ee686..81cf6a2e 100755 --- a/src/test/java/org/mskcc/cbio/portal/pancancer/TestPanCancerStudySummaryImport.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/pancancer/TestPanCancerStudySummaryImport.java @@ -1,11 +1,18 @@ -package org.mskcc.cbio.portal.pancancer; +package org.mskcc.cbio.portal.integrationTest.pancancer; import org.junit.After; import org.junit.Before; import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; -import org.mskcc.cbio.portal.dao.*; +import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoClinicalData; +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.dao.DaoGeneOptimized; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; +import org.mskcc.cbio.portal.dao.DaoPatient; +import org.mskcc.cbio.portal.dao.DaoSample; +import org.mskcc.cbio.portal.dao.DaoTypeOfCancer; import org.mskcc.cbio.portal.model.CancerStudy; import org.mskcc.cbio.portal.model.CanonicalGene; import org.mskcc.cbio.portal.model.ClinicalAttribute; @@ -13,10 +20,10 @@ import org.mskcc.cbio.portal.model.TypeOfCancer; import org.mskcc.cbio.portal.scripts.ImportCancerStudy; import org.mskcc.cbio.portal.scripts.ImportClinicalData; -import org.mskcc.cbio.portal.scripts.ImportSampleList; import org.mskcc.cbio.portal.scripts.ImportProfileData; -import org.mskcc.cbio.portal.util.*; -import org.mskcc.cbio.portal.web_api.GetSampleLists; +import org.mskcc.cbio.portal.scripts.ImportSampleList; +import org.mskcc.cbio.portal.util.ConsoleUtil; +import org.mskcc.cbio.portal.util.ProgressMonitor; import org.springframework.test.annotation.Rollback; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestGenerateMutationData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestGenerateMutationData.java similarity index 94% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestGenerateMutationData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestGenerateMutationData.java index 9217f91e..66926984 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestGenerateMutationData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestGenerateMutationData.java @@ -30,26 +30,26 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; +import org.mskcc.cbio.portal.scripts.GenerateMutationData; import org.mskcc.cbio.portal.util.ProgressMonitor; 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.File; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + /** * JUnit test for GenerateMutationData class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCaisesClinicalXML.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCaisesClinicalXML.java similarity index 97% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportCaisesClinicalXML.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCaisesClinicalXML.java index d139a87f..e0532c90 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCaisesClinicalXML.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCaisesClinicalXML.java @@ -30,9 +30,7 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; - -import java.io.File; +package org.mskcc.cbio.portal.integrationTest.scripts; import org.junit.Before; import org.junit.Ignore; @@ -46,11 +44,14 @@ import org.mskcc.cbio.portal.model.Patient; import org.mskcc.cbio.portal.model.Sample; import org.mskcc.cbio.portal.model.TypeOfCancer; +import org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML; 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 java.io.File; + /** * * @author jgao diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportClinicalData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportClinicalData.java similarity index 96% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportClinicalData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportClinicalData.java index df3e1fbd..6d1475f2 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportClinicalData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportClinicalData.java @@ -30,28 +30,38 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; import org.junit.Before; -import org.junit.Ignore; import org.junit.Rule; import org.junit.Test; import org.junit.rules.ExpectedException; import org.junit.runner.RunWith; -import org.mskcc.cbio.portal.dao.*; -import org.mskcc.cbio.portal.model.*; +import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoClinicalData; +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.model.CancerStudy; +import org.mskcc.cbio.portal.model.ClinicalParameterMap; +import org.mskcc.cbio.portal.model.Patient; +import org.mskcc.cbio.portal.scripts.ImportClinicalData; import org.mskcc.cbio.portal.util.ConsoleUtil; import org.mskcc.cbio.portal.util.ProgressMonitor; -import org.mskcc.cbio.portal.scripts.ImportClinicalData; 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.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Set; -import java.io.*; -import java.util.*; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; /** * Tests Import of Clinical Data. @@ -61,8 +71,6 @@ * @author Pieter Lukasse */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCnaDiscreteLongData.java similarity index 96% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCnaDiscreteLongData.java index 0f3703af..d317aa03 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCnaDiscreteLongData.java @@ -25,15 +25,28 @@ * @author Sander Tan */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import com.fasterxml.jackson.databind.*; -import org.junit.*; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.After; +import org.junit.Assert; +import org.junit.Before; +import org.junit.Test; import org.junit.runner.RunWith; -import org.mskcc.cbio.portal.dao.*; +import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoCnaEvent; +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.dao.DaoGeneOptimized; +import org.mskcc.cbio.portal.dao.DaoGeneticAlteration; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; +import org.mskcc.cbio.portal.dao.DaoSample; +import org.mskcc.cbio.portal.dao.DaoSampleProfile; +import org.mskcc.cbio.portal.dao.JdbcUtil; +import org.mskcc.cbio.portal.dao.MySQLbulkLoader; import org.mskcc.cbio.portal.model.CnaEvent; import org.mskcc.cbio.portal.model.GeneticProfile; import org.mskcc.cbio.portal.model.Sample; +import org.mskcc.cbio.portal.scripts.ImportCnaDiscreteLongData; import org.mskcc.cbio.portal.util.StableIdUtil; import org.springframework.test.annotation.Rollback; import org.springframework.test.context.ContextConfiguration; @@ -45,7 +58,10 @@ import java.sql.PreparedStatement; import java.sql.ResultSet; import java.sql.SQLException; -import java.util.*; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; +import java.util.Set; import static com.google.common.collect.Lists.newArrayList; import static com.google.common.collect.Sets.newHashSet; @@ -54,11 +70,10 @@ import static org.cbioportal.model.MolecularProfile.DataType.DISCRETE; import static org.cbioportal.model.MolecularProfile.ImportType.DISCRETE_LONG; import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = {"classpath:/applicationContext-dao.xml"}) @Rollback @Transactional @@ -565,8 +580,8 @@ private void assertSampleExistsInGeneticProfile(String sampleId) throws DaoExcep geneticProfile.getCancerStudyId(), sampleStableId ); - Assert.assertNotNull(sample); - Assert.assertTrue(DaoSampleProfile.sampleExistsInGeneticProfile( + assertNotNull(sample); + assertTrue(DaoSampleProfile.sampleExistsInGeneticProfile( sample.getInternalId(), geneticProfile.getGeneticProfileId() )); diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCopyNumberSegmentData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCopyNumberSegmentData.java similarity index 97% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportCopyNumberSegmentData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCopyNumberSegmentData.java index a68270ce..7cc50cff 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCopyNumberSegmentData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCopyNumberSegmentData.java @@ -21,18 +21,9 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; - -import java.io.BufferedReader; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileReader; -import java.io.IOException; -import java.util.ArrayList; -import java.util.List; +package org.mskcc.cbio.portal.integrationTest.scripts; import org.junit.Before; -import org.junit.Ignore; import org.junit.Rule; import org.junit.Test; import org.junit.rules.ExpectedException; @@ -45,6 +36,7 @@ import org.mskcc.cbio.portal.model.CancerStudy; import org.mskcc.cbio.portal.model.Patient; import org.mskcc.cbio.portal.model.Sample; +import org.mskcc.cbio.portal.scripts.ImportCopyNumberSegmentData; import org.mskcc.cbio.portal.util.SpringUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.ApplicationContext; @@ -53,13 +45,19 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.transaction.annotation.Transactional; +import java.io.BufferedReader; +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileReader; +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; + /** * Test the import of Segment data into database. * @author pieterlukasse */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportExtendedMutationData.java similarity index 93% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportExtendedMutationData.java index 9f3ad075..b76c33d8 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportExtendedMutationData.java @@ -30,38 +30,57 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; import org.junit.Before; -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.util.*; +import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoClinicalAttributeMeta; +import org.mskcc.cbio.portal.dao.DaoClinicalData; +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.dao.DaoGeneOptimized; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; +import org.mskcc.cbio.portal.dao.DaoMutation; +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.ClinicalAttribute; +import org.mskcc.cbio.portal.model.ClinicalData; +import org.mskcc.cbio.portal.model.ExtendedMutation; +import org.mskcc.cbio.portal.model.GeneticAlterationType; +import org.mskcc.cbio.portal.model.GeneticProfile; +import org.mskcc.cbio.portal.model.Patient; +import org.mskcc.cbio.portal.model.Sample; +import org.mskcc.cbio.portal.scripts.ImportExtendedMutationData; +import org.mskcc.cbio.portal.util.ConsoleUtil; +import org.mskcc.cbio.portal.util.ProgressMonitor; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.context.ApplicationContext; 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 com.google.common.collect.Sets.newHashSet; -import static org.junit.Assert.*; - -import java.io.*; +import java.io.File; +import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.HashSet; import java.util.List; import java.util.Set; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.context.ApplicationContext; + +import static com.google.common.collect.Sets.newHashSet; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertNull; /** * @author Arthur Goldberg goldberg@cbio.mskcc.org */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/integrationTestScript.xml", "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGeneData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGeneData.java similarity index 92% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportGeneData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGeneData.java index c192a46e..aa182c36 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGeneData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGeneData.java @@ -30,33 +30,27 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; - -import static org.junit.Assert.assertEquals; - -import java.io.File; - import org.mskcc.cbio.portal.dao.DaoGeneOptimized; -import org.mskcc.cbio.portal.dao.DaoReferenceGenomeGene; import org.mskcc.cbio.portal.model.CanonicalGene; -import org.mskcc.cbio.portal.model.ReferenceGenome; -import org.mskcc.cbio.portal.model.ReferenceGenomeGene; +import org.mskcc.cbio.portal.scripts.ImportGeneData; import org.mskcc.cbio.portal.util.ProgressMonitor; 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 java.io.File; + +import static org.junit.Assert.assertEquals; + /** * JUnit tests for ImportGeneData class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenericAssayData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenericAssayData.java similarity index 98% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenericAssayData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenericAssayData.java index 38b099e1..a0a33c6d 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenericAssayData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenericAssayData.java @@ -25,39 +25,36 @@ * @author Pim van Nierop, pim@thehyve.nl */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; - -import java.io.File; -import java.sql.Connection; -import java.sql.PreparedStatement; -import java.sql.ResultSet; -import java.sql.SQLException; - -import org.cbioportal.model.EntityType; import org.cbioportal.model.meta.GenericAssayMeta; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.dao.DaoGenericAssay; import org.mskcc.cbio.portal.dao.DaoGeneticEntity; import org.mskcc.cbio.portal.dao.JdbcUtil; import org.mskcc.cbio.portal.model.GeneticAlterationType; +import org.mskcc.cbio.portal.scripts.ImportGenericAssayEntity; import org.mskcc.cbio.portal.util.ProgressMonitor; 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 java.io.File; +import java.sql.Connection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; + /* * JUnit tests for ImportTreatmentData class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenericAssayPatientLevelData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenericAssayPatientLevelData.java similarity index 87% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenericAssayPatientLevelData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenericAssayPatientLevelData.java index 4599dc7f..123715f8 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenericAssayPatientLevelData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenericAssayPatientLevelData.java @@ -30,41 +30,49 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import java.io.BufferedReader; +import org.cbioportal.model.GeneticEntity; import org.junit.Before; -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.cbioportal.model.GeneticEntity; -import org.mskcc.cbio.portal.util.*; +import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.dao.DaoGeneOptimized; +import org.mskcc.cbio.portal.dao.DaoGenericAssay; +import org.mskcc.cbio.portal.dao.DaoGeneticAlteration; +import org.mskcc.cbio.portal.dao.DaoGeneticEntity; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; +import org.mskcc.cbio.portal.dao.DaoPatient; +import org.mskcc.cbio.portal.dao.DaoSample; +import org.mskcc.cbio.portal.dao.DaoSampleProfile; +import org.mskcc.cbio.portal.dao.MySQLbulkLoader; +import org.mskcc.cbio.portal.model.CancerStudy; +import org.mskcc.cbio.portal.model.GeneticAlterationType; +import org.mskcc.cbio.portal.model.GeneticProfile; +import org.mskcc.cbio.portal.model.Patient; +import org.mskcc.cbio.portal.model.Sample; +import org.mskcc.cbio.portal.scripts.ImportGenericAssayPatientLevelData; +import org.mskcc.cbio.portal.util.FileUtil; +import org.mskcc.cbio.portal.util.ProgressMonitor; 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.File; -import java.io.FileNotFoundException; -import java.io.FileReader; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; -import java.util.HashSet; -import java.util.List; -import java.util.Set; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; /** * JUnit tests for ImportGenericAssayPatientLevelData class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenesetData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenesetData.java similarity index 94% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenesetData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenesetData.java index 74825b3d..a345f722 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenesetData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenesetData.java @@ -19,46 +19,39 @@ * * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . -*/ + */ /* * @author Sander Tan -*/ + */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; - -import static org.junit.Assert.assertEquals; - -import java.io.File; - import org.mskcc.cbio.portal.dao.DaoGeneset; import org.mskcc.cbio.portal.model.Geneset; +import org.mskcc.cbio.portal.scripts.ImportGenesetData; import org.mskcc.cbio.portal.util.ProgressMonitor; 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; -/* - * JUnit tests for ImportGenesetData class. -*/ +import java.io.File; -@RunWith(SpringJUnit4ClassRunner.class) -@Ignore +import static org.junit.Assert.assertEquals; +@RunWith(SpringJUnit4ClassRunner.class) @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional public class TestImportGenesetData { - @Test + @Test public void testImportGenesetData() throws Exception { ProgressMonitor.setConsoleMode(false); - + // Open genesets test data file File file = new File("src/test/resources/genesets/unit-test1_genesets.gmt"); boolean updateInfo = false; @@ -68,23 +61,23 @@ public void testImportGenesetData() throws Exception { // Open supplementary file file = new File("src/test/resources/genesets/unit-test1_supp-genesets.txt"); ImportGenesetData.importSuppGenesetData(file); - + // Test database entries Geneset geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET5"); assertEquals("UNITTEST_GENESET5", geneset.getExternalId()); geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET10"); assertEquals("http://www.broadinstitute.org/gsea/msigdb/cards/GCNP_SHH_UP_EARLY.V1_UP", geneset.getRefLink()); - + // Test warning message assertEquals(5, skippedGenes); - + // Test database entries supplementary file geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET2"); assertEquals("Genes up-regulated in RK3E cells (kidney epithelium) over-expressing GLI1 [GeneID=2735].", geneset.getDescription()); geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET8"); assertEquals("UNITTEST_GENESET8", geneset.getName()); - - // Test update of genes + + // Test update of genes // Open genesets test data file file = new File("src/test/resources/genesets/unit-test2_genesets.gmt"); newVersion = false; @@ -94,13 +87,13 @@ public void testImportGenesetData() throws Exception { // Open supplementary file file = new File("src/test/resources/genesets/unit-test2_supp-genesets.txt"); ImportGenesetData.importSuppGenesetData(file); - + geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET2"); assertEquals("A made up description is suited for this a fake gene.", geneset.getDescription()); geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET1"); assertEquals("Thought of new nice name for this geneset", geneset.getName()); geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET1"); assertEquals("http://www.thehyve.nl/", geneset.getRefLink()); - + } } diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenesetHierarchyData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenesetHierarchyData.java similarity index 96% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenesetHierarchyData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenesetHierarchyData.java index 5befd914..8e63b1ed 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportGenesetHierarchyData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenesetHierarchyData.java @@ -25,42 +25,40 @@ * @author Sander Tan */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; - -import static org.junit.Assert.assertEquals; - -import java.io.File; -import java.sql.Connection; -import java.sql.PreparedStatement; -import java.sql.ResultSet; -import java.sql.SQLException; -import java.util.List; - import org.mskcc.cbio.portal.dao.DaoException; import org.mskcc.cbio.portal.dao.DaoGeneset; -import org.mskcc.cbio.portal.dao.DaoGenesetHierarchyNode; import org.mskcc.cbio.portal.dao.DaoGenesetHierarchyLeaf; +import org.mskcc.cbio.portal.dao.DaoGenesetHierarchyNode; import org.mskcc.cbio.portal.dao.JdbcUtil; import org.mskcc.cbio.portal.model.Geneset; import org.mskcc.cbio.portal.model.GenesetHierarchy; import org.mskcc.cbio.portal.model.GenesetHierarchyLeaf; +import org.mskcc.cbio.portal.scripts.ImportGenesetData; +import org.mskcc.cbio.portal.scripts.ImportGenesetHierarchy; import org.mskcc.cbio.portal.util.ProgressMonitor; 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 java.io.File; +import java.sql.Connection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.List; + +import static org.junit.Assert.assertEquals; + /* * JUnit tests for ImportGenesetData class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportProfileData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportProfileData.java similarity index 99% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportProfileData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportProfileData.java index 79054c65..f1cc61fe 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportProfileData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportProfileData.java @@ -21,18 +21,12 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotEquals; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertNull; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.List; - -import org.junit.*; +import org.junit.After; +import org.junit.Before; +import org.junit.Rule; +import org.junit.Test; import org.junit.rules.ExpectedException; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.dao.DaoCancerStudy; @@ -55,11 +49,10 @@ import org.mskcc.cbio.portal.model.CnaEvent; import org.mskcc.cbio.portal.model.ExtendedMutation; import org.mskcc.cbio.portal.model.GeneticProfile; -import org.mskcc.cbio.portal.model.GeneticAlterationType; import org.mskcc.cbio.portal.model.Patient; import org.mskcc.cbio.portal.model.Sample; import org.mskcc.cbio.portal.model.StructuralVariant; - +import org.mskcc.cbio.portal.scripts.ImportProfileData; import org.mskcc.cbio.portal.util.ConsoleUtil; import org.mskcc.cbio.portal.util.ProgressMonitor; import org.springframework.test.annotation.Rollback; @@ -67,12 +60,20 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.transaction.annotation.Transactional; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotEquals; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertNull; + /** * @author Pieter Lukasse pieter@thehyve.nl */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportReferenceGenome.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportReferenceGenome.java similarity index 92% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportReferenceGenome.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportReferenceGenome.java index 8749febb..a59ba407 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportReferenceGenome.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportReferenceGenome.java @@ -1,27 +1,24 @@ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; - -import static org.junit.Assert.assertEquals; - -import java.io.File; - import org.mskcc.cbio.portal.dao.DaoReferenceGenome; import org.mskcc.cbio.portal.model.ReferenceGenome; +import org.mskcc.cbio.portal.scripts.ImportReferenceGenome; import org.mskcc.cbio.portal.util.ProgressMonitor; 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 java.io.File; + +import static org.junit.Assert.assertEquals; + /** * JUnit tests for ImportGeneData class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportStructuralVariantData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportStructuralVariantData.java similarity index 90% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportStructuralVariantData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportStructuralVariantData.java index 25442ea0..76a58f85 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportStructuralVariantData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportStructuralVariantData.java @@ -25,28 +25,38 @@ * @author Sander Tan */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; +import com.fasterxml.jackson.databind.ObjectMapper; import junitparams.JUnitParamsRunner; import junitparams.Parameters; -import org.apache.commons.lang3.StringEscapeUtils; -import com.fasterxml.jackson.databind.ObjectMapper; -import org.junit.*; +import org.junit.Before; +import org.junit.ClassRule; +import org.junit.Ignore; +import org.junit.Rule; +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.util.*; +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.DaoStructuralVariant; +import org.mskcc.cbio.portal.dao.MySQLbulkLoader; +import org.mskcc.cbio.portal.model.StructuralVariant; +import org.mskcc.cbio.portal.scripts.ImportStructuralVariantData; +import org.mskcc.cbio.portal.util.ProgressMonitor; import org.springframework.test.annotation.Rollback; import org.springframework.test.context.ContextConfiguration; -import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.test.context.junit4.rules.SpringClassRule; import org.springframework.test.context.junit4.rules.SpringMethodRule; import org.springframework.transaction.annotation.Transactional; +import java.io.File; +import java.io.IOException; +import java.util.List; +import java.util.Set; + import static com.google.common.collect.Sets.newHashSet; -import static org.junit.Assert.*; -import java.io.*; -import java.util.*; +import static org.junit.Assert.assertEquals; /** * Test class to test functionality of ImportStructralVariantData @@ -57,7 +67,7 @@ @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional -public class TestImportStructuralVariantData{ +public class TestImportStructuralVariantData { int studyId; int geneticProfileId; Set noNamespaces = null; diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportTabDelimData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportTabDelimData.java similarity index 94% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportTabDelimData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportTabDelimData.java index 03522f6f..33779cd3 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportTabDelimData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportTabDelimData.java @@ -30,23 +30,40 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; -import java.io.BufferedReader; import org.junit.Before; -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.util.*; +import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.dao.DaoGeneOptimized; +import org.mskcc.cbio.portal.dao.DaoGeneset; +import org.mskcc.cbio.portal.dao.DaoGeneticAlteration; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; +import org.mskcc.cbio.portal.dao.DaoPatient; +import org.mskcc.cbio.portal.dao.DaoSample; +import org.mskcc.cbio.portal.dao.DaoSampleProfile; +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.CopyNumberStatus; +import org.mskcc.cbio.portal.model.Geneset; +import org.mskcc.cbio.portal.model.GeneticAlterationType; +import org.mskcc.cbio.portal.model.GeneticProfile; +import org.mskcc.cbio.portal.model.Patient; +import org.mskcc.cbio.portal.model.Sample; +import org.mskcc.cbio.portal.scripts.ImportGenesetData; +import org.mskcc.cbio.portal.scripts.ImportTabDelimData; +import org.mskcc.cbio.portal.util.ConsoleUtil; +import org.mskcc.cbio.portal.util.FileUtil; +import org.mskcc.cbio.portal.util.ProgressMonitor; 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.BufferedReader; import java.io.File; import java.io.FileNotFoundException; import java.io.FileReader; @@ -58,12 +75,13 @@ import java.util.List; import java.util.Set; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + /** * JUnit tests for ImportTabDelimData class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional @@ -509,5 +527,4 @@ private void addTestPatientAndSampleRecords(File file) throws FileNotFoundExcept } MySQLbulkLoader.flushAll(); } - } diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportUsers.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportUsers.java similarity index 92% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestImportUsers.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportUsers.java index 63dce370..d70ea0b0 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestImportUsers.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportUsers.java @@ -30,29 +30,30 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; // imports -import org.junit.Ignore; + import org.junit.Test; import org.junit.runner.RunWith; -import org.mskcc.cbio.portal.model.User; import org.mskcc.cbio.portal.dao.DaoUser; -import org.mskcc.cbio.portal.model.UserAuthorities; import org.mskcc.cbio.portal.dao.DaoUserAuthorities; +import org.mskcc.cbio.portal.model.User; +import org.mskcc.cbio.portal.model.UserAuthorities; +import org.mskcc.cbio.portal.scripts.ImportUsers; 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.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; /** * JUnit test for ImportUsers class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestIntegrationTest.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestIntegrationTest.java similarity index 99% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestIntegrationTest.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestIntegrationTest.java index e5e1c41b..bc3bbac1 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestIntegrationTest.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestIntegrationTest.java @@ -21,31 +21,13 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; - -import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.io.InputStream; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.HashMap; -import java.util.HashSet; -import java.util.List; -import java.util.Map; -import java.util.Set; +package org.mskcc.cbio.portal.integrationTest.scripts; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.core.JsonParseException; import com.fasterxml.jackson.databind.JsonMappingException; import com.fasterxml.jackson.databind.ObjectMapper; - import org.cbioportal.model.GenericAssayData; import org.cbioportal.model.GenesetMolecularData; import org.cbioportal.model.StructuralVariant; @@ -59,28 +41,29 @@ import org.junit.Test; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoClinicalAttributeMeta; +import org.mskcc.cbio.portal.dao.DaoClinicalData; import org.mskcc.cbio.portal.dao.DaoException; import org.mskcc.cbio.portal.dao.DaoGeneOptimized; import org.mskcc.cbio.portal.dao.DaoGeneset; +import org.mskcc.cbio.portal.dao.DaoGeneticAlteration; import org.mskcc.cbio.portal.dao.DaoGeneticEntity; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; import org.mskcc.cbio.portal.dao.DaoGistic; -import org.mskcc.cbio.portal.dao.DaoSampleList; -import org.mskcc.cbio.portal.dao.MySQLbulkLoader; import org.mskcc.cbio.portal.dao.DaoMutation; +import org.mskcc.cbio.portal.dao.DaoSampleList; import org.mskcc.cbio.portal.dao.DaoTypeOfCancer; -import org.mskcc.cbio.portal.dao.DaoClinicalData; -import org.mskcc.cbio.portal.dao.DaoGeneticProfile; -import org.mskcc.cbio.portal.dao.DaoGeneticAlteration; -import org.mskcc.cbio.portal.dao.DaoClinicalAttributeMeta; -import org.mskcc.cbio.portal.model.ClinicalData; -import org.mskcc.cbio.portal.model.ClinicalAttribute; -import org.mskcc.cbio.portal.model.GeneticProfile; -import org.mskcc.cbio.portal.model.SampleList; +import org.mskcc.cbio.portal.dao.MySQLbulkLoader; import org.mskcc.cbio.portal.model.CancerStudy; -import org.mskcc.cbio.portal.model.TypeOfCancer; import org.mskcc.cbio.portal.model.CanonicalGene; +import org.mskcc.cbio.portal.model.ClinicalAttribute; +import org.mskcc.cbio.portal.model.ClinicalData; import org.mskcc.cbio.portal.model.ExtendedMutation; +import org.mskcc.cbio.portal.model.GeneticProfile; import org.mskcc.cbio.portal.model.Gistic; +import org.mskcc.cbio.portal.model.SampleList; +import org.mskcc.cbio.portal.model.TypeOfCancer; +import org.mskcc.cbio.portal.scripts.ImportGenePanel; import org.mskcc.cbio.portal.util.ConsoleUtil; import org.mskcc.cbio.portal.util.ProgressMonitor; import org.mskcc.cbio.portal.util.SpringUtil; @@ -92,6 +75,23 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.transaction.annotation.Transactional; +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.InputStream; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertTrue; + /** * Integration test using the same data that is used by validation system test * "study_es_0". In the validation system test for "study_es_0" it is checked if @@ -103,8 +103,6 @@ */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/integrationTestScript.xml", "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestMutationFilter.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestMutationFilter.java similarity index 98% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestMutationFilter.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestMutationFilter.java index 6e4abce3..2c193723 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestMutationFilter.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestMutationFilter.java @@ -30,30 +30,28 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; - -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertTrue; +package org.mskcc.cbio.portal.integrationTest.scripts; import org.junit.Before; -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.model.CanonicalGene; import org.mskcc.cbio.portal.model.ExtendedMutation; +import org.mskcc.cbio.portal.scripts.MutationFilter; 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.assertFalse; +import static org.junit.Assert.assertTrue; + /** * JUnit tests for MutationFilter class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestNormalizeExpressionLevels.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestNormalizeExpressionLevels.java similarity index 94% rename from src/test/java/org/mskcc/cbio/portal/scripts/TestNormalizeExpressionLevels.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestNormalizeExpressionLevels.java index bb857d32..964ccee3 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestNormalizeExpressionLevels.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestNormalizeExpressionLevels.java @@ -30,17 +30,14 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.scripts; +package org.mskcc.cbio.portal.integrationTest.scripts; import org.junit.Before; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; - -import static org.junit.Assert.*; - -import org.mskcc.cbio.portal.model.CanonicalGene; import org.mskcc.cbio.portal.dao.DaoGeneOptimized; +import org.mskcc.cbio.portal.model.CanonicalGene; +import org.mskcc.cbio.portal.scripts.NormalizeExpressionLevels; import org.springframework.test.annotation.Rollback; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; @@ -51,9 +48,11 @@ import java.net.URL; import java.util.ArrayList; -@RunWith(SpringJUnit4ClassRunner.class) -@Ignore +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; +@RunWith(SpringJUnit4ClassRunner.class) @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/servlet/TestWebService.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/servlet/TestWebService.java similarity index 93% rename from src/test/java/org/mskcc/cbio/portal/servlet/TestWebService.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/servlet/TestWebService.java index fb2d968d..9b4917be 100644 --- a/src/test/java/org/mskcc/cbio/portal/servlet/TestWebService.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/servlet/TestWebService.java @@ -30,36 +30,50 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.servlet; - -import java.io.*; -import java.util.*; +package org.mskcc.cbio.portal.integrationTest.servlet; import jakarta.servlet.ServletException; - import org.junit.After; import org.junit.Before; -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.util.*; +import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.dao.DaoSampleList; +import org.mskcc.cbio.portal.model.CancerStudy; +import org.mskcc.cbio.portal.model.GeneticProfile; +import org.mskcc.cbio.portal.model.SampleList; +import org.mskcc.cbio.portal.model.SampleListCategory; +import org.mskcc.cbio.portal.model.User; +import org.mskcc.cbio.portal.servlet.NullHttpServletRequest; +import org.mskcc.cbio.portal.servlet.NullHttpServletResponse; +import org.mskcc.cbio.portal.servlet.WebService; +import org.mskcc.cbio.portal.util.AccessControl; +import org.mskcc.cbio.portal.util.SpringUtil; +import org.mskcc.cbio.portal.util.WebserviceParserUtils; import org.springframework.security.core.userdetails.UserDetails; 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.easymock.EasyMock.*; +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; + +import static org.easymock.EasyMock.createMock; +import static org.easymock.EasyMock.expect; +import static org.easymock.EasyMock.isA; +import static org.easymock.EasyMock.replay; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; /** * JUnit test for WebService class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/util/TestCancerStudyReader.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestCancerStudyReader.java similarity index 93% rename from src/test/java/org/mskcc/cbio/portal/util/TestCancerStudyReader.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestCancerStudyReader.java index d6c13b02..733cbc79 100644 --- a/src/test/java/org/mskcc/cbio/portal/util/TestCancerStudyReader.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestCancerStudyReader.java @@ -30,28 +30,27 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.util; +package org.mskcc.cbio.portal.integrationTest.util; -import java.io.File; - -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.dao.DaoCancerStudy; import org.mskcc.cbio.portal.model.CancerStudy; +import org.mskcc.cbio.portal.util.CancerStudyReader; 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.File; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.fail; /** * JUnit test for CancerStudyReader class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/util/TestGenePanelUtil.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestGenePanelUtil.java similarity index 96% rename from src/test/java/org/mskcc/cbio/portal/util/TestGenePanelUtil.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestGenePanelUtil.java index c4b05600..e86341d0 100644 --- a/src/test/java/org/mskcc/cbio/portal/util/TestGenePanelUtil.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestGenePanelUtil.java @@ -1,6 +1,5 @@ -package org.mskcc.cbio.portal.util; +package org.mskcc.cbio.portal.integrationTest.util; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.model.CanonicalGene; @@ -16,12 +15,13 @@ import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNull; -import static org.mskcc.cbio.portal.util.GenePanelUtil.*; +import static org.mskcc.cbio.portal.util.GenePanelUtil.Pair; +import static org.mskcc.cbio.portal.util.GenePanelUtil.extractGenes; +import static org.mskcc.cbio.portal.util.GenePanelUtil.extractPropertyValue; +import static org.mskcc.cbio.portal.util.GenePanelUtil.getAddRemove; @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = {"classpath:/applicationContext-dao.xml"}) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/util/TestGeneticProfileReader.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestGeneticProfileReader.java similarity index 96% rename from src/test/java/org/mskcc/cbio/portal/util/TestGeneticProfileReader.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestGeneticProfileReader.java index b8caceef..af6eaf95 100644 --- a/src/test/java/org/mskcc/cbio/portal/util/TestGeneticProfileReader.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestGeneticProfileReader.java @@ -30,9 +30,8 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.util; +package org.mskcc.cbio.portal.integrationTest.util; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.dao.DaoCancerStudy; @@ -41,23 +40,22 @@ import org.mskcc.cbio.portal.model.CancerStudy; import org.mskcc.cbio.portal.model.GeneticAlterationType; import org.mskcc.cbio.portal.model.GeneticProfile; +import org.mskcc.cbio.portal.util.GeneticProfileReader; 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.File; import java.io.IOException; import java.util.ArrayList; +import static org.junit.Assert.assertEquals; + /** * JUnit test for GeneticProfileReader class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/util/TestMutSigReader.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestMutSigReader.java similarity index 85% rename from src/test/java/org/mskcc/cbio/portal/util/TestMutSigReader.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestMutSigReader.java index bf46ab71..85c01d28 100644 --- a/src/test/java/org/mskcc/cbio/portal/util/TestMutSigReader.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestMutSigReader.java @@ -30,26 +30,30 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.util; +package org.mskcc.cbio.portal.integrationTest.util; import org.junit.Before; -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.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; +import org.mskcc.cbio.portal.dao.DaoMutSig; +import org.mskcc.cbio.portal.model.CanonicalGene; +import org.mskcc.cbio.portal.model.MutSig; +import org.mskcc.cbio.portal.util.MutSigReader; +import org.mskcc.cbio.portal.util.ProgressMonitor; 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.File; -@RunWith(SpringJUnit4ClassRunner.class) -@Ignore +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; +@RunWith(SpringJUnit4ClassRunner.class) @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/util/TestTransactionalScripts.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestTransactionalScripts.java similarity index 90% rename from src/test/java/org/mskcc/cbio/portal/util/TestTransactionalScripts.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestTransactionalScripts.java index 25b691ea..0bb03e57 100644 --- a/src/test/java/org/mskcc/cbio/portal/util/TestTransactionalScripts.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/util/TestTransactionalScripts.java @@ -1,10 +1,10 @@ -package org.mskcc.cbio.portal.util; +package org.mskcc.cbio.portal.integrationTest.util; import org.junit.Before; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.util.TransactionalScripts; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.ApplicationContext; import org.springframework.test.annotation.Rollback; @@ -13,8 +13,6 @@ import org.springframework.transaction.annotation.Transactional; @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/demoScript.xml", "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetGeneticProfiles.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetGeneticProfiles.java similarity index 94% rename from src/test/java/org/mskcc/cbio/portal/web_api/TestGetGeneticProfiles.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetGeneticProfiles.java index cd226089..ede6b433 100644 --- a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetGeneticProfiles.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetGeneticProfiles.java @@ -30,25 +30,23 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.web_api; +package org.mskcc.cbio.portal.integrationTest.web_api; -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.web_api.GetGeneticProfiles; 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.assertTrue; /** * JUnit test for GeneticProfile class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetMutSig.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetMutSig.java similarity index 94% rename from src/test/java/org/mskcc/cbio/portal/web_api/TestGetMutSig.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetMutSig.java index 6b074c3f..e7d33db7 100644 --- a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetMutSig.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetMutSig.java @@ -30,37 +30,35 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.web_api; +package org.mskcc.cbio.portal.integrationTest.web_api; import org.junit.Before; -import org.junit.Ignore; import org.junit.Test; 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.DaoGeneOptimized; import org.mskcc.cbio.portal.dao.DaoGeneticProfile; import org.mskcc.cbio.portal.dao.DaoMutSig; -import org.mskcc.cbio.portal.model.CancerStudy; import org.mskcc.cbio.portal.model.CanonicalGene; import org.mskcc.cbio.portal.model.MutSig; -import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.web_api.GetMutSig; 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.io.*; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; /** * @author Lennart Bastian */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetProfileData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetProfileData.java similarity index 88% rename from src/test/java/org/mskcc/cbio/portal/web_api/TestGetProfileData.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetProfileData.java index 37439531..8fdff896 100644 --- a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetProfileData.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetProfileData.java @@ -30,32 +30,36 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.web_api; +package org.mskcc.cbio.portal.integrationTest.web_api; import org.junit.Before; -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.util.*; +import org.mskcc.cbio.portal.dao.DaoCancerStudy; +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.dao.DaoGeneOptimized; +import org.mskcc.cbio.portal.dao.DaoGeneticProfile; +import org.mskcc.cbio.portal.dao.DaoPatient; +import org.mskcc.cbio.portal.dao.DaoSample; +import org.mskcc.cbio.portal.model.CanonicalGene; +import org.mskcc.cbio.portal.model.GeneticAlterationType; +import org.mskcc.cbio.portal.model.GeneticProfile; +import org.mskcc.cbio.portal.web_api.GetProfileData; 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.File; import java.io.IOException; import java.util.ArrayList; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + /** * JUnit test for GetProfileData class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetSampleList.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetSampleList.java similarity index 93% rename from src/test/java/org/mskcc/cbio/portal/web_api/TestGetSampleList.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetSampleList.java index dc91d80e..598269ce 100644 --- a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetSampleList.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetSampleList.java @@ -30,24 +30,22 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.web_api; +package org.mskcc.cbio.portal.integrationTest.web_api; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; +import org.mskcc.cbio.portal.web_api.GetSampleLists; 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.assertTrue; /** * JUnit test for GetSampleLists class. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetTypesOfCancer.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetTypesOfCancer.java similarity index 96% rename from src/test/java/org/mskcc/cbio/portal/web_api/TestGetTypesOfCancer.java rename to src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetTypesOfCancer.java index a28a89f6..51b1d78d 100644 --- a/src/test/java/org/mskcc/cbio/portal/web_api/TestGetTypesOfCancer.java +++ b/src/test/java/org/mskcc/cbio/portal/integrationTest/web_api/TestGetTypesOfCancer.java @@ -30,12 +30,11 @@ * along with this program. If not, see . */ -package org.mskcc.cbio.portal.web_api; +package org.mskcc.cbio.portal.integrationTest.web_api; import org.junit.After; import org.junit.Before; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.dao.DaoCancerStudy; @@ -43,23 +42,25 @@ import org.mskcc.cbio.portal.dao.DaoTypeOfCancer; import org.mskcc.cbio.portal.model.CancerStudy; import org.mskcc.cbio.portal.model.TypeOfCancer; +import org.mskcc.cbio.portal.web_api.GetTypesOfCancer; +import org.mskcc.cbio.portal.web_api.ProtocolException; 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 static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; +import static org.junit.Assert.fail; + /** * JUnit Tests for GetTypes of Cancer. * * @author Ethan Cerami, Arthur Goldberg, Ersin Ciftci. */ @RunWith(SpringJUnit4ClassRunner.class) -@Ignore - @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) @Rollback @Transactional diff --git a/src/test/java/org/mskcc/cbio/portal/scripts/TestCutInvalidCases.java b/src/test/java/org/mskcc/cbio/portal/scripts/TestCutInvalidCases.java index fbb6fa6a..1b576c74 100644 --- a/src/test/java/org/mskcc/cbio/portal/scripts/TestCutInvalidCases.java +++ b/src/test/java/org/mskcc/cbio/portal/scripts/TestCutInvalidCases.java @@ -34,10 +34,11 @@ import org.junit.Test; -import static org.junit.Assert.*; - import java.io.File; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.fail; + /** * JUnit test for CutInvalidCases class. */ diff --git a/src/test/java/org/mskcc/cbio/portal/stats/TestOddsRatio.java b/src/test/java/org/mskcc/cbio/portal/stats/TestOddsRatio.java index 108fdb57..adad5c30 100644 --- a/src/test/java/org/mskcc/cbio/portal/stats/TestOddsRatio.java +++ b/src/test/java/org/mskcc/cbio/portal/stats/TestOddsRatio.java @@ -56,7 +56,7 @@ public void testFisherExact() throws IOException { GeneticAlterationType.COPY_NUMBER_ALTERATION, "DISCRETE", "CNA", "CNA", true); // TBD: change this to use getResourceAsStream() - String matrix0[][] = WebFileConnect.retrieveMatrix(new File("target/test-classes/cna_sample2.txt")); + String matrix0[][] = WebFileConnect.retrieveMatrix(new File("src/test/resources/cna_sample2.txt")); ProfileData data0 = new ProfileData(profile0, matrix0); profileList.add(data0); diff --git a/src/test/resources/applicationContext-dao.xml b/src/test/resources/applicationContext-dao.xml index e0fbe55b..7992c0f9 100644 --- a/src/test/resources/applicationContext-dao.xml +++ b/src/test/resources/applicationContext-dao.xml @@ -9,17 +9,6 @@ http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx.xsd"> - - - - - - - - - - - @@ -89,26 +78,22 @@ - - - - - - allowLoadLocalInfile - true - - - + - - - -