Author: kono Date: 2012-05-18 18:09:15 -0700 (Fri, 18 May 2012) New Revision: 29301
Added: core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/AbstractSessionTest.java core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/BasicIntegrationTest.java core3/impl/trunk/session-impl/integration-test/src/test/resources/ core3/impl/trunk/session-impl/integration-test/src/test/resources/testData/ core3/impl/trunk/session-impl/integration-test/src/test/resources/testData/smallSession.cys Modified: core3/impl/trunk/session-impl/integration-test/pom.xml Log: refs #6 First version of pax exam integration test for automating session loading/saving test. Modified: core3/impl/trunk/session-impl/integration-test/pom.xml =================================================================== --- core3/impl/trunk/session-impl/integration-test/pom.xml 2012-05-19 00:21:59 UTC (rev 29300) +++ core3/impl/trunk/session-impl/integration-test/pom.xml 2012-05-19 01:09:15 UTC (rev 29301) @@ -1,5 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> -<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> +<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> <parent> <artifactId>session-impl-parent</artifactId> @@ -10,52 +11,152 @@ <properties> <bundle.symbolicName>org.cytoscape.session-impl-integration-test</bundle.symbolicName> <bundle.namespace>org.cytoscape.session</bundle.namespace> + + <!-- Karaf + Pax Exam --> + <exam.version>2.4.0</exam.version> + <paxrunnerversion>1.7.6</paxrunnerversion> + <url.version>1.3.3</url.version> + <felixversion>3.2.2</felixversion> </properties> <modelVersion>4.0.0</modelVersion> - <groupId>org.cytoscape</groupId> <artifactId>session-impl-integration-test</artifactId> - <name>Cytoscape Session Impl Integration Test (${project.artifactId})</name> + <name>Cytoscape Session Impl Integration Test (${project.artifactId})</name> <packaging>jar</packaging> <build> <plugins> - <plugin> - <groupId>org.ops4j.pax.exam</groupId> - <artifactId>maven-paxexam-plugin</artifactId> - <version>${maven-paxexam-plugin.version}</version> - <executions> - <execution> - <id>generate-config</id> - <goals> - <goal>generate-config</goal> - </goals> - </execution> - </executions> - <configuration> - <options> - <platform>felix</platform> - <version>${felix.version}</version> - <profiles>spring.dm/${spring.osgi.version}</profiles> - </options> - </configuration> - </plugin> + </plugins> + </build> - <!-- - This is where any additional implementation dependencies necessary for - running the integration tests should reside, NOT in the top level pom.xml. - --> + <!-- Build minimal application to test session mechanism. --> <dependencies> <dependency> <groupId>org.cytoscape</groupId> + <artifactId>event-impl</artifactId> + <version>${project.version}</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>model-impl</artifactId> + <version>${project.version}</version> + <scope>test</scope> + </dependency> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>ding-presentation-impl</artifactId> + <version>${project.version}</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>vizmap-impl</artifactId> + <version>${project.version}</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>org.cytoscape</groupId> <artifactId>session-impl</artifactId> <version>${project.version}</version> - <scope>provided</scope> + <scope>test</scope> </dependency> + + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>io-impl</artifactId> + <version>${project.version}</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>application-impl</artifactId> + <version>${project.version}</version> + <scope>test</scope> + </dependency> + + + <!-- Pax Exam Dependencies --> + <!-- Pax Exam Dependencies --> + + <dependency> + <groupId>org.glassfish.hk2.external</groupId> + <artifactId>javax.inject</artifactId> + <version>2.1.3</version> + </dependency> + + <dependency> + <groupId>org.ops4j.pax.exam</groupId> + <artifactId>pax-exam-container-forked</artifactId> + <version>${exam.version}</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>org.ops4j.pax.exam</groupId> + <artifactId>pax-exam-junit4</artifactId> + <version>${exam.version}</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>org.ops4j.pax.exam</groupId> + <artifactId>pax-exam-link-mvn</artifactId> + <version>${exam.version}</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>org.ops4j.pax.url</groupId> + <artifactId>pax-url-aether</artifactId> + <version>${url.version}</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>org.apache.felix</groupId> + <artifactId>org.apache.felix.framework</artifactId> + <version>4.0.2</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>ch.qos.logback</groupId> + <artifactId>logback-core</artifactId> + <version>0.9.29</version> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>ch.qos.logback</groupId> + <artifactId>logback-classic</artifactId> + <version>0.9.29</version> + <scope>test</scope> + </dependency> + + + + + + + + <!-- Karaf Extension --> + <dependency> + <groupId>org.apache.karaf.tooling</groupId> + <artifactId>org.apache.karaf.tooling.testing</artifactId> + <version>2.2.7</version> + <scope>test</scope> + </dependency> + + </dependencies> </project> Added: core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/AbstractSessionTest.java =================================================================== --- core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/AbstractSessionTest.java (rev 0) +++ core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/AbstractSessionTest.java 2012-05-19 01:09:15 UTC (rev 29301) @@ -0,0 +1,147 @@ +package org.cytoscape.session; + +import static org.mockito.Mockito.mock; + +import java.io.File; +import java.io.InputStream; +import java.net.URL; +import java.util.Properties; + +import org.cytoscape.equations.EquationCompiler; +import org.cytoscape.equations.EquationParser; +import org.cytoscape.equations.Interpreter; +import org.cytoscape.equations.internal.EquationCompilerImpl; +import org.cytoscape.equations.internal.EquationParserImpl; +import org.cytoscape.equations.internal.interpreter.InterpreterImpl; +import org.cytoscape.event.CyEventHelper; +import org.cytoscape.event.internal.CyEventHelperImpl; +import org.cytoscape.event.internal.CyListenerAdapter; +import org.cytoscape.io.BasicCyFileFilter; +import org.cytoscape.io.DataCategory; +import org.cytoscape.io.internal.read.CyNetworkReaderManagerImpl; +import org.cytoscape.io.internal.read.CyPropertyReaderManagerImpl; +import org.cytoscape.io.internal.read.VizmapReaderManagerImpl; +import org.cytoscape.io.internal.read.datatable.CSVCyReaderFactory; +import org.cytoscape.io.internal.read.session.Cy3SessionReaderImpl; +import org.cytoscape.io.internal.read.vizmap.VizmapXMLFileFilter; +import org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory; +import org.cytoscape.io.internal.util.ReadCache; +import org.cytoscape.io.internal.util.StreamUtilImpl; +import org.cytoscape.io.internal.util.vizmap.CalculatorConverterFactory; +import org.cytoscape.io.internal.util.vizmap.VisualStyleSerializer; +import org.cytoscape.io.read.CyNetworkReaderManager; +import org.cytoscape.io.read.CyPropertyReaderManager; +import org.cytoscape.io.read.CySessionReader; +import org.cytoscape.io.read.VizmapReaderManager; +import org.cytoscape.io.util.StreamUtil; +import org.cytoscape.model.CyNetworkTableManager; +import org.cytoscape.model.CyTableFactory; +import org.cytoscape.model.internal.CyNetworkTableManagerImpl; +import org.cytoscape.model.internal.CyRootNetworkManagerImpl; +import org.cytoscape.model.internal.CyTableFactoryImpl; +import org.cytoscape.model.subnetwork.CyRootNetworkManager; +import org.cytoscape.property.CyProperty; +import org.cytoscape.service.util.CyServiceRegistrar; +import org.cytoscape.service.util.internal.CyServiceRegistrarImpl; +import org.cytoscape.work.TaskMonitor; +import org.junit.After; +import org.junit.Before; +import org.junit.Test; +import org.osgi.framework.BundleContext; + +/** + * Build real application with minimal functionality. + * + */ +public class AbstractSessionTest { + + private CySessionReader sessionReader; + + private URL session1; + private TaskMonitor taskMonitor = mock(TaskMonitor.class); + + @Before + public void setUp() throws Exception { + buildHeadlessApplication(); + } + + @After + public void tearDown() throws Exception { + } + + @Test + public void test() throws Exception { + + //sessionReader.run(taskMonitor); + } + + private void buildHeadlessApplication() throws Exception { + BundleContext bc = mock(BundleContext.class); + CyListenerAdapter normal = new CyListenerAdapter(bc); + CyEventHelper cyEventHelper = new CyEventHelperImpl(normal); + + final File sessionFile1 = new File("./src/test/resources/testData/" + "smallSession.cys"); + + final URL sessionFileURL1 = sessionFile1.toURI().toURL(); + InputStream sourceInputStream = sessionFileURL1.openStream(); + + final ReadCache cache = new ReadCache(); + CyProperty<Properties> prop = new CyProperty<Properties>() { + + @Override + public String getName() { + // TODO Auto-generated method stub + return null; + } + + @Override + public Properties getProperties() { + // TODO Auto-generated method stub + return null; + } + + @Override + public org.cytoscape.property.CyProperty.SavePolicy getSavePolicy() { + // TODO Auto-generated method stub + return null; + } + + @Override + public Class<? extends Properties> getPropertyType() { + // TODO Auto-generated method stub + return null; + } + + }; + StreamUtil streamUtil = new StreamUtilImpl(prop); + CyNetworkReaderManager networkReaderMgr = new CyNetworkReaderManagerImpl(streamUtil); + CyPropertyReaderManager propertyReaderMgr = new CyPropertyReaderManagerImpl(streamUtil); + VizmapReaderManager vizmapReaderMgr = new VizmapReaderManagerImpl(streamUtil); + + CalculatorConverterFactory calculatorConverterFactory = new CalculatorConverterFactory(); + +// VisualStyleSerializer visualStyleSerializer = new VisualStyleSerializer(calculatorConverterFactory,visualStyleFactoryServiceRef,visualMappingManagerServiceRef,renderingEngineManagerServiceRef,discreteMappingFactoryServiceRef,continuousMappingFactoryServiceRef,passthroughMappingFactoryServiceRef); +// VizmapXMLFileFilter vizmapXMLFilter = new VizmapXMLFileFilter(new String[]{"xml"}, new String[]{}, "Vizmap XML files",DataCategory.VIZMAP, streamUtil); +// VizmapXMLReaderFactory vizmapXMLReaderFactory = new VizmapXMLReaderFactory(vizmapXMLFilter,visualStyleSerializer); + + + + + Interpreter interpreter = new InterpreterImpl(); + CyServiceRegistrar serviceRegistrar = new CyServiceRegistrarImpl(bc); + CyTableFactory tableFactory = new CyTableFactoryImpl(cyEventHelper, interpreter, serviceRegistrar); + EquationParser parser = new EquationParserImpl(); + EquationCompiler compiler = new EquationCompilerImpl(parser); + + BasicCyFileFilter sessionTableFilter = new BasicCyFileFilter(new String[] { "cytable" }, + new String[] { "text/plain" }, "Session table file", DataCategory.TABLE, streamUtil); + + CSVCyReaderFactory sessionTableReaderFactory = new CSVCyReaderFactory(sessionTableFilter, true, true, + tableFactory, compiler); + + CyNetworkTableManager networkTableMgr = new CyNetworkTableManagerImpl(); + CyRootNetworkManager rootNetworkMgr = new CyRootNetworkManagerImpl(); + sessionReader = new Cy3SessionReaderImpl(sourceInputStream, cache, networkReaderMgr, propertyReaderMgr, + vizmapReaderMgr, sessionTableReaderFactory, networkTableMgr, rootNetworkMgr); + } +} Added: core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/BasicIntegrationTest.java =================================================================== --- core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/BasicIntegrationTest.java (rev 0) +++ core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/BasicIntegrationTest.java 2012-05-19 01:09:15 UTC (rev 29301) @@ -0,0 +1,199 @@ +/* + * Copyright (C) 2011 Toni Menzel + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.cytoscape.session; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; +import static org.ops4j.pax.exam.CoreOptions.felix; +import static org.ops4j.pax.exam.CoreOptions.junitBundles; +import static org.ops4j.pax.exam.CoreOptions.mavenBundle; +import static org.ops4j.pax.exam.CoreOptions.options; +import static org.ops4j.pax.exam.CoreOptions.repository; + +import java.io.File; +import java.util.Set; + +import javax.inject.Inject; + +import org.cytoscape.model.CyNetwork; +import org.cytoscape.model.CyNetworkFactory; +import org.cytoscape.model.CyNetworkManager; +import org.cytoscape.task.read.OpenSessionTaskFactory; +import org.cytoscape.view.model.VisualLexicon; +import org.cytoscape.view.presentation.RenderingEngineManager; +import org.cytoscape.work.SynchronousTaskManager; +import org.cytoscape.work.TaskIterator; +import org.junit.After; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.ops4j.pax.exam.Option; +import org.ops4j.pax.exam.junit.Configuration; +import org.ops4j.pax.exam.junit.ExamReactorStrategy; +import org.ops4j.pax.exam.junit.JUnit4TestRunner; +import org.ops4j.pax.exam.spi.reactors.AllConfinedStagedReactorFactory; +import org.ops4j.pax.exam.util.Filter; +import org.osgi.framework.Bundle; +import org.osgi.framework.BundleContext; +import org.osgi.framework.ServiceReference; + +@RunWith(JUnit4TestRunner.class) +@ExamReactorStrategy( AllConfinedStagedReactorFactory.class ) +public class BasicIntegrationTest { + + final String API_BUNDLE_VERSION = "3.0.0-beta2-SNAPSHOT"; + final String IMPL_BUNDLE_VERSION = "3.0.0-alpha9-SNAPSHOT"; + + @Inject + private BundleContext bundleContext; + + @Inject + private CyNetworkManager networkManager; + @Inject + private CyNetworkFactory networkFactory; + + @Inject + private CySessionManager sessionManager; + + @Inject + private RenderingEngineManager renderingEngineManager; + + @Inject @Filter("(id=ding)") + private VisualLexicon lexicon; + + @Inject + private OpenSessionTaskFactory openSessionTF; + + @Inject + private SynchronousTaskManager tm; + + /** + * Build minimal set of bundles. + */ + @Configuration + public Option[] config() { + return options( + junitBundles(), + felix(), + repository("http://code.cytoscape.org/nexus/content/repositories/snapshots/";), + + + + // Misc. bundles required to run minimal Cytoscape + mavenBundle().groupId("cytoscape-sun").artifactId("jhall").version("1.0"), + // API bundles + + + + mavenBundle().groupId("org.cytoscape").artifactId("event-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("model-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("group-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("viewmodel-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("presentation-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("vizmap-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("session-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("io-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("property-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("work-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("core-task-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("application-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("layout-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("datasource-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("vizmap-gui-api").version(API_BUNDLE_VERSION), + + mavenBundle().groupId("org.cytoscape").artifactId("work-swing-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("swing-application-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("equations-api").version(API_BUNDLE_VERSION), + + mavenBundle().groupId("org.cytoscape").artifactId("swing-application-api").version(API_BUNDLE_VERSION), + + mavenBundle().groupId("org.cytoscape").artifactId("service-api").version(API_BUNDLE_VERSION), + + mavenBundle().groupId("com.googlecode.guava-osgi").artifactId("guava-osgi").version("9.0.0"), + mavenBundle().groupId("cytoscape-temp").artifactId("parallelcolt").version("0.9.4"), + mavenBundle().groupId("cytoscape-temp").artifactId("opencsv").version("2.1"), + mavenBundle().groupId("com.lowagie.text").artifactId("com.springsource.com.lowagie.text").version("2.0.8"), + mavenBundle().groupId("cytoscape-temp").artifactId("freehep-graphicsio").version("2.1.3"), + mavenBundle().groupId("cytoscape-temp").artifactId("freehep-graphicsio-svg").version("2.1.3"), + mavenBundle().groupId("cytoscape-temp").artifactId("freehep-graphicsio-ps").version("2.1.3"), + mavenBundle().groupId("cytoscape-temp").artifactId("freehep-graphics2d").version("2.1.3"), + mavenBundle().groupId("cytoscape-temp").artifactId("l2fprod-common-shared").version("7.3"), + mavenBundle().groupId("cytoscape-temp").artifactId("l2fprod-common-fontchooser").version("7.3"), + mavenBundle().groupId("cytoscape-temp").artifactId("l2fprod-common-sheet").version("7.3"), + mavenBundle().groupId("cytoscape-temp").artifactId("org.swinglabs.swingx").version("1.6.1"), + mavenBundle().groupId("cytoscape-temp").artifactId("freehep-export").version("2.1.1"), + mavenBundle().groupId("cytoscape-temp").artifactId("freehep-util").version("2.0.2"), + + + mavenBundle().groupId("org.cytoscape").artifactId("property-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("datasource-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("equations-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("event-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("swing-util-api").version(API_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("model-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("group-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("work-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("work-headless-impl").version(IMPL_BUNDLE_VERSION), + + mavenBundle().groupId("org.cytoscape").artifactId("layout-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("viewmodel-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("presentation-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("vizmap-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("application-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("session-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("ding-presentation-impl").version(IMPL_BUNDLE_VERSION), + + mavenBundle().groupId("org.cytoscape").artifactId("io-impl").version(IMPL_BUNDLE_VERSION), + mavenBundle().groupId("org.cytoscape").artifactId("core-task-impl").version(IMPL_BUNDLE_VERSION), + + mavenBundle().groupId("org.cytoscape").artifactId("vizmap-gui-impl").version(IMPL_BUNDLE_VERSION) + ); + } + + @Test + public void test() throws Exception { + assertNotNull(bundleContext); + Bundle[] bundles = bundleContext.getBundles(); + + for(Bundle bundle:bundles) { + System.out.println(bundle.getState() + ": Bundle: " + bundle.getSymbolicName() + " Correct state=" + Bundle.ACTIVE); + ServiceReference<?>[] services = bundle.getRegisteredServices(); + if(services != null) + System.out.println("# service: " + services.length); + } + assertNotNull(bundles); + assertNotNull(networkManager); + assertNotNull(networkFactory); + assertNotNull(sessionManager); + assertNotNull(renderingEngineManager); + + assertNotNull(tm); + assertNotNull(openSessionTF); + + final File sessionFile1 = new File("./src/test/resources/testData/" + "smallSession.cys"); + final TaskIterator ti = openSessionTF.createTaskIterator(sessionFile1); + tm.execute(ti); + } + + @After + public void confirm() { + Set<CyNetwork> networks = networkManager.getNetworkSet(); + assertEquals(2, networks.size()); +// CyNetwork net1 = networks.iterator().next(); +// CyNetwork net2 = networks.iterator().next(); +// assertEquals(22, net1.getNodeCount()); + } + +} Added: core3/impl/trunk/session-impl/integration-test/src/test/resources/testData/smallSession.cys =================================================================== (Binary files differ) Property changes on: core3/impl/trunk/session-impl/integration-test/src/test/resources/testData/smallSession.cys ___________________________________________________________________ Added: svn:mime-type + application/octet-stream -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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