LMS-1957 first approach

SVN: 19368

rtd_phosphonetx/.classpath

@@ -32,5 +32,8 @@
 	<classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
 	<classpathentry kind="lib" path="/libraries/fastutil/fastutil.jar" sourcepath="/libraries/fastutil/fastutil-src.zip"/>
 	<classpathentry kind="lib" path="/libraries/spring/test/spring-test.jar" sourcepath="/libraries/spring/test/src.jar"/>
+	<classpathentry kind="lib" path="/libraries/csv/csv.jar" sourcepath="/libraries/csv/src.zip"/>
+	<classpathentry kind="lib" path="/libraries/activation/activation.jar"/>
+	<classpathentry kind="lib" path="/libraries/mail/mail.jar"/>
 	<classpathentry kind="output" path="targets/www/WEB-INF/classes"/>
 </classpath>

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/ProteinTableReportTest.java

+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * 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 ch.systemsx.cisd.openbis.dss.phosphonetx.server.plugins;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.Properties;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.openbis.generic.shared.dto.builders.DatasetDescriptionBuilder;
+
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+@Friend(toClasses=ProteinTableReport.class)
+public class ProteinTableReportTest extends AbstractFileSystemTestCase
+{
+    private static final String EXAMPLE_PROTEINS =
+            "# Protein abundances computed from file 'result.consensusXML'\n"
+                    + "# Parameters (relevant only): top=3, average=median, include_all, consensus:normalize\n"
+                    + "# Files/samples associated with abundance values below:"
+                    + " 0: '/cluster/weisserh_B1012_053.featureXML',"
+                    + " 1: '/cluster/weisserh_B1012_057.featureXML'\n"
+                    + "\"protein\",\"n_proteins\",\"protein_score\",\"n_peptides\",\"abundance_0\",\"abundance_1\"\n"
+                    + "\"13621327\",1,1,5,7846763.86498425,8159570.13467505\n"
+                    + "\"13621329\",1,1,6,2976845.93289974,3670078.89677526\n"
+                    + "\"13621337\",1,1,14,18114384.6420854,14119249.6148974\n";
+
+    @BeforeMethod
+    public void beforeMethod()
+    {
+        File originalFolder = new File(new File(workingDirectory, "1"), "original");
+        originalFolder.mkdirs();
+        File dataSetFolder = new File(originalFolder, "data-set-folder");
+        dataSetFolder.mkdirs();
+        FileUtilities.writeToFile(new File(dataSetFolder, ProteinTableReport.PROTEIN_FILE_NAME), EXAMPLE_PROTEINS);
+    }
+    
+    @Test
+    public void test()
+    {
+        ProteinTableReport report = new ProteinTableReport(new Properties(), workingDirectory);
+        DataSetProcessingContext context = new DataSetProcessingContext(Collections.<String, String>emptyMap(), null, "a@bc.de");
+        DatasetDescriptionBuilder ds1 = new DatasetDescriptionBuilder("ds1").location("1");
+        List<DatasetDescription> dataSets = Arrays.asList(ds1.getDatasetDescription());
+        report.process(dataSets, context);
+    }
+}