LMS-1485 more unit tests

SVN: 15474

eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractor.java

@@ -34,6 +34,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
 class LcaMicDataSetPropertiesExtractor extends TimeSeriesDataSetPropertiesExtractor
 {
 
+    static final String GROWTH_RATE = "GROWTH_RATE";
+
     LcaMicDataSetPropertiesExtractor(Properties properties)
     {
         super(properties);
@@ -49,7 +51,7 @@ class LcaMicDataSetPropertiesExtractor extends TimeSeriesDataSetPropertiesExtrac
             throw new UserFailureException("Empty file: " + file);
         }
         String[] items = StringUtils.split(lines.get(0), " \t");
-        NewProperty growthRate = new NewProperty("GROWTH_RATE", items[items.length - 1]);
+        NewProperty growthRate = new NewProperty(GROWTH_RATE, items[items.length - 1]);
         List<NewProperty> properties =
                 HeaderUtils.extractHeaderProperties(incomingDataSetPath, ignoreEmptyLines, true, true);
         properties.add(growthRate);

eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetUploader.java

@@ -66,7 +66,7 @@ class LcaMicDataSetUploader extends AbstractDataSetUploader
         super(dataSource, service, parameters);
     }
 
-    public LcaMicDataSetUploader(ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
+    LcaMicDataSetUploader(ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
             TimeSeriesDataSetUploaderParameters parameters)
     {
         super(dao, service, parameters);

eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractorTest.java

+/*
+ * Copyright 2010 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 eu.basysbio.cisd.dss;
+
+import static eu.basysbio.cisd.dss.HeaderUtils.TIME_SERIES_HEADER_PROPERTIES;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class LcaMicDataSetPropertiesExtractorTest extends AbstractFileSystemTestCase
+{
+    static final String EXAMPLE =
+            "# Ma::MS::B1::NT::EX::T1::NC::GrowthRate::Value[h^(-1)]::LIN::BBA9001#A_S20090325-2::NC\t0.68\n"
+                    + "Time (s)\t"
+                    + "Ma::MS::B1::NT::EX::T1::NC::LcaMicCfd::Value[um]::LIN::BBA9001#A_S20090325-2::NC\t"
+                    + "Ma::MS::B1::NT::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::BBA9001#A_S20090325-2::NC\t"
+                    + "Ma::MS::B1::NT::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::BBA9001#A_S20090325-2::NC\n";
+
+    @Test
+    public void test() throws IOException
+    {
+        File ds = new File(workingDirectory, "ds");
+        ds.mkdirs();
+        File file = new File(ds, "t.txt");
+        FileUtilities.writeToFile(file, EXAMPLE);
+        IDataSetPropertiesExtractor extractor =
+                new LcaMicDataSetPropertiesExtractor(new Properties());
+        List<NewProperty> props = extractor.extractDataSetProperties(ds);
+        assertEquals(TIME_SERIES_HEADER_PROPERTIES.length + 1, props.size());
+        Map<String, String> map = new HashMap<String, String>();
+        for (NewProperty property : props)
+        {
+            map.put(property.getPropertyCode(), property.getValue());
+        }
+        assertEquals("BBA9001#A_S20090325-2", map.get(TimeSeriesPropertyType.BI_ID.toString()));
+        assertEquals("B1", map.get(TimeSeriesPropertyType.BIOLOGICAL_REPLICATE_CODE.toString()));
+        assertEquals("NC", map.get(TimeSeriesPropertyType.CEL_LOC.toString()));
+        assertEquals("NC", map.get(TimeSeriesPropertyType.CG_LIST.toString()));
+        assertEquals("MS", map.get(TimeSeriesPropertyType.CULTIVATION_METHOD_EXPERIMENT_CODE.toString()));
+        assertEquals("Ma", map.get(TimeSeriesPropertyType.EXPERIMENT_CODE.toString()));
+        assertEquals("LIN", map.get(TimeSeriesPropertyType.SCALE_LIST.toString()));
+        assertEquals("T1", map.get(TimeSeriesPropertyType.TECHNICAL_REPLICATE_CODE_LIST.toString()));
+        assertEquals("0", map.get(TimeSeriesPropertyType.TIME_POINT_LIST.toString()));
+        assertEquals("LcaMicAbsFl, LcaMicCfd", map.get(TimeSeriesPropertyType.TIME_SERIES_DATA_SET_TYPE.toString()));
+        assertEquals(null, map.get(TimeSeriesPropertyType.UPLOADER_EMAIL.toString()));
+        assertEquals("Mean[Au], Std[Au], Value[um]", map.get(TimeSeriesPropertyType.VALUE_TYPE_LIST.toString()));
+        assertEquals("0.68", map.get(LcaMicDataSetPropertiesExtractor.GROWTH_RATE));
+    }
+    
+}

eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetUploaderTest.java

+/*
+ * Copyright 2010 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 eu.basysbio.cisd.dss;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.util.List;
+import java.util.Properties;
+
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.etlserver.cifex.CifexExtractorHelper;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class LcaMicDataSetUploaderTest extends AbstractFileSystemTestCase
+{
+    private static FilenameFilter TXT_FILTER = new FilenameFilter()
+        {
+            public boolean accept(File dir, String name)
+            {
+                return name.endsWith(".txt");
+            }
+        };
+
+    private static FilenameFilter PROPERTIES_FILTER = new FilenameFilter()
+        {
+            public boolean accept(File dir, String name)
+            {
+                return name.equals(CifexExtractorHelper.REQUEST_PROPERTIES_FILE);
+            }
+        };
+
+    private Mockery context;
+    private ITimeSeriesDAO dao;
+    private IEncapsulatedOpenBISService service;
+    private LcaMicDataSetUploader uploader;
+    private IDropBoxFeeder feeder;
+    private File dropBox;
+
+    @BeforeMethod
+    public void beforeMethod()
+    {
+        context = new Mockery();
+        dao = context.mock(ITimeSeriesDAO.class);
+        service = context.mock(IEncapsulatedOpenBISService.class);
+        feeder = context.mock(IDropBoxFeeder.class);
+        dropBox = new File(workingDirectory, "drop-box");
+        dropBox.mkdirs();
+        Properties properties = new Properties();
+        properties.setProperty(
+                TimeSeriesDataSetUploaderParameters.TIME_SERIES_DATA_SET_DROP_BOX_PATH, dropBox
+                        .toString());
+        uploader =
+                new LcaMicDataSetUploader(dao, service, new TimeSeriesDataSetUploaderParameters(
+                        properties, true));
+    }
+    
+    @AfterMethod
+    public void tearDown()
+    {
+        // To following line of code should also be called at the end of each test method.
+        // Otherwise one does not known which test failed.
+        context.assertIsSatisfied();
+    }
+    
+    @Test
+    public void test()
+    {
+        File tsvFile = new File(workingDirectory, "data.tsv");
+        FileUtilities.writeToFile(tsvFile, LcaMicDataSetPropertiesExtractorTest.EXAMPLE 
+                + "12\t2.5\t5.5\tN/A\n42\t42.5\t45.5\t3.25\n");
+        
+        DataSetInformation dataSetInformation = new DataSetInformation();
+        dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier("p1", "e1"));
+        dataSetInformation.setDataSetCode("abc-1");
+        dataSetInformation.setUploadingUserEmail("ab@c.de");
+        uploader.handleTSVFile(tsvFile, dataSetInformation, feeder);
+        
+        List<String> data = getData(1);
+        assertEquals("BBA ID\t" +
+        		"Ma::MS::B1::12::EX::T1::NC::LcaMicCfd::Value[um]::LIN::NB::NC\t" +
+        		"Ma::MS::B1::42::EX::T1::NC::LcaMicCfd::Value[um]::LIN::NB::NC", data.get(0));
+        assertEquals("BBA9001#A_S20090325-2\t2.5\t42.5", data.get(1));
+        checkProperties(1);
+        data = getData(2);
+        assertEquals("BBA ID\t" +
+                "Ma::MS::B1::12::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::NB::NC\t" +
+                "Ma::MS::B1::42::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::NB::NC", data.get(0));
+        assertEquals("BBA9001#A_S20090325-2\t5.5\t45.5", data.get(1));
+        checkProperties(2);
+        data = getData(3);
+        assertEquals("BBA ID\t" +
+                "Ma::MS::B1::12::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::NB::NC\t" +
+                "Ma::MS::B1::42::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::NB::NC", data.get(0));
+        assertEquals("BBA9001#A_S20090325-2\tN/A\t3.25", data.get(1));
+        checkProperties(3);
+        context.assertIsSatisfied();
+    }
+
+    private List<String> getData(int number)
+    {
+        File ds = new File(dropBox, DataSetHandler.LCA_MIC_TIME_SERIES + number);
+        List<String> data = FileUtilities.loadToStringList(ds.listFiles(TXT_FILTER)[0]);
+        assertEquals(2, data.size());
+        return data;
+    }
+
+    private void checkProperties(int number)
+    {
+        File ds = new File(dropBox, DataSetHandler.LCA_MIC_TIME_SERIES + number);
+        List<String> data = FileUtilities.loadToStringList(ds.listFiles(PROPERTIES_FILTER)[0]);
+        assertEquals(2, data.size());
+        assertEquals("comment=null,p1/e1,abc-1,LCA_MIC_TIME_SERIES,PROPRIETARY", data.get(0));
+        assertEquals("user-email=ab@c.de", data.get(1));
+    }
+    
+}