LMS-1397 yeastx: introduce label, mz1 and mz2 columns

SVN: 15051

rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java

@@ -26,6 +26,7 @@ import javax.sql.DataSource;
 import net.lemnik.eodsql.DataIterator;
 import net.lemnik.eodsql.QueryTool;
 
+import ch.rinn.restrictions.Private;
 import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
 import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
 import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
@@ -49,7 +50,7 @@ public class EICMLChromatogramImagesReporter extends AbstractDatastorePlugin imp
     private static final String CHROMATOGRAM_SERVLET = "chromatogram";
 
     private static final int THUMBNAIL_WIDTH = 150;
-    
+
     private static final int THUMBNAIL_HEIGHT = 150;
 
     private static final int IMAGE_WIDTH = 1066;
@@ -61,7 +62,7 @@ public class EICMLChromatogramImagesReporter extends AbstractDatastorePlugin imp
     private final IEICMSRunDAO query;
 
     /**
-     * An internal helper class for storing the information for the query paramters to the image
+     * An internal helper class for storing the information for the query parameters to the image
      * servlet.
      * 
      * @author Chandrasekhar Ramakrishnan
@@ -169,12 +170,68 @@ public class EICMLChromatogramImagesReporter extends AbstractDatastorePlugin imp
         imageCell.addParameter(EICMLChromatogramGeneratorServlet.CHROMATOGRAM_CODE_PARAM,
                 chromatogram.getId());
 
+        String chromatogramLabel = chromatogram.getLabel();
+        row.add(SimpleTableModelBuilder.asText(chromatogramLabel));
+        int mz1 = getMz1(chromatogramLabel);
+        row.add(SimpleTableModelBuilder.asNum(mz1));
+        int mz2 = getMz2(chromatogramLabel);
+        row.add(SimpleTableModelBuilder.asNum(mz2));
         row.add(imageCell);
         return row;
     }
 
+    // All eic_chromatograms.label values have a format [-]EIC mz1[>mz2].
+    @Private
+    static int getMz1(String chromatogramLabel)
+    {
+        String textBefore = "EIC ";
+        int ixEic = chromatogramLabel.indexOf(textBefore);
+        if (ixEic == -1)
+        {
+            return -1;
+        }
+        int ixGt = chromatogramLabel.indexOf(">");
+        if (ixGt == -1)
+        {
+            ixGt = chromatogramLabel.length();
+        }
+        if (ixGt < ixEic)
+        {
+            return -1;
+        }
+        String text = chromatogramLabel.substring(ixEic + textBefore.length(), ixGt);
+        return parseNumber(text, -1);
+    }
+
+    // All eic_chromatograms.label values have a format [-]EIC mz1[>mz2].
+    @Private
+    static int getMz2(String chromatogramLabel)
+    {
+        int ixGt = chromatogramLabel.indexOf(">");
+        if (ixGt == -1)
+        {
+            return -1;
+        }
+        String text = chromatogramLabel.substring(ixGt + 1);
+        return parseNumber(text, -1);
+    }
+
+    private static int parseNumber(String text, int defaultValue)
+    {
+        try
+        {
+            return Integer.parseInt(text);
+        } catch (NumberFormatException ex)
+        {
+            return defaultValue;
+        }
+    }
+
     private static void addReportHeaders(SimpleTableModelBuilder builder)
     {
+        builder.addHeader("Label");
+        builder.addHeader("m/z 1");
+        builder.addHeader("m/z 2");
         builder.addHeader("Chromatogram");
     }
 }

rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporterTest.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 ch.systemsx.cisd.yeastx.eicml;
+
+import static ch.systemsx.cisd.yeastx.eicml.EICMLChromatogramImagesReporter.getMz1;
+import static ch.systemsx.cisd.yeastx.eicml.EICMLChromatogramImagesReporter.getMz2;
+import static org.testng.AssertJUnit.assertEquals;
+
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+
+/**
+ * Test of {@link EICMLChromatogramImagesReporter}
+ * 
+ * @author Tomasz Pylak
+ */
+@Friend(toClasses = EICMLChromatogramImagesReporter.class)
+public class EICMLChromatogramImagesReporterTest
+{
+    @Test
+    public void testLabelParsing()
+    {
+        assertEquals(10, getMz1("-EIC 10>23"));
+        assertEquals(10, getMz1("EIC 10>23"));
+        assertEquals(10, getMz1("-EIC 10"));
+        assertEquals(23, getMz2("-EIC 10>23"));
+        assertEquals(23, getMz2("EIC 10>23"));
+        assertEquals(-1, getMz2("-EIC 10"));
+
+    }
+}