From 6cd595c0e86547259edecf09476dfa39ad7e7d08 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Thu, 4 Mar 2010 23:32:38 +0000
Subject: [PATCH] LMS-1397 yeastx: introduce label, mz1 and mz2 columns
SVN: 15051
---
.../EICMLChromatogramImagesReporter.java | 61 ++++++++++++++++++-
.../EICMLChromatogramImagesReporterTest.java | 46 ++++++++++++++
2 files changed, 105 insertions(+), 2 deletions(-)
create mode 100644 rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporterTest.java
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java
index 4652de5cab1..d4164b7c8b8 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java
+++ b/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");
}
}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporterTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporterTest.java
new file mode 100644
index 00000000000..adc44046d88
--- /dev/null
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporterTest.java
@@ -0,0 +1,46 @@
+/*
+ * 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"));
+
+ }
+}
--
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