diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
index 0c6b2da27aa827f0e3972be1a96423bf0f9646f4..42a0ac587b56ca0afd5566d5699b43ff801e2f3a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -70,14 +70,14 @@ public class TabularDataGraphServlet extends AbstractDatasetDownloadServlet
private final String filePath;
- private final String graphTypeCode;
+ private final String graphName;
public RequestParams(HttpServletRequest request)
{
sessionId = getRequiredParameter(request, SESSION_ID_PARAM);
datasetCode = getRequiredParameter(request, DATASET_CODE_PARAM);
filePath = getRequiredParameter(request, FILE_PATH_PARAM);
- graphTypeCode = getRequiredParameter(request, GRAPH_TYPE_CODE);
+ graphName = getRequiredParameter(request, GRAPH_TYPE_CODE);
}
private static String getRequiredParameter(final HttpServletRequest request,
@@ -135,7 +135,7 @@ public class TabularDataGraphServlet extends AbstractDatasetDownloadServlet
// Generate an image image into the stream
ITabularDataGraph generator =
- configuration.getGraph(params.graphTypeCode, fileLines, response
+ configuration.getGraph(params.graphName, fileLines, response
.getOutputStream());
generator.generateImage();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
index 202adf9e9a20d6eaa82886eae519c00c5933d6fc..a4e3bf4522feb34e8432ec6c512f9790fa4d0d84 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
@@ -63,6 +63,20 @@ abstract class AbstractTabularDataGraph<T extends TabularDataGraphConfiguration>
.getImageHeight());
}
+ /**
+ * Create an image,overriding the width and height in the configuration from the file lines and
+ * write it to the output stream.
+ *
+ * @param imageWidth The desired width of the image
+ * @param imageHeight The desired height of the image
+ * @throws IOException
+ */
+ public void generateImage(int imageWidth, int imageHeight) throws IOException
+ {
+ JFreeChart chart = createChart();
+ ChartUtilities.writeChartAsPNG(out, chart, imageWidth, imageHeight);
+ }
+
// For Subclasses
/**
* Return the configuration for this graph.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
index 19bf44fa8b7628db2ec9ab3d207bf0559087b879..3e6bbdee632cf3fe53dc197df528a2e17553febc 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
@@ -29,6 +29,8 @@ import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PropertyParametersUtil;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PropertyParametersUtil.SectionProperties;
/**
* @author Chandrasekhar Ramakrishnan
@@ -39,18 +41,59 @@ public class TabularDataGraphCollectionConfiguration
private static final String IGNORE_COMMENTS_PROPERTY_KEY = "ignore-comments";
- // the seperator in the file
- private final char separator;
+ // the full width of the graphs when requested
+ private static final String IMAGE_WIDTH_KEY = "full-width";
+
+ // the full height of the graphs when requested
+ private static final String IMAGE_HEIGHT_KEY = "full-height";
+
+ // the width of the thumbnails shown in the report
+ private static final String THUMBNAIL_WIDTH_KEY = "column-width";
+
+ // the height of the thumbnails shown in the report
+ private static final String THUMBNAIL_HEIGHT_KEY = "column-height";
+
+ // the graphs to display -- each one is shown in a column.
+ private static final String GRAPHS_KEY = "graphs";
+
+ // the type of graph. See @{link GraphType} for valid types.
+ private static final String GRAPHS_TYPES_KEY = "graph-type";
+
+ // keys for the different kinds of graphs
+ private static final String TITLE_KEY = "title";
+
+ private static final String X_AXIS_KEY = "x-axis";
+
+ private static final String Y_AXIS_KEY = "y-axis";
+
+ private static final String COLUMN_KEY = "column";
+
+ private static final String NUMBER_OF_BINS_KEY = "number-of-bins";
+
+ private final char columnDelimiter;
private final boolean ignoreComments;
// the comment marker in the file
private final char comment;
- private final ArrayList<String> graphTypeCodes;
+ private final int imageWidth;
+
+ private final int imageHeight;
+
+ private final int thumbnailWidth;
+
+ private final int thumbnailHeight;
+
+ private final ArrayList<String> graphNames;
private final HashMap<String, TabularDataGraphConfiguration> graphTypeMap;
+ private enum GraphType
+ {
+ SCATTERPLOT, HISTOGRAM, HEATMAP
+ }
+
/**
* Create a configuration from the properties file located at path.
*
@@ -82,34 +125,93 @@ public class TabularDataGraphCollectionConfiguration
{
comment = '#';
- this.separator = PropertyUtils.getChar(properties, SEPARATOR_PROPERTY_KEY, ';');
+ this.columnDelimiter = PropertyUtils.getChar(properties, SEPARATOR_PROPERTY_KEY, ';');
this.ignoreComments =
PropertyUtils.getBoolean(properties, IGNORE_COMMENTS_PROPERTY_KEY, true);
- graphTypeCodes = new ArrayList<String>();
+
+ imageWidth = PropertyUtils.getInt(properties, IMAGE_WIDTH_KEY, 800);
+
+ imageHeight = PropertyUtils.getInt(properties, IMAGE_HEIGHT_KEY, 600);
+
+ thumbnailWidth = PropertyUtils.getInt(properties, THUMBNAIL_WIDTH_KEY, 300);
+
+ thumbnailHeight = PropertyUtils.getInt(properties, THUMBNAIL_HEIGHT_KEY, 200);
+
+ graphNames = new ArrayList<String>();
+ initializeGraphTypeCodes(properties);
graphTypeMap = new HashMap<String, TabularDataGraphConfiguration>();
initialzeGraphTypeMap(properties);
}
+ private void initializeGraphTypeCodes(Properties properties)
+ {
+ String graphTypeCodesString = properties.getProperty(GRAPHS_KEY, "");
+ String[] typeCodeArray = graphTypeCodesString.split(",");
+ for (String typeCode : typeCodeArray)
+ {
+ graphNames.add(typeCode.trim());
+ }
+ }
+
private void initialzeGraphTypeMap(Properties properties)
{
- TabularDataGraphConfiguration config =
- new TabularDataGraphConfiguration("Test", "TotalCells", "InfectedCells", 300, 200);
- graphTypeMap.put("scatter", config);
- graphTypeCodes.add("scatter");
+ SectionProperties[] pluginServicesProperties =
+ PropertyParametersUtil.extractSectionProperties(properties, GRAPHS_KEY, false);
+
+ for (SectionProperties sectionProp : pluginServicesProperties)
+ {
+ TabularDataGraphConfiguration config = getConfiguration(sectionProp);
+ graphTypeMap.put(sectionProp.getKey(), config);
+ }
+ }
+
+ private TabularDataGraphConfiguration getConfiguration(SectionProperties sectionProp)
+ {
+ Properties props = sectionProp.getProperties();
+ String graphTypeValue = PropertyUtils.getMandatoryProperty(props, GRAPHS_TYPES_KEY);
+ GraphType type = GraphType.valueOf(graphTypeValue.toUpperCase());
+ String title = props.getProperty(TITLE_KEY, sectionProp.getKey());
+ switch (type)
+ {
+ case HEATMAP:
+ String xAxis = PropertyUtils.getMandatoryProperty(props, X_AXIS_KEY);
+ String yAxis = PropertyUtils.getMandatoryProperty(props, Y_AXIS_KEY);
+ String zAxis = PropertyUtils.getMandatoryProperty(props, COLUMN_KEY);
+ if (xAxis.equals(yAxis))
+ {
+ return new TabularDataHeatmapConfiguration(title, xAxis, zAxis,
+ getThumbnailWidth(), getThumbnailHeight());
+ } else
+ {
+ return new TabularDataHeatmapConfiguration(title, xAxis, yAxis, zAxis,
+ getThumbnailWidth(), getThumbnailHeight());
+ }
+ case HISTOGRAM:
+ return new TabularDataHistogramConfiguration(title, PropertyUtils
+ .getMandatoryProperty(props, COLUMN_KEY), getThumbnailWidth(),
+ getThumbnailHeight(), PropertyUtils.getInt(props, NUMBER_OF_BINS_KEY, 10));
+ case SCATTERPLOT:
+ return new TabularDataGraphConfiguration(title, PropertyUtils.getMandatoryProperty(
+ props, X_AXIS_KEY), PropertyUtils.getMandatoryProperty(props, Y_AXIS_KEY),
+ getThumbnailWidth(), getThumbnailHeight());
+ }
+
+ // should never get here
+ return null;
}
/**
* Return the graph configuration associated with the graphTypeCode.
*
- * @param graphTypeCode The name of the graph type
+ * @param graphName The name of the graph type
*/
- public TabularDataGraphConfiguration getGraphConfiguration(String graphTypeCode)
+ public TabularDataGraphConfiguration getGraphConfiguration(String graphName)
{
- TabularDataGraphConfiguration config = graphTypeMap.get(graphTypeCode);
+ TabularDataGraphConfiguration config = graphTypeMap.get(graphName);
if (null == config)
{
- throw new IllegalArgumentException("No graph associated with code " + graphTypeCode);
+ throw new IllegalArgumentException("No graph associated with code " + graphName);
}
return config;
}
@@ -118,24 +220,23 @@ public class TabularDataGraphCollectionConfiguration
* Return the graph generator associated with the graphTypeCode, initialized by the fileLines
* and out.
*
- * @param graphTypeCode The name of the graph type
+ * @param graphName The name of the graph type
* @param fileLines The data to generate a graph from
* @param out The stream to write the graph to
*/
- public ITabularDataGraph getGraph(String graphTypeCode, DatasetFileLines fileLines,
- OutputStream out)
+ public ITabularDataGraph getGraph(String graphName, DatasetFileLines fileLines, OutputStream out)
{
- TabularDataGraphConfiguration config = graphTypeMap.get(graphTypeCode);
+ TabularDataGraphConfiguration config = graphTypeMap.get(graphName);
if (null == config)
{
- throw new IllegalArgumentException("No graph associated with code " + graphTypeCode);
+ throw new IllegalArgumentException("No graph associated with code " + graphName);
}
return new TabularDataScatterplot(config, fileLines, out);
}
public char getColumnDelimiter()
{
- return separator;
+ return columnDelimiter;
}
/**
@@ -153,26 +254,26 @@ public class TabularDataGraphCollectionConfiguration
public int getImageWidth()
{
- return 800;
+ return imageWidth;
}
public int getImageHeight()
{
- return 600;
+ return imageHeight;
}
public int getThumbnailWidth()
{
- return 300;
+ return thumbnailWidth;
}
public int getThumbnailHeight()
{
- return 200;
+ return thumbnailHeight;
}
- public List<String> getGraphTypeCodes()
+ public List<String> getGraphNames()
{
- return graphTypeCodes;
+ return graphNames;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisGraphReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisGraphReportingPlugin.java
index 6431cae5d3132ffb055035549042bc74962a896c..c28bccc8ac266c819adc16722ca48ccc5c1e14ac 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisGraphReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisGraphReportingPlugin.java
@@ -131,7 +131,7 @@ public class ImageAnalysisGraphReportingPlugin extends AbstractDataMergingReport
private List<String> getGraphTypeCodes()
{
- return configuration.getGraphTypeCodes();
+ return configuration.getGraphNames();
}
private int getImageWidth()
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfigurationTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfigurationTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..75ce8c95693c3ccd90530ec4b0a37df2cea4625f
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfigurationTest.java
@@ -0,0 +1,67 @@
+/*
+ * 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.openbis.dss.generic.server.graph;
+
+import java.net.URL;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphCollectionConfiguration;
+import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphConfiguration;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class TabularDataGraphCollectionConfigurationTest extends AssertJUnit
+{
+
+ @Test
+ public void testGoodConfigurationFile()
+ {
+ URL propertiesUrl = getClass().getResource("graph.properties");
+ String propertiesFilePath = propertiesUrl.getFile();
+ TabularDataGraphCollectionConfiguration configuration =
+ TabularDataGraphCollectionConfiguration.getConfiguration(propertiesFilePath);
+
+ // test the file global stuff
+ assertEquals(',', configuration.getColumnDelimiter());
+ assertFalse(configuration.isIgnoreComments());
+ assertEquals(1024, configuration.getImageWidth());
+ assertEquals(768, configuration.getImageHeight());
+ assertEquals(30, configuration.getThumbnailWidth());
+ assertEquals(30, configuration.getThumbnailHeight());
+
+ // test the graph configurations
+ assertEquals(4, configuration.getGraphNames().size());
+
+ List<String> graphNames = configuration.getGraphNames();
+ assertEquals("scatter1", graphNames.get(0));
+ TabularDataGraphConfiguration graphConfig =
+ configuration.getGraphConfiguration(graphNames.get(0));
+ // If not specified, the title should default to the name
+ assertEquals("scatter1", graphConfig.getTitle());
+ assertEquals(30, graphConfig.getImageHeight());
+ assertEquals(30, graphConfig.getImageWidth());
+
+ assertEquals("hist", graphNames.get(1));
+ assertEquals("heat", graphNames.get(2));
+ assertEquals("scatter2", graphNames.get(3));
+
+ }
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/graph.properties b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/graph.properties
new file mode 100644
index 0000000000000000000000000000000000000000..534639217f9e96e3825a4d4fb3bdbf8ca59d169d
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/graph.properties
@@ -0,0 +1,44 @@
+# ------------------------------------------------------------------
+# Properties File For Generating Graphs From Tabular Data
+# ------------------------------------------------------------------
+
+# The column delimiter
+separator = ,
+
+# Should comments be ignored?
+ignore-comments = false
+
+# The width of the full image
+full-width = 1024
+
+# The height of the full image
+full-height = 768
+
+# The width of the table column
+column-width = 30
+
+# The height of the table row
+column-height = 30
+
+# The graphs shown per row
+graphs = scatter1, hist, heat, scatter2
+
+# The properties for the first scatter plot
+scatter1.graph-type = scatterplot
+scatter1.x-axis = TotalCells
+scatter1.y-axis = InfectedCells
+
+# The properties for the histogram
+hist.graph-type = histogram
+hist.column = TotalCells
+
+# The properties for the heatmap
+heat.graph-type = heatmap
+heat.x-axis = WellName
+heat.y-axis = WellName
+heat.column = InfectedCells
+
+# The properties for the second scatter plot
+scatter2.graph-type = scatterplot
+scatter2.x-axis = TotalCells
+scatter2.y-axis = RelativeInfectionIndex
\ No newline at end of file