LMS-1483 Further work on the graph/plot framework.

SVN: 15486

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();
 

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.

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;
     }
 }

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()

screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfigurationTest.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.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));
+
+    }
+}

screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/graph.properties

+# ------------------------------------------------------------------
+# 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