From 23c18ca9bcc2a87eb61e8e2ad2021ec149140d82 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Thu, 15 Apr 2010 17:24:59 +0000
Subject: [PATCH] LMS-1483 Handling of configuration parameters for graph
generation.
SVN: 15490
---
screening/etc/tabular-data-graph.properties | 42 +++++++++++++++++++
.../server/TabularDataGraphServlet.java | 40 ++++++++++++++++--
.../server/graph/ITabularDataGraph.java | 10 +++++
...bularDataGraphCollectionConfiguration.java | 31 ++++++++++----
.../graph/TabularDataGraphConfiguration.java | 15 ++++++-
.../server/graph/TabularDataHeatmap.java | 3 --
.../TabularDataHeatmapConfiguration.java | 4 +-
.../TabularDataHistogramConfiguration.java | 2 +-
.../server/graph/TabularDataScatterplot.java | 5 ++-
.../TabularDataScatterplotConfiguration.java | 41 ++++++++++++++++++
...rDataGraphCollectionConfigurationTest.java | 7 +++-
.../server/graph/TabularDataHeatmapTest.java | 2 +-
.../graph/TabularDataScatterplotTest.java | 14 ++++---
.../dss/generic/server/graph/graph.properties | 4 +-
14 files changed, 190 insertions(+), 30 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotConfiguration.java
diff --git a/screening/etc/tabular-data-graph.properties b/screening/etc/tabular-data-graph.properties
index 9c3080b9185..04cb84acd09 100644
--- a/screening/etc/tabular-data-graph.properties
+++ b/screening/etc/tabular-data-graph.properties
@@ -1,3 +1,45 @@
# ------------------------------------------------------------------
# Properties File For Generating Graphs From Tabular Data
# ------------------------------------------------------------------
+# ------------------------------------------------------------------
+# Properties File For Generating Graphs From Tabular Data
+# ------------------------------------------------------------------
+
+# The width of the full image
+full-width = 800
+
+# The height of the full image
+full-height = 600
+
+# The width of the table column
+column-width = 300
+
+# The height of the table row
+column-height = 200
+
+# 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
+scatter1.title = Total vs. Infected
+
+# The properties for the histogram
+hist.graph-type = histogram
+hist.column = TotalCells
+hist.title = Total Cells Histogram
+
+# The properties for the heatmap
+heat.graph-type = heatmap
+heat.x-axis = WellName
+heat.y-axis = WellName
+heat.column = InfectionIndex
+heat.title = Infection Index
+
+# The properties for the second scatter plot
+scatter2.graph-type = scatterplot
+scatter2.x-axis = TotalCells
+scatter2.y-axis = RelativeInfectionIndex
+scatter2.title = Total vs. Rel Infection
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 42a0ac587b5..0e9ce3ec0fc 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
@@ -64,6 +64,11 @@ public class TabularDataGraphServlet extends AbstractDatasetDownloadServlet
*/
private static class RequestParams
{
+ // optional parameters
+ public final static String WIDTH_PARAM = "w";
+
+ public final static String HEIGHT_PARAM = "h";
+
private final String sessionId;
private final String datasetCode;
@@ -72,12 +77,35 @@ public class TabularDataGraphServlet extends AbstractDatasetDownloadServlet
private final String graphName;
+ private final int width;
+
+ private final int height;
+
public RequestParams(HttpServletRequest request)
{
sessionId = getRequiredParameter(request, SESSION_ID_PARAM);
datasetCode = getRequiredParameter(request, DATASET_CODE_PARAM);
filePath = getRequiredParameter(request, FILE_PATH_PARAM);
graphName = getRequiredParameter(request, GRAPH_TYPE_CODE);
+ width = getIntParam(request, WIDTH_PARAM, 0);
+ height = getIntParam(request, HEIGHT_PARAM, 0);
+ }
+
+ private static int getIntParam(HttpServletRequest request, String paramName,
+ int defaultValue)
+ {
+ String value = request.getParameter(paramName);
+ if (value == null)
+ return defaultValue;
+
+ try
+ {
+ return Integer.valueOf(value);
+ } catch (NumberFormatException e)
+ {
+ throw new UserFailureException("parameter " + paramName
+ + " should be an integer, but is: " + value);
+ }
}
private static String getRequiredParameter(final HttpServletRequest request,
@@ -135,9 +163,15 @@ public class TabularDataGraphServlet extends AbstractDatasetDownloadServlet
// Generate an image image into the stream
ITabularDataGraph generator =
- configuration.getGraph(params.graphName, fileLines, response
- .getOutputStream());
- generator.generateImage();
+ configuration.getGraph(params.graphName, fileLines, response.getOutputStream());
+
+ if (params.height > 0 && params.width > 0)
+ {
+ generator.generateImage(params.width, params.height);
+ } else
+ {
+ generator.generateImage();
+ }
} catch (Exception e)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/ITabularDataGraph.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/ITabularDataGraph.java
index 59c01edd377..724bbd49ae7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/ITabularDataGraph.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/ITabularDataGraph.java
@@ -32,4 +32,14 @@ public interface ITabularDataGraph
*/
public abstract void generateImage() throws IOException;
+ /**
+ * 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 abstract void generateImage(int imageWidth, int imageHeight) throws IOException;
+
}
\ No newline at end of file
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 3e6bbdee632..77b57e02b1d 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
@@ -28,6 +28,7 @@ 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.graph.TabularDataGraphConfiguration.GraphType;
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;
@@ -89,11 +90,6 @@ public class TabularDataGraphCollectionConfiguration
private final HashMap<String, TabularDataGraphConfiguration> graphTypeMap;
- private enum GraphType
- {
- SCATTERPLOT, HISTOGRAM, HEATMAP
- }
-
/**
* Create a configuration from the properties file located at path.
*
@@ -192,9 +188,10 @@ public class TabularDataGraphCollectionConfiguration
.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());
+ return new TabularDataScatterplotConfiguration(title, PropertyUtils
+ .getMandatoryProperty(props, X_AXIS_KEY), PropertyUtils
+ .getMandatoryProperty(props, Y_AXIS_KEY), getThumbnailWidth(),
+ getThumbnailHeight());
}
// should never get here
@@ -231,7 +228,23 @@ public class TabularDataGraphCollectionConfiguration
{
throw new IllegalArgumentException("No graph associated with code " + graphName);
}
- return new TabularDataScatterplot(config, fileLines, out);
+ GraphType type = config.getGraphType();
+ switch (type)
+ {
+ case HEATMAP:
+ return new TabularDataHeatmap((TabularDataHeatmapConfiguration) config, fileLines,
+ out);
+ case HISTOGRAM:
+ return new TabularDataHistogram((TabularDataHistogramConfiguration) config,
+ fileLines, out);
+ case SCATTERPLOT:
+ return new TabularDataScatterplot((TabularDataScatterplotConfiguration) config,
+ fileLines, out);
+
+ }
+
+ // should never get here
+ return null;
}
public char getColumnDelimiter()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphConfiguration.java
index 5a45d0bcde3..b60d7ccea51 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphConfiguration.java
@@ -23,6 +23,13 @@ package ch.systemsx.cisd.openbis.dss.generic.server.graph;
*/
public class TabularDataGraphConfiguration
{
+ public enum GraphType
+ {
+ SCATTERPLOT, HISTOGRAM, HEATMAP
+ }
+
+ private final GraphType graphType;
+
private final String title;
// the column that is used as the x-axis
@@ -44,9 +51,10 @@ public class TabularDataGraphConfiguration
* @param imageWidth The desired width of the resulting image
* @param imageHeight The desired height of the resulting image
*/
- public TabularDataGraphConfiguration(String title, String xAxisColumn,
+ protected TabularDataGraphConfiguration(GraphType graphType, String title, String xAxisColumn,
String yAxisColumn, int imageWidth, int imageHeight)
{
+ this.graphType = graphType;
this.title = title;
this.xAxisColumn = xAxisColumn;
this.yAxisColumn = yAxisColumn;
@@ -62,6 +70,11 @@ public class TabularDataGraphConfiguration
return title;
}
+ public GraphType getGraphType()
+ {
+ return graphType;
+ }
+
/**
* The name of the column from which the x values come.
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java
index ed8e3c3e07f..f58c5d45cb0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java
@@ -165,9 +165,6 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
{
heatmapData.maxY = element.y;
}
-
- // DEBUG
- System.out.println("" + element.x + "," + element.y + "," + element.z);
}
return heatmapData;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapConfiguration.java
index 3a4a0d7234e..7fe7b85aa3d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapConfiguration.java
@@ -40,7 +40,7 @@ public class TabularDataHeatmapConfiguration extends TabularDataGraphConfigurati
protected TabularDataHeatmapConfiguration(String title, String xAxisColumn, String yAxisColumn,
String zAxisColumn, int imageWidth, int imageHeight)
{
- super(title, xAxisColumn, yAxisColumn, imageWidth, imageHeight);
+ super(GraphType.HISTOGRAM, title, xAxisColumn, yAxisColumn, imageWidth, imageHeight);
this.zAxisColumn = zAxisColumn;
isXYSplit = true;
}
@@ -58,7 +58,7 @@ public class TabularDataHeatmapConfiguration extends TabularDataGraphConfigurati
protected TabularDataHeatmapConfiguration(String title, String indexColumn, String zAxisColumn,
int imageWidth, int imageHeight)
{
- super(title, indexColumn, indexColumn, imageWidth, imageHeight);
+ super(GraphType.HEATMAP, title, indexColumn, indexColumn, imageWidth, imageHeight);
this.zAxisColumn = zAxisColumn;
isXYSplit = false;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogramConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogramConfiguration.java
index 58eaefbdc80..2fd73e71d85 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogramConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogramConfiguration.java
@@ -36,7 +36,7 @@ public class TabularDataHistogramConfiguration extends TabularDataGraphConfigura
protected TabularDataHistogramConfiguration(String title, String histogramColumn,
int imageWidth, int imageHeight, int numberOfBins)
{
- super(title, histogramColumn, histogramColumn, imageWidth, imageHeight);
+ super(GraphType.HISTOGRAM, title, histogramColumn, histogramColumn, imageWidth, imageHeight);
assert numberOfBins > 0;
this.numberOfBins = numberOfBins;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplot.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplot.java
index bf775ba3eab..ac9f36ec863 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplot.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplot.java
@@ -31,13 +31,14 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLine
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class TabularDataScatterplot extends AbstractTabularDataGraph<TabularDataGraphConfiguration>
+public class TabularDataScatterplot extends
+ AbstractTabularDataGraph<TabularDataScatterplotConfiguration>
{
/**
* @param configuration
*/
- public TabularDataScatterplot(TabularDataGraphConfiguration configuration,
+ public TabularDataScatterplot(TabularDataScatterplotConfiguration configuration,
DatasetFileLines fileLines, OutputStream out)
{
super(configuration, fileLines, out);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotConfiguration.java
new file mode 100644
index 00000000000..05d91f218d0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotConfiguration.java
@@ -0,0 +1,41 @@
+/*
+ * 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;
+
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class TabularDataScatterplotConfiguration extends TabularDataGraphConfiguration
+{
+
+ /**
+ * Construct a configuration for a scatterplot.
+ *
+ * @param title
+ * @param xAxisColumn
+ * @param yAxisColumn
+ * @param imageWidth
+ * @param imageHeight
+ */
+ public TabularDataScatterplotConfiguration(String title, String xAxisColumn,
+ String yAxisColumn, int imageWidth, int imageHeight)
+ {
+ super(GraphType.SCATTERPLOT, title, xAxisColumn, yAxisColumn, imageWidth, imageHeight);
+ }
+
+}
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
index 75ce8c95693..09c7360fb3e 100644
--- 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
@@ -60,8 +60,13 @@ public class TabularDataGraphCollectionConfigurationTest extends AssertJUnit
assertEquals(30, graphConfig.getImageWidth());
assertEquals("hist", graphNames.get(1));
+ graphConfig = configuration.getGraphConfiguration(graphNames.get(1));
+ assertEquals("Total Cells Histogram", graphConfig.getTitle());
+
assertEquals("heat", graphNames.get(2));
- assertEquals("scatter2", graphNames.get(3));
+ graphConfig = configuration.getGraphConfiguration(graphNames.get(2));
+ assertEquals("Infected Cells", graphConfig.getTitle());
+ assertEquals("scatter2", graphNames.get(3));
}
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapTest.java
index b8ca69d7222..94f1bd136e5 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapTest.java
@@ -29,7 +29,7 @@ public class TabularDataHeatmapTest extends AbstractTabularDataGraphTest
@Test
public void testHeatmap() throws IOException
{
- File outputFile = getImageOutputFile();
+ File outputFile = getTestImageOutputFile();
TabularDataHeatmapConfiguration config =
new TabularDataHeatmapConfiguration("Test", "WellName", "InfectionIndex", 300, 200);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotTest.java
index e77a0b0e146..ae7be7358d1 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotTest.java
@@ -31,9 +31,10 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
{
File outputFile = getImageOutputFile();
- TabularDataGraphConfiguration config =
- new TabularDataGraphConfiguration("Test", "TotalCells", "InfectedCells", 300, 200);
- AbstractTabularDataGraph<TabularDataGraphConfiguration> graph =
+ TabularDataScatterplotConfiguration config =
+ new TabularDataScatterplotConfiguration("Test", "TotalCells", "InfectedCells", 300,
+ 200);
+ TabularDataScatterplot graph =
new TabularDataScatterplot(config, getDatasetFileLines(),
getOutputStream(outputFile));
assertNotSame(graph.tryXColumnNumber(), graph.tryYColumnNumber());
@@ -48,9 +49,10 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
{
File outputFile = getImageOutputFile();
- TabularDataGraphConfiguration config =
- new TabularDataGraphConfiguration("Test", "TotalCells", "Non-existant", 300, 200);
- AbstractTabularDataGraph<TabularDataGraphConfiguration> graph =
+ TabularDataScatterplotConfiguration config =
+ new TabularDataScatterplotConfiguration("Test", "TotalCells", "Non-existant", 300,
+ 200);
+ TabularDataScatterplot graph =
new TabularDataScatterplot(config, getDatasetFileLines(),
getOutputStream(outputFile));
assertTrue(graph.tryYColumnNumber() < 0);
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
index 534639217f9..6605628eba3 100644
--- 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
@@ -31,14 +31,16 @@ scatter1.y-axis = InfectedCells
# The properties for the histogram
hist.graph-type = histogram
hist.column = TotalCells
+hist.title = Total Cells Histogram
# The properties for the heatmap
heat.graph-type = heatmap
heat.x-axis = WellName
heat.y-axis = WellName
heat.column = InfectedCells
+heat.title = Infected Cells
# 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
+scatter2.y-axis = RelativeInfectionIndex
--
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