diff --git a/screening/etc/service.properties b/screening/etc/service.properties
index 014b948454598501ac86f21a464671cb256e285b..36f93e28c1d2255367867a7c87f4d5ce15cb5dc3 100644
--- a/screening/etc/service.properties
+++ b/screening/etc/service.properties
@@ -79,7 +79,7 @@ quiet-period = 3
# ---------------------------------------------------------------------------
# Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name.
-reporting-plugins = plate-image-reporter, plate-image-params-reporter, plate-image-analysis-merger, demo-reporter
+reporting-plugins = plate-image-reporter, plate-image-params-reporter, plate-image-analysis-merger, plate-image-analysis-graph, demo-reporter
# Label of the plugin which will be shown for the users.
demo-reporter.label = Show Dataset Size
@@ -113,6 +113,12 @@ plate-image-analysis-merger.dataset-types = HCS_IMAGE_ANALYSIS_DATA
plate-image-analysis-merger.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisMergedRowsReportingPlugin
plate-image-analysis-merger.properties-file =
+plate-image-analysis-graph.label = Show Image Analysis Graphs
+plate-image-analysis-graph.dataset-types = HCS_IMAGE_ANALYSIS_DATA
+plate-image-analysis-graph.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisGraphReportingPlugin
+plate-image-analysis-graph.servlet-path = datastore_server_graph/
+plate-image-analysis-graph.properties-file = etc/tabular-data-graph.properties
+
# ---------------------------------------------------------------------------
# Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name.
@@ -134,13 +140,18 @@ hierarchical-storage-updater.hierarchy-root-dir = targets/hierarchical-store
# ---------------------------------------------------------------------------
# list of additional web servlets which will be exposed
-plugin-services = screening-image-download-servlet
+plugin-services = screening-image-download-servlet, tabular-data-graph-servlet
# class of the web servlet
#screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet
screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.SplittingImagesDownloadServlet
# URL which will be mapped to this servlet
screening-image-download-servlet.path = /datastore_server_screening/*
+tabular-data-graph-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.TabularDataGraphServlet
+# URL which will be mapped to this servlet
+tabular-data-graph-servlet.path = /datastore_server_graph/*
+tabular-data-graph-servlet.properties-file = etc/tabular-data-graph.properties
+
# ---------------------------------------------------------------------------
# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
diff --git a/screening/etc/tabular-data-graph.properties b/screening/etc/tabular-data-graph.properties
new file mode 100644
index 0000000000000000000000000000000000000000..9c3080b91851b38697b87b2c6134516d45d59781
--- /dev/null
+++ b/screening/etc/tabular-data-graph.properties
@@ -0,0 +1,3 @@
+# ------------------------------------------------------------------
+# Properties File For Generating Graphs From Tabular Data
+# ------------------------------------------------------------------
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphGeneratorServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphGeneratorServlet.java
deleted file mode 100644
index 95c58d2db477225a563bd1f23cb04ea780350ffc..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphGeneratorServlet.java
+++ /dev/null
@@ -1,206 +0,0 @@
-/*
- * 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;
-
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Properties;
-
-import javax.servlet.ServletConfig;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import javax.servlet.http.HttpSession;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphGenerator;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class TabularDataGraphGeneratorServlet extends AbstractDatasetDownloadServlet
-{
-
- private static final long serialVersionUID = 1L;
-
- // Required servlet parameters
-
- public final static String DATASET_CODE_PARAM = "dataset";
-
- public final static String GRAPH_TYPE_CODE = "type";
-
- // Optional, but recommended servlet parameters
-
- public final static String IMAGE_WIDTH_PARAM = "w";
-
- public final static String IMAGE_HEIGHT_PARAM = "h";
-
- // Default values for optional parameters
- public final static int DEFAULT_WIDTH = 300;
-
- public final static int DEFAULT_HEIGHT = 200;
-
- /**
- * A utility class for dealing with the parameters required to generate an image from a
- * chromatogram. This class makes sure all the required parameters are in the request (it throws
- * exceptions otherwise), and it defaults values for all optional parameters if they are not in
- * the request.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- private static class RequestParams
- {
- private final String sessionId;
-
- private final String datasetCode;
-
- private final String graphTypeCode;
-
- private final int width;
-
- private final int height;
-
- public RequestParams(HttpServletRequest request)
- {
- sessionId = getParam(request, SESSION_ID_PARAM);
- datasetCode = getParam(request, DATASET_CODE_PARAM);
- graphTypeCode = getParam(request, GRAPH_TYPE_CODE);
- width = getIntParam(request, IMAGE_WIDTH_PARAM, DEFAULT_WIDTH);
- height = getIntParam(request, IMAGE_HEIGHT_PARAM, DEFAULT_HEIGHT);
- }
-
- 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 getParam(final HttpServletRequest request, String paramName)
- {
- String value = request.getParameter(paramName);
- if (value == null)
- {
- throw new UserFailureException("no value for the parameter " + paramName
- + " found in the URL");
- }
- return value;
- }
-
- public String getSessionId()
- {
- return sessionId;
- }
-
- public String getDatasetCode()
- {
- return datasetCode;
- }
-
- public String getGraphTypeCode()
- {
- return graphTypeCode;
- }
-
- public int getWidth()
- {
- return width;
- }
-
- public int getHeight()
- {
- return height;
- }
- }
-
- // The properties needed for connecting to the database
- private Properties dbProperties;
-
- @Override
- protected synchronized void doSpecificInitialization(Enumeration<String> parameterNames,
- ServletConfig servletConfig)
- {
- // Only initialize the db properties once
- if (dbProperties != null)
- return;
-
- dbProperties = new Properties();
- String name;
- while (parameterNames.hasMoreElements())
- {
- name = parameterNames.nextElement();
- dbProperties.setProperty(name, servletConfig.getInitParameter(name));
- }
- }
-
- @Override
- protected final void doGet(final HttpServletRequest request, final HttpServletResponse response)
- throws ServletException, IOException
- {
- try
- {
- // Get the parameters from the request
- RequestParams params = new RequestParams(request);
- String sessionId = params.getSessionId();
- String datasetCode = params.getDatasetCode();
- int height = params.getHeight();
- int width = params.getWidth();
-
- // Get the session and user from the request
- HttpSession session = tryGetOrCreateSession(request, sessionId);
- if (session == null)
- {
- printSessionExpired(response);
- return;
- }
- // Check that the user has view access to the chromatogram data
- // NOTE: This throws an exception -- it may be nicer to return an image for a
- // non-accessible chromatogram...
- ensureDatasetAccessible(datasetCode, session, sessionId);
-
- // Get the chromatogram data
- DatasetFileLines fileLines = tryDatasetLinesForParameters(params);
-
- // Generate a chromatogram image into the stream
- TabularDataGraphGenerator generator =
- new TabularDataGraphGenerator(fileLines, response.getOutputStream(), width,
- height);
- generator.generateImage();
-
- } catch (Exception e)
- {
- printErrorResponse(response, "Invalid Request");
- e.printStackTrace();
- }
- }
-
- private DatasetFileLines tryDatasetLinesForParameters(RequestParams params)
- {
- return null;
- }
-}
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
new file mode 100644
index 0000000000000000000000000000000000000000..0c6b2da27aa827f0e3972be1a96423bf0f9646f4
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -0,0 +1,184 @@
+/*
+ * 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;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+
+import javax.servlet.ServletConfig;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import javax.servlet.http.HttpSession;
+
+import com.csvreader.CsvReader;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.graph.ITabularDataGraph;
+import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphCollectionConfiguration;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class TabularDataGraphServlet extends AbstractDatasetDownloadServlet
+{
+ // Required servlet parameters
+ public final static String DATASET_CODE_PARAM = "dataset";
+
+ public final static String FILE_PATH_PARAM = "file";
+
+ public final static String GRAPH_TYPE_CODE = "type";
+
+ private static final long serialVersionUID = 1L;
+
+ private TabularDataGraphCollectionConfiguration configuration;
+
+ private final static String PROPERTIES_FILE_KEY = "properties-file";
+
+ /**
+ * A utility class for dealing with the URL parameters required to generate an image. This class
+ * makes sure all the required parameters are in the request (it throws exceptions otherwise),
+ * and it defaults values for all optional parameters if they are not in the request.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+ private static class RequestParams
+ {
+ private final String sessionId;
+
+ private final String datasetCode;
+
+ private final String filePath;
+
+ private final String graphTypeCode;
+
+ 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);
+ }
+
+ private static String getRequiredParameter(final HttpServletRequest request,
+ String paramName)
+ {
+ String value = request.getParameter(paramName);
+ if (value == null)
+ {
+ throw new UserFailureException("no value for the parameter " + paramName
+ + " found in the URL");
+ }
+ return value;
+ }
+ }
+
+ @Override
+ protected synchronized void doSpecificInitialization(Enumeration<String> parameterNames,
+ ServletConfig servletConfig)
+ {
+ // Only initialize the db properties once
+ if (configuration != null)
+ return;
+
+ String propertiesFilePath = servletConfig.getInitParameter(PROPERTIES_FILE_KEY);
+ configuration =
+ TabularDataGraphCollectionConfiguration.getConfiguration(propertiesFilePath);
+ }
+
+ @Override
+ protected final void doGet(final HttpServletRequest request, final HttpServletResponse response)
+ throws ServletException, IOException
+ {
+ try
+ {
+ // Get the parameters from the request
+ RequestParams params = new RequestParams(request);
+ String sessionId = params.sessionId;
+ String datasetCode = params.datasetCode;
+ String filePath = params.filePath;
+
+ // Get the session and user from the request
+ HttpSession session = tryGetOrCreateSession(request, sessionId);
+ if (session == null)
+ {
+ printSessionExpired(response);
+ return;
+ }
+ // Check that the user has view access to the data
+ // NOTE: This throws an exception -- it may be nicer to return an image for a
+ // non-accessible dataset...
+ ensureDatasetAccessible(datasetCode, session, sessionId);
+
+ // Get the tabular data
+ DatasetFileLines fileLines = getDatasetFileLines(filePath);
+
+ // Generate an image image into the stream
+ ITabularDataGraph generator =
+ configuration.getGraph(params.graphTypeCode, fileLines, response
+ .getOutputStream());
+ generator.generateImage();
+
+ } catch (Exception e)
+ {
+ printErrorResponse(response, "Invalid Request");
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Return the tabular data as a DatasetFileLines.
+ */
+ private DatasetFileLines getDatasetFileLines(String path) throws IOException
+ {
+ File file = new File(path);
+ CsvReader reader = getCsvReader(file);
+ List<String[]> lines = new ArrayList<String[]>();
+ while (reader.readRecord())
+ {
+ lines.add(reader.getValues());
+ }
+
+ return new DatasetFileLines(file, path, lines);
+ }
+
+ /**
+ * Get a CsvReader for parsing a tabular data file.
+ */
+ private CsvReader getCsvReader(File file) throws IOException
+ {
+ if (file.isFile() == false)
+ {
+ throw new UserFailureException(file + " does not exist or is not a file.");
+ }
+ FileInputStream fileInputStream = new FileInputStream(file);
+
+ CsvReader csvReader = new CsvReader(fileInputStream, Charset.defaultCharset());
+ csvReader.setDelimiter(configuration.getColumnDelimiter());
+ csvReader.setSkipEmptyRecords(true);
+ csvReader.setUseComments(configuration.isIgnoreComments());
+ csvReader.setComment(configuration.getCommentDelimiter());
+
+ return csvReader;
+ }
+}
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 926a5bbc575b9b0f998c0488c0692181c964c0f6..202adf9e9a20d6eaa82886eae519c00c5933d6fc 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
@@ -34,7 +34,8 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLine
*
* @author Chandrasekhar Ramakrishnan
*/
-public abstract class AbstractTabularDataGraph<T extends TabularDataGraphConfiguration>
+abstract class AbstractTabularDataGraph<T extends TabularDataGraphConfiguration> implements
+ ITabularDataGraph
{
protected final T configuration;
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
new file mode 100644
index 0000000000000000000000000000000000000000..59c01edd3775176cdc932e0a14facc6ab441875e
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/ITabularDataGraph.java
@@ -0,0 +1,35 @@
+/*
+ * 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.io.IOException;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public interface ITabularDataGraph
+{
+
+ // Public API
+ /**
+ * Create an image from the file lines and write it to the output stream.
+ *
+ * @throws IOException
+ */
+ public abstract void generateImage() 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
new file mode 100644
index 0000000000000000000000000000000000000000..19bf44fa8b7628db2ec9ab3d207bf0559087b879
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
@@ -0,0 +1,178 @@
+/*
+ * 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.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+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;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class TabularDataGraphCollectionConfiguration
+{
+ private static final String SEPARATOR_PROPERTY_KEY = "separator";
+
+ private static final String IGNORE_COMMENTS_PROPERTY_KEY = "ignore-comments";
+
+ // the seperator in the file
+ private final char separator;
+
+ private final boolean ignoreComments;
+
+ // the comment marker in the file
+ private final char comment;
+
+ private final ArrayList<String> graphTypeCodes;
+
+ private final HashMap<String, TabularDataGraphConfiguration> graphTypeMap;
+
+ /**
+ * Create a configuration from the properties file located at path.
+ *
+ * @param path Path to the properties file.
+ */
+ public static TabularDataGraphCollectionConfiguration getConfiguration(String path)
+ throws EnvironmentFailureException
+ {
+ Properties configurationProps = new Properties();
+ try
+ {
+ configurationProps.load(new FileInputStream(path));
+ } catch (FileNotFoundException ex)
+ {
+ throw new EnvironmentFailureException("Could not find the configuration file "
+ + new File(path).getAbsolutePath());
+ } catch (IOException ex)
+ {
+ throw new EnvironmentFailureException("Could not read the configuration file " + path);
+ }
+
+ return new TabularDataGraphCollectionConfiguration(configurationProps);
+ }
+
+ /**
+ * Initialize the configuration based on the properties object.
+ */
+ private TabularDataGraphCollectionConfiguration(Properties properties)
+ {
+ comment = '#';
+
+ this.separator = PropertyUtils.getChar(properties, SEPARATOR_PROPERTY_KEY, ';');
+ this.ignoreComments =
+ PropertyUtils.getBoolean(properties, IGNORE_COMMENTS_PROPERTY_KEY, true);
+ graphTypeCodes = new ArrayList<String>();
+ graphTypeMap = new HashMap<String, TabularDataGraphConfiguration>();
+ initialzeGraphTypeMap(properties);
+
+ }
+
+ private void initialzeGraphTypeMap(Properties properties)
+ {
+ TabularDataGraphConfiguration config =
+ new TabularDataGraphConfiguration("Test", "TotalCells", "InfectedCells", 300, 200);
+ graphTypeMap.put("scatter", config);
+ graphTypeCodes.add("scatter");
+ }
+
+ /**
+ * Return the graph configuration associated with the graphTypeCode.
+ *
+ * @param graphTypeCode The name of the graph type
+ */
+ public TabularDataGraphConfiguration getGraphConfiguration(String graphTypeCode)
+ {
+ TabularDataGraphConfiguration config = graphTypeMap.get(graphTypeCode);
+ if (null == config)
+ {
+ throw new IllegalArgumentException("No graph associated with code " + graphTypeCode);
+ }
+ return config;
+ }
+
+ /**
+ * Return the graph generator associated with the graphTypeCode, initialized by the fileLines
+ * and out.
+ *
+ * @param graphTypeCode 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)
+ {
+ TabularDataGraphConfiguration config = graphTypeMap.get(graphTypeCode);
+ if (null == config)
+ {
+ throw new IllegalArgumentException("No graph associated with code " + graphTypeCode);
+ }
+ return new TabularDataScatterplot(config, fileLines, out);
+ }
+
+ public char getColumnDelimiter()
+ {
+ return separator;
+ }
+
+ /**
+ * Should comments be ignored?
+ */
+ public boolean isIgnoreComments()
+ {
+ return ignoreComments;
+ }
+
+ public char getCommentDelimiter()
+ {
+ return comment;
+ }
+
+ public int getImageWidth()
+ {
+ return 800;
+ }
+
+ public int getImageHeight()
+ {
+ return 600;
+ }
+
+ public int getThumbnailWidth()
+ {
+ return 300;
+ }
+
+ public int getThumbnailHeight()
+ {
+ return 200;
+ }
+
+ public List<String> getGraphTypeCodes()
+ {
+ return graphTypeCodes;
+ }
+}
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 b7cf659499c631bf04c36bcb441c2884d0593280..5a45d0bcde3111f58df452d3aaa777b3352a1465 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
@@ -44,7 +44,7 @@ public class TabularDataGraphConfiguration
* @param imageWidth The desired width of the resulting image
* @param imageHeight The desired height of the resulting image
*/
- protected TabularDataGraphConfiguration(String title, String xAxisColumn,
+ public TabularDataGraphConfiguration(String title, String xAxisColumn,
String yAxisColumn, int imageWidth, int imageHeight)
{
this.title = title;
@@ -57,7 +57,7 @@ public class TabularDataGraphConfiguration
/**
* The title for the resulting image.
*/
- protected String getTitle()
+ public String getTitle()
{
return title;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphGenerator.java
deleted file mode 100644
index 0dd108990b3cef36612cc92096eeacf40d0c5d1f..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphGenerator.java
+++ /dev/null
@@ -1,302 +0,0 @@
-/*
- * 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.awt.Color;
-import java.awt.Font;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.util.List;
-
-import org.jfree.chart.ChartFactory;
-import org.jfree.chart.ChartUtilities;
-import org.jfree.chart.JFreeChart;
-import org.jfree.chart.axis.Axis;
-import org.jfree.chart.axis.ValueAxis;
-import org.jfree.chart.plot.PlotOrientation;
-import org.jfree.chart.plot.XYPlot;
-import org.jfree.chart.renderer.xy.XYBarRenderer;
-import org.jfree.chart.renderer.xy.XYItemRenderer;
-import org.jfree.chart.renderer.xy.XYSplineRenderer;
-import org.jfree.data.xy.IntervalXYDataset;
-import org.jfree.data.xy.XYSeries;
-import org.jfree.data.xy.XYSeriesCollection;
-
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
-
-/**
- * Generates a graph from tabular data. Both the graph type and the columns used for the graph can
- * be configured.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class TabularDataGraphGenerator
-{
- public static enum ChartType
- {
- AREA, BAR, LINE, SPLINE
- }
-
- public final static ChartType DEFAULT_CHART_TYPE = ChartType.LINE;
-
- private final String title;
-
- private final String xAxisHeader;
-
- private final String yAxisHeader;
-
- private final DatasetFileLines fileLines;
-
- private final int imageWidth;
-
- private final int imageHeight;
-
- private final ChartType chartType;
-
- private final OutputStream out;
-
- /**
- * Initialize a chromatogram generator. The chart type is defaulted to DEFAULT_CHART_TYPE.
- *
- * @param fileLines The data to generate a graph from.
- * @param out The stream to write the image to
- * @param imageWidth The width in pixels of the generated image
- * @param imageHeight The height in pixels of the generated image
- */
- public TabularDataGraphGenerator(DatasetFileLines fileLines, OutputStream out,
- int imageWidth, int imageHeight)
- {
- this("Chart", "TotalCells", "InfectedCells", imageWidth, imageHeight, DEFAULT_CHART_TYPE,
- fileLines, out);
- }
-
- /**
- * Initialize a chromatogram generator.
- *
- * @param title The title of the graph
- * @param xAxisColumnHeader The header of the data column used to create the x-axis
- * @param yAxisColumnHeader The header of the data column used to create the y-axis
- * @param imageWidth The width in pixels of the generated image
- * @param imageHeight The height in pixels of the generated image
- * @param chartType One of AREA, BAR, LINE, or SPLINE
- * @param fileLines The data to generate a graph from.
- * @param out The stream to write the image to.
- */
- public TabularDataGraphGenerator(String title, String xAxisColumnHeader,
- String yAxisColumnHeader, int imageWidth, int imageHeight, ChartType chartType,
- DatasetFileLines fileLines, OutputStream out)
- {
- this.title = title;
- this.xAxisHeader = xAxisColumnHeader;
- this.yAxisHeader = yAxisColumnHeader;
- this.imageWidth = imageWidth;
- this.imageHeight = imageHeight;
- this.chartType = chartType;
- this.fileLines = fileLines;
- this.out = out;
- }
-
- /**
- * Create an image from the chromatogram and write it to the output stream.
- *
- * @throws IOException
- */
- public void generateImage() throws IOException
- {
- JFreeChart chart = createChart(tryCreateDataset());
- ChartUtilities.writeChartAsPNG(out, chart, imageWidth, imageHeight);
- }
-
- private JFreeChart createChart(IntervalXYDataset dataset)
- {
- JFreeChart chart = null;
- switch (chartType)
- {
- case AREA:
- chart = createAreaChart(dataset);
- break;
- case BAR:
- chart = createBarChart(dataset);
- break;
- case LINE:
- chart = createLineChart(dataset);
- break;
- case SPLINE:
- chart = createSplineChart(dataset);
- break;
- }
-
- return chart;
- }
-
- private JFreeChart createBarChart(IntervalXYDataset dataset)
- {
- JFreeChart chart = ChartFactory.createXYBarChart(title, // title
- "Run Time", // x-axis label
- false, // use date axis?
- "Intensity", // y-axis label
- dataset, // data
- PlotOrientation.VERTICAL, // plot orientation
- false, // create legend?
- false, // generate tooltips?
- false // generate URLs?
- );
-
- XYPlot plot = configureChart(chart);
-
- XYItemRenderer r = plot.getRenderer();
- if (r instanceof XYBarRenderer)
- {
- XYBarRenderer renderer = (XYBarRenderer) r;
- renderer.setShadowVisible(false);
- }
-
- return chart;
- }
-
- private JFreeChart createLineChart(IntervalXYDataset dataset)
- {
- JFreeChart chart = ChartFactory.createXYLineChart(title, // title
- "run time", // x-axis label
- "intensity", // y-axis label
- dataset, // data
- PlotOrientation.VERTICAL, // plot orientation
- false, // create legend?
- false, // generate tooltips?
- false // generate URLs?
- );
-
- configureChart(chart);
-
- return chart;
- }
-
- private JFreeChart createSplineChart(IntervalXYDataset dataset)
- {
- JFreeChart chart = ChartFactory.createXYLineChart(title, // title
- "run time", // x-axis label
- "intensity", // y-axis label
- dataset, // data
- PlotOrientation.VERTICAL, // plot orientation
- false, // create legend?
- false, // generate tooltips?
- false // generate URLs?
- );
-
- XYPlot plot = configureChart(chart);
-
- XYSplineRenderer renderer = new XYSplineRenderer();
- renderer.setSeriesShapesVisible(0, false);
- plot.setRenderer(renderer);
-
- return chart;
- }
-
- private JFreeChart createAreaChart(IntervalXYDataset dataset)
- {
- JFreeChart chart = ChartFactory.createXYAreaChart(title, // title
- "run time", // x-axis label
- "intensity", // y-axis label
- dataset, // data
- PlotOrientation.VERTICAL, // plot orientation
- false, // create legend?
- false, // generate tooltips?
- false // generate URLs?
- );
-
- configureChart(chart);
-
- return chart;
- }
-
- /**
- * Create a JFreeChart dataset from the chromatogram data.
- */
- private IntervalXYDataset tryCreateDataset()
- {
- XYSeries s1 = new XYSeries(title);
- String[] headers = fileLines.getHeaderTokens();
- // figure out which indices are used for the x- and y-axes
- int xIndex = -1, yIndex = -1, i = 0;
- for (String header : headers)
- {
- if (xAxisHeader.equals(header))
- {
- xIndex = i;
- } else if (yAxisHeader.equals(header))
- {
- yIndex = i;
- }
- ++i;
- }
-
- // The data set did not contain the expected headers.
- if (xIndex < 0 || yIndex < 0)
- {
- return null;
- }
-
- List<String[]> lines = fileLines.getDataLines();
- for (String[] line : lines)
- {
- float x = Float.valueOf(line[xIndex]);
- float y = Float.valueOf(line[yIndex]);
- s1.add(x, y);
- }
-
- XYSeriesCollection dataset = new XYSeriesCollection();
- dataset.addSeries(s1);
-
- return dataset;
- }
-
- /**
- * Apply the visual preferences to the chart.
- */
- private XYPlot configureChart(JFreeChart chart)
- {
- Font font = JFreeChart.DEFAULT_TITLE_FONT;
- chart.getTitle().setFont(cloneFontWithNewSize(font, Math.max(11, imageHeight / 30)));
- chart.setBackgroundPaint(Color.WHITE);
-
- XYPlot plot = (XYPlot) chart.getPlot();
- setAxisLabelFontSize(plot.getDomainAxis());
- setAxisLabelFontSize(plot.getRangeAxis());
- plot.setBackgroundPaint(Color.WHITE);
- plot.setDomainGridlinesVisible(false);
- plot.setRangeGridlinesVisible(true);
- plot.setRangeGridlinePaint(Color.LIGHT_GRAY);
- plot.setDomainCrosshairVisible(false);
- plot.setRangeCrosshairVisible(false);
-
- ValueAxis axis = plot.getDomainAxis();
- axis.setAutoRange(true);
-
- return plot;
- }
-
- private void setAxisLabelFontSize(Axis axis)
- {
- Font labelFont = axis.getLabelFont();
- axis.setLabelFont(cloneFontWithNewSize(labelFont, Math.max(10, imageHeight / 40)));
- }
-
- private Font cloneFontWithNewSize(Font font, int newSize)
- {
- return new Font(font.getName(), font.getStyle(), newSize);
- }
-}
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 4ec497952ef1af961e98e78fcc0f96c330324e03..ed8e3c3e07fb4321f1abb5fd823db68127c137ab 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
@@ -25,6 +25,7 @@ import java.util.regex.Pattern;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.axis.NumberTickUnit;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.GrayPaintScale;
@@ -46,6 +47,8 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLine
public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeatmapConfiguration>
{
+ private final Pattern xySplitterPattern;
+
/**
* @param configuration
*/
@@ -53,6 +56,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
DatasetFileLines fileLines, OutputStream out)
{
super(configuration, fileLines, out);
+ xySplitterPattern = Pattern.compile("([A-Z])([0-9]*)");
}
@Override
@@ -103,6 +107,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
}
NumberAxis xAxis = new NumberAxis(xAxisLabel);
xAxis.setAutoRangeIncludesZero(false);
+ xAxis.setTickUnit(new NumberTickUnit(1.));
NumberAxis yAxis = new NumberAxis(yAxisLabel);
XYBlockRenderer renderer = new XYBlockRenderer();
@@ -170,7 +175,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
private void splitColumnIntoXandY(String string, HeatmapElement element)
{
- Pattern p = Pattern.compile("([A-Z])([0-9]*)");
+ Pattern p = xySplitterPattern;
Matcher m = p.matcher(string);
if (m.matches())
{
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
new file mode 100644
index 0000000000000000000000000000000000000000..6431cae5d3132ffb055035549042bc74962a896c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisGraphReportingPlugin.java
@@ -0,0 +1,156 @@
+/*
+ * Copyright 2009 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.plugins;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.TabularDataGraphServlet;
+import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphCollectionConfiguration;
+import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphConfiguration;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDataMergingReportingPlugin;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GeneratedImageTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ * Reporting plugin that returns a table in which each column contains a graph. The number and
+ * format of the graphs can be configured in a properties file.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ImageAnalysisGraphReportingPlugin extends AbstractDataMergingReportingPlugin
+{
+ private static final long serialVersionUID = 1L;
+
+ private final String graphServletPath;
+
+ private final TabularDataGraphCollectionConfiguration configuration;
+
+ // Keys for the properties
+ private final String SERVLET_PATH_PROP = "servlet-path";
+
+ private final static String PROPERTIES_FILE_KEY = "properties-file";
+
+ public ImageAnalysisGraphReportingPlugin(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot, SEMICOLON_SEPARATOR);
+ graphServletPath = properties.getProperty(SERVLET_PATH_PROP, "datastore_server_graph/");
+ String propertiesFilePath = properties.getProperty(PROPERTIES_FILE_KEY);
+ if (propertiesFilePath == null)
+ {
+ throw new EnvironmentFailureException(
+ "ImageAnalysisGraphReportingPlugin requires a properties file (specified with the "
+ + PROPERTIES_FILE_KEY + "key).");
+ }
+
+ configuration =
+ TabularDataGraphCollectionConfiguration.getConfiguration(propertiesFilePath);
+ }
+
+ public TableModel createReport(List<DatasetDescription> datasets)
+ {
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
+ addHeaders(builder);
+ if (datasets.isEmpty())
+ {
+ return builder.getTableModel();
+ }
+ for (DatasetDescription dataset : datasets)
+ {
+ final File dir = getDataSubDir(dataset);
+ List<File> matchingFiles = findMatchingFiles(dataset, dir);
+ if (matchingFiles.size() > 1)
+ {
+ throw UserFailureException.fromTemplate(
+ "Found multiple candidate files in the dataset %s ", dataset
+ .getDatasetCode());
+ }
+ builder.addRow(createRow(dataset.getDatasetCode(), matchingFiles.get(0)));
+ }
+ return builder.getTableModel();
+ }
+
+ /**
+ * Add the headers to the table -- these depend on the configuration
+ */
+ private void addHeaders(SimpleTableModelBuilder builder)
+ {
+ builder.addHeader("Data Set Code");
+ int width = getThumbnailWidth();
+ for (String graphTypeCode : getGraphTypeCodes())
+ {
+ TabularDataGraphConfiguration graphConfig =
+ configuration.getGraphConfiguration(graphTypeCode);
+ builder.addHeader(graphConfig.getTitle(), width);
+ }
+ }
+
+ private List<ISerializableComparable> createRow(String datasetCode, File file)
+ {
+ List<ISerializableComparable> row = new ArrayList<ISerializableComparable>();
+
+ // The data set code
+ row.add(SimpleTableModelBuilder.asText(datasetCode));
+
+ for (String graphTypeCode : getGraphTypeCodes())
+ {
+
+ GeneratedImageTableCell imageCell =
+ new GeneratedImageTableCell(graphServletPath, getImageWidth(),
+ getImageHeight(), getThumbnailWidth(), getThumbnailHeight());
+ imageCell.addParameter(TabularDataGraphServlet.DATASET_CODE_PARAM, datasetCode);
+ imageCell.addParameter(TabularDataGraphServlet.FILE_PATH_PARAM, file.getAbsolutePath());
+ imageCell.addParameter(TabularDataGraphServlet.GRAPH_TYPE_CODE, graphTypeCode);
+
+ row.add(imageCell);
+ }
+
+ return row;
+ }
+
+ private List<String> getGraphTypeCodes()
+ {
+ return configuration.getGraphTypeCodes();
+ }
+
+ private int getImageWidth()
+ {
+ return configuration.getImageWidth();
+ }
+
+ private int getImageHeight()
+ {
+ return configuration.getImageHeight();
+ }
+
+ private int getThumbnailWidth()
+ {
+ return configuration.getThumbnailWidth();
+ }
+
+ private int getThumbnailHeight()
+ {
+ return configuration.getThumbnailHeight();
+ }
+}
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 94f1bd136e5e48606f59a151b485a16b4eb9d06c..b8ca69d7222434c7c35339e52bca911b10585aa4 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 = getTestImageOutputFile();
+ File outputFile = getImageOutputFile();
TabularDataHeatmapConfiguration config =
new TabularDataHeatmapConfiguration("Test", "WellName", "InfectionIndex", 300, 200);