From ddeb74bf92374d7d9f65d99288388f17b057c517 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 10 Aug 2010 10:58:52 +0000
Subject: [PATCH] LMS-1632 Generalize the graph generation code to accept
tabular data, either from a file or from the DB.
SVN: 17377
---
.../AbstractTabularDataGraphServlet.java | 202 ++++++++++++++++++
.../server/ImagingDataGraphServlet.java | 194 +++++++++++++++++
.../server/TabularDataGraphServlet.java | 156 +-------------
.../graph/AbstractTabularDataGraph.java | 6 +-
...bularDataGraphCollectionConfiguration.java | 4 +-
.../server/graph/TabularDataHeatmap.java | 4 +-
.../server/graph/TabularDataHistogram.java | 4 +-
.../server/graph/TabularDataScatterplot.java | 4 +-
...baseImageAnalysisGraphReportingPlugin.java | 152 +++++++++++++
...sedImageAnalysisGraphReportingPlugin.java} | 18 +-
10 files changed, 579 insertions(+), 165 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractTabularDataGraphServlet.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImagingDataGraphServlet.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DatabaseImageAnalysisGraphReportingPlugin.java
rename screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/{ImageAnalysisGraphReportingPlugin.java => FileBasedImageAnalysisGraphReportingPlugin.java} (86%)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractTabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractTabularDataGraphServlet.java
new file mode 100644
index 00000000000..c755bb227fa
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractTabularDataGraphServlet.java
@@ -0,0 +1,202 @@
+/*
+ * 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 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.ITabularDataGraph;
+import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphCollectionConfiguration;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public abstract class AbstractTabularDataGraphServlet extends AbstractDatasetDownloadServlet
+{
+ private static final long serialVersionUID = 1L;
+
+ public static final String DATASET_CODE_PARAM = "dataset";
+
+ public static final String GRAPH_TYPE_CODE = "type";
+
+ protected TabularDataGraphCollectionConfiguration configuration;
+
+ private static final String PROPERTIES_FILE_KEY = "properties-file";
+
+ public static final String FILE_PATH_PARAM = "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
+ */
+ protected 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;
+
+ private final String filePathOrNull;
+
+ 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);
+ filePathOrNull = getOptionalParameter(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 getOptionalParameter(final HttpServletRequest request,
+ String paramName)
+ {
+ String value = request.getParameter(paramName);
+ return value;
+ }
+
+ 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;
+ }
+ }
+
+ /**
+ *
+ *
+ */
+ public AbstractTabularDataGraphServlet()
+ {
+ super();
+ }
+
+ /**
+ * @param applicationContext
+ */
+ public AbstractTabularDataGraphServlet(ApplicationContext applicationContext)
+ {
+ super(applicationContext);
+ }
+
+ @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 filePathOrNull = params.filePathOrNull;
+
+ // 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
+ ITabularData fileLines = getDatasetLines(datasetCode, filePathOrNull);
+
+ // Generate an image into the stream
+ ITabularDataGraph generator =
+ 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)
+ {
+ e.printStackTrace();
+ printErrorResponse(response, "Invalid Request");
+ }
+ }
+
+ protected abstract ITabularData getDatasetLines(String dataSetCode, String filePathOrNull)
+ throws IOException;
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImagingDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImagingDataGraphServlet.java
new file mode 100644
index 00000000000..3aa322e29f9
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImagingDataGraphServlet.java
@@ -0,0 +1,194 @@
+/*
+ * 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.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+
+/**
+ * Create a graph from the imaging database.
+ * <p>
+ * TODO 2010-08-09, CR, LMS-1692, This implementation is inefficient. The better way to implement
+ * this would be to lazily get feature vectors necessary for generating the graph, not to egerly get
+ * all feature vectors.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ImagingDataGraphServlet extends AbstractTabularDataGraphServlet
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private IImagingQueryDAO imagingDbDao;
+
+ private IEncapsulatedOpenBISService openBisService;
+
+ /**
+ * An CSV-file-like interface to feature data from the database.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+ private final class ImagingTabularData implements ITabularData
+ {
+ private static final String WELL_NAME_COLUMN = "WellName";
+
+ private static final String WELL_ROW_COLUMN = "Row";
+
+ private static final String WELL_COLUMN_COLUMN = "Column";
+
+ private final IImagingQueryDAO dao;
+
+ private final IEncapsulatedOpenBISService service;
+
+ private final String dataSetCode;
+
+ private String[] headerTokens;
+
+ private ArrayList<String[]> lines;
+
+ private ImagingTabularData(IImagingQueryDAO dao, IEncapsulatedOpenBISService service,
+ String dataSetCode)
+ {
+ this.dao = dao;
+ this.service = service;
+ this.dataSetCode = dataSetCode;
+ initialize();
+ }
+
+ private void initialize()
+ {
+ final FeatureTableBuilder tableBuilder = new FeatureTableBuilder(dao, service);
+ tableBuilder.addFeatureVectorsOfDataSet(dataSetCode);
+
+ List<String> featureNames = tableBuilder.getFeatureNames();
+ int headerTokensLength = featureNames.size() + 3;
+ headerTokens = new String[headerTokensLength];
+ headerTokens[0] = WELL_NAME_COLUMN;
+ headerTokens[1] = WELL_ROW_COLUMN;
+ headerTokens[2] = WELL_COLUMN_COLUMN;
+
+ int i = 1;
+ for (String name : featureNames)
+ {
+ headerTokens[i++] = name;
+ }
+
+ lines = new ArrayList<String[]>();
+
+ final List<FeatureTableRow> rows = tableBuilder.createFeatureTableRows();
+ for (FeatureTableRow row : rows)
+ {
+ String[] line = new String[headerTokensLength];
+ WellPosition pos = row.getWellPosition();
+ String rowLetter = PlateUtils.translateRowNumberIntoLetterCode(pos.getWellRow());
+ String columnNumber = Integer.toString(row.getWellPosition().getWellColumn());
+ line[0] = rowLetter + columnNumber;
+ line[1] = rowLetter;
+ line[2] = columnNumber;
+ i = 1;
+ float[] values = row.getFeatureValues();
+ for (float value : values)
+ {
+ line[i++] = Float.toString(value);
+ }
+ lines.add(line);
+ }
+ // final ImgDatasetDTO dataSet = dao.tryGetDatasetByPermId(dataSetCode);
+ // if (dataSet == null)
+ // {
+ // throw new UserFailureException("Unkown data set " + dataSetCode);
+ // }
+ //
+ // final List<ImgFeatureDefDTO> featureDefinitions =
+ // dao.listFeatureDefsByDataSetId(dataSet.getId());
+ //
+ // int headersLength = featureDefinitions.size();
+ // headerTokens = new String[headersLength];
+ // lines = new ArrayList<String[]>();
+ // int featureDefCount = 0;
+ // for (ImgFeatureDefDTO featureDefinition : featureDefinitions)
+ // {
+ // headerTokens[featureDefCount++] = featureDefinition.getName();
+ // }
+ // int numRows = dataSet.getFieldNumberOfRows();
+ // int numCols = dataSet.getFieldNumberOfColumns();
+ // for (int row = 0; row < numRows; ++row)
+ // {
+ // for (int col = 0; col < numCols; ++col)
+ // {
+ // for (ImgFeatureDefDTO featureDefinition : featureDefinitions)
+ // {
+ // List<ImgFeatureValuesDTO> featureValues =
+ // dao.getFeatureValues(featureDefinition);
+ // }
+ // }
+ // }
+ }
+
+ public List<String[]> getDataLines()
+ {
+ return lines;
+ }
+
+ public String[] getHeaderTokens()
+ {
+ return headerTokens;
+ }
+
+ }
+
+ @Override
+ protected ITabularData getDatasetLines(String dataSetCode, String filePathOrNull)
+ throws IOException
+ {
+ return new ImagingTabularData(getDAO(), getService(), dataSetCode);
+ }
+
+ private IImagingQueryDAO getDAO()
+ {
+ synchronized (this)
+ {
+ if (imagingDbDao == null)
+ {
+ imagingDbDao = DssScreeningUtils.createQuery();
+ }
+ }
+ return imagingDbDao;
+ }
+
+ private IEncapsulatedOpenBISService getService()
+ {
+ synchronized (this)
+ {
+ if (openBisService == null)
+ {
+ openBisService = ServiceProvider.getOpenBISService();
+ }
+ }
+ return openBisService;
+ }
+
+}
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 a3da0caf8f7..7fc440aef44 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
@@ -18,168 +18,30 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.File;
import java.io.IOException;
-import java.util.Enumeration;
-
-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.ITabularDataGraph;
-import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphCollectionConfiguration;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
import ch.systemsx.cisd.utils.CsvFileReaderHelper;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class TabularDataGraphServlet extends AbstractDatasetDownloadServlet
+public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
{
- // 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
+ * Return the tabular data from a file as a DatasetFileLines.
*/
- 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;
-
- private final String filePath;
-
- 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,
- 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)
+ protected ITabularData getDatasetLines(String dataSetCode, String pathOrNull)
+ throws IOException
{
- // 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
+ if (pathOrNull == null)
{
- // 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.graphName, fileLines, response.getOutputStream());
-
- if (params.height > 0 && params.width > 0)
- {
- generator.generateImage(params.width, params.height);
- } else
- {
- generator.generateImage();
- }
-
- } catch (Exception e)
- {
- e.printStackTrace();
- printErrorResponse(response, "Invalid Request");
+ throw new UserFailureException("No value for the parameter " + FILE_PATH_PARAM
+ + " found in the URL");
}
- }
-
- /**
- * Return the tabular data as a DatasetFileLines.
- */
- private DatasetFileLines getDatasetFileLines(String path) throws IOException
- {
- return CsvFileReaderHelper.getDatasetFileLines(new File(path), configuration);
+ return CsvFileReaderHelper.getDatasetFileLines(new File(pathOrNull), configuration);
}
}
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 db83f51b5e4..d01086793ea 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
@@ -32,7 +32,7 @@ import org.jfree.chart.plot.XYPlot;
import org.jfree.data.general.Dataset;
import org.jfree.data.xy.DefaultXYDataset;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
/**
* Abstract superclass for the different kinds of graphs.
@@ -44,11 +44,11 @@ abstract class AbstractTabularDataGraph<T extends TabularDataGraphConfiguration>
{
protected final T configuration;
- protected final DatasetFileLines fileLines;
+ protected final ITabularData fileLines;
protected final OutputStream out;
- protected AbstractTabularDataGraph(T configuration, DatasetFileLines fileLines, OutputStream out)
+ protected AbstractTabularDataGraph(T configuration, ITabularData fileLines, OutputStream out)
{
this.configuration = configuration;
this.fileLines = fileLines;
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 6521373bd4a..bd66d97e497 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
@@ -31,7 +31,7 @@ import ch.systemsx.cisd.common.utilities.PropertyParametersUtil;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.common.utilities.PropertyParametersUtil.SectionProperties;
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.server.plugins.tasks.ITabularData;
import ch.systemsx.cisd.utils.CsvFileReaderHelper.ICsvFileReaderConfiguration;
/**
@@ -222,7 +222,7 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
* @param fileLines The data to generate a graph from
* @param out The stream to write the graph to
*/
- public ITabularDataGraph getGraph(String graphName, DatasetFileLines fileLines, OutputStream out)
+ public ITabularDataGraph getGraph(String graphName, ITabularData fileLines, OutputStream out)
{
TabularDataGraphConfiguration config = graphTypeMap.get(graphName);
if (null == config)
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 d8f83735aef..2cd95f05f0a 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
@@ -40,7 +40,7 @@ import org.jfree.ui.RectangleEdge;
import org.jfree.ui.RectangleInsets;
import ch.systemsx.cisd.bds.hcs.Location;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
/**
* @author Chandrasekhar Ramakrishnan
@@ -52,7 +52,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
* @param configuration
*/
public TabularDataHeatmap(TabularDataHeatmapConfiguration configuration,
- DatasetFileLines fileLines, OutputStream out)
+ ITabularData fileLines, OutputStream out)
{
super(configuration, fileLines, out);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java
index afeadce9c61..91b32532964 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java
@@ -28,7 +28,7 @@ import org.jfree.chart.renderer.xy.XYItemRenderer;
import org.jfree.data.general.Dataset;
import org.jfree.data.statistics.HistogramDataset;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
/**
* @author Chandrasekhar Ramakrishnan
@@ -41,7 +41,7 @@ public class TabularDataHistogram extends
* @param configuration
*/
public TabularDataHistogram(TabularDataHistogramConfiguration configuration,
- DatasetFileLines fileLines, OutputStream out)
+ ITabularData fileLines, OutputStream out)
{
super(configuration, fileLines, out);
}
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 98adb20c9dd..fa68501d706 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
@@ -29,7 +29,7 @@ import org.jfree.data.xy.XYDataset;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
/**
* @author Chandrasekhar Ramakrishnan
@@ -42,7 +42,7 @@ public class TabularDataScatterplot extends
* @param configuration
*/
public TabularDataScatterplot(TabularDataScatterplotConfiguration configuration,
- DatasetFileLines fileLines, OutputStream out)
+ ITabularData fileLines, OutputStream out)
{
super(configuration, fileLines, out);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DatabaseImageAnalysisGraphReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DatabaseImageAnalysisGraphReportingPlugin.java
new file mode 100644
index 00000000000..b0b7400e664
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DatabaseImageAnalysisGraphReportingPlugin.java
@@ -0,0 +1,152 @@
+/*
+ * 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.openbis.dss.generic.server.AbstractTabularDataGraphServlet;
+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.
+ * <p>
+ * This plugin reads data from a the imaging database. The
+ * {@link FileBasedImageAnalysisGraphReportingPlugin} reads from a file.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class DatabaseImageAnalysisGraphReportingPlugin 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 DatabaseImageAnalysisGraphReportingPlugin(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(
+ "DatabaseImageAnalysisGraphReportingPlugin 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)
+ {
+ builder.addRow(createRow(dataset));
+ }
+ return builder.getTableModel();
+ }
+
+ /**
+ * Add the headers to the table -- these depend on the configuration
+ */
+ private void addHeaders(SimpleTableModelBuilder builder)
+ {
+ builder.addHeader("Data Set Code");
+ builder.addHeader("Sample Code");
+ int width = getThumbnailWidth();
+ for (String graphTypeCode : getGraphTypeCodes())
+ {
+ TabularDataGraphConfiguration graphConfig =
+ configuration.getGraphConfiguration(graphTypeCode);
+ builder.addHeader(graphConfig.getTitle(), width);
+ }
+ }
+
+ private List<ISerializableComparable> createRow(DatasetDescription dataset)
+ {
+ List<ISerializableComparable> row = new ArrayList<ISerializableComparable>();
+
+ // The data set and sample code
+ row.add(SimpleTableModelBuilder.asText(dataset.getDatasetCode()));
+ row.add(SimpleTableModelBuilder.asText(dataset.getSampleCode()));
+
+ for (String graphTypeCode : getGraphTypeCodes())
+ {
+
+ GeneratedImageTableCell imageCell =
+ new GeneratedImageTableCell(graphServletPath, getImageWidth(),
+ getImageHeight(), getThumbnailWidth(), getThumbnailHeight());
+ imageCell.addParameter(AbstractTabularDataGraphServlet.DATASET_CODE_PARAM, dataset
+ .getDatasetCode());
+ imageCell.addParameter(AbstractTabularDataGraphServlet.GRAPH_TYPE_CODE, graphTypeCode);
+
+ row.add(imageCell);
+ }
+
+ return row;
+ }
+
+ private List<String> getGraphTypeCodes()
+ {
+ return configuration.getGraphNames();
+ }
+
+ 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/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisGraphReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FileBasedImageAnalysisGraphReportingPlugin.java
similarity index 86%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisGraphReportingPlugin.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FileBasedImageAnalysisGraphReportingPlugin.java
index 936d4f4975c..1c2d1dc5f67 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/FileBasedImageAnalysisGraphReportingPlugin.java
@@ -23,7 +23,7 @@ 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.AbstractTabularDataGraphServlet;
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;
@@ -36,10 +36,13 @@ 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.
+ * <p>
+ * This plugin reads data from a file. The {@link DatabaseImageAnalysisGraphReportingPlugin} reads
+ * from the imaging db.
*
* @author Chandrasekhar Ramakrishnan
*/
-public class ImageAnalysisGraphReportingPlugin extends AbstractDataMergingReportingPlugin
+public class FileBasedImageAnalysisGraphReportingPlugin extends AbstractDataMergingReportingPlugin
{
private static final long serialVersionUID = 1L;
@@ -52,7 +55,7 @@ public class ImageAnalysisGraphReportingPlugin extends AbstractDataMergingReport
private final static String PROPERTIES_FILE_KEY = "properties-file";
- public ImageAnalysisGraphReportingPlugin(Properties properties, File storeRoot)
+ public FileBasedImageAnalysisGraphReportingPlugin(Properties properties, File storeRoot)
{
super(properties, storeRoot, SEMICOLON_SEPARATOR);
graphServletPath = properties.getProperty(SERVLET_PATH_PROP, "datastore_server_graph/");
@@ -60,7 +63,7 @@ public class ImageAnalysisGraphReportingPlugin extends AbstractDataMergingReport
if (propertiesFilePath == null)
{
throw new EnvironmentFailureException(
- "ImageAnalysisGraphReportingPlugin requires a properties file (specified with the "
+ "DatabaseImageAnalysisGraphReportingPlugin requires a properties file (specified with the "
+ PROPERTIES_FILE_KEY + "key).");
}
@@ -121,10 +124,11 @@ public class ImageAnalysisGraphReportingPlugin extends AbstractDataMergingReport
GeneratedImageTableCell imageCell =
new GeneratedImageTableCell(graphServletPath, getImageWidth(),
getImageHeight(), getThumbnailWidth(), getThumbnailHeight());
- imageCell.addParameter(TabularDataGraphServlet.DATASET_CODE_PARAM, dataset
+ imageCell.addParameter(AbstractTabularDataGraphServlet.DATASET_CODE_PARAM, dataset
.getDatasetCode());
- imageCell.addParameter(TabularDataGraphServlet.FILE_PATH_PARAM, file.getAbsolutePath());
- imageCell.addParameter(TabularDataGraphServlet.GRAPH_TYPE_CODE, graphTypeCode);
+ imageCell.addParameter(AbstractTabularDataGraphServlet.FILE_PATH_PARAM, file
+ .getAbsolutePath());
+ imageCell.addParameter(AbstractTabularDataGraphServlet.GRAPH_TYPE_CODE, graphTypeCode);
row.add(imageCell);
}
--
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