diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EICMLChromatogramGeneratorServlet.java b/rtd_yeastx/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EICMLChromatogramGeneratorServlet.java
new file mode 100644
index 0000000000000000000000000000000000000000..52284791dcc6f6aa8a6d8f9256101ab5e7313e3f
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EICMLChromatogramGeneratorServlet.java
@@ -0,0 +1,172 @@
+/*
+ * 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 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.AbstractDatasetDownloadServlet;
+import ch.systemsx.cisd.yeastx.eicml.ChromatogramDTO;
+import ch.systemsx.cisd.yeastx.eicml.EICMLChromatogramImageGenerator;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class EICMLChromatogramGeneratorServlet extends AbstractDatasetDownloadServlet
+{
+
+ private static final long serialVersionUID = 1L;
+
+ // Required servlet parameters
+
+ public final static String DATASET_CODE_PARAM = "dataset";
+
+ public final static String CHROMATOGRAM_CODE_PARAM = "chromatogram";
+
+ // Optional, but recommended servlet parameters
+
+ public final static String IMAGE_WIDTH_PARAM = "w";
+
+ public final static String IMAGE_HEIGHT_PARAM = "h";
+
+ /**
+ * A utility class for dealing with the parameters required to generate an image from a
+ * chromatogram.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+ private static class RequestParams
+ {
+ private final String sessionId;
+
+ private final String datasetCode;
+
+ private final int width;
+
+ private final int height;
+
+ public RequestParams(HttpServletRequest request)
+ {
+ sessionId = getParam(request, SESSION_ID_PARAM);
+ datasetCode = getParam(request, DATASET_CODE_PARAM);
+ width = getIntParam(request, IMAGE_WIDTH_PARAM);
+ height = getIntParam(request, IMAGE_HEIGHT_PARAM);
+ }
+
+ private static int getIntParam(HttpServletRequest request, String paramName)
+ {
+ String value = getParam(request, paramName);
+ 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 int getWidth()
+ {
+ return width;
+ }
+
+ public int getHeight()
+ {
+ return height;
+ }
+ }
+
+ // private static IEICMSRunDAO createQuery(Properties properties)
+ // {
+ // final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
+ // DataSource dataSource = dbContext.getDataSource();
+ // return QueryTool.getQuery(dataSource, IEICMSRunDAO.class);
+ // }
+
+ @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);
+
+ // TODO Get the chromatogram data
+ ChromatogramDTO chromatogram = getChromatogramForId(null);
+
+ // Generate a chromatogram image into the stream
+ EICMLChromatogramImageGenerator generator =
+ new EICMLChromatogramImageGenerator(chromatogram, response.getOutputStream(),
+ width, height);
+ generator.generateImage();
+
+ } catch (Exception e)
+ {
+ printErrorResponse(response, "Error: " + e.getMessage());
+ e.printStackTrace();
+ }
+ }
+
+ ChromatogramDTO getChromatogramForId(String id)
+ {
+ return null;
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java
new file mode 100644
index 0000000000000000000000000000000000000000..3579a518a659faaeeef885ba9a2bdd4e437944da
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java
@@ -0,0 +1,147 @@
+/*
+ * 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.yeastx.eicml;
+
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asText;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.QueryTool;
+
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.openbis.dss.generic.server.EICMLChromatogramGeneratorServlet;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ImageTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
+
+/**
+ * Reporting plugin which shows images for the chromatograms contained in the specified datasets.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class EICMLChromatogramImagesReporter extends AbstractDatastorePlugin implements
+ IReportingPluginTask
+{
+ private static final String CHROMATOGRAM_SERVLET = "chromatogram";
+
+ private static final int THUMBNAIL_SIZE = 60;
+
+ private static final long serialVersionUID = 1L;
+
+ private final IEICMSRunDAO query;
+
+ public EICMLChromatogramImagesReporter(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ this.query = createQuery(properties);
+ }
+
+ private static IEICMSRunDAO createQuery(Properties properties)
+ {
+ final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
+ DataSource dataSource = dbContext.getDataSource();
+ return QueryTool.getQuery(dataSource, IEICMSRunDAO.class);
+ }
+
+ public TableModel createReport(List<DatasetDescription> datasets)
+ {
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
+ addReportHeaders(builder);
+ List<EICMSRunDTO> runs = fetchRuns(datasets);
+ for (EICMSRunDTO run : runs)
+ {
+ DataIterator<ChromatogramDTO> chromatograms = query.getChromatogramsForRun(run);
+ addRun(builder, run, chromatograms);
+ }
+ return builder.getTableModel();
+ }
+
+ private List<EICMSRunDTO> fetchRuns(List<DatasetDescription> datasets)
+ {
+ List<EICMSRunDTO> runs = new ArrayList<EICMSRunDTO>();
+ for (DatasetDescription dataset : datasets)
+ {
+ EICMSRunDTO run = query.getMSRunByDatasetPermId(dataset.getDatasetCode());
+ if (run != null)
+ {
+ runs.add(run);
+ }
+ }
+ return runs;
+ }
+
+ private static void addRun(SimpleTableModelBuilder builder, EICMSRunDTO run,
+ DataIterator<ChromatogramDTO> chromatograms)
+ {
+ for (ChromatogramDTO chromatogram : chromatograms)
+ {
+ builder.addRow(createRow(builder, run, chromatogram));
+ }
+ }
+
+ private static List<ISerializableComparable> createRow(SimpleTableModelBuilder builder,
+ EICMSRunDTO run, ChromatogramDTO chromatogram)
+ {
+ List<ISerializableComparable> row = new ArrayList<ISerializableComparable>();
+
+ row.add(asText(chromatogram.getLabel()));
+
+ StringBuffer imageURL = new StringBuffer();
+
+ imageURL.append(CHROMATOGRAM_SERVLET);
+
+ imageURL.append("?");
+ imageURL.append(EICMLChromatogramGeneratorServlet.DATASET_CODE_PARAM);
+ imageURL.append("=");
+ imageURL.append(run.getId());
+
+ imageURL.append("&");
+ imageURL.append(EICMLChromatogramGeneratorServlet.CHROMATOGRAM_CODE_PARAM);
+ imageURL.append("=");
+ imageURL.append(chromatogram.getId());
+
+ imageURL.append("&");
+ imageURL.append(EICMLChromatogramGeneratorServlet.IMAGE_WIDTH_PARAM);
+ imageURL.append("=");
+ imageURL.append(THUMBNAIL_SIZE);
+
+ imageURL.append("&");
+ imageURL.append(EICMLChromatogramGeneratorServlet.IMAGE_HEIGHT_PARAM);
+ imageURL.append("=");
+ imageURL.append(THUMBNAIL_SIZE);
+
+ row.add(new ImageTableCell(imageURL.toString(), THUMBNAIL_SIZE, THUMBNAIL_SIZE));
+ return row;
+ }
+
+ private static void addReportHeaders(SimpleTableModelBuilder builder)
+ {
+ builder.addHeader("Label");
+ builder.addHeader("Chromatogram");
+ }
+}