diff --git a/screening/dist/etc/service.properties b/screening/dist/etc/service.properties
index cb5fb7967b15d46046b73ba4d8ead547ccab6fc6..b2400892d2ac5a98da3cf8b417b115fab9c15c75 100644
--- a/screening/dist/etc/service.properties
+++ b/screening/dist/etc/service.properties
@@ -112,7 +112,7 @@ default-plate-image-analysis.properties-file =
plate-image-analysis-graph.label = Image Analysis Graphs
plate-image-analysis-graph.dataset-types = HCS_IMAGE_ANALYSIS_DATA, HCS_ANALYSIS_PER_GENE
-plate-image-analysis-graph.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.DatabaseImageAnalysisGraphReportingPlugin
+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
@@ -128,7 +128,7 @@ screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.se
# 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.ImagingDataGraphServlet
+tabular-data-graph-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.TabularDataGraphServlet
tabular-data-graph-servlet.path = /datastore_server_graph/*
tabular-data-graph-servlet.properties-file = etc/tabular-data-graph.properties
diff --git a/screening/etc/service.properties b/screening/etc/service.properties
index e002a253193edaf568ef8fb6d5e1d673a944aa49..31c0a913abb6169d322979c35d0b3667db69b74e 100644
--- a/screening/etc/service.properties
+++ b/screening/etc/service.properties
@@ -106,7 +106,7 @@ default-plate-image-analysis.properties-file =
plate-image-analysis-graph.label = Image Analysis Graphs
plate-image-analysis-graph.dataset-types = HCS_IMAGE_ANALYSIS_DATA, HCS_ANALYSIS_PER_GENE
-plate-image-analysis-graph.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.DatabaseImageAnalysisGraphReportingPlugin
+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
@@ -122,7 +122,7 @@ screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.se
# 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.ImagingDataGraphServlet
+tabular-data-graph-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.TabularDataGraphServlet
tabular-data-graph-servlet.path = /datastore_server_graph/*
tabular-data-graph-servlet.properties-file = etc/tabular-data-graph.properties
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FileTabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FileTabularDataGraphServlet.java
new file mode 100644
index 0000000000000000000000000000000000000000..df7ed6ce97e2c3288d1282b4aa8e168bfe8af24a
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FileTabularDataGraphServlet.java
@@ -0,0 +1,47 @@
+/*
+ * 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.IOException;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
+import ch.systemsx.cisd.utils.CsvFileReaderHelper;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class FileTabularDataGraphServlet extends AbstractTabularDataGraphServlet
+{
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Return the tabular data from a file as a DatasetFileLines.
+ */
+ @Override
+ protected ITabularData getDatasetLines(String dataSetCode, String pathOrNull)
+ throws IOException
+ {
+ if (pathOrNull == null)
+ {
+ throw new UserFailureException("No value for the parameter " + FILE_PATH_PARAM
+ + " found in the URL");
+ }
+ return CsvFileReaderHelper.getDatasetFileLines(new File(pathOrNull), configuration);
+ }
+}
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
deleted file mode 100644
index 3aa322e29f9344bd78d728e937cc84fc67d20a57..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImagingDataGraphServlet.java
+++ /dev/null
@@ -1,194 +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.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 7fc440aef448b2eef2d03c66849e968bbece40f8..d988553b942530b6dafdc98c3cabbf205abc08bb 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
@@ -16,32 +16,179 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
-import java.io.File;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
-import ch.systemsx.cisd.utils.CsvFileReaderHelper;
+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 TabularDataGraphServlet extends AbstractTabularDataGraphServlet
{
+
private static final long serialVersionUID = 1L;
+ private IImagingQueryDAO imagingDbDao;
+
+ private IEncapsulatedOpenBISService openBisService;
+
/**
- * Return the tabular data from a file as a DatasetFileLines.
+ * 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 pathOrNull)
+ protected ITabularData getDatasetLines(String dataSetCode, String filePathOrNull)
throws IOException
{
- if (pathOrNull == null)
+ return new ImagingTabularData(getDAO(), getService(), dataSetCode);
+ }
+
+ private IImagingQueryDAO getDAO()
+ {
+ synchronized (this)
{
- throw new UserFailureException("No value for the parameter " + FILE_PATH_PARAM
- + " found in the URL");
+ if (imagingDbDao == null)
+ {
+ imagingDbDao = DssScreeningUtils.createQuery();
+ }
}
- return CsvFileReaderHelper.getDatasetFileLines(new File(pathOrNull), configuration);
+ 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/plugins/FileBasedImageAnalysisGraphReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FileBasedImageAnalysisGraphReportingPlugin.java
index 1c2d1dc5f67c85dbb76603f098ac04c430860316..14fde7f96d2df93252b2ae323711e9b90acac4c3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FileBasedImageAnalysisGraphReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FileBasedImageAnalysisGraphReportingPlugin.java
@@ -37,7 +37,7 @@ 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
+ * This plugin reads data from a file. The {@link ImageAnalysisGraphReportingPlugin} reads
* from the imaging db.
*
* @author Chandrasekhar Ramakrishnan
@@ -63,7 +63,7 @@ public class FileBasedImageAnalysisGraphReportingPlugin extends AbstractDataMerg
if (propertiesFilePath == null)
{
throw new EnvironmentFailureException(
- "DatabaseImageAnalysisGraphReportingPlugin requires a properties file (specified with the "
+ "ImageAnalysisGraphReportingPlugin requires a properties file (specified with the "
+ PROPERTIES_FILE_KEY + "key).");
}
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/ImageAnalysisGraphReportingPlugin.java
similarity index 94%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DatabaseImageAnalysisGraphReportingPlugin.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisGraphReportingPlugin.java
index b0b7400e664c99235384cc1ed378714688446bb1..a175ff96145b3262724ab2b1726928ec458aab5b 100644
--- 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/ImageAnalysisGraphReportingPlugin.java
@@ -41,7 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
*
* @author Chandrasekhar Ramakrishnan
*/
-public class DatabaseImageAnalysisGraphReportingPlugin extends AbstractDataMergingReportingPlugin
+public class ImageAnalysisGraphReportingPlugin extends AbstractDataMergingReportingPlugin
{
private static final long serialVersionUID = 1L;
@@ -54,7 +54,7 @@ public class DatabaseImageAnalysisGraphReportingPlugin extends AbstractDataMergi
private final static String PROPERTIES_FILE_KEY = "properties-file";
- public DatabaseImageAnalysisGraphReportingPlugin(Properties properties, File storeRoot)
+ public ImageAnalysisGraphReportingPlugin(Properties properties, File storeRoot)
{
super(properties, storeRoot, SEMICOLON_SEPARATOR);
graphServletPath = properties.getProperty(SERVLET_PATH_PROP, "datastore_server_graph/");
@@ -62,7 +62,7 @@ public class DatabaseImageAnalysisGraphReportingPlugin extends AbstractDataMergi
if (propertiesFilePath == null)
{
throw new EnvironmentFailureException(
- "DatabaseImageAnalysisGraphReportingPlugin requires a properties file (specified with the "
+ "ImageAnalysisGraphReportingPlugin requires a properties file (specified with the "
+ PROPERTIES_FILE_KEY + "key).");
}