BIS-224 SP-333 : Scaffolding for implementation of SP-333

SVN: 28409

datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractTabularDataGraphServlet.java

@@ -79,7 +79,7 @@ public abstract class AbstractTabularDataGraphServlet extends AbstractDatasetDow
             sessionId = getRequiredParameter(request, Utils.SESSION_ID_PARAM);
             datasetCode = getRequiredParameter(request, DATASET_CODE_PARAM);
             filePathOrNull = getOptionalParameter(request, FILE_PATH_PARAM);
-            graphName = getRequiredParameter(request, GRAPH_TYPE_CODE);
+            graphName = getOptionalParameter(request, GRAPH_TYPE_CODE, "dynamic");
             width = getIntParam(request, WIDTH_PARAM, 0);
             height = getIntParam(request, HEIGHT_PARAM, 0);
         }
@@ -108,6 +108,17 @@ public abstract class AbstractTabularDataGraphServlet extends AbstractDatasetDow
             return value;
         }
 
+        private static String getOptionalParameter(final HttpServletRequest request,
+                String paramName, String defaultValue)
+        {
+            String value = request.getParameter(paramName);
+            if (null == value)
+            {
+                return defaultValue;
+            }
+            return value;
+        }
+
         private static String getRequiredParameter(final HttpServletRequest request,
                 String paramName)
         {
@@ -119,6 +130,11 @@ public abstract class AbstractTabularDataGraphServlet extends AbstractDatasetDow
             }
             return value;
         }
+
+        public String getSessionId()
+        {
+            return sessionId;
+        }
     }
 
     /**
@@ -176,11 +192,12 @@ public abstract class AbstractTabularDataGraphServlet extends AbstractDatasetDow
             ensureDatasetAccessible(datasetCode, session, sessionId);
 
             // Get the tabular data
-            ITabularData fileLines = getDatasetLines(datasetCode, filePathOrNull);
+            ITabularData fileLines = getDatasetLines(request, datasetCode, filePathOrNull);
 
             // Generate an image into the stream
             ITabularDataGraph generator =
-                    configuration.getGraph(params.graphName, fileLines, response.getOutputStream());
+                    getConfiguration(request).getGraph(params.graphName, fileLines,
+                            response.getOutputStream());
 
             response.setContentType(Utils.CONTENT_TYPE_PNG);
             String headerContentDisposition = "inline; filename=plot_" + (new Date().getTime());
@@ -201,7 +218,16 @@ public abstract class AbstractTabularDataGraphServlet extends AbstractDatasetDow
         }
     }
 
-    protected abstract ITabularData getDatasetLines(String dataSetCode, String filePathOrNull)
+    /**
+     * Get the configuration for this graph. Defaults to the configuration ivar. Subclasses may
+     * override.
+     */
+    protected TabularDataGraphCollectionConfiguration getConfiguration(HttpServletRequest request)
+    {
+        return configuration;
+    }
+
+    protected abstract ITabularData getDatasetLines(HttpServletRequest request, String dataSetCode, String filePathOrNull)
             throws IOException;
 
 }
\ No newline at end of file

datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DynamicFileTabularDataGraphServlet.java

+/*
+ * Copyright 2013 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.util.Enumeration;
+import java.util.Properties;
+
+import javax.servlet.ServletConfig;
+import javax.servlet.http.HttpServletRequest;
+
+import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphCollectionConfiguration;
+import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphCollectionConfiguration.DynamicTabularDataGraphCollectionConfiguration;
+
+/**
+ * @author cramakri
+ */
+public class DynamicFileTabularDataGraphServlet extends FileTabularDataGraphServlet
+{
+
+    private static final String DYNAMIC_GRAPH_NAME = "dynamic";
+
+    private static final long serialVersionUID = 1L;
+
+    @Override
+    protected TabularDataGraphCollectionConfiguration getConfiguration(HttpServletRequest request)
+    {
+        // TODO Implement this properly
+        DynamicTabularDataGraphCollectionConfiguration config =
+                new DynamicTabularDataGraphCollectionConfiguration();
+        config.setColumnDelimiter('\t');
+        Properties props = new Properties();
+        props.setProperty(TabularDataGraphCollectionConfiguration.GRAPHS_KEY,
+                DynamicTabularDataGraphCollectionConfiguration.DYNAMIC_GRAPH_NAME);
+        props.setProperty(DYNAMIC_GRAPH_NAME + "."
+                + TabularDataGraphCollectionConfiguration.TITLE_KEY, "Title");
+        props.setProperty(DYNAMIC_GRAPH_NAME + "."
+                + TabularDataGraphCollectionConfiguration.GRAPHS_TYPES_KEY, "SCATTERPLOT");
+        props.setProperty(DYNAMIC_GRAPH_NAME + "."
+                + TabularDataGraphCollectionConfiguration.X_AXIS_KEY, "col1");
+        props.setProperty(DYNAMIC_GRAPH_NAME + "."
+                + TabularDataGraphCollectionConfiguration.Y_AXIS_KEY, "col2");
+        config.setProperties(props);
+
+        return TabularDataGraphCollectionConfiguration.getConfiguration(config);
+    }
+
+    @Override
+    protected synchronized void doSpecificInitialization(Enumeration<String> parameterNames,
+            ServletConfig servletConfig)
+    {
+        // Do not initialize the configuration variable -- we never use it
+        configuration = null;
+    }
+
+}

datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FileTabularDataGraphServlet.java

@@ -16,10 +16,14 @@
 
 package ch.systemsx.cisd.openbis.dss.generic.server;
 
-import java.io.File;
 import java.io.IOException;
 
+import javax.servlet.http.HttpServletRequest;
+
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
 import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper;
 import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ITabularData;
 
@@ -34,14 +38,27 @@ public class FileTabularDataGraphServlet extends AbstractTabularDataGraphServlet
      * Return the tabular data from a file as a DatasetFileLines.
      */
     @Override
-    protected ITabularData getDatasetLines(String dataSetCode, String pathOrNull)
-            throws IOException
+    protected ITabularData getDatasetLines(HttpServletRequest request, 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);
+
+        RequestParams requestParams = new RequestParams(request);
+
+        IHierarchicalContentProvider contentProvider =
+                applicationContext.getHierarchicalContentProvider(requestParams.getSessionId());
+        IHierarchicalContent content = contentProvider.asContent(dataSetCode);
+        IHierarchicalContentNode node = content.getNode(pathOrNull);
+
+        ITabularData data =
+                CsvFileReaderHelper.getDatasetFileLines(node.getFile(), getConfiguration(request));
+
+        content.close();
+
+        return data;
     }
 }

datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java

@@ -46,7 +46,7 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
 
     private static final String LABEL_POSTFIX = ".label";
 
-    private static final String SEPARATOR_PROPERTY_KEY = "separator";
+    public static final String SEPARATOR_PROPERTY_KEY = "separator";
 
     private static final String IGNORE_COMMENTS_PROPERTY_KEY = "ignore-comments";
 
@@ -63,17 +63,17 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
     private static final String THUMBNAIL_HEIGHT_KEY = "column-height";
 
     // the graphs to display -- each one is shown in a column.
-    private static final String GRAPHS_KEY = "graphs";
+    public static final String GRAPHS_KEY = "graphs";
 
     // the type of graph. See @{link GraphType} for valid types.
-    private static final String GRAPHS_TYPES_KEY = "graph-type";
+    public static final String GRAPHS_TYPES_KEY = "graph-type";
 
     // keys for the different kinds of graphs
-    private static final String TITLE_KEY = "title";
+    public static final String TITLE_KEY = "title";
 
-    private static final String X_AXIS_KEY = "x-axis";
+    public static final String X_AXIS_KEY = "x-axis";
 
-    private static final String Y_AXIS_KEY = "y-axis";
+    public static final String Y_AXIS_KEY = "y-axis";
 
     private static final String COLUMN_KEY = "column";
 
@@ -98,6 +98,101 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
 
     private final HashMap<String, TabularDataGraphConfiguration> graphTypeMap;
 
+    /**
+     * Class used to dynamically initialize a TabularDataGraphCollectionConfiguration;
+     * 
+     * @author cramakri
+     */
+    public static class DynamicTabularDataGraphCollectionConfiguration
+    {
+        public static String DYNAMIC_GRAPH_NAME = "dynamic";
+
+        private char columnDelimiter = ';';
+
+        private boolean ignoreComments = true;
+
+        private int imageWidth = 800;
+
+        private int imageHeight = 600;
+
+        private int thumbnailWidth = 300;
+
+        private int thumbnailHeight = 200;
+
+        private Properties properties = new Properties();
+
+        public char getColumnDelimiter()
+        {
+            return columnDelimiter;
+        }
+
+        public void setColumnDelimiter(char columnDelimiter)
+        {
+            this.columnDelimiter = columnDelimiter;
+        }
+
+        public boolean isIgnoreComments()
+        {
+            return ignoreComments;
+        }
+
+        public void setIgnoreComments(boolean ignoreComments)
+        {
+            this.ignoreComments = ignoreComments;
+        }
+
+        public int getImageWidth()
+        {
+            return imageWidth;
+        }
+
+        public void setImageWidth(int imageWidth)
+        {
+            this.imageWidth = imageWidth;
+        }
+
+        public int getImageHeight()
+        {
+            return imageHeight;
+        }
+
+        public void setImageHeight(int imageHeight)
+        {
+            this.imageHeight = imageHeight;
+        }
+
+        public int getThumbnailWidth()
+        {
+            return thumbnailWidth;
+        }
+
+        public void setThumbnailWidth(int thumbnailWidth)
+        {
+            this.thumbnailWidth = thumbnailWidth;
+        }
+
+        public int getThumbnailHeight()
+        {
+            return thumbnailHeight;
+        }
+
+        public void setThumbnailHeight(int thumbnailHeight)
+        {
+            this.thumbnailHeight = thumbnailHeight;
+        }
+
+        public Properties getProperties()
+        {
+            return properties;
+        }
+
+        public void setProperties(Properties properties)
+        {
+            this.properties = properties;
+        }
+
+    }
+
     /**
      * Create a configuration from the properties file located at path.
      * 
@@ -122,6 +217,18 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
         return new TabularDataGraphCollectionConfiguration(configurationProps);
     }
 
+    /**
+     * Create a configuration from the properties file located at path.
+     * 
+     * @param path Path to the properties file.
+     */
+    public static TabularDataGraphCollectionConfiguration getConfiguration(
+            DynamicTabularDataGraphCollectionConfiguration config)
+            throws EnvironmentFailureException
+    {
+        return new TabularDataGraphCollectionConfiguration(config);
+    }
+
     /**
      * Initialize the configuration based on the properties object.
      */
@@ -148,6 +255,27 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
 
     }
 
+    /**
+     * Initialize the configuration based on the configuration object.
+     */
+    private TabularDataGraphCollectionConfiguration(
+            DynamicTabularDataGraphCollectionConfiguration config)
+    {
+        comment = '#';
+
+        this.columnDelimiter = config.getColumnDelimiter();
+        this.ignoreComments = config.isIgnoreComments();
+        imageWidth = config.getImageWidth();
+        imageHeight = config.getImageHeight();
+        thumbnailWidth = config.getThumbnailWidth();
+        thumbnailHeight = config.getThumbnailHeight();
+
+        graphNames = new ArrayList<String>();
+        graphNames.add(DynamicTabularDataGraphCollectionConfiguration.DYNAMIC_GRAPH_NAME);
+        graphTypeMap = new HashMap<String, TabularDataGraphConfiguration>();
+        initialzeGraphTypeMap(config.getProperties());
+    }
+
     private void initializeGraphTypeCodes(Properties properties)
     {
         String graphTypeCodesString = properties.getProperty(GRAPHS_KEY, "");