From bd60a43d3da4ff549c14f57c1d9af884d3d4520d Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Thu, 21 Feb 2013 21:10:12 +0000
Subject: [PATCH] BIS-224 SP-333 : Scaffolding for implementation of SP-333
SVN: 28409
---
.../AbstractTabularDataGraphServlet.java | 34 ++++-
.../DynamicFileTabularDataGraphServlet.java | 69 +++++++++
.../server/FileTabularDataGraphServlet.java | 25 +++-
...bularDataGraphCollectionConfiguration.java | 140 +++++++++++++++++-
4 files changed, 254 insertions(+), 14 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DynamicFileTabularDataGraphServlet.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractTabularDataGraphServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractTabularDataGraphServlet.java
index b08582f26b0..0cd37ed6e18 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractTabularDataGraphServlet.java
+++ b/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
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DynamicFileTabularDataGraphServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DynamicFileTabularDataGraphServlet.java
new file mode 100644
index 00000000000..8662ed82c7b
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DynamicFileTabularDataGraphServlet.java
@@ -0,0 +1,69 @@
+/*
+ * 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;
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FileTabularDataGraphServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FileTabularDataGraphServlet.java
index 9e64544eb8f..4f056fd39dd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FileTabularDataGraphServlet.java
+++ b/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;
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
index f4d697ee098..ca1328f2b8b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
+++ b/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, "");
--
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