Author: rozagh
Date: 2012-03-29 16:32:04 -0700 (Thu, 29 Mar 2012)
New Revision: 28702
Removed:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyFileFilterImpl.java
Modified:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/BasicCyFileFilter.java
Log:
Fixes for the bug in the reader selection based on the file filter. The accepts
method in BasicCyFileFilter now only checks for the extension as the extentions
are unique for each table reader. Readers with shared extensions have their
specified file filter with an accept method re-implemented.
Modified:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/BasicCyFileFilter.java
===================================================================
---
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/BasicCyFileFilter.java
2012-03-29 23:17:58 UTC (rev 28701)
+++
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/BasicCyFileFilter.java
2012-03-29 23:32:04 UTC (rev 28702)
@@ -90,15 +90,41 @@
if (category != this.category)
return false;
+ if (extensionsMatch(uri))
+ return true;
+ else
+ return false;
+
+ }
+
+ private boolean extensionsMatch(URI uri){
+ String extension = getExtension(uri.toString());
+ //logger.info("******URI extension is" + extension + "the task
extension is" + this.extensions);
+
+ if (extension != null && extensions.contains(extension))
+ return true;
+ else
+ return false;
+ }
+
+
+ /*
+ * The content types are not checked anymore since some of
+ * readers have similar content types. Hence, the correct reader
+ * wasn't picked up.
+ */
+ private boolean contentTypesMatch(URI uri){
try {
final URLConnection connection =
streamUtil.getURLConnection(uri.toURL());
final String contentType = connection.getContentType();
+ //logger.info("******URI content type is" + contentType
+ "the task content type is" + this.contentTypes);
// Check for matching content type
if ((contentType != null) &&
contentTypes.contains(contentType)) {
logger.info("content type matches: " +
contentType);
return true;
- }
+ }else
+ return false;
} catch (IOException ioe) {
@@ -106,15 +132,8 @@
return false;
}
- // No content-type match -- try for an extension match
- // if no extensions are listed, then match by default
- String extension = getExtension(uri.toString());
- if ((extension != null) && (extensions.contains(extension) ||
extensions.size() == 0 ))
- return true;
-
- return false;
}
-
+
/**
* This method always returns false in this particular implementation.
You must extend
* this class and override this method to get alternative behavior.
Ideally this method
Deleted:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyFileFilterImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyFileFilterImpl.java
2012-03-29 23:17:58 UTC (rev 28701)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyFileFilterImpl.java
2012-03-29 23:32:04 UTC (rev 28702)
@@ -1,232 +0,0 @@
-/*
- File: CyFileFilter.java
-
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-package org.cytoscape.io.internal;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-import java.net.URI;
-import java.net.URLConnection;
-import java.util.Set;
-
-import javax.swing.filechooser.FileFilter;
-
-import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.DataCategory;
-import org.cytoscape.io.util.StreamUtil;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class CyFileFilterImpl implements CyFileFilter {
-
- private final Set<String> extensions;
- private final Set<String> contentTypes;
- private final String description;
- private final StreamUtil streamUtil;
-
- protected final DataCategory category;
- private static final Logger logger =
LoggerFactory.getLogger(CyFileFilterImpl.class);
-
- /**
- * Creates a file filter from the specified arguments.
- * Note that the "." before the extension is not needed and will be
ignored.
- */
- public CyFileFilterImpl(final Set<String> extensions,
- final Set<String> contentTypes, final String
description,
- final DataCategory category, StreamUtil streamUtil) {
-
- this.extensions = extensions;
- this.contentTypes = contentTypes;
- this.category = category;
-
- String d = description == null ? "(" : description + " (";
-
- for (String ex : extensions)
- d += "*." + ex + ", ";
- d = d.substring(0, d.length() - 2);
- d += ")";
-
- this.description = d;
- this.streamUtil = streamUtil;
-
- }
-
- /**
- * Returns true if this class is capable of processing the specified URL
- *
- * @param url
- * the URL
- * @param contentType
- * the content-type of the URL
- * @throws IOException
- * @throws MalformedURLException
- *
- */
- public boolean accepts(URI uri, DataCategory category) {
-
- // Check data category
- if (category != this.category)
- return false;
-
- try {
-
- final URLConnection connection =
streamUtil.getURLConnection(uri.toURL());
- final String contentType = connection.getContentType();
-
- // Check for matching content type
- if ((contentType != null) &&
contentTypes.contains(contentType)) {
- logger.debug("content type matches: " +
contentType);
- return true;
- }
-
-
- } catch (IOException ioe) {
- logger.warn("Caught an exception trying to check
content type",ioe);
- return false;
- }
-
- // No content-type match -- try for an extension match
- // if no extensions are listed, then match by default
- String extension = getExtension(uri.toString());
- if ((extension != null) && (extensions.contains(extension) ||
extensions.size() == 0 ))
- return true;
-
- return false;
- }
-
- /**
- * Must be overridden by subclasses.
- */
- public boolean accepts(InputStream stream, DataCategory category) {
- return false;
- }
-
- public Set<String> getExtensions() {
- return extensions;
- }
-
- public Set<String> getContentTypes() {
- return contentTypes;
- }
-
- /**
- * Returns the human readable description of this filter. For example:
- * "JPEG and GIF Image Files (*.jpg, *.gif)"
- *
- * @see setDescription
- * @see setExtensionListInDescription
- * @see isExtensionListInDescription
- * @see FileFilter#getDescription
- */
- public String getDescription() {
- return description;
- }
-
- private String getExtension(String filename) {
- if (filename != null) {
- int i = filename.lastIndexOf('.');
-
- if ((i > 0) && (i < (filename.length() - 1))) {
- return filename.substring(i + 1).toLowerCase();
- }
- }
-
- return null;
- }
-
- public DataCategory getDataCategory() {
- return category;
- }
-
- protected String getHeader(InputStream stream, int numLines) {
-
- String header;
- BufferedReader br = new BufferedReader(new
InputStreamReader(stream));
-
- try {
- header = parseHeader(br, numLines);
- } catch (IOException ioe) {
- logger.warn("failed to read header from stream", ioe);
- header = "";
- } finally {
- if (br != null)
- try { br.close(); } catch (IOException e) {}
-
- br = null;
- }
-
- return header;
- }
-
- private String parseHeader(BufferedReader bufferedReader, int numLines)
- throws IOException {
- StringBuilder header = new StringBuilder();
-
- try {
- String line = bufferedReader.readLine();
-
- int lineCount = 0;
-
- while ((line != null) && (lineCount < numLines)) {
- header.append(line + "\n");
- line = bufferedReader.readLine();
- lineCount++;
- }
- } finally {
- if (bufferedReader != null)
- bufferedReader.close();
- }
-
- return header.toString();
- }
-
- public String toString() {
- String s = description + " [category: " + category + "]
[extensions: ";
- for ( String ext : extensions )
- s += ext + ",";
- s += "] [contentTypes: ";
- for ( String c : contentTypes )
- s += c + ",";
- s += "]";
-
- return s;
- }
-
-}
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