Author: mes
Date: 2012-03-13 09:17:43 -0700 (Tue, 13 Mar 2012)
New Revision: 28514
Removed:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/write/filter/StreamUtilImpl.java
Modified:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/util/StreamUtil.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/StreamUtilImpl.java
core3/impl/trunk/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiCyFileFilterTest.java
core3/impl/trunk/sbml-impl/src/test/java/org/cytoscape/sbml/internal/SBMLFileFilterTest.java
Log:
added another method ot StreamUtil
Modified:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/util/StreamUtil.java
===================================================================
--- core3/api/trunk/io-api/src/main/java/org/cytoscape/io/util/StreamUtil.java
2012-03-13 16:00:54 UTC (rev 28513)
+++ core3/api/trunk/io-api/src/main/java/org/cytoscape/io/util/StreamUtil.java
2012-03-13 16:17:43 UTC (rev 28514)
@@ -12,7 +12,21 @@
*/
public interface StreamUtil {
+ String URL_PATTERN =
"^(jar\\:)?((http|https|ftp|file)+\\:\\/+\\S+)(\\!\\/\\S*)?$";
+
/**
+ * Gets the input stream from given a string. Attempts to
+ * determine if the string is a URL or a File and then creates
+ * the appropriate InputStream.
+ * Proxy will be used if available.
+ *
+ * @param source The string from which to generate the InputStream.
+ * @return An input stream from the specified string.
+ * @throws IOException
+ */
+ InputStream getInputStream(final String source) throws IOException;
+
+ /**
* Gets the input stream from given {@link java.net.URL}.
* Proxy will be used if available.
*
Deleted:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/write/filter/StreamUtilImpl.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/write/filter/StreamUtilImpl.java
2012-03-13 16:00:54 UTC (rev 28513)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/write/filter/StreamUtilImpl.java
2012-03-13 16:17:43 UTC (rev 28514)
@@ -1,208 +0,0 @@
-/*
- * Copyright (c) 2006, 2007, 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.filter.internal.write.filter;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.Proxy;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.jar.JarInputStream;
-import java.util.zip.GZIPInputStream;
-import java.util.zip.ZipInputStream;
-
-import org.cytoscape.io.util.StreamUtil;
-
-/**
- *
- */
-public class StreamUtilImpl implements StreamUtil {
-
- private static final String GZIP = ".gz";
-
- private static final String ZIP = ".zip";
-
- private static final String JAR = ".jar";
-
- private static int msConnectionTimeout = 2000;
- /**
- *
- */
- public static boolean STOP = false;
-
- /**
- * Gets the an input stream given a URL.
- *
- * @param source
- * URL source for a zip or jar file.
- * @return InputStream for given URL
- * @throws IOException
- *
- */
- public InputStream getInputStream(URL source) throws IOException {
- final InputStream newIs;
- final InputStream proxyIs;
- proxyIs = getBasicInputStream(source);
- if (source.toString().toLowerCase().endsWith(GZIP)) {
- newIs = new GZIPInputStream(proxyIs);
- } else if (source.toString().toLowerCase().endsWith(ZIP)) {
- // System.err.println(source.toString() + " ZIP ");
- newIs = new ZipInputStream(proxyIs);
- } else if (source.toString().toLowerCase().endsWith(JAR)) {
- newIs = new JarInputStream(proxyIs);
- } else {
- newIs = proxyIs;
- }
- return newIs;
- }
-
- /**
- * Obtain an InputStream for a given URL. Ensure proxy servers and an
input
- * stream to the real URL source is created--not a locally cached and
out of
- * date source. Proxy servers and other characteristics can cause pages
to
- * be cached.
- *
- * @param source
- * the non-null URL from which to obtain an InputStream.
- * @return InputStream from the source URL.
- * @throws IllegalStateException
- * if source is null.
- * @throws IOException
- * if a connection to the URL can't be opened or a problem
- * occurs with the InputStream.
- */
- public InputStream getBasicInputStream(URL source) throws IOException {
- if (source == null) {
- throw new IllegalStateException(
- "getBasicInputStream was given a null
'source' argument.");
- }
- URLConnection uc = getURLConnection(source);
- return uc.getInputStream();
- }
-
- /**
- * Obtain a URLConnection for a given URL. Ensure proxy servers are
- * considered and page caching is ignored.
- *
- * @param source
- * the non-null URL from which to obtain a URLConnection.
- * @return URLConnection to the source URL.
- * @throws IllegalStateException
- * if source is null.
- * @throws IOException
- * if a connection to the URL can't be opened.
- */
- public URLConnection getURLConnection(URL source) throws IOException {
- if (source == null) {
- throw new IllegalStateException(
- "getURLConnection was given a null
'source' argument.");
- }
- // TODO add proxy support back -- should be inserted as a
service
- Proxy cytoProxy = null; // ProxyHandler.getProxyServer();
- URLConnection uc = null;
- if (cytoProxy == null) {
- uc = source.openConnection();
- } else {
- try {
- uc = source.openConnection(cytoProxy);
- } catch (UnsupportedOperationException e) {
- // This happens when we have a URL whose
- // protocol handler doesn't take a proxy
- // argument (such as a URL referring to inside
- // a jar file). In this case, just use the
- // normal way to open a connection:
- uc = source.openConnection();
- }
- }
- uc.setUseCaches(false); // don't use a cached page
- uc.setConnectTimeout(msConnectionTimeout); // set timeout for
connection
- return uc;
- }
-
- // /**
- // * Download the file specified by the url string to the given File
object
- // *
- // * @param urlString
- // * @param downloadFile
- // * @param taskMonitor
- // * @return
- // * @throws IOException
- // */
- // public static void download(String urlString, File downloadFile,
- // TaskMonitor taskMonitor) throws IOException {
- // URL url = new URL(urlString);
- // InputStream is = null;
- // int maxCount = 0; // -1 if unknown
- // int progressCount = 0;
- // URLConnection conn = getURLConnection(url);
- // maxCount = conn.getContentLength();
- // is = conn.getInputStream();
- // FileOutputStream os = new FileOutputStream(downloadFile);
- // double percent = 0.0d;
- // byte[] buffer = new byte[1];
- // while (((is.read(buffer)) != -1) && !STOP) {
- // progressCount += buffer.length;
- // // Report on Progress
- // if (taskMonitor != null) {
- // percent = ((double) progressCount / maxCount) * 100.0;
- // if (maxCount == -1) { // file size unknown
- // percent = -1;
- // }
- // JTask jTask = (JTask) taskMonitor;
- // if (jTask.haltRequested()) { // abort
- // downloadFile = null;
- // taskMonitor.setStatus("Canceling the download ...");
- // taskMonitor.setPercentCompleted(100);
- // break;
- // }
- // taskMonitor.setPercentCompleted((int) percent);
- // }
- // os.write(buffer);
- // }
- // os.flush();
- // os.close();
- // is.close();
- // if (STOP) {
- // downloadFile.delete();
- // }
- // }
- //
- // /**
- // * Get the the contents of the given URL as a string.
- // *
- // * @param source
- // * @return String
- // * @throws IOException
- // */
- // public static String download(URL source) throws IOException {
- // InputStream is = getInputStream(source);
- // StringBuffer buffer = new StringBuffer();
- // int c;
- // while ((c = is.read()) != -1) {
- // buffer.append((char) c);
- // }
- // is.close();
- // return buffer.toString();
- // }
-}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/StreamUtilImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/StreamUtilImpl.java
2012-03-13 16:00:54 UTC (rev 28513)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/StreamUtilImpl.java
2012-03-13 16:17:43 UTC (rev 28514)
@@ -25,6 +25,7 @@
import java.io.IOException;
import java.io.InputStream;
+import java.io.FileInputStream;
import java.net.InetSocketAddress;
import java.net.Proxy;
import java.net.Proxy.Type;
@@ -38,11 +39,15 @@
import org.cytoscape.io.util.StreamUtil;
import org.cytoscape.property.CyProperty;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
*
*/
public class StreamUtilImpl implements StreamUtil {
+ private static final Logger logger =
LoggerFactory.getLogger(StreamUtilImpl.class);
private static final String GZIP = ".gz";
private static final String ZIP = ".zip";
private static final String JAR = ".jar";
@@ -53,6 +58,14 @@
public StreamUtilImpl(CyProperty<Properties> proxyProperties) {
properties = proxyProperties.getProperties();
}
+
+ @Override
+ public InputStream getInputStream(String name) throws IOException {
+ if (name.matches(StreamUtil.URL_PATTERN))
+ return getInputStream(new URL(name));
+ else
+ return new FileInputStream(name);
+ }
/**
* Gets the an input stream given a URL.
Modified:
core3/impl/trunk/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiCyFileFilterTest.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiCyFileFilterTest.java
2012-03-13 16:00:54 UTC (rev 28513)
+++
core3/impl/trunk/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiCyFileFilterTest.java
2012-03-13 16:17:43 UTC (rev 28514)
@@ -26,6 +26,11 @@
StreamUtil streamUtil = new StreamUtil() {
@Override
+ public InputStream getInputStream(String s) throws
IOException {
+ return null;
+ }
+
+ @Override
public URLConnection getURLConnection(URL source)
throws IOException {
return null;
}
Modified:
core3/impl/trunk/sbml-impl/src/test/java/org/cytoscape/sbml/internal/SBMLFileFilterTest.java
===================================================================
---
core3/impl/trunk/sbml-impl/src/test/java/org/cytoscape/sbml/internal/SBMLFileFilterTest.java
2012-03-13 16:00:54 UTC (rev 28513)
+++
core3/impl/trunk/sbml-impl/src/test/java/org/cytoscape/sbml/internal/SBMLFileFilterTest.java
2012-03-13 16:17:43 UTC (rev 28514)
@@ -32,6 +32,11 @@
public InputStream getInputStream(URL source) throws
IOException {
return source.openStream();
}
+
+ @Override
+ public InputStream getInputStream(String source) throws
IOException {
+ return null;
+ }
};
filter = new SBMLFileFilter("SBML", streamUtil);
}
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