X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2FEnfinEnvision2OneWay.java;h=a11542c79856353706d11eebd1a1bf6b8636f6f0;hb=3bb3bf052916ca69a915a48324a122b0e3f20651;hp=ae2792c3580b48a4168a1b1b76fe5ce5622b803f;hpb=a124e525dece0edc422cd2f8888d03ea14f65f15;p=jalview.git
diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index ae2792c..a11542c 100644
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -1,5 +1,5 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@ -25,6 +25,7 @@ import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
import java.awt.Component;
import java.awt.Cursor;
@@ -32,12 +33,21 @@ import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.io.BufferedOutputStream;
import java.io.BufferedReader;
import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
import java.net.URL;
+import java.net.URLEncoder;
+import java.nio.charset.Charset;
+import java.nio.charset.CharsetEncoder;
import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
+import java.util.regex.Pattern;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
@@ -47,10 +57,15 @@ import javax.swing.event.MenuListener;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
+import org.apache.axis.utils.StringUtils;
+import org.apache.http.client.utils.URLEncodedUtils;
+import org.apache.http.entity.StringEntity;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;
+import com.lowagie.text.html.HtmlEncoder;
+
/**
* Lightweight runnable to discover dynamic 'one way' group URL services
*
@@ -137,19 +152,31 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
System.err.println("Adding entry for " + wfname + " " + description);
if (wfname.toLowerCase().indexOf("funcnet") == -1)
{
+ description = Pattern.compile("\\s+",Pattern.MULTILINE).matcher(description).replaceAll(" ");
groupURLdescr.addElement(description);
groupURLdescr.addElement(description);
+ String urlstub=wfname;
+ if (wfname.indexOf(" ")>-1)
+ {
+ // make the name safe!
+ try {
+ urlstub = URLEncoder.encode(wfname,"utf-8");
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
groupURLLinks
.addElement(wfname
+ "|"
+ "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
- + wfname
+ + urlstub
+ "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
groupURLLinks
.addElement(wfname
+ "|"
+ "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
- + wfname
+ + urlstub
+ "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
}
}
@@ -283,7 +310,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
* Object array returned from the makeUrlStubs function.
*/
private void addshowLink(JMenu linkMenu, String label, String descr,
- String dbname, final GroupUrlLink urlgenerator, final Object[] urlstub)
+ String dbname, final GroupUrlLink urlgenerator,
+ final Object[] urlstub)
{
Component[] jmi = linkMenu.getMenuComponents();
for (int i = 0; i < jmi.length; i++)
@@ -295,20 +323,24 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
return;
}
}
+ try {
+ descr = HtmlEncoder.encode(descr);
+ } catch (Exception e){};
+
boolean seqsorids = (urlgenerator.getGroupURLType() & urlgenerator.SEQUENCEIDS) == 0;
int i = urlgenerator.getNumberInvolved(urlstub);
JMenuItem item = new JMenuItem(label);
- //
- if (dbname==null || dbname.trim().length()==0)
+ //
+ if (dbname == null || dbname.trim().length() == 0)
{
dbname = "";
}
item.setToolTipText(""
- + JvSwingUtils.wrapTooltip("Submit " + i + " " +
- dbname +" "
- + (seqsorids ? "sequence" : "sequence id") + (i > 1 ? "s" : "")
-
- + " to
" + descr) + "");
+ + JvSwingUtils.wrapTooltip("Submit " + i + " " + dbname + " "
+ + (seqsorids ? "sequence" : "sequence id")
+ + (i > 1 ? "s" : "")
+
+ + " to
" + descr) + "