X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2FEnfinEnvision2OneWay.java;h=239a62687082f286aa5362ea1083dc589a0e9df9;hb=61c62b2455f3e25a14587aa37e4a2949184041a2;hp=8e596b77949d510b335df073114c21e7ec38bc5f;hpb=486e70a70e56b8ac23fd191c2ac9f8c7366f4fd7;p=jalview.git
diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 8e596b7..239a626 100644
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -1,5 +1,22 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
@@ -9,18 +26,21 @@ import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
import jalview.util.GroupUrlLink;
+import jalview.util.MessageManager;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
+import java.awt.Component;
import java.awt.Cursor;
import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
import java.net.URL;
+import java.net.URLEncoder;
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;
@@ -34,91 +54,152 @@ 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
+ *
+ * as of Jalview 2.8.1 this class is mothballed and will be dropped in v3.
+ *
* @author JimP
- *
+ * @deprecated
+ *
*/
-public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSMenuEntryProviderI
+public class EnfinEnvision2OneWay extends DefaultHandler implements
+ Runnable, WSMenuEntryProviderI
{
- private static EnfinEnvision2OneWay groupURLLinksGatherer=null;
- public static EnfinEnvision2OneWay getInstance() {
- if (groupURLLinksGatherer==null) {
+ private static EnfinEnvision2OneWay groupURLLinksGatherer = null;
+
+ public static EnfinEnvision2OneWay getInstance()
+ {
+ if (groupURLLinksGatherer == null)
+ {
groupURLLinksGatherer = new EnfinEnvision2OneWay();
}
return groupURLLinksGatherer;
}
- private void waitForCompletion() {
+
+ private void waitForCompletion()
+ {
if (groupURLLinksGatherer.isRunning())
{
- // wait around and show a visual delay indicator
- Cursor oldCursor = Desktop.instance.getCursor();
- Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- while (groupURLLinksGatherer.isRunning())
- {
- try {
- Thread.sleep(100);
- } catch (InterruptedException e ){};
+ // wait around and show a visual delay indicator
+ Cursor oldCursor = Desktop.instance.getCursor();
+ Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ while (groupURLLinksGatherer.isRunning())
+ {
+ try
+ {
+ Thread.sleep(100);
+ } catch (InterruptedException e)
+ {
+ }
+ ;
+ }
+ Desktop.instance.setCursor(oldCursor);
}
- Desktop.instance.setCursor(oldCursor);
- }
}
- public Vector getEnvisionServiceGroupURLS() {
+
+ public Vector getEnvisionServiceGroupURLS()
+ {
waitForCompletion();
return groupURLLinks;
}
+
/**
- * indicate if
+ * indicate if
*/
- private static String BACKGROUND="BACKGROUNDPARAM";
+ private static String BACKGROUND = "BACKGROUNDPARAM";
+
/**
- * contains null strings or one of the above constants - indicate if this URL is a special case.
+ * contains null strings or one of the above constants - indicate if this URL
+ * is a special case.
*/
private Vector additionalPar = new Vector();
+
/**
* the enfin service URL
*/
- private String enfinService=null;
- private String description=null;
+ private String enfinService = null;
+
+ private String description = null;
+
private String wfname;
- /* (non-Javadoc)
- * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String, java.lang.String)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
+ * java.lang.String, java.lang.String)
*/
public void endElement(String uri, String localName, String qName)
throws SAXException
{
-
-// System.err.println("End element: : '"+uri+" "+localName+" "+qName);
- if (qName.equalsIgnoreCase("workflow") && description!=null && description.length()>0)
+
+ // System.err.println("End element: : '"+uri+" "+localName+" "+qName);
+ if (qName.equalsIgnoreCase("workflow") && description != null
+ && description.length() > 0)
{
- //groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
- //groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
- System.err.println("Adding entry for "+wfname+" "+description);
- if (wfname.toLowerCase().indexOf("funcnet")==-1)
+ // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
+ // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
+ 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);
- groupURLLinks.addElement(wfname+"|"+"http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="+wfname+"&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+"&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+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="
+ + 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="
+ + urlstub
+ + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
}
}
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
*/
public void characters(char[] ch, int start, int length)
throws SAXException
{
- if (description!=null) {
- for (int i=start; i 1 ? "s" : "")})));
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -218,7 +345,13 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
public void run()
{
- showLink(urlgenerator.constructFrom(urlstub));
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException ex)
+ {
+ Cache.log.warn("Not showing link: URL is too long!", ex);
+ }
}
}).start();
@@ -230,6 +363,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
/**
* open the given link in a new browser window
+ *
* @param url
*/
public void showLink(String url)
@@ -242,44 +376,53 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
+
/**
* called by a web service menu instance when it is opened.
+ *
* @param enfinServiceMenu
* @param alignFrame
*/
private void buildGroupLinkMenu(JMenu enfinServiceMenu,
AlignFrame alignFrame)
{
+ if (running || !started)
+ {
+ return;
+ }
SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
- if (sg==null) {
+ if (sg == null)
+ {
// consider visible regions here/
}
enfinServiceMenu.removeAll();
- JMenu entries = buildGroupURLMenu(seqs,sg);
- if (entries!=null)
+ JMenu entries = buildGroupURLMenu(seqs, sg);
+ if (entries != null)
{
- for (int i=0,iSize=entries.getMenuComponentCount();iend)
+ // we skip sequences which do not have any non-gaps in the region of
+ // interest
+ if (start > end)
{
continue;
}
// just collect ids from dataset sequence
- // TODO: check if IDs collected from selecton group intersects with the current selection, too
+ // TODO: check if IDs collected from selecton group intersects with the
+ // current selection, too
SequenceI sqi = seqs[sq];
- while (sqi.getDatasetSequence()!=null) {
- sqi = sqi.getDatasetSequence(); }
+ while (sqi.getDatasetSequence() != null)
+ {
+ sqi = sqi.getDatasetSequence();
+ }
DBRefEntry[] dbr = sqi.getDBRef();
- if (dbr!=null && dbr.length>0)
+ if (dbr != null && dbr.length > 0)
{
- for (int d=0;d gurlMenus = new Hashtable();
+ /**
+ * last number of sequences where URL generation failed
+ */
+ int[] nsqtype = new int[]
+ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
+ for (int i = 0; i < groupURLLinks.size(); i++)
+ {
+ String link = (String) groupURLLinks.elementAt(i);
+ String descr = (String) groupURLdescr.elementAt(i);
+
+ // boolean specialCase =
+ // additionalPar.elementAt(i).toString().equals(BACKGROUND);
+ GroupUrlLink urlLink = null;
+ try
+ {
+ urlLink = new GroupUrlLink(link);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+ + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ // create/recover the sub menus that might be populated for this link.
+ JMenu[] wflinkMenus = gurlMenus.get(label);
+ if (wflinkMenus == null)
+ {
+ // three types of url that might be
+ // created.
+ wflinkMenus = new JMenu[]
+ { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) };
+ gurlMenus.put(label, wflinkMenus);
+ }
+
+ boolean usingNames = false;
+ // Now see which parts of the group apply for this URL
+ String ltarget;
+ String[] seqstr, ids; // input to makeUrl
+ for (int t = 0; t < allowedDb.length; t++)
+ {
+ ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
- String[] seqstr,ids; // input to makeUrl
- if (idset!=null)
+ if (idset != null)
{
- int numinput = ((int[])idset[0])[0];
- String[] allids = ((String[])idset[1]);
+ int numinput = ((int[]) idset[0])[0];
+ String[] allids = ((String[]) idset[1]);
seqstr = new String[numinput];
ids = new String[numinput];
- for (int sq=0,idcount=0;sq 0
+ && numinput >= nsqtype[urlLink.getGroupURLType()])
{
- if (allids[sq]!=null) {
+ continue;
+ }
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
+ {
+ if (allids[sq] != null)
+ {
ids[idcount] = allids[sq];
seqstr[idcount++] = idandseqs[1][sq];
}
}
- } else {
- // just use the id/seq set
- seqstr = idandseqs[1];
- ids = idandseqs[0];
- usingNames=true;
- }
- // and try and make the groupURL!
-
- Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
- if (urlset!=null)
- {
- int type = urlLink.getGroupURLType() & 3;
- //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
- // first two bits ofurlLink type bitfield are sequenceids and sequences
- // TODO: FUTURE: ensure the groupURL menu structure can be generalised
- addshowLink(linkMenus[type], label + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), descr, urlLink, urlset);
- addMenu = true;
+ try
+ {
+ createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
+ descr, ids, seqstr);
+ } catch (UrlStringTooLongException ex)
+ {
+ nsqtype[urlLink.getGroupURLType()] = numinput;
+ }
}
}
- if (addMenu)
+ // also do names only.
+ seqstr = idandseqs[1];
+ ids = idandseqs[0];
+ if (nsqtype[urlLink.getGroupURLType()] > 0
+ && idandseqs[0].length >= nsqtype[urlLink.getGroupURLType()])
+ {
+ continue;
+ }
+
+ try
+ {
+ createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
+ ids, seqstr);
+ } catch (UrlStringTooLongException ex)
+ {
+ nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length;
+ }
+ }
+ boolean anyadded = false; // indicates if there are any group links to give
+ // to user
+ for (Map.Entry menues : gurlMenus.entrySet())
{
- groupLinksMenu = new JMenu("Group Links");
- for (int m=0;m0)
+ if (wflinkMenus[m] != null
+ && wflinkMenus[m].getMenuComponentCount() > 0)
{
- groupLinksMenu.add(linkMenus[m]);
+ anyadded = true;
+ grouplinkset.add(wflinkMenus[m]);
}
}
-
+ groupLinksMenu.add(grouplinkset);
+ }
+ if (anyadded)
+ {
return groupLinksMenu;
}
return null;
}
- /// end of stuff copied from popupmenu
- public void attachWSMenuEntry(final JMenu wsmenu, final AlignFrame alignFrame)
+ private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
+ GroupUrlLink urlLink, String label, String ltarget, String descr,
+ String[] ids, String[] seqstr) throws UrlStringTooLongException
+ {
+ Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
+ + System.currentTimeMillis(), false);
+
+ if (urlset != null)
+ {
+ int type = urlLink.getGroupURLType() & 3;
+ // System.out.println(urlLink.getGroupURLType()
+ // +" "+((String[])urlset[3])[0]);
+ // first two bits ofurlLink type bitfield are sequenceids and sequences
+ // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+ addshowLink(
+ linkMenus[type],
+ label
+ + " "
+ + (ltarget == null ? (((type & 1) == 1 ? "ID"
+ : "Sequence") + (urlLink
+ .getNumberInvolved(urlset) > 1 ? "s" : ""))
+ : (usingNames ? (((type & 1) == 1) ? "(Names)"
+ : "")
+ : ("(" + ltarget + ")"))), descr,
+ usingNames ? null : label, urlLink, urlset);
+ return true;
+ }
+ return false;
+ }
+
+ // / end of stuff copied from popupmenu
+ public void attachWSMenuEntry(final JMenu wsmenu,
+ final AlignFrame alignFrame)
{
final JMenu enfinServiceMenu = new JMenu("Envision 2");
wsmenu.add(enfinServiceMenu);
enfinServiceMenu.setEnabled(false);
wsmenu.addMenuListener(new MenuListener()
- {
- // this listener remembers when the menu was first selected, and
- // doesn't rebuild the session list until it has been cleared and
- // reselected again.
- boolean refresh = true;
+ {
+ // this listener remembers when the menu was first selected, and
+ // doesn't rebuild the session list until it has been cleared and
+ // reselected again.
+ boolean refresh = true;
- public void menuCanceled(MenuEvent e)
- {
- refresh = true;
- }
+ public void menuCanceled(MenuEvent e)
+ {
+ refresh = true;
+ }
- public void menuDeselected(MenuEvent e)
- {
- refresh = true;
- }
+ public void menuDeselected(MenuEvent e)
+ {
+ refresh = true;
+ }
- public void menuSelected(MenuEvent e)
+ public void menuSelected(MenuEvent e)
+ {
+ if (refresh && !isRunning())
{
- if (refresh)
+ new Thread(new Runnable()
{
- try {
- buildGroupLinkMenu(enfinServiceMenu,alignFrame);
- } catch (OutOfMemoryError ex)
+ public void run()
{
- Cache.log.error("Out of memory when calculating the Envision2 links.",ex);
- enfinServiceMenu.setEnabled(false);
+ try
+ {
+ buildGroupLinkMenu(enfinServiceMenu, alignFrame);
+ } catch (OutOfMemoryError ex)
+ {
+ Cache.log
+ .error("Out of memory when calculating the Envision2 links.",
+ ex);
+ enfinServiceMenu.setEnabled(false);
+ }
}
- refresh = false;
- }
+ }).start();
+ refresh = false;
}
- });
-
-
+ }
+ });
+
}
}