X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;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) + ""); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -318,7 +350,13 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements 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(); @@ -360,6 +398,10 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements private void buildGroupLinkMenu(JMenu enfinServiceMenu, AlignFrame alignFrame) { + if (running || !started) + { + return; + } SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence(); SequenceGroup sg = alignFrame.getViewport().getSelectionGroup(); if (sg == null) @@ -394,7 +436,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements */ private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg) { - + if (groupURLdescr == null || groupURLLinks == null) + return null; // TODO: usability: thread off the generation of group url content so root // menu appears asap // sequence only URLs @@ -462,10 +505,15 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements } // now create group links for all distinct ID/sequence sets. Hashtable 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 = groupURLLinks.elementAt(i).toString(); - String descr = groupURLdescr.elementAt(i).toString(); + String link = (String) groupURLLinks.elementAt(i); + String descr = (String) groupURLdescr.elementAt(i); // boolean specialCase = // additionalPar.elementAt(i).toString().equals(BACKGROUND); @@ -512,6 +560,11 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements String[] allids = ((String[]) idset[1]); seqstr = new String[numinput]; ids = new String[numinput]; + if (nsqtype[urlLink.getGroupURLType()] > 0 + && numinput >= nsqtype[urlLink.getGroupURLType()]) + { + continue; + } for (int sq = 0, idcount = 0; sq < seqs.length; sq++) { if (allids[sq] != null) @@ -520,15 +573,33 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements seqstr[idcount++] = idandseqs[1][sq]; } } - createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null, - descr, ids, seqstr); + try + { + createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null, + descr, ids, seqstr); + } catch (UrlStringTooLongException ex) + { + nsqtype[urlLink.getGroupURLType()] = numinput; + } } } // also do names only. seqstr = idandseqs[1]; ids = idandseqs[0]; - createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr, - ids, seqstr); + 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 @@ -556,10 +627,11 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames, GroupUrlLink urlLink, String label, String ltarget, String descr, - String[] ids, String[] seqstr) + String[] ids, String[] seqstr) throws UrlStringTooLongException { Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview" + System.currentTimeMillis(), false); + if (urlset != null) { int type = urlLink.getGroupURLType() & 3; @@ -609,18 +681,24 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements public void menuSelected(MenuEvent e) { - if (refresh) + if (refresh && !isRunning()) { - try - { - buildGroupLinkMenu(enfinServiceMenu, alignFrame); - } catch (OutOfMemoryError ex) + new Thread(new Runnable() { - Cache.log.error( - "Out of memory when calculating the Envision2 links.", - ex); - enfinServiceMenu.setEnabled(false); - } + public void run() + { + try + { + buildGroupLinkMenu(enfinServiceMenu, alignFrame); + } catch (OutOfMemoryError ex) + { + Cache.log + .error("Out of memory when calculating the Envision2 links.", + ex); + enfinServiceMenu.setEnabled(false); + } + } + }).start(); refresh = false; } }