X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FEnfinEnvision2OneWay.java;h=edc7fb781237a2a9e203a6cd7741d524db3d9436;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=f40831ca2041c7ac2f9ac8f33916fc8365b05a04;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java index f40831c..edc7fb7 100644 --- a/src/jalview/ws/EnfinEnvision2OneWay.java +++ b/src/jalview/ws/EnfinEnvision2OneWay.java @@ -1,19 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 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; @@ -30,15 +31,13 @@ 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; @@ -52,10 +51,14 @@ 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 @@ -138,19 +141,34 @@ 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+"#"); } } @@ -284,7 +302,8 @@ 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++) @@ -296,20 +315,28 @@ 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) @@ -319,7 +346,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements public void run() { - try { + try + { showLink(urlgenerator.constructFrom(urlstub)); } catch (UrlStringTooLongException ex) { @@ -404,7 +432,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements */ private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg) { - if (groupURLdescr==null || groupURLLinks==null) + if (groupURLdescr == null || groupURLLinks == null) return null; // TODO: usability: thread off the generation of group url content so root // menu appears asap @@ -476,7 +504,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements /** * last number of sequences where URL generation failed */ - int[] nsqtype = new int[] { 0,0,0,0,0,0,0,0,0,0}; + 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); @@ -527,7 +556,8 @@ 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()]) + if (nsqtype[urlLink.getGroupURLType()] > 0 + && numinput >= nsqtype[urlLink.getGroupURLType()]) { continue; } @@ -539,8 +569,10 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements seqstr[idcount++] = idandseqs[1][sq]; } } - try {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; @@ -550,14 +582,17 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements // also do names only. seqstr = idandseqs[1]; ids = idandseqs[0]; - if (nsqtype[urlLink.getGroupURLType()]>0 && idandseqs[0].length>=nsqtype[urlLink.getGroupURLType()]) + 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) + + try + { + createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr, + ids, seqstr); + } catch (UrlStringTooLongException ex) { nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length; } @@ -590,7 +625,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements GroupUrlLink urlLink, String label, String ltarget, String descr, String[] ids, String[] seqstr) throws UrlStringTooLongException { - Object[] urlset= urlLink.makeUrlStubs(ids, seqstr, "FromJalview" + Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview" + System.currentTimeMillis(), false); if (urlset != null) @@ -615,6 +650,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements } return false; } + // / end of stuff copied from popupmenu public void attachWSMenuEntry(final JMenu wsmenu, final AlignFrame alignFrame) @@ -643,19 +679,22 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements { if (refresh && !isRunning()) { - new Thread(new Runnable() { - public void run() { - 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); - } - }}).start(); + 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; } }