forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.archaeopteryx;
  27
  28 import java.io.File;
  29 import java.io.IOException;
  30 import java.net.MalformedURLException;
  31 import java.net.URL;
  32
  33 import javax.net.ssl.HttpsURLConnection;
  34 import javax.swing.JOptionPane;
  35
  36 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  37 import org.forester.archaeopteryx.webservices.WebserviceUtil;
  38 import org.forester.archaeopteryx.webservices.WebservicesManager;
  39 import org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat;
  40 import org.forester.io.parsers.PhylogenyParser;
  41 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  42 import org.forester.io.parsers.nhx.NHXParser;
  43 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  44 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  45 import org.forester.io.parsers.tol.TolParser;
  46 import org.forester.phylogeny.Phylogeny;
  47 import org.forester.phylogeny.PhylogenyMethods;
  48 import org.forester.phylogeny.data.Identifier;
  49 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  50 import org.forester.phylogeny.factories.PhylogenyFactory;
  51 import org.forester.util.ForesterUtil;
  52 import org.forester.util.TrustManager;
  53
  54 public class UrlTreeReader implements Runnable {
  55
  56     private final MainFrame _main_frame;
  57     private final int       _webservice_client_index;
  58
  59     UrlTreeReader( final MainFrame mf, final int webservice_client_index ) {
  60         _main_frame = mf;
  61         _webservice_client_index = webservice_client_index;
  62     }
  63
  64     @Override
  65     public void run() {
  66         readPhylogeniesFromWebservice();
  67     }
  68
  69     synchronized void readPhylogeniesFromWebservice() {
  70         URL url = null;
  71         Phylogeny[] trees = null;
  72         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
  73         final PhylogeniesWebserviceClient client = webservices_manager
  74                 .getAvailablePhylogeniesWebserviceClient( _webservice_client_index );
  75         String identifier = JOptionPane.showInputDialog( _main_frame, client.getInstructions() + "\n(Reference: "
  76                 + client.getReference() + ")", client.getDescription(), JOptionPane.QUESTION_MESSAGE );
  77         if ( ( identifier != null ) && ( identifier.trim().length() > 0 ) ) {
  78             identifier = identifier.trim();
  79             if ( client.isQueryInteger() ) {
  80                 identifier = identifier.replaceAll( "^\\D+", "" );
  81                 int id = -1;
  82                 try {
  83                     id = Integer.parseInt( identifier );
  84                 }
  85                 catch ( final NumberFormatException e ) {
  86                     id = -1;
  87                 }
  88                 if ( id < 1 ) {
  89                     JOptionPane.showMessageDialog( _main_frame,
  90                                                    "Identifier is expected to be a number",
  91                                                    "Can not open URL",
  92                                                    JOptionPane.ERROR_MESSAGE );
  93                     return;
  94                 }
  95                 identifier = id + "";
  96             }
  97             boolean exception = false;
  98             try {
  99                 String url_str = client.getUrl();
 100                 url_str = url_str.replaceFirst( PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier );
 101                 url = new URL( url_str );
 102                 PhylogenyParser parser = null;
 103                 switch ( client.getReturnFormat() ) {
 104                     case TOL_XML_RESPONSE:
 105                         parser = new TolParser();
 106                         break;
 107                     case NEXUS:
 108                         parser = new NexusPhylogeniesParser();
 109                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
 110                         break;
 111                     case TREEBASE_TREE:
 112                         parser = new NexusPhylogeniesParser();
 113                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
 114                         ( ( NexusPhylogeniesParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
 115                         break;
 116                     case TREEBASE_STUDY:
 117                         parser = new NexusPhylogeniesParser();
 118                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
 119                         ( ( NexusPhylogeniesParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
 120                         break;
 121                     case NH:
 122                         parser = new NHXParser();
 123                         ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
 124                         ( ( NHXParser ) parser ).setReplaceUnderscores( true );
 125                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 126                         break;
 127                     case NH_EXTRACT_TAXONOMY:
 128                         parser = new NHXParser();
 129                         ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
 130                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 131                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 132                         break;
 133                     case PFAM:
 134                         parser = new NHXParser();
 135                         ( ( NHXParser ) parser )
 136                                 .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
 137                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 138                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 139                         break;
 140                     case NHX:
 141                         parser = new NHXParser();
 142                         ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
 143                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 144                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 145                         break;
 146                     case PHYLOXML:
 147                         parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
 148                         break;
 149                     default:
 150                         throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
 151                 }
 152                 if ( _main_frame.getMainPanel().getCurrentTreePanel() != null ) {
 153                     _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
 154                 }
 155                 else {
 156                     _main_frame.getMainPanel().setWaitCursor();
 157                 }
 158                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 159
 160                 if (client.getReturnFormat()== WebservicesManager.WsPhylogenyFormat.TREEBASE_TREE
 161                     || client.getReturnFormat()== WebservicesManager.WsPhylogenyFormat.TREEBASE_STUDY) {
 162
 163                     final HttpsURLConnection con = TrustManager.makeHttpsURLConnection( url );
 164                     trees = factory.create( con.getInputStream(), parser );
 165                 }
 166                 else {
 167                     trees = factory.create( url.openStream(), parser );
 168                 }
 169             }
 170             catch ( final MalformedURLException e ) {
 171                 exception = true;
 172                 JOptionPane.showMessageDialog( _main_frame,
 173                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
 174                                                "Malformed URL",
 175                                                JOptionPane.ERROR_MESSAGE );
 176             }
 177             catch ( final IOException e ) {
 178                 exception = true;
 179                 JOptionPane.showMessageDialog( _main_frame,
 180                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 181                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 182                                                JOptionPane.ERROR_MESSAGE );
 183             }
 184             catch ( final NumberFormatException e ) {
 185                 exception = true;
 186                 JOptionPane.showMessageDialog( _main_frame,
 187                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 188                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 189                                                JOptionPane.ERROR_MESSAGE );
 190             }
 191             catch ( final Exception e ) {
 192                 exception = true;
 193                 e.printStackTrace();
 194                 JOptionPane.showMessageDialog( _main_frame,
 195                                                e.getLocalizedMessage(),
 196                                                "Unexpected Exception",
 197                                                JOptionPane.ERROR_MESSAGE );
 198             }
 199             finally {
 200                 if ( _main_frame.getCurrentTreePanel() != null ) {
 201                     _main_frame.getCurrentTreePanel().setArrowCursor();
 202                 }
 203                 else {
 204                     _main_frame.getMainPanel().setArrowCursor();
 205                 }
 206             }
 207             if ( ( trees != null ) && ( trees.length > 0 ) ) {
 208                 for( final Phylogeny phylogeny : trees ) {
 209                     if ( !phylogeny.isEmpty() ) {
 210                         if ( client.getName().equals( WebserviceUtil.TREE_FAM_NAME ) ) {
 211                             phylogeny.setRerootable( false );
 212                             phylogeny.setRooted( true );
 213                         }
 214                         if ( client.getProcessingInstructions() != null ) {
 215                             try {
 216                                 WebserviceUtil.processInstructions( client, phylogeny );
 217                             }
 218                             catch ( final PhyloXmlDataFormatException e ) {
 219                                 JOptionPane.showMessageDialog( _main_frame,
 220                                                                "Error:\n" + e.getLocalizedMessage(),
 221                                                                "Error",
 222                                                                JOptionPane.ERROR_MESSAGE );
 223                             }
 224                         }
 225                         if ( client.getNodeField() != null ) {
 226                             try {
 227                                 PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField(), false );
 228                             }
 229                             catch ( final PhyloXmlDataFormatException e ) {
 230                                 JOptionPane.showMessageDialog( _main_frame,
 231                                                                "Error:\n" + e.getLocalizedMessage(),
 232                                                                "Error",
 233                                                                JOptionPane.ERROR_MESSAGE );
 234                             }
 235                         }
 236                         phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) );
 237                         _main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() );
 238                         _main_frame.getMenuBarOfMainFrame().add( _main_frame.getHelpMenu() );
 239                         _main_frame.getMainPanel().addPhylogenyInNewTab( phylogeny,
 240                                                                          _main_frame.getConfiguration(),
 241                                                                          new File( url.getFile() ).getName(),
 242                                                                          url.toString() );
 243                         String my_name_for_file = "";
 244                         if ( !ForesterUtil.isEmpty( phylogeny.getName() ) ) {
 245                             my_name_for_file = new String( phylogeny.getName() ).replaceAll( " ", "_" );
 246                         }
 247                         else if ( phylogeny.getIdentifier() != null ) {
 248                             final StringBuffer sb = new StringBuffer();
 249                             if ( !ForesterUtil.isEmpty( phylogeny.getIdentifier().getProvider() ) ) {
 250                                 sb.append( phylogeny.getIdentifier().getProvider() );
 251                                 sb.append( "_" );
 252                             }
 253                             sb.append( phylogeny.getIdentifier().getValue() );
 254                             my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
 255                         }
 256                         _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
 257                         AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
 258                                 .getControlPanel(), _main_frame.getConfiguration() );
 259                         _main_frame.getMainPanel().getControlPanel().showWhole();
 260                     }
 261                 }
 262             }
 263             else if ( !exception ) {
 264                 JOptionPane.showMessageDialog( null, ForesterUtil.wordWrap( "Failed to read in tree(s) from [" + url
 265                         + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
 266             }
 267             _main_frame.getContentPane().repaint();
 268             if ( ( trees != null ) && ( trees.length > 0 ) ) {
 269                 try {
 270                     JOptionPane.showMessageDialog( null,
 271                                                    ForesterUtil.wordWrap( "Successfully read in " + trees.length
 272                                                            + " tree(s) from [" + url + "]", 80 ),
 273                                                    "Success",
 274                                                    JOptionPane.INFORMATION_MESSAGE );
 275                 }
 276                 catch ( final Exception e ) {
 277                     // Not important if this fails, do nothing.
 278                 }
 279                 _main_frame.getContentPane().repaint();
 280             }
 281         }
 282         _main_frame.activateSaveAllIfNeeded();
 283         System.gc();
 284     }
 285 }