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.swing.JOptionPane;
  34
  35 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  36 import org.forester.archaeopteryx.webservices.WebserviceUtil;
  37 import org.forester.archaeopteryx.webservices.WebservicesManager;
  38 import org.forester.io.parsers.PhylogenyParser;
  39 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  40 import org.forester.io.parsers.nhx.NHXParser;
  41 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  42 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  43 import org.forester.io.parsers.tol.TolParser;
  44 import org.forester.phylogeny.Phylogeny;
  45 import org.forester.phylogeny.PhylogenyMethods;
  46 import org.forester.phylogeny.data.Identifier;
  47 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  48 import org.forester.phylogeny.factories.PhylogenyFactory;
  49 import org.forester.util.ForesterUtil;
  50
  51 public class UrlTreeReader implements Runnable {
  52
  53     private final MainFrame _main_frame;
  54     private final int       _webservice_client_index;
  55
  56     UrlTreeReader( final MainFrame mf, final int webservice_client_index ) {
  57         _main_frame = mf;
  58         _webservice_client_index = webservice_client_index;
  59     }
  60
  61     @Override
  62     public void run() {
  63         readPhylogeniesFromWebservice();
  64     }
  65
  66     synchronized void readPhylogeniesFromWebservice() {
  67         URL url = null;
  68         Phylogeny[] trees = null;
  69         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
  70         final PhylogeniesWebserviceClient client = webservices_manager
  71                 .getAvailablePhylogeniesWebserviceClient( _webservice_client_index );
  72         String identifier = JOptionPane.showInputDialog( _main_frame, client.getInstructions() + "\n(Reference: "
  73                 + client.getReference() + ")", client.getDescription(), JOptionPane.QUESTION_MESSAGE );
  74         if ( ( identifier != null ) && ( identifier.trim().length() > 0 ) ) {
  75             identifier = identifier.trim();
  76             if ( client.isQueryInteger() ) {
  77                 identifier = identifier.replaceAll( "^\\D+", "" );
  78                 int id = -1;
  79                 try {
  80                     id = Integer.parseInt( identifier );
  81                 }
  82                 catch ( final NumberFormatException e ) {
  83                     id = -1;
  84                 }
  85                 if ( id < 1 ) {
  86                     JOptionPane.showMessageDialog( _main_frame,
  87                                                    "Identifier is expected to be a number",
  88                                                    "Can not open URL",
  89                                                    JOptionPane.ERROR_MESSAGE );
  90                     return;
  91                 }
  92                 identifier = id + "";
  93             }
  94             boolean exception = false;
  95             try {
  96                 String url_str = client.getUrl();
  97                 url_str = url_str.replaceFirst( PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier );
  98                 url = new URL( url_str );
  99                 PhylogenyParser parser = null;
 100                 switch ( client.getReturnFormat() ) {
 101                     case TOL_XML_RESPONSE:
 102                         parser = new TolParser();
 103                         break;
 104                     case NEXUS:
 105                         parser = new NexusPhylogeniesParser();
 106                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
 107                         break;
 108                     case TREEBASE_TREE:
 109                         parser = new NexusPhylogeniesParser();
 110                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
 111                         ( ( NexusPhylogeniesParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
 112                         break;
 113                     case TREEBASE_STUDY:
 114                         parser = new NexusPhylogeniesParser();
 115                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
 116                         ( ( NexusPhylogeniesParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
 117                         break;
 118                     case NH:
 119                         parser = new NHXParser();
 120                         ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
 121                         ( ( NHXParser ) parser ).setReplaceUnderscores( true );
 122                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 123                         break;
 124                     case NH_EXTRACT_TAXONOMY:
 125                         parser = new NHXParser();
 126                         ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
 127                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 128                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 129                         break;
 130                     case PFAM:
 131                         parser = new NHXParser();
 132                         ( ( NHXParser ) parser )
 133                                 .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
 134                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 135                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 136                         break;
 137                     case NHX:
 138                         parser = new NHXParser();
 139                         ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
 140                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 141                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 142                         break;
 143                     case PHYLOXML:
 144                         parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
 145                         break;
 146                     default:
 147                         throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
 148                 }
 149                 if ( _main_frame.getMainPanel().getCurrentTreePanel() != null ) {
 150                     _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
 151                 }
 152                 else {
 153                     _main_frame.getMainPanel().setWaitCursor();
 154                 }
 155                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 156                 trees = factory.create( url.openStream(), parser );
 157             }
 158             catch ( final MalformedURLException e ) {
 159                 exception = true;
 160                 JOptionPane.showMessageDialog( _main_frame,
 161                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
 162                                                "Malformed URL",
 163                                                JOptionPane.ERROR_MESSAGE );
 164             }
 165             catch ( final IOException e ) {
 166                 exception = true;
 167                 JOptionPane.showMessageDialog( _main_frame,
 168                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 169                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 170                                                JOptionPane.ERROR_MESSAGE );
 171             }
 172             catch ( final NumberFormatException e ) {
 173                 exception = true;
 174                 JOptionPane.showMessageDialog( _main_frame,
 175                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 176                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 177                                                JOptionPane.ERROR_MESSAGE );
 178             }
 179             catch ( final Exception e ) {
 180                 exception = true;
 181                 e.printStackTrace();
 182                 JOptionPane.showMessageDialog( _main_frame,
 183                                                e.getLocalizedMessage(),
 184                                                "Unexpected Exception",
 185                                                JOptionPane.ERROR_MESSAGE );
 186             }
 187             finally {
 188                 if ( _main_frame.getCurrentTreePanel() != null ) {
 189                     _main_frame.getCurrentTreePanel().setArrowCursor();
 190                 }
 191                 else {
 192                     _main_frame.getMainPanel().setArrowCursor();
 193                 }
 194             }
 195             if ( ( trees != null ) && ( trees.length > 0 ) ) {
 196                 for( final Phylogeny phylogeny : trees ) {
 197                     if ( !phylogeny.isEmpty() ) {
 198                         if ( client.getName().equals( WebserviceUtil.TREE_FAM_NAME ) ) {
 199                             phylogeny.setRerootable( false );
 200                             phylogeny.setRooted( true );
 201                         }
 202                         if ( client.getProcessingInstructions() != null ) {
 203                             try {
 204                                 WebserviceUtil.processInstructions( client, phylogeny );
 205                             }
 206                             catch ( final PhyloXmlDataFormatException e ) {
 207                                 JOptionPane.showMessageDialog( _main_frame,
 208                                                                "Error:\n" + e.getLocalizedMessage(),
 209                                                                "Error",
 210                                                                JOptionPane.ERROR_MESSAGE );
 211                             }
 212                         }
 213                         if ( client.getNodeField() != null ) {
 214                             try {
 215                                 PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField(), false );
 216                             }
 217                             catch ( final PhyloXmlDataFormatException e ) {
 218                                 JOptionPane.showMessageDialog( _main_frame,
 219                                                                "Error:\n" + e.getLocalizedMessage(),
 220                                                                "Error",
 221                                                                JOptionPane.ERROR_MESSAGE );
 222                             }
 223                         }
 224                         phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) );
 225                         _main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() );
 226                         _main_frame.getMenuBarOfMainFrame().add( _main_frame.getHelpMenu() );
 227                         _main_frame.getMainPanel().addPhylogenyInNewTab( phylogeny,
 228                                                                          _main_frame.getConfiguration(),
 229                                                                          new File( url.getFile() ).getName(),
 230                                                                          url.toString() );
 231                         String my_name_for_file = "";
 232                         if ( !ForesterUtil.isEmpty( phylogeny.getName() ) ) {
 233                             my_name_for_file = new String( phylogeny.getName() ).replaceAll( " ", "_" );
 234                         }
 235                         else if ( phylogeny.getIdentifier() != null ) {
 236                             final StringBuffer sb = new StringBuffer();
 237                             if ( !ForesterUtil.isEmpty( phylogeny.getIdentifier().getProvider() ) ) {
 238                                 sb.append( phylogeny.getIdentifier().getProvider() );
 239                                 sb.append( "_" );
 240                             }
 241                             sb.append( phylogeny.getIdentifier().getValue() );
 242                             my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
 243                         }
 244                         _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
 245                         AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
 246                                 .getControlPanel(), _main_frame.getConfiguration() );
 247                         _main_frame.getMainPanel().getControlPanel().showWhole();
 248                     }
 249                 }
 250             }
 251             else if ( !exception ) {
 252                 JOptionPane.showMessageDialog( null, ForesterUtil.wordWrap( "Failed to read in tree(s) from [" + url
 253                         + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
 254             }
 255             _main_frame.getContentPane().repaint();
 256             if ( ( trees != null ) && ( trees.length > 0 ) ) {
 257                 try {
 258                     JOptionPane.showMessageDialog( null,
 259                                                    ForesterUtil.wordWrap( "Successfully read in " + trees.length
 260                                                            + " tree(s) from [" + url + "]", 80 ),
 261                                                    "Success",
 262                                                    JOptionPane.INFORMATION_MESSAGE );
 263                 }
 264                 catch ( final Exception e ) {
 265                     // Not important if this fails, do nothing.
 266                 }
 267                 _main_frame.getContentPane().repaint();
 268             }
 269         }
 270         _main_frame.activateSaveAllIfNeeded();
 271         System.gc();
 272     }
 273 }