src/org/biojava/dasobert/dasregistry/Das1Validator.java

   1 /*                    BioJava development code
   2  *
   3  * This code may be freely distributed and modified under the
   4  * terms of the GNU Lesser General Public Licence.  This should
   5  * be distributed with the code.  If you do not have a copy,
   6  * see:
   7  *
   8  *      http://www.gnu.org/copyleft/lesser.html
   9  *
  10  * Copyright for this code is held jointly by the individual
  11  * authors.  These should be listed in @author doc comments.
  12  *
  13  * For more information on the BioJava project and its aims,
  14  * or to join the biojava-l mailing list, visit the home page
  15  * at:
  16  *
  17  *      http://www.biojava.org/
  18  *
  19  * Created on 30.08.2005
  20  * @author Andreas Prlic
  21  *
  22  */
  23
  24
  25 package org.biojava.dasobert.dasregistry ;
  26
  27 //import org.biojava.services.das.*;
  28 //xml stuff
  29 import org.xml.sax.*;
  30 import javax.xml.parsers.*;
  31 import java.util.ArrayList                    ;
  32 import java.util.Map                          ;
  33 import java.util.List                         ;
  34 import java.io.InputStream                    ;
  35
  36 import java.net.URL                           ;
  37
  38
  39 //for validation add dependency on SPICE... :-/
  40 import java.net.HttpURLConnection;
  41 import org.biojava.dasobert.das.*;
  42 import org.biojava.dasobert.das.DAS_Entry_Points_Handler;
  43 import org.biojava.dasobert.das.DAS_Types_Handler;
  44
  45
  46
  47 public class Das1Validator {
  48
  49     public final static String[] DAS_CAPABILITIES = {
  50         "sequence",
  51         "structure",
  52         "alignment",
  53         "types",
  54         "features",
  55         "entry_points",
  56         "dna",
  57         "stylesheet"
  58     } ;
  59
  60
  61     //private final static String DATASOURCE_NAME = "jdbc/mysql";
  62     String validationMessage;
  63
  64     public boolean VALIDATION = false; // DTD validation ..
  65
  66     List all_capabilities;
  67     public Das1Validator() {
  68         validationMessage = "" ;
  69         all_capabilities = new ArrayList();
  70         for ( int i = 0 ; i< DAS_CAPABILITIES.length; i++ ) {
  71             all_capabilities.add(DAS_CAPABILITIES[i]);
  72         }
  73     }
  74
  75     /** return which errors have been produced during validation... */
  76     public String getValidationMessage(){
  77         return validationMessage;
  78     }
  79
  80
  81
  82     public String[] validate(String url, DasCoordinateSystem[] coords, String[] capabilities){
  83         validationMessage="";
  84         // a list containing all valid DAS requests ...
  85
  86         List lst =new ArrayList();
  87
  88         char lastChar = url.charAt(url.length()-1);
  89         if ( lastChar  != '/')
  90             url += "/";
  91
  92         validateURL(url);
  93
  94
  95         // test if all specified capabilities really work
  96         for ( int c = 0 ; c < capabilities.length ; c++) {
  97             String capability = capabilities[c];
  98             if ( all_capabilities.contains(capability)) {
  99                 //System.out.println("testing " + capability);
 100
 101                 if ( capability.equals("sequence")) {
 102                     for ( int i=0;i< coords.length;i++){
 103                         DasCoordinateSystem ds =coords[i];
 104                         String testcode = ds.getTestCode();
 105
 106                         // do a DAS sequence retreive
 107                         if (  validateSequence(url,testcode) )
 108                             lst.add(capability);
 109
 110                     }
 111
 112                 }
 113                 else if ( capability.equals("structure")) {
 114
 115                 }
 116                 else if ( capability.equals("features")){
 117                     for ( int i=0;i< coords.length;i++){
 118                         DasCoordinateSystem ds =coords[i];
 119                         String testcode = ds.getTestCode();
 120
 121
 122                         if ( validateFeatures(url,testcode))
 123                             lst.add(capability);
 124
 125                     }
 126                 }
 127                 else if ( capability.equals("alignment")){
 128
 129                 } else if ( capability.equals("types")){
 130                     if ( validateTypes(url))
 131                         lst.add(capability);
 132                     //else
 133                     //    error =true ;
 134
 135                 } else if ( capability.equals("entry_points")) {
 136                     if ( validateEntry_Points(url))
 137                         lst.add(capability);
 138                     //else
 139                     //    error = true;
 140                 } else if ( capability.equals("stylesheet")) {
 141                     if ( validateStylesheet(url))
 142                         lst.add(capability);
 143                     //} else
 144                     //    error = true;
 145                 } else if ( capability.equals("dna")){
 146                     for ( int i=0;i< coords.length;i++){
 147                         DasCoordinateSystem ds =coords[i];
 148                         String testcode = ds.getTestCode();
 149
 150                         if ( validateDNA(url,testcode))
 151                             lst.add(capability);
 152                     }
 153                 }
 154                 else {
 155                     validationMessage += "<br/>---<br/> test of capability " + capability + " not implemented,yet.";
 156                     lst.add(capability);
 157                 }
 158             }
 159         }
 160
 161         //if ( error) {
 162         //    System.out.println("DasValidator: "+ validationMessage);
 163         //}
 164         //this.validationMessage = validationMessage;
 165         return (String[])lst.toArray(new String[lst.size()]);
 166
 167     }
 168
 169     /** make sure the URL matches the DAS spec
 170      returns true if URL looks o.k...
 171      */
 172     public  boolean validateURL(String url) {
 173         String[] spl = url.split("/");
 174
 175         //for (int i = 0 ; i < spl.length  ; i++ ) {
 176         //    System.out.println("spl["+i+"]:"+spl[i]);
 177         //}
 178
 179         if (spl == null ) {
 180             validationMessage +="---<br/> URL is not well formed" ;
 181             return false;
 182         }
 183
 184         if ( spl.length <= 4) {
 185             validationMessage +="---<br/> URL is not well formed <br/>" +
 186             "should be http[s]://site.specific.prefix/das/dassourcename/";
 187             return false;
 188         }
 189
 190         //System.out.println("split 0 : " + spl[0]);
 191         if ( ! (spl[0].equals("http:"))) {
 192             if ( ! ( spl[0].equals("https:"))){
 193                 validationMessage +="---<br/> URL is not well formed (does not start with http:// or https://)" ;
 194                 return false;
 195             }
 196
 197         }
 198
 199         String dastxt = spl[spl.length-2] ;
 200         //System.out.println("should be >das< " + dastxt);
 201         if ( ! dastxt.equals("das")) {
 202             String suggestion = spl[0] + "//" ;
 203             String wrong      = spl[0] + "//" ;
 204             for (int i = 2 ; i < spl.length -2 ; i++ ) {
 205                 suggestion += spl[i] + "/" ;
 206                 wrong += spl[i] + "/" ;
 207             }
 208             suggestion +="<b>das</b>/"+spl[spl.length-1];
 209             wrong +="<b>" + spl[spl.length-2] + "</b>/"+spl[spl.length-1];
 210             validationMessage +="--<br/> the URL does not match the DAS spec. it should be <br/>"+
 211             " http[s]://site.specific.prefix/das/dassourcename/ <br/>" +
 212             " found >" + dastxt +" < instead of >das< <br/>" +
 213             " suggested url: " + suggestion + "<br/>"+
 214             " instead of: " + wrong ;
 215             return false;
 216         }
 217         return true;
 218
 219     }
 220
 221     private boolean validateDNA(String url, String testcode){
 222         try {
 223             String cmd = url+"dna?segment="+testcode;
 224             URL strurl = new URL(cmd);
 225             InputStream dasInStream = open(strurl);
 226
 227             XMLReader xmlreader = getXMLReader();
 228
 229             DAS_DNA_Handler cont_handle = new DAS_DNA_Handler() ;
 230
 231             xmlreader.setContentHandler(cont_handle);
 232             xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
 233             InputSource insource = new InputSource() ;
 234
 235             insource.setByteStream(dasInStream);
 236             xmlreader.parse(insource);
 237             String sequence = cont_handle.get_sequence();
 238             if ( sequence.length() > 0 ) {
 239                 return true;
 240             } else {
 241                 validationMessage  +="<br/>---<br/> contacting " + cmd + "<br/>";
 242                 validationMessage += " no sequence was returned";
 243
 244                 return false;
 245             }
 246
 247
 248         } catch ( Exception e) {
 249             //e.printStackTrace();
 250             validationMessage += "<br/>---<br/> contacting " + url + "dna?segment="+testcode + "<br/>";
 251
 252             Throwable cause = e.getCause();
 253             if ( cause != null)
 254                 validationMessage += cause.toString();
 255             else
 256                 validationMessage += e.toString();
 257         }
 258         return false;
 259
 260     }
 261
 262     private boolean validateStylesheet(String url) {
 263         try {
 264             DAS_StylesheetRetrieve dsr = new DAS_StylesheetRetrieve();
 265             URL styleurl = new URL(url+"stylesheet");
 266
 267             Map[] stylesheet = dsr.retrieve(styleurl);
 268             if (( stylesheet != null ) && ( stylesheet.length > 0))
 269                 return true;
 270             else {
 271                 validationMessage  +="<br/>---<br/> contacting " + url + "stylesheet<br/>";
 272                 validationMessage += " no stylesheet was returned";
 273                 return false;
 274             }
 275         } catch (Exception e) {
 276             validationMessage += "<br/>---<br/> contacting " + url+"stylesheet <br/>";
 277
 278             Throwable cause = e.getCause();
 279             if ( cause != null)
 280                 validationMessage += cause.toString();
 281             else
 282                 validationMessage += e.toString();
 283         }
 284         return false;
 285     }
 286
 287
 288     private boolean validateEntry_Points(String url){
 289         try {
 290             URL u = new URL(url+"entry_points");
 291
 292             InputStream dasInStream = open(u);
 293
 294             XMLReader xmlreader = getXMLReader();
 295
 296             DAS_Entry_Points_Handler cont_handle = new DAS_Entry_Points_Handler() ;
 297
 298             xmlreader.setContentHandler(cont_handle);
 299             xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
 300             InputSource insource = new InputSource() ;
 301             insource.setByteStream(dasInStream);
 302             xmlreader.parse(insource);
 303             String version = cont_handle.getVersion();
 304             if ( version != null ) {
 305                 return true;
 306             } else {
 307                 validationMessage  +="<br/>---<br/> contacting " + url +"entry_points <br/>";
 308                 validationMessage += " no version was returned";
 309
 310                 return false;
 311             }
 312
 313
 314         } catch ( Exception e) {
 315             //e.printStackTrace();
 316             validationMessage += "<br/>---<br/> contacting " + url+ "types <br/>";
 317
 318             Throwable cause = e.getCause();
 319             if ( cause != null)
 320                 validationMessage += cause.toString();
 321             else
 322                 validationMessage += e.toString();
 323         }
 324         return false;
 325     }
 326
 327     private boolean validateTypes(String url){
 328         try {
 329             URL u = new URL(url+"types");
 330             InputStream dasInStream = open(u);
 331             XMLReader xmlreader = getXMLReader();
 332
 333             DAS_Types_Handler cont_handle = new DAS_Types_Handler() ;
 334
 335             xmlreader.setContentHandler(cont_handle);
 336             xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
 337             InputSource insource = new InputSource() ;
 338             insource.setByteStream(dasInStream);
 339             xmlreader.parse(insource);
 340             String[] types = cont_handle.getTypes();
 341             if ( types.length > 0 ) {
 342                 return true;
 343             } else {
 344                 validationMessage  +="<br/>---<br/> contacting " + url +"types <br/>";
 345                 validationMessage += " no types were returned";
 346
 347                 return false;
 348             }
 349
 350
 351         } catch ( Exception e) {
 352             //e.printStackTrace();
 353             validationMessage += "<br/>---<br/> contacting " + url+ "types <br/>";
 354
 355             Throwable cause = e.getCause();
 356             if ( cause != null)
 357                 validationMessage += cause.toString();
 358             else
 359                 validationMessage += e.toString();
 360         }
 361         return false;
 362     }
 363
 364
 365     private boolean validateFeatures(String url, String testcode){
 366         try {
 367             URL u = new URL(url+"features?segment="+testcode);
 368             InputStream dasInStream = open(u);
 369             XMLReader xmlreader = getXMLReader();
 370
 371             DAS_Feature_Handler cont_handle = new DAS_Feature_Handler() ;
 372             cont_handle.setDASCommand(url.toString());
 373             xmlreader.setContentHandler(cont_handle);
 374             xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
 375             InputSource insource = new InputSource() ;
 376             insource.setByteStream(dasInStream);
 377             xmlreader.parse(insource);
 378             List features = cont_handle.get_features();
 379             if ( features.size() > 0 ) {
 380                 return true;
 381             } else {
 382                 validationMessage  +="<br/>---<br/> contacting " + url+"features?segment="+testcode + "<br/>";
 383                 validationMessage += " no features were returned";
 384
 385                 return false;
 386             }
 387
 388         } catch ( Exception e) {
 389             //e.printStackTrace();
 390             validationMessage += "<br/>---<br/> contacting " + url+"features?segment="+testcode + "<br/>";
 391
 392             Throwable cause = e.getCause();
 393             if ( cause != null)
 394                 validationMessage += cause.toString();
 395             else
 396                 validationMessage += e.toString();
 397         }
 398         return false;
 399     }
 400      private boolean validateSequence(String url, String testcode) {
 401         URL dasUrl;
 402         String cmd = url+"sequence?segment="+testcode;
 403         try {
 404             dasUrl = new URL(cmd);
 405
 406         } catch ( Exception e) {
 407             e.printStackTrace();
 408             return false;
 409         }
 410         try {
 411             InputStream dasInStream =open(dasUrl);
 412             SAXParserFactory spfactory =
 413                 SAXParserFactory.newInstance();
 414             spfactory.setValidating(true);
 415
 416             SAXParser saxParser = null ;
 417
 418             try{
 419                 saxParser =
 420                     spfactory.newSAXParser();
 421             } catch (ParserConfigurationException e) {
 422                 e.printStackTrace();
 423             }
 424             XMLReader xmlreader = saxParser.getXMLReader();
 425
 426             try {
 427                 xmlreader.setFeature("http://xml.org/sax/features/validation", VALIDATION);
 428             } catch (SAXException e) {
 429                 e.printStackTrace();
 430             }
 431             try {
 432                 xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",VALIDATION);
 433             } catch (SAXNotRecognizedException e){
 434                 e.printStackTrace();
 435             }
 436
 437             DAS_Sequence_Handler cont_handle = new DAS_Sequence_Handler() ;
 438             xmlreader.setContentHandler(cont_handle);
 439             xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
 440             InputSource insource = new InputSource() ;
 441             insource.setByteStream(dasInStream);
 442             xmlreader.parse(insource);
 443             String sequence = cont_handle.get_sequence();
 444             if ( ( sequence==null) || (sequence.equals(""))) {
 445                 validationMessage += "---<br/>contacting " + cmd +"<br/>";
 446                 validationMessage += "no sequence found";
 447                 return false;
 448             }
 449             return true;
 450         } catch (Exception e) {
 451             validationMessage += "---<br/>contacting " + cmd +"<br/>";
 452
 453             Throwable cause = e.getCause();
 454             if ( cause != null)
 455                 validationMessage += cause.toString();
 456             else
 457                 validationMessage += e.toString();
 458             //e.printStackTrace();
 459         }
 460         return false;
 461     }
 462
 463     private XMLReader getXMLReader() throws SAXException{
 464         SAXParserFactory spfactory =
 465             SAXParserFactory.newInstance();
 466
 467         spfactory.setValidating(false) ;
 468         SAXParser saxParser = null ;
 469
 470         try{
 471             saxParser =
 472                 spfactory.newSAXParser();
 473         } catch (ParserConfigurationException e) {
 474             e.printStackTrace();
 475         }
 476
 477         XMLReader xmlreader = saxParser.getXMLReader();
 478         boolean validation = VALIDATION;
 479         //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
 480         try {
 481             xmlreader.setFeature("http://xml.org/sax/features/validation", validation);
 482         } catch (SAXException e) {
 483             e.printStackTrace();
 484         }
 485
 486         try {
 487             xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation);
 488         } catch (SAXNotRecognizedException e){
 489             e.printStackTrace();
 490         }
 491         return xmlreader;
 492
 493     }
 494
 495
 496
 497     private InputStream open(URL url) throws Exception{
 498
 499         // TODO Auto-generated method stub
 500
 501         InputStream inStream = null;
 502
 503         HttpURLConnection huc = null;
 504         huc = (HttpURLConnection) url.openConnection();
 505         //String contentEncoding = huc.getContentEncoding();
 506         inStream = huc.getInputStream();
 507         return inStream;
 508     }
 509
 510
 511
 512
 513
 514 }