+++ /dev/null
-/* BioJava development code
- *
- * This code may be freely distributed and modified under the
- * terms of the GNU Lesser General Public Licence. This should
- * be distributed with the code. If you do not have a copy,
- * see:
- *
- * http://www.gnu.org/copyleft/lesser.html
- *
- * Copyright for this code is held jointly by the individual
- * authors. These should be listed in @author doc comments.
- *
- * For more information on the BioJava project and its aims,
- * or to join the biojava-l mailing list, visit the home page
- * at:
- *
- * http://www.biojava.org/
- *
- * Created on 30.08.2005
- * @author Andreas Prlic
- *
- */
-
-
-package org.biojava.dasobert.dasregistry ;
-
-//import org.biojava.services.das.*;
-//xml stuff
-import org.xml.sax.*;
-import javax.xml.parsers.*;
-import java.util.ArrayList ;
-import java.util.Map ;
-import java.util.List ;
-import java.io.InputStream ;
-
-import java.net.URL ;
-
-
-//for validation add dependency on SPICE... :-/
-import java.net.HttpURLConnection;
-import org.biojava.dasobert.das.*;
-import org.biojava.dasobert.das.DAS_Entry_Points_Handler;
-import org.biojava.dasobert.das.DAS_Types_Handler;
-
-
-
-public class Das1Validator {
-
- public final static String[] DAS_CAPABILITIES = {
- "sequence",
- "structure",
- "alignment",
- "types",
- "features",
- "entry_points",
- "dna",
- "stylesheet"
- } ;
-
-
- //private final static String DATASOURCE_NAME = "jdbc/mysql";
- String validationMessage;
-
- public boolean VALIDATION = false; // DTD validation ..
-
- List all_capabilities;
- public Das1Validator() {
- validationMessage = "" ;
- all_capabilities = new ArrayList();
- for ( int i = 0 ; i< DAS_CAPABILITIES.length; i++ ) {
- all_capabilities.add(DAS_CAPABILITIES[i]);
- }
- }
-
- /** return which errors have been produced during validation... */
- public String getValidationMessage(){
- return validationMessage;
- }
-
-
-
- public String[] validate(String url, DasCoordinateSystem[] coords, String[] capabilities){
- validationMessage="";
- // a list containing all valid DAS requests ...
-
- List lst =new ArrayList();
-
- char lastChar = url.charAt(url.length()-1);
- if ( lastChar != '/')
- url += "/";
-
- validateURL(url);
-
-
- // test if all specified capabilities really work
- for ( int c = 0 ; c < capabilities.length ; c++) {
- String capability = capabilities[c];
- if ( all_capabilities.contains(capability)) {
- //System.out.println("testing " + capability);
-
- if ( capability.equals("sequence")) {
- for ( int i=0;i< coords.length;i++){
- DasCoordinateSystem ds =coords[i];
- String testcode = ds.getTestCode();
-
- // do a DAS sequence retreive
- if ( validateSequence(url,testcode) )
- lst.add(capability);
-
- }
-
- }
- else if ( capability.equals("structure")) {
-
- }
- else if ( capability.equals("features")){
- for ( int i=0;i< coords.length;i++){
- DasCoordinateSystem ds =coords[i];
- String testcode = ds.getTestCode();
-
-
- if ( validateFeatures(url,testcode))
- lst.add(capability);
-
- }
- }
- else if ( capability.equals("alignment")){
-
- } else if ( capability.equals("types")){
- if ( validateTypes(url))
- lst.add(capability);
- //else
- // error =true ;
-
- } else if ( capability.equals("entry_points")) {
- if ( validateEntry_Points(url))
- lst.add(capability);
- //else
- // error = true;
- } else if ( capability.equals("stylesheet")) {
- if ( validateStylesheet(url))
- lst.add(capability);
- //} else
- // error = true;
- } else if ( capability.equals("dna")){
- for ( int i=0;i< coords.length;i++){
- DasCoordinateSystem ds =coords[i];
- String testcode = ds.getTestCode();
-
- if ( validateDNA(url,testcode))
- lst.add(capability);
- }
- }
- else {
- validationMessage += "<br/>---<br/> test of capability " + capability + " not implemented,yet.";
- lst.add(capability);
- }
- }
- }
-
- //if ( error) {
- // System.out.println("DasValidator: "+ validationMessage);
- //}
- //this.validationMessage = validationMessage;
- return (String[])lst.toArray(new String[lst.size()]);
-
- }
-
- /** make sure the URL matches the DAS spec
- returns true if URL looks o.k...
- */
- public boolean validateURL(String url) {
- String[] spl = url.split("/");
-
- //for (int i = 0 ; i < spl.length ; i++ ) {
- // System.out.println("spl["+i+"]:"+spl[i]);
- //}
-
- if (spl == null ) {
- validationMessage +="---<br/> URL is not well formed" ;
- return false;
- }
-
- if ( spl.length <= 4) {
- validationMessage +="---<br/> URL is not well formed <br/>" +
- "should be http[s]://site.specific.prefix/das/dassourcename/";
- return false;
- }
-
- //System.out.println("split 0 : " + spl[0]);
- if ( ! (spl[0].equals("http:"))) {
- if ( ! ( spl[0].equals("https:"))){
- validationMessage +="---<br/> URL is not well formed (does not start with http:// or https://)" ;
- return false;
- }
-
- }
-
- String dastxt = spl[spl.length-2] ;
- //System.out.println("should be >das< " + dastxt);
- if ( ! dastxt.equals("das")) {
- String suggestion = spl[0] + "//" ;
- String wrong = spl[0] + "//" ;
- for (int i = 2 ; i < spl.length -2 ; i++ ) {
- suggestion += spl[i] + "/" ;
- wrong += spl[i] + "/" ;
- }
- suggestion +="<b>das</b>/"+spl[spl.length-1];
- wrong +="<b>" + spl[spl.length-2] + "</b>/"+spl[spl.length-1];
- validationMessage +="--<br/> the URL does not match the DAS spec. it should be <br/>"+
- " http[s]://site.specific.prefix/das/dassourcename/ <br/>" +
- " found >" + dastxt +" < instead of >das< <br/>" +
- " suggested url: " + suggestion + "<br/>"+
- " instead of: " + wrong ;
- return false;
- }
- return true;
-
- }
-
- private boolean validateDNA(String url, String testcode){
- try {
- String cmd = url+"dna?segment="+testcode;
- URL strurl = new URL(cmd);
- InputStream dasInStream = open(strurl);
-
- XMLReader xmlreader = getXMLReader();
-
- DAS_DNA_Handler cont_handle = new DAS_DNA_Handler() ;
-
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource() ;
-
- insource.setByteStream(dasInStream);
- xmlreader.parse(insource);
- String sequence = cont_handle.get_sequence();
- if ( sequence.length() > 0 ) {
- return true;
- } else {
- validationMessage +="<br/>---<br/> contacting " + cmd + "<br/>";
- validationMessage += " no sequence was returned";
-
- return false;
- }
-
-
- } catch ( Exception e) {
- //e.printStackTrace();
- validationMessage += "<br/>---<br/> contacting " + url + "dna?segment="+testcode + "<br/>";
-
- Throwable cause = e.getCause();
- if ( cause != null)
- validationMessage += cause.toString();
- else
- validationMessage += e.toString();
- }
- return false;
-
- }
-
- private boolean validateStylesheet(String url) {
- try {
- DAS_StylesheetRetrieve dsr = new DAS_StylesheetRetrieve();
- URL styleurl = new URL(url+"stylesheet");
-
- Map[] stylesheet = dsr.retrieve(styleurl);
- if (( stylesheet != null ) && ( stylesheet.length > 0))
- return true;
- else {
- validationMessage +="<br/>---<br/> contacting " + url + "stylesheet<br/>";
- validationMessage += " no stylesheet was returned";
- return false;
- }
- } catch (Exception e) {
- validationMessage += "<br/>---<br/> contacting " + url+"stylesheet <br/>";
-
- Throwable cause = e.getCause();
- if ( cause != null)
- validationMessage += cause.toString();
- else
- validationMessage += e.toString();
- }
- return false;
- }
-
-
- private boolean validateEntry_Points(String url){
- try {
- URL u = new URL(url+"entry_points");
-
- InputStream dasInStream = open(u);
-
- XMLReader xmlreader = getXMLReader();
-
- DAS_Entry_Points_Handler cont_handle = new DAS_Entry_Points_Handler() ;
-
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource() ;
- insource.setByteStream(dasInStream);
- xmlreader.parse(insource);
- String version = cont_handle.getVersion();
- if ( version != null ) {
- return true;
- } else {
- validationMessage +="<br/>---<br/> contacting " + url +"entry_points <br/>";
- validationMessage += " no version was returned";
-
- return false;
- }
-
-
- } catch ( Exception e) {
- //e.printStackTrace();
- validationMessage += "<br/>---<br/> contacting " + url+ "types <br/>";
-
- Throwable cause = e.getCause();
- if ( cause != null)
- validationMessage += cause.toString();
- else
- validationMessage += e.toString();
- }
- return false;
- }
-
- private boolean validateTypes(String url){
- try {
- URL u = new URL(url+"types");
- InputStream dasInStream = open(u);
- XMLReader xmlreader = getXMLReader();
-
- DAS_Types_Handler cont_handle = new DAS_Types_Handler() ;
-
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource() ;
- insource.setByteStream(dasInStream);
- xmlreader.parse(insource);
- String[] types = cont_handle.getTypes();
- if ( types.length > 0 ) {
- return true;
- } else {
- validationMessage +="<br/>---<br/> contacting " + url +"types <br/>";
- validationMessage += " no types were returned";
-
- return false;
- }
-
-
- } catch ( Exception e) {
- //e.printStackTrace();
- validationMessage += "<br/>---<br/> contacting " + url+ "types <br/>";
-
- Throwable cause = e.getCause();
- if ( cause != null)
- validationMessage += cause.toString();
- else
- validationMessage += e.toString();
- }
- return false;
- }
-
-
- private boolean validateFeatures(String url, String testcode){
- try {
- URL u = new URL(url+"features?segment="+testcode);
- InputStream dasInStream = open(u);
- XMLReader xmlreader = getXMLReader();
-
- DAS_Feature_Handler cont_handle = new DAS_Feature_Handler() ;
- cont_handle.setDASCommand(url.toString());
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource() ;
- insource.setByteStream(dasInStream);
- xmlreader.parse(insource);
- List features = cont_handle.get_features();
- if ( features.size() > 0 ) {
- return true;
- } else {
- validationMessage +="<br/>---<br/> contacting " + url+"features?segment="+testcode + "<br/>";
- validationMessage += " no features were returned";
-
- return false;
- }
-
- } catch ( Exception e) {
- //e.printStackTrace();
- validationMessage += "<br/>---<br/> contacting " + url+"features?segment="+testcode + "<br/>";
-
- Throwable cause = e.getCause();
- if ( cause != null)
- validationMessage += cause.toString();
- else
- validationMessage += e.toString();
- }
- return false;
- }
- private boolean validateSequence(String url, String testcode) {
- URL dasUrl;
- String cmd = url+"sequence?segment="+testcode;
- try {
- dasUrl = new URL(cmd);
-
- } catch ( Exception e) {
- e.printStackTrace();
- return false;
- }
- try {
- InputStream dasInStream =open(dasUrl);
- SAXParserFactory spfactory =
- SAXParserFactory.newInstance();
- spfactory.setValidating(true);
-
- SAXParser saxParser = null ;
-
- try{
- saxParser =
- spfactory.newSAXParser();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
- XMLReader xmlreader = saxParser.getXMLReader();
-
- try {
- xmlreader.setFeature("http://xml.org/sax/features/validation", VALIDATION);
- } catch (SAXException e) {
- e.printStackTrace();
- }
- try {
- xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",VALIDATION);
- } catch (SAXNotRecognizedException e){
- e.printStackTrace();
- }
-
- DAS_Sequence_Handler cont_handle = new DAS_Sequence_Handler() ;
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource() ;
- insource.setByteStream(dasInStream);
- xmlreader.parse(insource);
- String sequence = cont_handle.get_sequence();
- if ( ( sequence==null) || (sequence.equals(""))) {
- validationMessage += "---<br/>contacting " + cmd +"<br/>";
- validationMessage += "no sequence found";
- return false;
- }
- return true;
- } catch (Exception e) {
- validationMessage += "---<br/>contacting " + cmd +"<br/>";
-
- Throwable cause = e.getCause();
- if ( cause != null)
- validationMessage += cause.toString();
- else
- validationMessage += e.toString();
- //e.printStackTrace();
- }
- return false;
- }
-
- private XMLReader getXMLReader() throws SAXException{
- SAXParserFactory spfactory =
- SAXParserFactory.newInstance();
-
- spfactory.setValidating(false) ;
- SAXParser saxParser = null ;
-
- try{
- saxParser =
- spfactory.newSAXParser();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
-
- XMLReader xmlreader = saxParser.getXMLReader();
- boolean validation = VALIDATION;
- //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
- try {
- xmlreader.setFeature("http://xml.org/sax/features/validation", validation);
- } catch (SAXException e) {
- e.printStackTrace();
- }
-
- try {
- xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation);
- } catch (SAXNotRecognizedException e){
- e.printStackTrace();
- }
- return xmlreader;
-
- }
-
-
-
- private InputStream open(URL url) throws Exception{
-
- // TODO Auto-generated method stub
-
- InputStream inStream = null;
-
- HttpURLConnection huc = null;
- huc = (HttpURLConnection) url.openConnection();
- //String contentEncoding = huc.getContentEncoding();
- inStream = huc.getInputStream();
- return inStream;
- }
-
-
-
-
-
-}
git://source.jalview.org / jalview.git / blobdiff