--- /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