/*                    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;
    }





}