package uk.ac.vamsas.client.simpleclient;

import java.io.BufferedInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Vector;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.client.VorbaIdFactory;
import uk.ac.vamsas.client.VorbaXmlBinder;
import uk.ac.vamsas.objects.core.VAMSAS;
import uk.ac.vamsas.objects.core.VamsasDocument;
import uk.ac.vamsas.objects.utils.AppDataReference;
import uk.ac.vamsas.objects.utils.DocumentStuff;
import uk.ac.vamsas.objects.utils.ProvenanceStuff;
import uk.ac.vamsas.objects.utils.document.VersionEntries;

/**
 * Base class for SimpleClient Vamsas Document Object Manipulation
 * holds static vamsasDocument from XML routines and
 * state objects for a particular unmarshalled Document instance.
 * @author jimp
 */
  

public class SimpleDocBinding {

  protected VorbaIdFactory vorba;
  protected static Log log = LogFactory.getLog(SimpleDocBinding.class);

  /**
   * @return Returns the vorba.
   */
  public VorbaIdFactory getVorba() {
    return vorba;
  }

  /**
   * @param vorba The vorba to set.
   */
  public void setVorba(VorbaIdFactory vorba) {
    this.vorba = vorba;
  }

  /**
   * Uses VorbaXmlBinder to retrieve the VamsasDocument from the given stream
   */
  public VamsasDocument getVamsasDocument(VamsasArchiveReader oReader) throws IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
    if (oReader!=null) {
      // check the factory
      if (vorba==null) {
        log.error("Invalid SimpleDocument construction - no VorbaIdFactory defined!");
        return null;
      }
  
      if (oReader.isValid()) {
        // Read vamsasDocument.xsd instance
        InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
        Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vdoc, vorba, new VamsasDocument());
        if (unmarsh==null)
          log.fatal("Couldn't unmarshall document!");
        
        Vobject vobjs = (Vobject) unmarsh[0];
        if (vobjs!=null) { 
          VamsasDocument doc=(VamsasDocument) vobjs;
          if (doc!=null)
            return doc;
        }
        log.debug("Found no VamsasDocument object in properly formatted Vamsas Archive.");
      } else {        
        // deprecated data handler (vamsas.xsd instance)
        InputStream vxmlis = oReader.getVamsasXmlStream();
        if (vxmlis!=null) { // Might be an old vamsas file.
          BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
          InputStreamReader vxml = new InputStreamReader(ixml);
          Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vxml, vorba, new VAMSAS());
          
          if (unmarsh==null)
            log.fatal("Couldn't unmarshall document!");
          
          VAMSAS root[]= new VAMSAS[] { null};
          root[0] = (VAMSAS) unmarsh[0]; 
          
          if (root[0]==null) {
            log.debug("Found no VAMSAS object in VamsasXML stream.");
          } else {
            log.debug("Making new VamsasDocument from VamsasXML stream.");
            VamsasDocument doc = DocumentStuff.newVamsasDocument(root, 
                ProvenanceStuff.newProvenance(
                    vorba.getUserHandle().getFullName(), 
                    "Vamsas Document constructed from vamsas.xml"), VersionEntries.ALPHA_VERSION);
            // VAMSAS: decide on 'system' operations provenance form
            // LATER: implement classes for translating Vorba properties into provenance user fields.
            // VAMSAS: decide on machine readable info embedding in provenance should be done
            root[0]=null;
            root=null;
            return doc;
          }
        }
      }
    }
    // otherwise - there was no valid original document to read.
    return null;    
  }

  /**
   * Extract all jarEntries in an archive referenced by the vamsas document
   * LATER: a family of methods for finding extraneous jarEntries , and invalid appDataReferences
   * @param doc
   * @param oReader
   * @return array of the subset of JarEntry names that are referenced in doc 
   */
  public Vector getReferencedEntries(VamsasDocument doc, VamsasArchiveReader oReader) {
    if (oReader==null)
     return null;
    if (doc==null) {
     try { doc = getVamsasDocument(oReader); } 
     catch (Exception e) { log.warn("Failed to get document from "+oReader.jfileName); };
    }
    Vector docrefs = AppDataReference.getAppDataReferences(doc);
    if (docrefs==null)
      return null;
    Vector entries = oReader.getExtraEntries();
    if (entries!=null && entries.size()>0 && docrefs.size()>0) {
      int i=0, j=entries.size();
      do {
        if (!docrefs.contains(entries.get(i))) {
            entries.remove(i);
            j--;
        } else
          i++;
      } while (i<j);
    }
    return entries;
  }
}