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Revision 9352

Added by Lauren Walker about 9 years ago

Update the packageId attribute in EML documents on update. Never display the local docid in the rendered EML.

View differences:

src/edu/ucsb/nceas/metacat/dataone/D1NodeService.java
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package edu.ucsb.nceas.metacat.dataone;


  		




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import java.io.ByteArrayInputStream;


  		




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import java.io.ByteArrayOutputStream;


  		




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import java.io.File;


  		




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import java.io.FileNotFoundException;


  		




  ......




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import java.io.InputStream;


  		




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import java.io.OutputStream;


  		




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import java.io.OutputStreamWriter;


  		




  
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import java.io.StringReader;


  		




  
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import java.io.UnsupportedEncodingException;


  		




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import java.io.Writer;


  		




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import java.math.BigInteger;


  		




  
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import java.nio.charset.Charset;


  		




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import java.sql.PreparedStatement;


  		




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import java.sql.ResultSet;


  		




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import java.sql.SQLException;


  		




  ......




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import java.util.Vector;


  		




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import java.util.concurrent.locks.Lock;


  		




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import javax.xml.transform.Result;


  		




  
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import javax.xml.transform.Source;


  		




  
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import javax.xml.transform.TransformerException;


  		




  
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import javax.xml.transform.TransformerFactory;


  		




  
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import javax.xml.transform.dom.DOMSource;


  		




  
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import javax.xml.transform.stream.StreamResult;


  		




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import javax.servlet.http.HttpServletRequest;


  		




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import org.apache.commons.io.IOUtils;


  		




  ......




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import org.dataone.service.types.v1.util.AuthUtils;


  		




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import org.dataone.service.types.v1.util.ChecksumUtil;


  		




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import org.dataone.service.util.Constants;


  		




  
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import org.w3c.dom.Document;


  		




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import edu.ucsb.nceas.metacat.AccessionNumber;


  		




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import edu.ucsb.nceas.metacat.AccessionNumberException;


  		




  ......




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import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler;


  		




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import edu.ucsb.nceas.metacat.util.SkinUtil;


  		




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import edu.ucsb.nceas.utilities.PropertyNotFoundException;


  		




  
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import edu.ucsb.nceas.utilities.XMLUtilities;


  		




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public abstract class D1NodeService {


  		




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  public static final String DELETEDMESSAGE = "The object with the PID has been deleted from the node.";


  		




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  private static String XPATH_EML_ID = "/eml:eml/@packageId";


  		




  
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  private static Logger logMetacat = Logger.getLogger(D1NodeService.class);


  		




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  /** For logging the operations */


  		




  ......




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      return objectList;


  		




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  }


  		




  
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  /**


  		




  
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   * Update a science metadata document with its new Identifier  


  		




  
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   * 


  		




  
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   * @param session - the Session object containing the credentials for the Subject


  		




  
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   * @param object - the InputStream for the XML object to be edited


  		




  
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   * @param pid - the Identifier of the XML object to be updated


  		




  
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   * @param newPid = the new Identifier to give to the modified XML doc


  		




  
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   * 


  		




  
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   * @return newObject - The InputStream for the modified XML object


  		




  
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   * 


  		




  
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   * @throws ServiceFailure


  		




  
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   * @throws IOException


  		




  
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   * @throws UnsupportedEncodingException


  		




  
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   * @throws InvalidToken


  		




  
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   * @throws NotAuthorized


  		




  
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   * @throws NotFound


  		




  
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   * @throws NotImplemented


  		




  
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   */


  		




  
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  public InputStream editScienceMetadata(Session session, InputStream object, Identifier pid, Identifier newPid)


  		




  
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  	throws ServiceFailure, IOException, UnsupportedEncodingException, InvalidToken, NotAuthorized, NotFound, NotImplemented {


  		




  
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	logMetacat.debug("D1NodeService.editScienceMetadata() called.");


  		




  
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	 InputStream newObject = null;


  		




  
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    try{   	


  		




  
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    	//Get the root node of the XML document


  		




  
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    	byte[] xmlBytes  = IOUtils.toByteArray(object);


  		




  
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        String xmlStr = new String(xmlBytes, "UTF-8");


  		




  
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    	Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new StringReader(xmlStr));


  		




  
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	    org.w3c.dom.Node docNode = doc.getDocumentElement();


  		




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	    //Get the system metadata for this object


  		




  
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	    SystemMetadata sysMeta = null;


  		




  
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	    try{


  		




  
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	    	sysMeta = getSystemMetadata(session, pid);


  		




  
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	    } catch(NotAuthorized e){


  		




  
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	    	throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " + 


  		




  
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	    			"This session is not authorized to access the system metadata for " +


  		




  
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	    			pid.getValue() + " : " + e.getMessage());


  		




  
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	    } catch(NotFound e){


  		




  
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	    	throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " + 


  		




  
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	    			"Could not find the system metadata for " +


  		




  
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	    			pid.getValue() + " : " + e.getMessage());


  		




  
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	    }


  		




  
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	    //Get the formatId


  		




  
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        ObjectFormatIdentifier objFormatId = sysMeta.getFormatId();


  		




  
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        String formatId = objFormatId.getValue();


  		




  
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    	//For all EML formats


  		




  
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        if(formatId.indexOf("eml") == 0){


  		




  
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        	//Update or add the id attribute


  		




  
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    	    XMLUtilities.addAttributeNodeToDOMTree(docNode, XPATH_EML_ID, newPid.getValue());


  		




  
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        }


  		




  
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        //The modified object InputStream


  		




  
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	    ByteArrayOutputStream outputStream = new ByteArrayOutputStream();


  		




  
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	    Source xmlSource = new DOMSource(docNode);


  		




  
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	    Result outputTarget = new StreamResult(outputStream);


  		




  
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	    TransformerFactory.newInstance().newTransformer().transform(xmlSource, outputTarget);


  		




  
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	    newObject = new ByteArrayInputStream(outputStream.toByteArray());


  		




  
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    } catch(TransformerException e) {


  		




  
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    	throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +


  		




  
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                "Could not update the ID in the XML document for " +


  		




  
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                "pid " + pid.getValue() +" : " + e.getMessage());


  		




  
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    }


  		




  
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    return newObject;


  		




  
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  }


  		




  
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  /**


  		




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   * Update a systemMetadata document


  		




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   * 


  		












  

    
      src/edu/ucsb/nceas/metacat/dataone/MNodeService.java
    
  





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import java.io.Writer;


  		




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import java.math.BigInteger;


  		




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import java.net.URISyntaxException;


  		




  
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import java.nio.charset.Charset;


  		




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import java.security.NoSuchAlgorithmException;


  		




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import java.sql.SQLException;


  		




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import java.util.ArrayList;


  		




  ......




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                //String objectAsXML = "";


  		




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                try {


  		




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                    //objectAsXML = IOUtils.toString(object, "UTF-8");


  		




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                    // give the old pid so we can calculate the new local id 


  		




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                    localId = insertOrUpdateDocument(object, "UTF-8", pid, session, "update");


  		




  
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                	InputStream editedObject = editScienceMetadata(session, object, pid, newPid);


  		




  
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                    localId = insertOrUpdateDocument(editedObject, "UTF-8", pid, session, "update");


  		




  
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                    // register the newPid and the generated localId


  		




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                    if (newPid != null) {


  		




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                        IdentifierManager.getInstance().createMapping(newPid.getValue(), localId);


  		




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                    }


  		




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                } catch (IOException e) {


  		












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