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Revision 5958

Added by Chris Jones almost 14 years ago

To support generation of SystemMetadata and GUIDs, added a number of methods to MetacatHandler that are also in CrudService(). CrudService should eventually be refactored to use the handler methods. Added:
readFromFilesystem() - Read a file from Metacat's configured file system data directory, and return a FileInputStream. This code has been factored out of handleInsertOrUpdateAction().
Also updated the imports list to support new methods.

View differences:

src/edu/ucsb/nceas/metacat/MetacatHandler.java
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package edu.ucsb.nceas.metacat;


  		




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import au.com.bytecode.opencsv.CSVWriter;


  		




  
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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.IdentifierManager;


  		




  
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlException;


  		




  
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile;


  		




  
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlInterface;


  		




  
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlList;


  		




  
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import edu.ucsb.nceas.metacat.cart.CartManager;


  		




  
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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;


  		




  
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import edu.ucsb.nceas.metacat.database.DBConnection;


  		




  
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import edu.ucsb.nceas.metacat.database.DBConnectionPool;


  		




  
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import edu.ucsb.nceas.metacat.dataquery.DataQuery;


  		




  
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import edu.ucsb.nceas.metacat.properties.PropertyService;


  		




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


  		




  
  43
  
    
import edu.ucsb.nceas.metacat.service.SessionService;


  		




  
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import edu.ucsb.nceas.metacat.service.XMLSchemaService;


  		




  
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import edu.ucsb.nceas.metacat.shared.HandlerException;


  		




  
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import edu.ucsb.nceas.metacat.shared.MetacatUtilException;


  		




  
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import edu.ucsb.nceas.metacat.shared.ServiceException;


  		




  
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import edu.ucsb.nceas.metacat.spatial.SpatialHarvester;


  		




  
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import edu.ucsb.nceas.metacat.spatial.SpatialQuery;


  		




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


  		




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


  		




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


  		




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


  		




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


  		




  
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import edu.ucsb.nceas.utilities.FileUtil;


  		




  
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import edu.ucsb.nceas.utilities.LSIDUtil;


  		




  
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import edu.ucsb.nceas.utilities.ParseLSIDException;


  		




  
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;


  		




  
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import java.io.BufferedInputStream;


  		




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import java.io.ByteArrayInputStream;


  		




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import java.io.File;


  		




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import java.io.FileInputStream;


  		




  
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import java.io.FileOutputStream;


  		




  
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import java.io.FileNotFoundException;


  		




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import java.io.IOException;


  		




  
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import java.io.InputStream;


  		




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import java.io.InputStreamReader;


  		




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import java.io.OutputStream;


  		




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import java.io.OutputStreamWriter;


  		




  ......




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import java.io.Writer;


  		




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import java.net.MalformedURLException;


  		




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import java.net.URL;


  		




  
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import java.security.NoSuchAlgorithmException;


  		




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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.sql.Timestamp;


  		




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import java.text.ParseException;


  		




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import java.text.SimpleDateFormat;


  		




  
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import java.util.Date;


  		




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import java.util.Enumeration;


  		




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import java.util.HashMap;


  		




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import java.util.Hashtable;


  		




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import java.util.Iterator;


  		




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import java.util.Map;


  		




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import java.util.Timer;


  		




  
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import java.util.TimerTask;


  		




  
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import java.util.TimeZone;


  		




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import java.util.Vector;


  		




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import java.util.zip.ZipEntry;


  		




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import java.util.zip.ZipOutputStream;


  		




  ......




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import javax.servlet.http.HttpSession;


  		




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import javax.activation.MimetypesFileTypeMap;


  		




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import javax.xml.parsers.ParserConfigurationException;


  		




  
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import javax.xml.xpath.XPathExpressionException;


  		




  
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import org.apache.commons.io.input.XmlStreamReader;


  		




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import org.apache.log4j.Logger;


  		




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import org.ecoinformatics.eml.EMLParser;


  		




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import au.com.bytecode.opencsv.CSVWriter;


  		




  
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import org.dataone.eml.DataoneEMLParser;


  		




  
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import org.dataone.eml.EMLDocument;


  		




  
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import org.dataone.eml.EMLDocument.DistributionMetadata;


  		




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import org.dataone.service.exceptions.NotFound;


  		




  
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import org.dataone.service.types.NodeReference;


  		




  
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import org.dataone.service.types.util.ServiceTypeUtil;


  		




  
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import org.jibx.runtime.BindingDirectory;


  		




  
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import org.jibx.runtime.IBindingFactory;


  		




  
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import org.jibx.runtime.IMarshallingContext;


  		




  
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import org.jibx.runtime.IUnmarshallingContext;


  		




  
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import org.jibx.runtime.JiBXException;


  		




  
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import org.xml.sax.SAXException;


  		




  
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import com.oreilly.servlet.multipart.FilePart;


  		




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import com.oreilly.servlet.multipart.MultipartParser;


  		




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import com.oreilly.servlet.multipart.ParamPart;


  		




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import com.oreilly.servlet.multipart.Part;


  		




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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlException;


  		




  77
  
  
    
import edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile;


  		




  78
  
  
    
import edu.ucsb.nceas.metacat.accesscontrol.AccessControlInterface;


  		




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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlList;


  		




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import edu.ucsb.nceas.metacat.cart.CartManager;


  		




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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;


  		




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import edu.ucsb.nceas.metacat.database.DBConnection;


  		




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import edu.ucsb.nceas.metacat.database.DBConnectionPool;


  		




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import edu.ucsb.nceas.metacat.dataquery.DataQuery;


  		




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import edu.ucsb.nceas.metacat.properties.PropertyService;


  		




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


  		




  87
  
  
    
import edu.ucsb.nceas.metacat.service.SessionService;


  		




  88
  
  
    
import edu.ucsb.nceas.metacat.service.XMLSchemaService;


  		




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import edu.ucsb.nceas.metacat.shared.HandlerException;


  		




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import edu.ucsb.nceas.metacat.shared.MetacatUtilException;


  		




  91
  
  
    
import edu.ucsb.nceas.metacat.shared.ServiceException;


  		




  92
  
  
    
import edu.ucsb.nceas.metacat.spatial.SpatialHarvester;


  		




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import edu.ucsb.nceas.metacat.spatial.SpatialQuery;


  		




  94
  
  
    
import edu.ucsb.nceas.metacat.util.AuthUtil;


  		




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


  		




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


  		




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


  		




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


  		




  99
  
  
    
import edu.ucsb.nceas.utilities.FileUtil;


  		




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import edu.ucsb.nceas.utilities.LSIDUtil;


  		




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import edu.ucsb.nceas.utilities.ParseLSIDException;


  		




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import edu.ucsb.nceas.utilities.PropertyNotFoundException;


  		




  
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import org.dataone.service.types.AuthToken;


  		




  
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import org.dataone.service.types.Checksum;


  		




  
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import org.dataone.service.types.ChecksumAlgorithm;


  		




  
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import org.dataone.service.types.Identifier;


  		




  
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import org.dataone.service.types.ObjectFormat;


  		




  
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import org.dataone.service.types.Principal;


  		




  
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import org.dataone.service.types.SystemMetadata;


  		




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import org.dataone.service.exceptions.BaseException;


  		




  
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/**


  		




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 * General entry point for the Metacat server which is called from various 


  		




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 * mechanisms such as the standard MetacatServlet class and the various web


  		




  ......




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        //System.out.println("response from MetacatHandler.setAccess: " + resp);


  		




  967
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    }


  		




  968
  1008
  
    
    


  		




  
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    /**


  		




  
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     * Read a file from Metacat's configured file system data directory.


  		




  
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     *


  		




  
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     * @param filename  The full path file name of the file to read


  		




  
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     * 


  		




  
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     * @return fileInputStream  The file to read as a FileInputStream


  		




  
  1015
  
    
     */


  		




  
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    private FileInputStream readFromFilesystem(String filename) 


  		




  
  1017
  
    
      throws FileNotFoundException {


  		




  
  1018
  
    
        


  		




  
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        logMetacat.debug("MetacatHandler.readFromFilesystem() called.");


  		




  
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        FileInputStream fileInputStream = null;


  		




  
  1022
  
    
        


  		




  
  1023
  
    
        try {


  		




  
  1024
  
    
          fileInputStream = new FileInputStream(filename);


  		




  
  1025
  
    

  		




  
  1026
  
    
        } catch ( FileNotFoundException fnfe ) {


  		




  
  1027
  
    
          logMetacat.debug("There was an error reading the file " +


  		




  
  1028
  
    
                           filename + ". The error was: "         +


  		




  
  1029
  
    
                           fnfe.getMessage());


  		




  
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          throw fnfe;


  		




  
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        }


  		




  
  1033
  
    
        


  		




  
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      return fileInputStream;  


  		




  
  1035
  
    
    }


  		




  
  1036
  
    
    


  		




  969
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    /** read metadata or data from Metacat


  		




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     * @throws PropertyNotFoundException 


  		




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     * @throws ParseLSIDException 


  		












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