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Revision 6130

Added by ben leinfelder over 13 years ago

organize imports so that it is clearer what dependencies exist on the D1 jars

View differences:

test/edu/ucsb/nceas/metacat/dataone/MetadataTypeRegisterTest.java
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package edu.ucsb.nceas.metacat.dataone;


  		




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import edu.ucsb.nceas.MCTestCase;


  		




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import junit.framework.Test;


  		




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import junit.framework.TestSuite;


  		




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import org.dataone.client.ObjectFormatCache;


  		




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import org.dataone.service.exceptions.NotFound;


  		




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import org.dataone.service.types.*;


  		




  
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import org.dataone.service.types.ObjectFormat;


  		




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import edu.ucsb.nceas.MCTestCase;


  		




  
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/**


  		




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 * A JUnit test for testing the dataone MetadataTypeRegister class


  		




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 */


  		












  

    
      test/edu/ucsb/nceas/metacat/dataone/CNCoreTest.java
    
  





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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.NodeReference;


  		




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import org.dataone.service.types.ObjectFormat;


  		




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import org.dataone.service.types.Session;


  		




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import org.dataone.service.types.Subject;


  		




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import org.dataone.service.types.SystemMetadata;


  		












  

    
      src/edu/ucsb/nceas/metacat/restservice/ResourceHandler.java
    
  





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 */


  		




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package edu.ucsb.nceas.metacat.restservice;


  		




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import java.io.*;


  		




  
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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.IOException;


  		




  
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import java.io.InputStream;


  		




  
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import java.io.OutputStream;


  		




  
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import java.io.PrintWriter;


  		




  
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import java.io.StringReader;


  		




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import java.net.URL;


  		




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import java.util.*;


  		




  
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import java.text.DateFormat;


  		




  
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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.Hashtable;


  		




  
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import java.util.Iterator;


  		




  
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import java.util.List;


  		




  
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import java.util.Map;


  		




  
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import java.util.TimeZone;


  		




  
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import java.util.Timer;


  		




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import javax.mail.BodyPart;


  		




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import javax.mail.MessagingException;


  		




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import javax.mail.internet.MimeMultipart;


  		




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import javax.servlet.ServletContext;


  		




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import javax.servlet.http.HttpServletRequest;


  		




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import javax.servlet.http.HttpServletResponse;


  		




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import java.security.NoSuchAlgorithmException;


  		




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import java.sql.SQLException;


  		




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import java.text.DateFormat;


  		




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import java.text.ParseException;


  		




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import java.text.ParsePosition;


  		




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import java.text.SimpleDateFormat;


  		




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import org.apache.commons.io.IOUtils;


  		




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import org.apache.log4j.Logger;


  		




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import org.apache.maven.artifact.ant.shaded.IOUtil;


  		




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import org.dataone.service.exceptions.InvalidSystemMetadata;


  		




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import org.dataone.service.exceptions.InvalidToken;


  		




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import org.dataone.service.exceptions.NotAuthorized;


  		




  
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import org.dataone.service.exceptions.NotFound;


  		




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import org.dataone.service.exceptions.NotImplemented;


  		




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import org.dataone.service.exceptions.ServiceFailure;


  		




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import org.dataone.service.exceptions.UnsupportedType;


  		




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import org.dataone.service.exceptions.NotFound;


  		




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import org.dataone.service.types.*;


  		




  
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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.DescribeResponse;


  		




  
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import org.dataone.service.types.Event;


  		




  
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import org.dataone.service.types.Identifier;


  		




  
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import org.dataone.service.types.Log;


  		




  
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import org.dataone.service.types.Node;


  		




  
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import org.dataone.service.types.NodeList;


  		




  
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import org.dataone.service.types.NodeReference;


  		




  
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import org.dataone.service.types.NodeType;


  		




  
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import org.dataone.service.types.ObjectFormat;


  		




  
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import org.dataone.service.types.ObjectList;


  		




  
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import org.dataone.service.types.Service;


  		




  
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import org.dataone.service.types.ServiceMethod;


  		




  
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import org.dataone.service.types.Services;


  		




  
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import org.dataone.service.types.Session;


  		




  
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import org.dataone.service.types.SystemMetadata;


  		




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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 edu.ucsb.nceas.metacat.AccessionNumberException;


  		




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import edu.ucsb.nceas.metacat.DBUtil;


  		




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import edu.ucsb.nceas.metacat.IdentifierManager;


  		




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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;


  		




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import edu.ucsb.nceas.metacat.MetaCatServlet;


  		




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import edu.ucsb.nceas.metacat.MetacatHandler;


  		




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


  		




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import edu.ucsb.nceas.metacat.dataone.CNCoreImpl;


  		




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import edu.ucsb.nceas.metacat.dataone.CrudService;


  		




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import edu.ucsb.nceas.metacat.dataone.HealthService;


  		




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


  		




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


  		




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


  		




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


  		




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


  		




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


  		




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import edu.ucsb.nceas.utilities.PropertyNotFoundException;


  		




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import org.dataone.service.streaming.util.StreamUtil;


  		




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import com.gc.iotools.stream.is.InputStreamFromOutputStream;


  		




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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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/**


  		




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 * 


  		




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 * Implements Earthgrid REST API to Metacat <br/><br/> 


  		












  

    
      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.event.MetacatDocumentEvent;


  		




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import edu.ucsb.nceas.metacat.event.MetacatEventService;


  		




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


  		




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


  		




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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.ByteArrayOutputStream;


  		




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import java.io.File;


  		




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import java.io.FileInputStream;


  		




  
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import java.io.FileNotFoundException;


  		




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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.PrintWriter;


  		




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import java.io.Reader;


  		




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import java.io.StringReader;


  		




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import java.io.ByteArrayOutputStream;


  		




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import java.io.UnsupportedEncodingException;


  		




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import java.io.Writer;


  		




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import java.net.MalformedURLException;


  		




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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.TimeZone;


  		




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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.activation.MimetypesFileTypeMap;


  		




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import javax.servlet.ServletOutputStream;


  		




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import javax.servlet.http.HttpServletRequest;


  		




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import javax.servlet.http.HttpServletResponse;


  		




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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 org.dataone.client.ObjectFormatCache;


  		




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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.BaseException;


  		




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import org.dataone.service.exceptions.NotFound;


  		




  
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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.NodeReference;


  		




  
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import org.dataone.service.types.ObjectFormat;


  		




  
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import org.dataone.service.types.Subject;


  		




  
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import org.dataone.service.types.SystemMetadata;


  		




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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.ecoinformatics.eml.EMLParser;


  		




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import org.jibx.runtime.JiBXException;


  		




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import org.xml.sax.SAXException;


  		




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import au.com.bytecode.opencsv.CSVWriter;


  		




  
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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 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.Subject;


  		




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import org.dataone.service.types.SystemMetadata;


  		




  
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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.event.MetacatDocumentEvent;


  		




  
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import edu.ucsb.nceas.metacat.event.MetacatEventService;


  		




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


  		




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


  		




  
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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 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


  		












  

    
      src/edu/ucsb/nceas/metacat/service/ObjectFormatService.java
    
  





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package edu.ucsb.nceas.metacat.service;


  		




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import java.io.ByteArrayInputStream;


  		




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import java.io.FileInputStream;


  		




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import java.io.FileNotFoundException;


  		




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import java.io.InputStream;


  		




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import java.sql.SQLException;


  		




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import java.util.HashMap;


  		




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import java.util.List;


  		




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import org.apache.log4j.Logger;


  		




  
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import org.dataone.client.ObjectFormatCache;


  		




  
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import org.dataone.service.types.ObjectFormat;


  		




  
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import org.dataone.service.types.ObjectFormatList;


  		




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


  		




  
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import org.jibx.runtime.JiBXException;


  		




  
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import edu.ucsb.nceas.metacat.DBUtil;


  		




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import edu.ucsb.nceas.metacat.DocumentImpl;


  		




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import edu.ucsb.nceas.metacat.McdbException;


  		




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


  		




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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;


  		




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


  		




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


  		




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


  		




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import edu.ucsb.nceas.utilities.PropertyNotFoundException;


  		




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import org.apache.log4j.Logger;


  		




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import org.dataone.client.CNode;


  		




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import org.dataone.client.D1Client;


  		




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import org.dataone.client.ObjectFormatCache;


  		




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import org.dataone.service.exceptions.InsufficientResources;


  		




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import org.dataone.service.exceptions.InvalidRequest;


  		




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import org.dataone.service.exceptions.NotFound;


  		




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import org.dataone.service.exceptions.NotImplemented;


  		




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import org.dataone.service.exceptions.ServiceFailure;


  		




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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.ObjectFormatList;


  		




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//import org.dataone.service.types.ObjectFormatList;


  		




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


  		




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import org.jibx.runtime.JiBXException;


  		




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/**


  		




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 *  The ObjectFormatService manages the list of object formats registered


  		




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 *  within Metacat.  This includes schema types, mime types, and other


  		




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  private String coordinatingNodeBaseURL = null;


  		




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  /* The D1 coordinating node reference object used for object format lookups */


  		




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  private CNode cn = null;


  		




  
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  //private CNode cn = null;


  		




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  /* The D1 node type for this instance of metacat */


  		




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  private String nodeType;


  		












  

    
      src/edu/ucsb/nceas/metacat/admin/upgrade/GenerateSystemMetadata.java
    
  





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 */


  		




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import java.io.ByteArrayInputStream;


  		




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import java.io.IOException;


  		




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import java.io.InputStream;


  		




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import java.security.NoSuchAlgorithmException;


  		




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import java.sql.SQLException;


  		




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import java.util.Calendar;


  		




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import java.util.Date;


  		




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import java.util.Hashtable;


  		




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import java.util.List;


  		




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import java.util.TimeZone;


  		




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import java.util.Timer;


  		




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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.logging.Log;


  		




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import org.apache.commons.logging.LogFactory;


  		




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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.InvalidRequest;


  		




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import org.dataone.service.exceptions.InvalidToken;


  		




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import org.dataone.service.exceptions.NotAuthorized;


  		




  ......




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import org.dataone.service.exceptions.NotImplemented;


  		




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import org.dataone.service.exceptions.ServiceFailure;


  		




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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.NodeReference;


  		




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import org.dataone.service.types.ObjectFormat;


  		




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import org.dataone.service.types.Subject;


  		




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import org.dataone.service.types.SystemMetadata;


  		




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import org.xml.sax.SAXException;


  		




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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.DocumentImpl;


  		




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import edu.ucsb.nceas.metacat.IdentifierManager;


  		




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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;


  		




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import edu.ucsb.nceas.metacat.McdbException;


  		




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import edu.ucsb.nceas.metacat.MetacatHandler;


  		




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import edu.ucsb.nceas.metacat.admin.AdminException;


  		




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import edu.ucsb.nceas.metacat.dataone.CrudService;


  		




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


  		




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


  		




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import edu.ucsb.nceas.utilities.PropertyNotFoundException;


  		




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import edu.ucsb.nceas.utilities.SortedProperties;


  		




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