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Revision 6092

Added by Matt Jones almost 13 years ago

Modified Metacat to build against the D1_SCHEMA_0_6_1 branch of the dataone schemas by incorporating the 0.6.1-SNAPSHOT version of d1_common and d1_libclient libraries, and refactoring Metacat code references to the d1 schema changed types.

View differences:

test/edu/ucsb/nceas/metacat/dataone/CrudServiceTest.java
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import org.apache.commons.io.IOUtils;


  		




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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.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.ObjectFormat;


  		




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import org.dataone.service.types.ObjectInfo;


  		




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import org.dataone.service.types.ObjectList;


  		




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import org.dataone.service.types.Principal;


  		




  
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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.MCTestCase;


  		




  ......




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        //set the size


  		




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        sm.setSize(testDoc.getBytes(MetaCatServlet.DEFAULT_ENCODING).length);


  		




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        //submitter


  		




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        Principal p = new Principal();


  		




  
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        Subject p = new Subject();


  		




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        p.setValue("joe");


  		




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        sm.setSubmitter(p);


  		




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        sm.setRightsHolder(p);


  		












  

    
      src/upgrade-db-to-1.10.0-postgres.sql
    
  





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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




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  VALUES ('Schema', 'http://dataone.org/service/types/0.5.1', '/schema/D1_SCHEMA_0_5_1/dataoneTypes.xsd');


  		




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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




  
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  VALUES ('Schema', 'http://ns.dataone.org/service/types/0.6.1', '/schema/D1_SCHEMA_0_6_1/dataoneTypes.xsd');


  		




  
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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




  
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  VALUES ('Schema', 'http://ns.dataone.org/service/types/0.6.2', '/schema/D1_SCHEMA_0_6_2/dataoneTypes.xsd');


  		




  
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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




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  VALUES ('Schema', '@eml2_1_1namespace@', '/schema/eml-2.1.1/eml.xsd');  


  		




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/*


  		




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 * update the database version


  		












  

    
      src/loaddtdschema-postgres.sql
    
  





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  VALUES ('Schema', 'http://dataone.org/service/types/0.5.1', '/schema/D1_SCHEMA_0_5_1/dataoneTypes.xsd');


  		




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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




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  VALUES ('Schema', 'http://ns.dataone.org/service/types/0.6.0', '/schema/D1_SCHEMA_0_6_0/dataoneTypes.xsd');


  		




  
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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




  
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  VALUES ('Schema', 'http://ns.dataone.org/service/types/0.6.1', '/schema/D1_SCHEMA_0_6_1/dataoneTypes.xsd');


  		




  
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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




  
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  VALUES ('Schema', 'http://ns.dataone.org/service/types/0.6.2', '/schema/D1_SCHEMA_0_6_2/dataoneTypes.xsd');


  		




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INSERT INTO db_version (version, status, date_created) 


  		




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  VALUES ('1.10.0',1,CURRENT_DATE);


  		












  

    
      src/upgrade-db-to-1.10.0-oracle.sql
    
  





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 */


  		




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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




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  VALUES ('Schema', 'http://dataone.org/service/types/0.5.1', '/schema/D1_SCHEMA_0_5_1/dataoneTypes.xsd');


  		




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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




  
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  VALUES ('Schema', 'http://ns.dataone.org/service/types/0.6.1', '/schema/D1_SCHEMA_0_6_1/dataoneTypes.xsd');


  		




  
  40
  
    
INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




  
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  VALUES ('Schema', 'http://ns.dataone.org/service/types/0.6.2', '/schema/D1_SCHEMA_0_6_2/dataoneTypes.xsd');


  		




  
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INSERT INTO xml_catalog (entry_type, public_id, system_id)


  		




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  VALUES ('Schema', '@eml2_1_1namespace@', '/schema/eml-2.1.1/eml.xsd');


  		




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/*


  		












  

    
      src/edu/ucsb/nceas/metacat/MetacatHandler.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.ObjectFormat;


  		




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import org.dataone.service.types.Principal;


  		




  
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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.exceptions.BaseException;


  		




  ......




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      sysMeta.setSize(sizeOfStream(inputStream));


  		




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      //submitter


  		




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      Principal principal = new Principal();


  		




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      principal.setValue((String) docInfo.get("user_owner"));


  		




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      sysMeta.setSubmitter(principal);


  		




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      sysMeta.setRightsHolder(principal);


  		




  
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      Subject subject = new Subject();


  		




  
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      subject.setValue((String) docInfo.get("user_owner"));


  		




  
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      sysMeta.setSubmitter(subject);


  		




  
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      sysMeta.setRightsHolder(subject);


  		




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      try {


  		




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        SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-DD");


  		












  

    
      src/edu/ucsb/nceas/metacat/util/MetacatPopulator.java
    
  





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 */


  		




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package edu.ucsb.nceas.metacat.util;


  		




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import java.io.ByteArrayInputStream;


  		




  
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import java.io.InputStream;


  		




  
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import java.io.OutputStream;


  		




  
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import java.net.HttpURLConnection;


  		




  
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import java.net.URL;


  		




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import java.security.MessageDigest;


  		




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import java.util.*;


  		




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import java.io.*;


  		




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import java.net.*;


  		




  
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import java.util.Calendar;


  		




  
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import java.util.Date;


  		




  
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import java.util.Vector;


  		




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import javax.activation.DataHandler;


  		




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import javax.activation.DataSource;


  		




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import javax.mail.MessagingException;


  		




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import javax.mail.internet.MimeBodyPart;


  		




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import javax.mail.internet.MimeMultipart;


  		




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import javax.xml.parsers.DocumentBuilder;


  		




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import javax.xml.parsers.DocumentBuilderFactory;


  		




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import javax.xml.parsers.ParserConfigurationException;


  		




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import org.apache.commons.io.IOUtils;


  		




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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.MetacatResultSet;


  		




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import edu.ucsb.nceas.metacat.MetacatResultSet.Document;


  		




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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.restservice.InputStreamDataSource;


  		




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import org.dataone.service.exceptions.InvalidSystemMetadata;


  		




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import org.dataone.service.exceptions.ServiceFailure;


  		




  
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import org.dataone.client.D1Client;


  		




  
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import org.dataone.client.MNode;


  		




  
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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.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.Principal;


  		




  
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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.Identifier;


  		




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import org.dataone.client.D1Client;


  		




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import org.dataone.client.MNode;


  		




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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 sun.tools.jstat.Identifier;


  		




  
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import edu.ucsb.nceas.metacat.MetaCatServlet;


  		




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


  		




  
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import edu.ucsb.nceas.metacat.restservice.InputStreamDataSource;


  		




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


  		




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/**


  		




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 * @author berkley


  		




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 * A class to populate a metacat instance based on documents returned from a query


  		




  ......




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        sm.setSize(doc.doctext.getBytes(MetaCatServlet.DEFAULT_ENCODING).length);


  		




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        //submitter


  		




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        Principal p = new Principal();


  		




  
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        Subject p = new Subject();


  		




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        p.setValue("unknown");


  		




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        sm.setSubmitter(p);


  		




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        sm.setRightsHolder(p);


  		












  

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





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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.ObjectList;


  		




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import org.dataone.service.types.Principal;


  		




  
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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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  ......




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            NodeReference memberNode = new NodeReference();


  		




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            memberNode.setValue(ipAddress);


  		




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            le.setMemberNode(memberNode);


  		




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            Principal princ = new Principal();


  		




  
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            Subject princ = new Subject();


  		




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            princ.setValue(principal);


  		




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            le.setPrincipal(princ);


  		




  
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            le.setSubject(princ);


  		




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            le.setUserAgent("metacat/RESTService");


  		




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            if(event == null)


  		




  ......




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    	sm.setSize(sizeOfStream(is));


  		




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    	//submitter


  		




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    	Principal p = new Principal();


  		




  
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    	Subject p = new Subject();


  		




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    	p.setValue((String) docInfo.get("user_owner"));


  		




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    	sm.setSubmitter(p);


  		




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    	sm.setRightsHolder(p);


  		












  

    
      build.xml
    
  





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		<property name="eml2_0_1-schema-tag" value="RELEASE_EML_2_0_1" />


  		




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		<property name="eml2_1_0-schema-tag" value="RELEASE_EML_2_1_0" />


  		




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		<property name="eml2_1_1-schema-tag" value="RELEASE_EML_2_1_1_RC_2" />


  		




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		<property name="dataone-schema-tag" value="D1_SCHEMA_0_5_1" />


  		




  
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		<property name="dataone-schema-tag" value="D1_SCHEMA_0_6_1" />


  		




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		<property name="eml2-style-tag" value="RELEASE_EML_UTILS_1_0_0_RC12" />


  		




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		<property name="eml2_0_0namespace"


  		




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			value="eml://ecoinformatics.org/eml-2.0.0" />


  		




  ......




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		<property name="svn.eml211SchemaUrl"


  		




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			value="https://code.ecoinformatics.org/code/eml/tags/${eml2_1_1-schema-tag}" />


  		




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		<property name="svn.dataone-0.1-schema-url"


  		




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			value="https://repository.dataone.org/software/cicore/tags/${dataone-schema-tag}" />


  		




  
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			value="https://repository.dataone.org/software/cicore/branches/${dataone-schema-tag}" />


  		




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		<property name="svn.eml2StyleUrl"


  		




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			value="https://code.ecoinformatics.org/code/eml/tags/${eml2-style-tag}" />


  		




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