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Revision 6134

Added by ben leinfelder over 13 years ago

use Data Manager Library to parse EML when needed in DataONE classes.
(augmented DML to parse data format elements in EML to estimate MIME type)
https://redmine.dataone.org/issues/1634

View differences:

src/edu/ucsb/nceas/metacat/MetacatHandler.java
74 74 
import org.apache.commons.io.input.XmlStreamReader;
75 75 
import org.apache.log4j.Logger;
76 76 
import org.dataone.client.ObjectFormatCache;
77 
import org.dataone.eml.DataoneEMLParser;
78 
import org.dataone.eml.EMLDocument;
79 
import org.dataone.eml.EMLDocument.DistributionMetadata;
80 77 
import org.dataone.service.exceptions.BaseException;
81 78 
import org.dataone.service.exceptions.NotFound;
82 79 
import org.dataone.service.types.Checksum;
......
87 84 
import org.dataone.service.types.Subject;
88 85 
import org.dataone.service.types.SystemMetadata;
89 86 
import org.dataone.service.types.util.ServiceTypeUtil;
87 
import org.ecoinformatics.datamanager.DataManager;
88 
import org.ecoinformatics.datamanager.database.DatabaseConnectionPoolInterface;
89 
import org.ecoinformatics.datamanager.parser.DataPackage;
90 
import org.ecoinformatics.datamanager.parser.TextComplexDataFormat;
90 91 
import org.ecoinformatics.eml.EMLParser;
91 92 
import org.jibx.runtime.JiBXException;
92 93 
import org.xml.sax.SAXException;
......
107 108 
import edu.ucsb.nceas.metacat.database.DBConnection;
108 109 
import edu.ucsb.nceas.metacat.database.DBConnectionPool;
109 110 
import edu.ucsb.nceas.metacat.dataquery.DataQuery;
111 
import edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory;
110 112 
import edu.ucsb.nceas.metacat.event.MetacatDocumentEvent;
111 113 
import edu.ucsb.nceas.metacat.event.MetacatEventService;
112 114 
import edu.ucsb.nceas.metacat.properties.PropertyService;
......
3611 3613 
           format == ObjectFormatCache.getFormat("eml://ecoinformatics.org/eml-2.1.1") ) {
3612 3614
3613 3615 
        try {
3614 
          DataoneEMLParser emlParser = DataoneEMLParser.getInstance();
3615 
          EMLDocument emlDocument = emlParser.parseDocument(inputStream);
3616
3617 
        	DatabaseConnectionPoolInterface connectionPool = MetacatDatabaseConnectionPoolFactory.getDatabaseConnectionPoolInterface();
3618 
        	DataManager dataManager = DataManager.getInstance(connectionPool, connectionPool.getDBAdapterName());
3619 
        	DataPackage dataPackage = dataManager.parseMetadata(inputStream);
3616 3620
3617 3621 
          // iterate through the data objects in the EML doc and add sysmeta
3618 3622 
          logMetacat.debug("In createSystemMetadata() the number of data " +
3619 
            "entities is: " + emlDocument.distributionMetadata.size());
3623 
            "entities is: " + dataPackage.getEntityNumber());
3620 3624
3621 3625 
          // iterate through data objects described by the EML
3622 
          for( int j = 0; j < emlDocument.distributionMetadata.size(); j++ ) {
3626 
          for (int j = 0; j < dataPackage.getEntityList().length; j++) {
3623 3627
3624 
            DistributionMetadata distMetadata =
3625 
              emlDocument.distributionMetadata.elementAt(j);
3626 
            String dataDocUrl = distMetadata.url;
3627 
            String dataDocMimeType = "";
3628 
            if (distMetadata.mimeType == null) {
3628
3629 
            String dataDocUrl = dataPackage.getEntityList()[j].getURL();
3630 
            String dataDocMimeType = dataPackage.getEntityList()[j].getDataFormat();
3631 
            // default to binary
3632 
            if (dataDocMimeType == null) {
3629 3633 
                dataDocMimeType =
3630 3634 
                	ObjectFormatCache.getFormat("application/octet-stream").getFmtid().getValue();
3631 
            } else {
3632 
                dataDocMimeType = distMetadata.mimeType;
3633 3635 
            }
3634 3636 
            String dataDocLocalId = "";
3635 3637 
            logMetacat.debug("Data local ID: " + dataDocLocalId);
......
3726 3728 
        } catch ( XPathExpressionException xpee ) {
3727 3729 
          logMetacat.debug("There was a problem searching the EML document. " +
3728 3730 
                           "The error message was: " + xpee.getMessage());
3731 
        } catch ( Exception e ) {
3732 
            logMetacat.debug("There was a problem creating System Metadata. " +
3733 
                    "The error message was: " + e.getMessage());
3729 3734 
        } // end try()
3730 3735
3731 3736 
      } // end if()
src/edu/ucsb/nceas/metacat/util/MetacatPopulator.java
44 44 
import org.dataone.client.D1Client;
45 45 
import org.dataone.client.MNode;
46 46 
import org.dataone.client.ObjectFormatCache;
47 
import org.dataone.eml.DataoneEMLParser;
48 
import org.dataone.eml.EMLDocument;
49 
import org.dataone.eml.EMLDocument.DistributionMetadata;
50 47 
import org.dataone.service.types.AuthToken;
51 48 
import org.dataone.service.types.Checksum;
52 49 
import org.dataone.service.types.ChecksumAlgorithm;
......
55 52 
import org.dataone.service.types.ObjectFormat;
56 53 
import org.dataone.service.types.Subject;
57 54 
import org.dataone.service.types.SystemMetadata;
55 
import org.ecoinformatics.datamanager.DataManager;
56 
import org.ecoinformatics.datamanager.database.DatabaseConnectionPoolInterface;
57 
import org.ecoinformatics.datamanager.parser.DataPackage;
58 58 

  		




  59
  59
  
    
import edu.ucsb.nceas.metacat.MetaCatServlet;


  		




  
  60
  
    
import edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory;


  		




  60
  61
  
    
import edu.ucsb.nceas.metacat.properties.PropertyService;


  		




  61
  62
  
    
import edu.ucsb.nceas.metacat.restservice.InputStreamDataSource;


  		




  62
  63
  
    

  		




  ......




  139
  140
  
    
            System.out.println("doctext: " + doctext);


  		




  140
  141
  
    
            is = stringToStream(doctext);


  		




  141
  142
  
    
            //parse the document


  		




  142
  
  
    
            DataoneEMLParser parser = DataoneEMLParser.getInstance();


  		




  143
  
  
    
            EMLDocument emld = parser.parseDocument(is);


  		




  144
  
  
    
            if(emld == null)


  		




  
  143
  
    
            DatabaseConnectionPoolInterface connectionPool = MetacatDatabaseConnectionPoolFactory.getDatabaseConnectionPoolInterface();


  		




  
  144
  
    
        	DataManager dataManager = DataManager.getInstance(connectionPool, connectionPool.getDBAdapterName());


  		




  
  145
  
    
        	DataPackage dataPackage = dataManager.parseMetadata(is);


  		




  
  146
  
    
        	


  		




  
  147
  
    
            if(dataPackage == null)


  		




  145
  148
  
    
            {


  		




  146
  149
  
    
                continue;


  		




  147
  150
  
    
            }


  		




  ......




  152
  155
  
    

  		




  153
  156
  
    
            printHeader("creating document on destination " + destinationUrl);            


  		




  154
  157
  
    
            SystemMetadata sysmeta = generateSystemMetadata(doc);


  		




  155
  
  
    
            for(int j=0; j<emld.distributionMetadata.size(); j++)


  		




  
  158
  
    
            for(int j=0; j < dataPackage.getEntityList().length; j++)


  		




  156
  159
  
    
            {


  		




  157
  
  
    
                Identifier emlId = sysmeta.getIdentifier();


  		




  158
  
  
    
                DistributionMetadata dm = emld.distributionMetadata.elementAt(j);


  		




  159
  
  
    
                String dataDocUrl = dm.url;


  		




  160
  
  
    
                String dataDocMimeType = dm.mimeType;


  		




  
  160
  
    
                String dataDocUrl = dataPackage.getEntityList()[j].getURL();


  		




  
  161
  
    
                String dataDocMimeType = 


  		




  
  162
  
    
                	dataPackage.getEntityList()[j].getDataFormat();


  		




  
  163
  
    
                if (dataDocMimeType == null) {


  		




  
  164
  
    
	                dataDocMimeType = 


  		




  
  165
  
    
	                	ObjectFormatCache.getFormat("application/octet-stream").getFmtid().getValue();


  		




  
  166
  
    
                }


  		




  161
  167
  
    
                String dataDocLocalId = "";


  		




  162
  168
  
    
                if(dataDocUrl.trim().startsWith("ecogrid://knb/"))


  		




  163
  169
  
    
                { //we only handle ecogrid urls right now


  		




  ......




  248
  254
  
    
        logout();


  		




  249
  255
  
    
    }


  		




  250
  256
  
    
    


  		




  251
  
  
    
    /**


  		




  252
  
  
    
     * create the documents listed by an eml document as described in the 


  		




  253
  
  
    
     * new system


  		




  254
  
  
    
     * @param doc


  		




  255
  
  
    
     * @param emld


  		




  256
  
  
    
     */


  		




  257
  
  
    
    private void createDescribedDocuments(Document doc, EMLDocument emld)


  		




  258
  
  
    
    {


  		




  259
  
  
    
        


  		




  260
  
  
    
    }


  		




  
  257
  
    

  		




  261
  258
  
    
    


  		




  262
  259
  
    
    /**


  		




  263
  260
  
    
     * @param doc


  		












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