Project

General

Profile

« Previous | Next » 

Revision 8711

Added by ben leinfelder over 10 years ago

Include method to look up annotation classes from BioPortal. We still have OBOE-SBC in there, and theyhave the SWEET ontology. The suggestions returned are not perfect, but they can be better than nothing. Ideally, we'd only query a few ontologies so we don't end up using terms from medical ontologies that aren't really appropriate for our domain. https://projects.ecoinformatics.org/ecoinfo/issues/6256

View differences:

src/edu/ucsb/nceas/metacat/annotation/DatapackageSummarizer.java
1 1 
package edu.ucsb.nceas.metacat.annotation;
2 2 

  		




  3
  3
  
    
import java.io.InputStream;


  		




  
  4
  
    
import java.io.InputStreamReader;


  		




  4
  5
  
    
import java.io.StringWriter;


  		




  
  6
  
    
import java.net.URL;


  		




  
  7
  
    
import java.net.URLEncoder;


  		




  5
  8
  
    
import java.sql.PreparedStatement;


  		




  6
  9
  
    
import java.sql.SQLException;


  		




  7
  10
  
    
import java.util.ArrayList;


  		




  ......




  21
  24
  
    
import org.ecoinformatics.datamanager.parser.Entity;


  		




  22
  25
  
    
import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;


  		




  23
  26
  
    
import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser;


  		




  
  27
  
    
import org.w3c.dom.Document;


  		




  
  28
  
    
import org.w3c.dom.NodeList;


  		




  24
  29
  
    

  		




  25
  30
  
    
import com.hp.hpl.jena.ontology.AllValuesFromRestriction;


  		




  26
  31
  
    
import com.hp.hpl.jena.ontology.Individual;


  		




  ......




  44
  49
  
    
import edu.ucsb.nceas.metacat.replication.ReplicationService;


  		




  45
  50
  
    
import edu.ucsb.nceas.metacat.util.DocumentUtil;


  		




  46
  51
  
    
import edu.ucsb.nceas.utilities.SortedProperties;


  		




  
  52
  
    
import edu.ucsb.nceas.utilities.XMLUtilities;


  		




  47
  53
  
    

  		




  48
  54
  
    
public class DatapackageSummarizer {


  		




  49
  55
  
    

  		




  ......




  64
  70
  
    
    public static String prov_source = "http://www.w3.org/ns/prov.owl";


  		




  65
  71
  
    
    public static String cito =  "http://purl.org/spar/cito/";


  		




  66
  72
  
    
    


  		




  
  73
  
    
    // for looking up concepts in BioPortal


  		




  
  74
  
    
    static final String REST_URL = "http://data.bioontology.org";


  		




  
  75
  
    
    static final String API_KEY = "24e4775e-54e0-11e0-9d7b-005056aa3316";


  		




  
  76
  
    
    


  		




  67
  77
  
    
    // package visibility for testing only


  		




  68
  78
  
    
    boolean randomize = false;


  		




  69
  79
  
    

  		




  ......




  230
  240
  
    
				return subclass;


  		




  231
  241
  
    
			}


  		




  232
  242
  
    
		}


  		




  233
  
  
    
		return null;


  		




  
  243
  
    
		// try to look it up if we got this far


  		




  
  244
  
    
		return this.lookupRemoteAnnotationClass(standardClass, unit);


  		




  234
  245
  
    
	}


  		




  235
  246
  
    
	


  		




  236
  247
  
    
	private Resource lookupCharacteristic(OntClass characteristicClass, Attribute attribute) {


  		




  ......




  262
  273
  
    
				return subclass;


  		




  263
  274
  
    
			}


  		




  264
  275
  
    
		}


  		




  
  276
  
    
		


  		




  
  277
  
    
		// try to look it up if we got this far


  		




  
  278
  
    
		return this.lookupRemoteAnnotationClass(characteristicClass, attribute.getDefinition());


  		




  
  279
  
    
		


  		




  
  280
  
    
	}


  		




  
  281
  
    
	


  		




  
  282
  
    
	private Resource lookupRemoteAnnotationClass(OntClass superClass, String text) {


  		




  
  283
  
    
		


  		




  
  284
  
    
		


  		




  
  285
  
    
		try {


  		




  
  286
  
    
			


  		




  
  287
  
    
			String urlParameters = "apikey=" + API_KEY;


  		




  
  288
  
    
			urlParameters += "&format=xml";


  		




  
  289
  
    
//			urlParameters += "&ontologies=OBOE-SBC";


  		




  
  290
  
    
			urlParameters += "&ontologies=SWEET";


  		




  
  291
  
    
			urlParameters += "&text=" + URLEncoder.encode(text, "UTF-8");


  		




  
  292
  
    
			


  		




  
  293
  
    
			String url = REST_URL + "/annotator?" + urlParameters ;


  		




  
  294
  
    
			URL restURL = new URL(url);


  		




  
  295
  
    
			InputStream is = ReplicationService.getURLStream(restURL);


  		




  
  296
  
    
			Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new InputStreamReader(is, "UTF-8"));


  		




  
  297
  
    
			NodeList classNodeList = XMLUtilities.getNodeListWithXPath(doc, "//annotation/annotatedClass/id");


  		




  
  298
  
    
			if (classNodeList != null && classNodeList.getLength() > 0) {


  		




  
  299
  
    
				String classURI = classNodeList.item(0).getFirstChild().getNodeValue();


  		




  
  300
  
    
				logMetacat.info("annotator suggested: " + classURI);


  		




  
  301
  
    
				Resource subclass = superClass.getModel().getResource(classURI);


  		




  
  302
  
    
				// TODO: check that it is a subclass of superClass?


  		




  
  303
  
    
				return subclass;


  		




  
  304
  
    
			}


  		




  
  305
  
    
		} catch (Exception e) {


  		




  
  306
  
    
			logMetacat.error("Could not lookup BioPortal annotation for text= " + text, e);


  		




  
  307
  
    
		}


  		




  
  308
  
    
		


  		




  265
  309
  
    
		return null;


  		




  266
  310
  
    
	}


  		




  267
  311
  
    
	


  		












Also available in:  Unified diff