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Revision 8768

Added by ben leinfelder over 10 years ago

process all the returned annotation suggestions until we find one that is appropriately located in the subclass hierarchy for the given superclass.

View differences:

src/edu/ucsb/nceas/metacat/annotation/BioPortalService.java
9 9 
import org.w3c.dom.Document;
10 10 
import org.w3c.dom.NodeList;
11 11 

  		




  
  12
  
    
import com.hp.hpl.jena.ontology.ConversionException;


  		




  12
  13
  
    
import com.hp.hpl.jena.ontology.OntClass;


  		




  13
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import com.hp.hpl.jena.rdf.model.Resource;


  		




  14
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  ......




  31
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	 */


  		




  32
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	public static Resource lookupAnnotationClass(OntClass superClass, String text, String ontologies) {


  		




  33
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  35
  
    
		// no point calling the service


  		




  
  36
  
    
		if (text == null || text.length() == 0) {


  		




  
  37
  
    
			return null;


  		




  
  38
  
    
		}


  		




  
  39
  
    
		


  		




  34
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		try {


  		




  35
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  36
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			String urlParameters = "apikey=" + API_KEY;


  		




  ......




  46
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			Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new InputStreamReader(is, "UTF-8"));


  		




  47
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			NodeList classNodeList = XMLUtilities.getNodeListWithXPath(doc, "//annotation/annotatedClass/id");


  		




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


  		




  49
  
  
    
				String classURI = classNodeList.item(0).getFirstChild().getNodeValue();


  		




  50
  
  
    
				logMetacat.info("annotator suggested: " + classURI);


  		




  51
  
  
    
				Resource subclass = superClass.getModel().getResource(classURI);


  		




  52
  
  
    
				// check that it is a subclass of superClass


  		




  53
  
  
    
				if (superClass.hasSubClass(subclass)) {


  		




  54
  
  
    
					return subclass;


  		




  
  55
  
    
				for (int i = 0; i < classNodeList.getLength(); i++) {


  		




  
  56
  
    
					String classURI = classNodeList.item(i).getFirstChild().getNodeValue();


  		




  
  57
  
    
					logMetacat.info("annotator suggested: " + classURI);


  		




  
  58
  
    
					Resource subclass = superClass.getModel().getResource(classURI);


  		




  
  59
  
    
					// check that it is a subclass of superClass


  		




  
  60
  
    
					boolean isSubclass = false;


  		




  
  61
  
    
					try {


  		




  
  62
  
    
						isSubclass = superClass.hasSubClass(subclass);


  		




  
  63
  
    
					} catch (ConversionException ce) {


  		




  
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						logMetacat.warn("Skipping unknown subclass: " + classURI, ce);


  		




  
  65
  
    
						// try the next one


  		




  
  66
  
    
						continue;


  		




  
  67
  
    
					}


  		




  
  68
  
    
					if (isSubclass) {


  		




  
  69
  
    
						return subclass;


  		




  
  70
  
    
					}


  		




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				}


  		




  
  72
  
    
				


  		




  56
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			}


  		




  57
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		} catch (Exception e) {


  		




  58
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			logMetacat.error("Could not lookup BioPortal annotation for text=" + text, e);


  		












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