Hi again
My project is basically: 1) to come in with an abstract/ scientific
article, 2) call an existing Annotator from Parser.java, 3) get good
labels, and 4) return model with all the new labels to Parser.java.
I have created my jena model in Parser.java, and wish to call
TextAnnotation.java to load the "preferred labels" into my model, via the
property AnnotationLabel in TextAnnotation.java.
The labels are loaded in the printAnnotations method of class
TextAnnotation. (I need to return model back to Parser.java.)
I wish to use only one model. I am running into compile time errors.
THANKS in ADVANCE for your help.
Mona
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.Property;
public class Parser {
public static Model model = ModelFactory.createDefaultModel();
/* create the Resource, using the product URI */
Resource softwareproduct =
model.createResource(urlAddress);
//create the properties
Property extracteddata = model.createProperty("
http://www.mydirectory.com/softwareproduct#extracteddata";);
Property annotationLabel = model.createProperty("
http://www.mydirectory.com/softwareproduct#softwareannotation";);
...
SAXparsingExtractedText saxparser = new
SAXparsingExtractedText();
abstractinfo = saxparser.parseDocument(urlAddress);
softwareproduct.addProperty(extracteddata,
abstractinfo);
//-------> I call the TEXT ANNOTATOR with abstractinfo
and model (??) and url address
TextAnnotation annotateText = new
TextAnnotation();
annotateText.stringToAnnotate(abstractinfo,
model, urlAddress);
}
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource;
public class TextAnnotation {
static final String REST_URL = "http://data.bioontology.org";;
static final ObjectMapper mapper = new ObjectMapper();
public void stringToAnnotate(String abstractInfo, Model model2, String
URLaddress) throws UnsupportedEncodingException {
String textToAnnotate = URLEncoder.encode(abstractInfo, "UTF-8");
Resource SoftwareProduct = model2.createResource(URLaddress);
Property AnnotationLabel = model2.createProperty("
http://www.mydirectory.com/softwareproduct#softwareannotation";);
// Get just annotations
JsonNode annotations = jsonToNode(get(REST_URL +
"/annotator?ontologies=NCIT&text=" + textToAnnotate));
printAnnotations(annotations);
}
private model2 printAnnotations(JsonNode annotations) {
for (JsonNode annotation : annotations) {
// Get the details for the class that was found in the
annotation and print
JsonNode classDetails =
jsonToNode(get(annotation.get("annotatedClass").get("links").get("self").asText()));
//Don't print "preferred Labels", load "prefLabels" into the
model
// System.out.println("\tprefLabel: " +
classDetails.get("prefLabel").asText());
SoftwareProduct.addProperty(AnnotationLabel,
classDetails.get("prefLabel").asText());
}
}
}
}
private static JsonNode jsonToNode(String json) {
JsonNode root = null;
try {
root = mapper.readTree(json);
} catch (JsonProcessingException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
return root;
}
private static String get(String urlToGet) {
URL url;
HttpURLConnection conn;
BufferedReader rd;
String line;
String result = "";
try {
url = new URL(urlToGet);
conn = (HttpURLConnection) url.openConnection();
conn.setRequestMethod("GET");
conn.setRequestProperty("Authorization", "apikey token=" +
API_KEY);
conn.setRequestProperty("Accept", "application/json");
rd = new BufferedReader(
new InputStreamReader(conn.getInputStream()));
while ((line = rd.readLine()) != null) {
result += line;
}
rd.close();
} catch (Exception e) {
e.printStackTrace();
}
return result;
}
}
Compilation errors:
Exception in thread "main" java.lang.Error: Unresolved compilation
problems:
SoftwareProduct cannot be resolved
AnnotationLabel cannot be resolved to a variable
at TextAnnotation.printAnnotations(TextAnnotation.java:47)
at TextAnnotation.stringToAnnotate(TextAnnotation.java:32)
at Parser.getTitle(Parser.java:291)
at Parser.getAllUrlNames(Parser.java:118)
at Parser.main(Parser.java:723)
On Mon, Jan 27, 2014 at 3:36 PM, Joshua TAYLOR <joshuaaa...@gmail.com>wrote:
> You can pass models as parameters to methods (just like any other Java
> object). The code in this message looks like it may have been mangled
> on its way to the list. It's certainly not in a compilable state at
> the moment. E.g., lines like
>
> Product.addProperty(category_n, classDetails.get( );
>
> don't even have balanced parentheses. It will be much easier to see
> what the problem is if you can provide a minimal example that other
> people can use to reproduce the error, and if you show what error
> you're actually getting. E.g., when you say that "[you] tried
> passing the model in a parameter list from Parser.java. It did not
> work: `Annotator.printAnnotations(model).`", what do you mean that it
> didn't work? Did you get a compilation error? Were you able to run
> it, but it produced different results than what you'd been expected?
> Or something else entirely?
>
>
>
> On Mon, Jan 27, 2014 at 6:10 PM, Mona Salem <monasalem...@gmail.com>
> wrote:
> > Hi
> >
> > I am a newbie to Jena.
> >
> > I want to be able to add rdf statements to my model in two different
> .java
> > classes; ie Parser.java and Annotator.java
> >
> > I did the following:
> >
> > public class Parser {
> >
> >
> >
> > public static Model model = ModelFactory.createDefaultModel();
> >
> >
> >
> >
> >
> > Resource Product = model.createResource(ItemAddress);
> >
> >
> >
> > //create the properties
> >
> > Property category1 = model.createProperty("http: .);
> >
> > Property category2 = model.createProperty("http: .);
> >
> > Property category3 = model.createProperty("http: .);
> >
> > .
> >
> > .
> >
> > .
> >
> > Property category_n = model.createProperty("http: .);
> >
> >
> >
> > //add object
> >
> > Product.addProperty(category1, );
> >
> > Product.addProperty(category2, );
> >
> > .
> >
> > .
> >
> > .
> >
> >
> >
> > }
> >
> >
> >
> > I want to load values for category_n in a method of the second class:
> >
> >
> >
> > public class Annotator{
> >
> >
> >
> > private static void printAnnotations(JsonNode annotations){
> >
> > for (JsonNode annotation : annotations){
> >
> >
> >
> > System.out.println(" something here");
> >
> >
> >
> > Product.addProperty(category_n, classDetails.get( );
> >
> >
> >
> > }
> >
> > }
> >
> >
> >
> > Note that the loop in the printAnnotations method will create multiple
> rdf
> > statements with same pair resource/predicate and multiple objects.
> >
> >
> >
> > I tried passing the model in a parameter list from Parser.java. It did
> not
> > work
> >
> > Annotator.printAnnotations(model).
> >
> >
> >
> > I thought making the model public would make this work.
> >
> >
> >
> > Should I use an array in Annotator to collect the values in the loop?
> >
> >
> >
> > Thanks for the help.
> >
> > Mona
> >
> >
> >
>
>
>
> --
> Joshua Taylor, http://www.cs.rpi.edu/~tayloj/
>
