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Posted to dev@uima.apache.org by Syed Moinuddin <mo...@gmail.com> on 2016/11/28 06:48:04 UTC
Getting output in json
HI,
I want to get the output in json, I'm trying the following program,
public static void main(final String... args) throws IOException,
UIMAException, SAXException {
final String note = "Serum Cholesterol 154 150 250
mgs/dl\n-\nSerum Triglycerides 67 90 200 mgs /dl\n-\nSerum HDL:
Cholesterol 38 35 55 mgs /dl\n-\nSerum LDL: Cholesterol 49 85 150
mgs/d1\n-\nSerum VLDL: Cholesterol 13 10 40 mgs/dl\n-\nTotal
Cholesterol / HDL Ratio: 3.90\";
final JCas jcas = JCasFactory.createJCas();
jcas.setDocumentText(note);
// final AnalysisEngineDescription aed = getDefaultPipeline();
final AnalysisEngineDescription aed = getFastPipeline(); //
Outputs from default and fast pipeline are identical
SimplePipeline.runPipeline(jcas, aed);
Collection<TOP> codes = JCasUtil.selectAll(jcas);
List<TOP> list = new ArrayList<>(codes)
TOP [] res = list.toArray(new TOP[list.size()]);
// System.out.println(Arrays.toString(res));
String json = new Gson().toJson(res);
System.out.println(json);
}
But this gives following error,
Exception in thread "main" java.lang.IllegalArgumentException: class
org.apache.uima.jcas.tcas.DocumentAnnotation_Type declares multiple
JSON fields named fsGenerator
at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getBoundFields(ReflectiveTypeAdapterFactory.java:122)
at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.create(ReflectiveTypeAdapterFactory.java:72)
at com.google.gson.Gson.getAdapter(Gson.java:353)
at com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper.write(TypeAdapterRuntimeTypeWrapper.java:55)
at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.write(ReflectiveTypeAdapterFactory.java:89)
at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.write(ReflectiveTypeAdapterFactory.java:195)
at com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper.write(TypeAdapterRuntimeTypeWrapper.java:68)
at com.google.gson.internal.bind.ArrayTypeAdapter.write(ArrayTypeAdapter.java:93)
at com.google.gson.Gson.toJson(Gson.java:586)
at com.google.gson.Gson.toJson(Gson.java:565)
at com.google.gson.Gson.toJson(Gson.java:520)
at com.google.gson.Gson.toJson(Gson.java:500)
at org.apache.ctakes.clinicalpipeline.ExtractNEs.main(ExtractNEs.java:146)
Any guidance would be really helpful.
Thanks
Re: Getting output in json
Posted by Marshall Schor <ms...@schor.com>.
I'm not very familiar with Gson, so I can't help there.
However, UIMA has built-in JSON serialization, described here:
http://uima.apache.org/d/uimaj-current/references.html#ugr.ref.json
This is built on the Jackson support for JSON.
-Marshall
On 11/28/2016 1:48 AM, Syed Moinuddin wrote:
> HI,
>
> I want to get the output in json, I'm trying the following program,
>
> public static void main(final String... args) throws IOException,
> UIMAException, SAXException {
> final String note = "Serum Cholesterol 154 150 250
> mgs/dl\n-\nSerum Triglycerides 67 90 200 mgs /dl\n-\nSerum HDL:
> Cholesterol 38 35 55 mgs /dl\n-\nSerum LDL: Cholesterol 49 85 150
> mgs/d1\n-\nSerum VLDL: Cholesterol 13 10 40 mgs/dl\n-\nTotal
> Cholesterol / HDL Ratio: 3.90\";
> final JCas jcas = JCasFactory.createJCas();
> jcas.setDocumentText(note);
> // final AnalysisEngineDescription aed = getDefaultPipeline();
> final AnalysisEngineDescription aed = getFastPipeline(); //
> Outputs from default and fast pipeline are identical
> SimplePipeline.runPipeline(jcas, aed);
>
> Collection<TOP> codes = JCasUtil.selectAll(jcas);
> List<TOP> list = new ArrayList<>(codes)
>
> TOP [] res = list.toArray(new TOP[list.size()]);
>
> // System.out.println(Arrays.toString(res));
>
> String json = new Gson().toJson(res);
> System.out.println(json);
>
> }
>
> But this gives following error,
>
> Exception in thread "main" java.lang.IllegalArgumentException: class
> org.apache.uima.jcas.tcas.DocumentAnnotation_Type declares multiple
> JSON fields named fsGenerator
> at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getBoundFields(ReflectiveTypeAdapterFactory.java:122)
> at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.create(ReflectiveTypeAdapterFactory.java:72)
> at com.google.gson.Gson.getAdapter(Gson.java:353)
> at com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper.write(TypeAdapterRuntimeTypeWrapper.java:55)
> at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.write(ReflectiveTypeAdapterFactory.java:89)
> at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.write(ReflectiveTypeAdapterFactory.java:195)
> at com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper.write(TypeAdapterRuntimeTypeWrapper.java:68)
> at com.google.gson.internal.bind.ArrayTypeAdapter.write(ArrayTypeAdapter.java:93)
> at com.google.gson.Gson.toJson(Gson.java:586)
> at com.google.gson.Gson.toJson(Gson.java:565)
> at com.google.gson.Gson.toJson(Gson.java:520)
> at com.google.gson.Gson.toJson(Gson.java:500)
> at org.apache.ctakes.clinicalpipeline.ExtractNEs.main(ExtractNEs.java:146)
>
> Any guidance would be really helpful.
>
> Thanks
>