use of com.github.phenomics.ontolib.formats.hpo.HpoTerm in project loinc2hpo by monarch-initiative.
the class UniversalLoinc2HPOAnnotationTest method testBuilderForAdvanced.
@Test
public void testBuilderForAdvanced() throws Exception {
Map<String, HpoTerm> hpoTermMap;
String hpo_obo = FhirObservationAnalyzerTest.class.getClassLoader().getResource("obo/hp.obo").getPath();
HpoOboParser hpoOboParser = new HpoOboParser(new File(hpo_obo));
HpoOntology hpo = null;
try {
hpo = hpoOboParser.parse();
} catch (IOException e) {
e.printStackTrace();
}
ImmutableMap.Builder<String, HpoTerm> termmap = new ImmutableMap.Builder<>();
if (hpo != null) {
List<HpoTerm> res = hpo.getTermMap().values().stream().distinct().collect(Collectors.toList());
res.forEach(term -> termmap.put(term.getName(), term));
}
hpoTermMap = termmap.build();
UniversalLoinc2HPOAnnotation.Builder loinc2HpoAnnotationBuilder = new UniversalLoinc2HPOAnnotation.Builder();
LoincId loincId = new LoincId("600-7");
LoincScale loincScale = LoincScale.string2enum("Nom");
HpoTerm forCode1 = hpoTermMap.get("Recurrent E. coli infections");
HpoTerm forCode2 = hpoTermMap.get("Recurrent Staphylococcus aureus infections");
HpoTerm positive = hpoTermMap.get("Recurrent bacterial infections");
Code code1 = Code.getNewCode().setSystem("http://snomed.info/sct").setCode("112283007");
Code code2 = Code.getNewCode().setSystem("http://snomed.info/sct").setCode("3092008");
loinc2HpoAnnotationBuilder.setLoincId(loincId).setLoincScale(loincScale).setHighValueHpoTerm(positive).addAdvancedAnnotation(code1, new HpoTermId4LoincTest(forCode1, false)).addAdvancedAnnotation(code2, new HpoTermId4LoincTest(forCode2, false));
UniversalLoinc2HPOAnnotation annotation600 = loinc2HpoAnnotationBuilder.build();
assertEquals("600-7", annotation600.getLoincId().toString());
Map<String, Code> internalCodes = CodeSystemConvertor.getCodeContainer().getCodeSystemMap().get(Loinc2HPOCodedValue.CODESYSTEM);
Code code4Pos = internalCodes.get("P");
assertEquals(positive.getId().getIdWithPrefix(), annotation600.getCandidateHpoTerms().get(code4Pos).getHpoTerm().getId().getIdWithPrefix());
assertEquals(false, annotation600.getCandidateHpoTerms().get(code4Pos).isNegated());
Code code4high = internalCodes.get("H");
assertEquals(positive.getId().getIdWithPrefix(), annotation600.getCandidateHpoTerms().get(code4high).getHpoTerm().getId().getIdWithPrefix());
assertEquals(false, annotation600.getCandidateHpoTerms().get(code4Pos).isNegated());
assertEquals(forCode1.getId().getIdWithPrefix(), annotation600.getCandidateHpoTerms().get(code1).getHpoTerm().getId().getIdWithPrefix());
assertEquals(false, annotation600.getCandidateHpoTerms().get(code1).isNegated());
assertEquals(forCode2.getId().getIdWithPrefix(), annotation600.getCandidateHpoTerms().get(code2).getHpoTerm().getId().getIdWithPrefix());
assertEquals(false, annotation600.getCandidateHpoTerms().get(code2).isNegated());
}
use of com.github.phenomics.ontolib.formats.hpo.HpoTerm in project loinc2hpo by monarch-initiative.
the class UniversalLoinc2HPOAnnotationTest method testWriteInOut.
@Test
@Ignore
public void testWriteInOut() throws Exception {
Map<String, HpoTerm> hpoTermMap;
Map<TermId, HpoTerm> hpoTermMap2;
String hpo_obo = FhirObservationAnalyzerTest.class.getClassLoader().getResource("obo/hp.obo").getPath();
HpoOboParser hpoOboParser = new HpoOboParser(new File(hpo_obo));
HpoOntology hpo = null;
try {
hpo = hpoOboParser.parse();
} catch (IOException e) {
e.printStackTrace();
}
ImmutableMap.Builder<String, HpoTerm> termmap = new ImmutableMap.Builder<>();
ImmutableMap.Builder<TermId, HpoTerm> termmap2 = new ImmutableMap.Builder<>();
if (hpo != null) {
List<HpoTerm> res = hpo.getTermMap().values().stream().distinct().collect(Collectors.toList());
res.forEach(term -> {
termmap.put(term.getName(), term);
termmap2.put(term.getId(), term);
});
}
hpoTermMap = termmap.build();
hpoTermMap2 = termmap2.build();
UniversalLoinc2HPOAnnotation.Builder loinc2HpoAnnotationBuilder = new UniversalLoinc2HPOAnnotation.Builder();
LoincId loincId = new LoincId("15074-8");
LoincScale loincScale = LoincScale.string2enum("Qn");
HpoTerm low = hpoTermMap.get("Hypoglycemia");
HpoTerm normal = hpoTermMap.get("Abnormality of blood glucose concentration");
HpoTerm hi = hpoTermMap.get("Hyperglycemia");
loinc2HpoAnnotationBuilder.setLoincId(loincId).setLoincScale(loincScale).setLowValueHpoTerm(low).setIntermediateValueHpoTerm(normal).setIntermediateNegated(true).setHighValueHpoTerm(hi);
UniversalLoinc2HPOAnnotation annotation15074 = loinc2HpoAnnotationBuilder.build();
Map<LoincId, UniversalLoinc2HPOAnnotation> testmap = new HashMap<>();
testmap.put(loincId, annotation15074);
loinc2HpoAnnotationBuilder = new UniversalLoinc2HPOAnnotation.Builder();
loincId = new LoincId("600-7");
loincScale = LoincScale.string2enum("Nom");
HpoTerm forCode1 = hpoTermMap.get("Recurrent E. coli infections");
HpoTerm forCode2 = hpoTermMap.get("Recurrent Staphylococcus aureus infections");
HpoTerm positive = hpoTermMap.get("Recurrent bacterial infections");
Code code1 = Code.getNewCode().setSystem("http://snomed.info/sct").setCode("112283007");
Code code2 = Code.getNewCode().setSystem("http://snomed.info/sct").setCode("3092008");
loinc2HpoAnnotationBuilder.setLoincId(loincId).setLoincScale(loincScale).setHighValueHpoTerm(positive).addAdvancedAnnotation(code1, new HpoTermId4LoincTest(forCode1, false)).addAdvancedAnnotation(code2, new HpoTermId4LoincTest(forCode2, false));
UniversalLoinc2HPOAnnotation annotation600 = loinc2HpoAnnotationBuilder.build();
testmap.put(loincId, annotation600);
assertEquals(2, testmap.size());
String filepath = temporaryFolder.newFile().getAbsolutePath();
WriteToFile.toTSVbasicAnnotations(filepath, testmap);
String filepath2 = temporaryFolder.newFile().getAbsolutePath();
WriteToFile.toTSVadvancedAnnotations(filepath2, testmap);
Map<LoincId, UniversalLoinc2HPOAnnotation> deserializedMap = WriteToFile.fromTSVBasic(filepath, hpoTermMap2);
WriteToFile.fromTSVAdvanced(filepath2, deserializedMap, hpoTermMap2);
assertEquals(2, deserializedMap.size());
deserializedMap.values().forEach(System.out::println);
}
use of com.github.phenomics.ontolib.formats.hpo.HpoTerm in project loinc2hpo by monarch-initiative.
the class UniversalLoinc2HPOAnnotationTest method testSerializeAdvancedAnnotation.
@Test
@Ignore
public void testSerializeAdvancedAnnotation() throws Exception {
Map<String, HpoTerm> hpoTermMap;
String hpo_obo = FhirObservationAnalyzerTest.class.getClassLoader().getResource("obo/hp.obo").getPath();
HpoOboParser hpoOboParser = new HpoOboParser(new File(hpo_obo));
HpoOntology hpo = null;
try {
hpo = hpoOboParser.parse();
} catch (IOException e) {
e.printStackTrace();
}
ImmutableMap.Builder<String, HpoTerm> termmap = new ImmutableMap.Builder<>();
if (hpo != null) {
List<HpoTerm> res = hpo.getTermMap().values().stream().distinct().collect(Collectors.toList());
res.forEach(term -> termmap.put(term.getName(), term));
}
hpoTermMap = termmap.build();
UniversalLoinc2HPOAnnotation.Builder loinc2HpoAnnotationBuilder = new UniversalLoinc2HPOAnnotation.Builder();
LoincId loincId = new LoincId("600-7");
LoincScale loincScale = LoincScale.string2enum("Nom");
HpoTerm forCode1 = hpoTermMap.get("Recurrent E. coli infections");
HpoTerm forCode2 = hpoTermMap.get("Recurrent Staphylococcus aureus infections");
HpoTerm positive = hpoTermMap.get("Recurrent bacterial infections");
Code code1 = Code.getNewCode().setSystem("http://snomed.info/sct").setCode("112283007");
Code code2 = Code.getNewCode().setSystem("http://snomed.info/sct").setCode("3092008");
loinc2HpoAnnotationBuilder.setLoincId(loincId).setLoincScale(loincScale).setHighValueHpoTerm(positive).addAdvancedAnnotation(code1, new HpoTermId4LoincTest(forCode1, false)).addAdvancedAnnotation(code2, new HpoTermId4LoincTest(forCode2, false));
UniversalLoinc2HPOAnnotation annotation600 = loinc2HpoAnnotationBuilder.build();
System.out.println(annotation600.getAdvancedAnnotationsString());
}
use of com.github.phenomics.ontolib.formats.hpo.HpoTerm in project loinc2hpo by monarch-initiative.
the class UniversalLoinc2HPOAnnotationTest method testSerializeBasicAnnotation.
@Test
@Ignore
public void testSerializeBasicAnnotation() throws Exception {
Map<String, HpoTerm> hpoTermMap;
String hpo_obo = FhirObservationAnalyzerTest.class.getClassLoader().getResource("obo/hp.obo").getPath();
HpoOboParser hpoOboParser = new HpoOboParser(new File(hpo_obo));
HpoOntology hpo = null;
try {
hpo = hpoOboParser.parse();
} catch (IOException e) {
e.printStackTrace();
}
ImmutableMap.Builder<String, HpoTerm> termmap = new ImmutableMap.Builder<>();
if (hpo != null) {
List<HpoTerm> res = hpo.getTermMap().values().stream().distinct().collect(Collectors.toList());
res.forEach(term -> termmap.put(term.getName(), term));
}
hpoTermMap = termmap.build();
UniversalLoinc2HPOAnnotation.Builder loinc2HpoAnnotationBuilder = new UniversalLoinc2HPOAnnotation.Builder();
LoincId loincId = new LoincId("15074-8");
LoincScale loincScale = LoincScale.string2enum("Qn");
HpoTerm low = hpoTermMap.get("Hypoglycemia");
HpoTerm normal = hpoTermMap.get("Abnormality of blood glucose concentration");
HpoTerm hi = hpoTermMap.get("Hyperglycemia");
loinc2HpoAnnotationBuilder.setLoincId(loincId).setLoincScale(loincScale).setLowValueHpoTerm(low).setIntermediateValueHpoTerm(normal).setIntermediateNegated(true).setHighValueHpoTerm(hi);
UniversalLoinc2HPOAnnotation annotation15074 = loinc2HpoAnnotationBuilder.build();
System.out.println(UniversalLoinc2HPOAnnotation.getHeaderBasic());
System.out.println(annotation15074.getBasicAnnotationsString().trim());
}
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