Examples with Code org.monarchinitiative.loinc2hpo.codesystems.Code used on opensource projects

Example 6 with Code

use of org.monarchinitiative.loinc2hpo.codesystems.Code in project loinc2hpo by monarch-initiative.

the class ObservationAnalysisFromQnValue method getHPOforObservation.

@Override
public HpoTermId4LoincTest getHPOforObservation() throws ReferenceNotFoundException, AmbiguousReferenceException, UnrecognizedCodeException {
    HpoTermId4LoincTest hpoTermId4LoincTest = null;
    // find applicable reference range
    List<Observation.ObservationReferenceRangeComponent> references = this.references.stream().filter(p -> withinAgeRange(p)).collect(Collectors.toList());
    if (references.size() < 1) {
        throw new ReferenceNotFoundException();
    } else if (references.size() == 1) {
        Observation.ObservationReferenceRangeComponent targetReference = references.get(0);
        double low = targetReference.hasLow() ? targetReference.getLow().getValue().doubleValue() : Double.MIN_VALUE;
        double high = targetReference.hasHigh() ? targetReference.getHigh().getValue().doubleValue() : Double.MAX_VALUE;
        double observed = valueQuantity.getValue().doubleValue();
        Loinc2HPOCodedValue result;
        if (observed < low) {
            result = Loinc2HPOCodedValue.fromCode("L");
        } else if (observed > high) {
            result = Loinc2HPOCodedValue.fromCode("H");
        } else {
            result = Loinc2HPOCodedValue.fromCode("N");
        }
        Code resultCode = Code.getNewCode().setSystem(Loinc2HPOCodedValue.CODESYSTEM).setCode(result.toCode());
        hpoTermId4LoincTest = annotationMap.get(loincId).loincInterpretationToHPO(resultCode);
    } else if (references.size() == 2) {
        // what does it mean with multiple references
        throw new AmbiguousReferenceException();
    } else if (references.size() == 3) {
    // it can happen when there is actually one range but coded in three ranges
    // e.g. normal 20-30
    // in this case, one range ([20, 30]) is sufficient;
    // however, it is written as three ranges: ( , 20) [20, 30] (30, )
    // We should handle this case
    } else {
        throw new AmbiguousReferenceException();
    }
    // if we can still not find an answer, it is probably that we did not have the annotation
    if (hpoTermId4LoincTest == null)
        throw new UnrecognizedCodeException();
    return hpoTermId4LoincTest;
}

Example 7 with Code

use of org.monarchinitiative.loinc2hpo.codesystems.Code in project loinc2hpo by monarch-initiative.

the class UniversalLoinc2HPOAnnotationTest method testToString.

@Test
public void testToString() 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();
    Map<LoincId, UniversalLoinc2HPOAnnotation> testmap = new HashMap<>();
    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");
    Map<String, Code> internalCodes = CodeSystemConvertor.getCodeContainer().getCodeSystemMap().get(Loinc2HPOCodedValue.CODESYSTEM);
    UniversalLoinc2HPOAnnotation glucoseAnnotation = new UniversalLoinc2HPOAnnotation.Builder().setLoincId(loincId).setLoincScale(loincScale).setLowValueHpoTerm(low).setIntermediateValueHpoTerm(normal).setHighValueHpoTerm(hi).setIntermediateNegated(true).build();
    testmap.put(loincId, glucoseAnnotation);
    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");
    UniversalLoinc2HPOAnnotation bacterialAnnotation = new UniversalLoinc2HPOAnnotation.Builder().setLoincId(loincId).setLoincScale(loincScale).addAdvancedAnnotation(code1, new HpoTermId4LoincTest(forCode1, false)).addAdvancedAnnotation(code2, new HpoTermId4LoincTest(forCode2, false)).addAdvancedAnnotation(internalCodes.get("P"), new HpoTermId4LoincTest(positive, false)).build();
    testmap.put(loincId, bacterialAnnotation);
    // testmap.entrySet().forEach(System.out::println);
    String path = temporaryFolder.newFile("testoutput.tsv").getPath();
    WriteToFile.writeToFile("", path);
    testmap.forEach((k, v) -> {
        WriteToFile.appendToFile(v.toString(), path);
        WriteToFile.appendToFile("\n", path);
    });
    // WriteToFile.appendToFile(glucoseAnnotation.toString(), path);
    BufferedReader reader = new BufferedReader(new FileReader(path));
    // System.out.println(UniversalLoinc2HPOAnnotation.getHeaderAdvanced());
    // reader.lines().forEach(System.out::println);
    String content = "15074-8\tQn\thttp://jax.org/loinc2hpo\tL\tHP:0001943\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "15074-8\tQn\thttp://jax.org/loinc2hpo\tN\tHP:0011015\ttrue\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "15074-8\tQn\thttp://jax.org/loinc2hpo\tH\tHP:0003074\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "15074-8\tQn\thttp://jax.org/loinc2hpo\tA\tHP:0011015\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "600-7\tNom\thttp://snomed.info/sct\t112283007\tHP:0002740\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "600-7\tNom\thttp://jax.org/loinc2hpo\tP\tHP:0002718\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "600-7\tNom\thttp://snomed.info/sct\t3092008\tHP:0002726\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull";
    assertEquals(9, reader.lines().collect(Collectors.toList()).size());
}

Example 8 with Code

use of org.monarchinitiative.loinc2hpo.codesystems.Code in project loinc2hpo by monarch-initiative.

the class UniversalLoinc2HPOAnnotationTest method testBuilderForBasicAnnotation.

@Test
public void testBuilderForBasicAnnotation() 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();
    assertEquals("15074-8", annotation15074.getLoincId().toString());
    assertEquals("Qn", annotation15074.getLoincScale().toString());
    Map<String, Code> internalCodes = CodeSystemConvertor.getCodeContainer().getCodeSystemMap().get(Loinc2HPOCodedValue.CODESYSTEM);
    Code code4low = internalCodes.get("L");
    assertEquals(low.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4low).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(false, annotation15074.getCandidateHpoTerms().get(code4low).isNegated());
    Code code4high = internalCodes.get("H");
    assertEquals(hi.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4high).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(false, annotation15074.getCandidateHpoTerms().get(code4high).isNegated());
    Code code4normal = internalCodes.get("N");
    assertEquals(normal.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4normal).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(true, annotation15074.getCandidateHpoTerms().get(code4normal).isNegated());
    Code code4Pos = internalCodes.get("P");
    assertEquals(hi.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4Pos).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(false, annotation15074.getCandidateHpoTerms().get(code4Pos).isNegated());
    Code code4NP = internalCodes.get("NP");
    assertEquals(normal.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4NP).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(true, annotation15074.getCandidateHpoTerms().get(code4NP).isNegated());
}

Example 9 with Code

use of org.monarchinitiative.loinc2hpo.codesystems.Code in project loinc2hpo by monarch-initiative.

the class FhirObservationAnalyzerTest method testUniversalAnnotation.

@Test
public void testUniversalAnnotation() throws Exception {
    FhirObservationAnalyzer.setObservation(observation);
    Map<LoincId, UniversalLoinc2HPOAnnotation> testmap = new HashMap<>();
    LoincId loincId = new LoincId("15074-8");
    LoincScale loincScale = LoincScale.string2enum("Qn");
    TermId low = hpoTermMap.get("Hypoglycemia").getId();
    TermId normal = hpoTermMap.get("Abnormality of blood glucose concentration").getId();
    TermId hi = hpoTermMap.get("Hyperglycemia").getId();
    Map<String, Code> internalCodes = CodeSystemConvertor.getCodeContainer().getCodeSystemMap().get(Loinc2HPOCodedValue.CODESYSTEM);
    /**
     *        UniversalLoinc2HPOAnnotation glucoseAnnotation = new UniversalLoinc2HPOAnnotation(loincId, loincScale);
     *        glucoseAnnotation.addAnnotation(internalCodes.get("L"), new HpoTermId4LoincTest(low, false))
     *                .addAnnotation(internalCodes.get("N"), new HpoTermId4LoincTest(normal, true))
     *                .addAnnotation(internalCodes.get("A"), new HpoTermId4LoincTest(normal, false))
     *                .addAnnotation(internalCodes.get("H"), new HpoTermId4LoincTest(hi, false));
     */
    UniversalLoinc2HPOAnnotation glucoseAnnotation = new UniversalLoinc2HPOAnnotation.Builder().setLoincId(loincId).setLoincScale(loincScale).setLowValueHpoTerm(hpoTermMap.get("Hypoglycemia")).setIntermediateValueHpoTerm(hpoTermMap.get("Abnormality of blood glucose concentration")).setHighValueHpoTerm(hpoTermMap.get("Hyperglycemia")).setIntermediateNegated(true).build();
    testmap.put(loincId, glucoseAnnotation);
    LabTestResultInHPO result = FhirObservationAnalyzer.getHPOFromInterpretation(FhirObservationAnalyzer.getObservation().getInterpretation(), testmap);
    System.out.println(result);
}

Example 10 with Code

use of org.monarchinitiative.loinc2hpo.codesystems.Code in project loinc2hpo by monarch-initiative.

the class WriteToFile method fromTSV.

/**
 * A method to deserialize annotation map from a TSV file.
 * @param path filepath to the TSV
 * @param hpoTermMap a HPO map from TermId to HpoTerm. Note: the key is TermId, instead of TermName
 * @return an annotation map
 * @throws FileNotFoundException
 */
public static Map<LoincId, UniversalLoinc2HPOAnnotation> fromTSV(String path, Map<TermId, HpoTerm> hpoTermMap) throws FileNotFoundException {
    Map<LoincId, UniversalLoinc2HPOAnnotation> deserializedMap = new LinkedHashMap<>();
    Map<LoincId, UniversalLoinc2HPOAnnotation.Builder> builderMap = new HashMap<>();
    Map<String, Code> internalCode = CodeSystemConvertor.getCodeContainer().getCodeSystemMap().get(Loinc2HPOCodedValue.CODESYSTEM);
    BufferedReader reader = new BufferedReader(new FileReader(path));
    reader.lines().forEach(serialized -> {
        String[] elements = serialized.split("\\t");
        if (elements.length == 13 && !serialized.startsWith("loincId")) {
            try {
                LoincId loincId = new LoincId(elements[0]);
                LoincScale loincScale = LoincScale.string2enum(elements[1]);
                String codeSystem = elements[2];
                String codeId = elements[3];
                TermPrefix prefix = new ImmutableTermPrefix(elements[4].substring(0, 2));
                String id = elements[4].substring(3);
                HpoTerm hpoTerm = hpoTermMap.get(new ImmutableTermId(prefix, id));
                boolean inverse = Boolean.parseBoolean(elements[5]);
                String note = elements[6].equals(MISSINGVALUE) ? null : elements[6];
                boolean flag = Boolean.parseBoolean(elements[7]);
                double version = Double.parseDouble(elements[8]);
                LocalDateTime createdOn = elements[9].equals(MISSINGVALUE) ? null : LocalDateTime.parse(elements[9]);
                String createdBy = elements[10].equals(MISSINGVALUE) ? null : elements[10];
                LocalDateTime lastEditedOn = elements[11].equals(MISSINGVALUE) ? null : LocalDateTime.parse(elements[11]);
                String lastEditedBy = elements[12].equals(MISSINGVALUE) ? null : elements[12];
                if (!builderMap.containsKey(loincId)) {
                    UniversalLoinc2HPOAnnotation.Builder builder = new UniversalLoinc2HPOAnnotation.Builder().setLoincId(loincId).setLoincScale(loincScale).setNote(note).setFlag(flag).setVersion(version).setCreatedOn(createdOn).setCreatedBy(createdBy).setLastEditedOn(lastEditedOn).setLastEditedBy(lastEditedBy);
                    builderMap.put(loincId, builder);
                }
                Code code = Code.getNewCode().setSystem(codeSystem).setCode(codeId);
                HpoTermId4LoincTest hpoTermId4LoincTest = new HpoTermId4LoincTest(hpoTerm, inverse);
                if (code.equals(internalCode.get("L"))) {
                    builderMap.get(loincId).setLowValueHpoTerm(hpoTermId4LoincTest.getHpoTerm());
                }
                if (code.equals(internalCode.get("N"))) {
                    builderMap.get(loincId).setIntermediateValueHpoTerm(hpoTermId4LoincTest.getHpoTerm());
                    builderMap.get(loincId).setIntermediateNegated(hpoTermId4LoincTest.isNegated());
                }
                if (code.equals(internalCode.get("H"))) {
                    builderMap.get(loincId).setHighValueHpoTerm(hpoTermId4LoincTest.getHpoTerm());
                }
                if (code.equals(internalCode.get("A")) || code.equals(internalCode.get("P")) || code.equals(internalCode.get("NP"))) {
                    // currently, we neglect those codes
                    // it will be wrong to do so if the user has manually changed what map to them
                    logger.info("!!!!!!!!!!!annotation neglected. MAY BE WRONG!!!!!!!!!!!!!!!");
                } else {
                    builderMap.get(loincId).addAdvancedAnnotation(code, hpoTermId4LoincTest);
                }
            } catch (MalformedLoincCodeException e) {
                logger.error("Malformed loinc code line: " + serialized);
            }
        } else {
            if (elements.length != 13) {
                logger.error(String.format("line does not have 13 elements, but has %d elements. Line: %s", elements.length, serialized));
            } else {
                logger.info("line is header: " + serialized);
            }
        }
    });
    try {
        reader.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
    builderMap.entrySet().forEach(b -> deserializedMap.put(b.getKey(), b.getValue().build()));
    return deserializedMap;
}