Examples with HpoTermId4LoincTest org.monarchinitiative.loinc2hpo.loinc.HpoTermId4LoincTest used on opensource projects

Example 1 with HpoTermId4LoincTest

use of org.monarchinitiative.loinc2hpo.loinc.HpoTermId4LoincTest in project loinc2hpo by monarch-initiative.

the class ObservationAnalysisFromCodedValues method getHPOforObservation.

@Override
public HpoTermId4LoincTest getHPOforObservation() throws AmbiguousResultsFoundException, UnrecognizedCodeException, AnnotationNotFoundException {
    if (annotationMap.get(loincId) == null)
        throw new AnnotationNotFoundException();
    Set<HpoTermId4LoincTest> results = new HashSet<>();
    codedValue.getCoding().stream().filter(p -> annotationMap.get(loincId).getCodes().contains(new Code(p))).forEach(p -> results.add(annotationMap.get(loincId).loincInterpretationToHPO(new Code(p))));
    if (results.size() > 1) {
        throw new AmbiguousResultsFoundException();
    }
    if (results.size() == 1) {
        return results.iterator().next();
    } else {
        throw new UnrecognizedCodeException();
    }
}

Example 2 with HpoTermId4LoincTest

use of org.monarchinitiative.loinc2hpo.loinc.HpoTermId4LoincTest in project loinc2hpo by monarch-initiative.

the class ObservationAnalysisFromInterpretation method getHPOforObservation.

@Override
public HpoTermId4LoincTest getHPOforObservation() throws UnsupportedCodingSystemException, AmbiguousResultsFoundException, AnnotationNotFoundException, UnrecognizedCodeException {
    // here we use a map to store the results: since there could be more than one interpretation coding system,
    // we try them all and store the results in a map <external code, result in internal code>
    Map<Code, Code> results = new HashMap<>();
    // get the annotation class for this loinc code
    UniversalLoinc2HPOAnnotation annotationForLoinc = annotationMap.get(this.loincId);
    if (annotationForLoinc == null)
        throw new AnnotationNotFoundException();
    // all interpretation codes in different coding systems. Expect one in most cases.
    Set<Code> interpretationCodes = getInterpretationCodes();
    interpretationCodes.stream().filter(p -> CodeSystemConvertor.getCodeContainer().getCodeSystemMap().containsKey(p.getSystem())).forEach(p -> {
        Code internalCode = null;
        try {
            internalCode = CodeSystemConvertor.convertToInternalCode(p);
            results.put(p, internalCode);
        } catch (InternalCodeNotFoundException e) {
            e.printStackTrace();
        }
    });
    List<Code> distinct = results.values().stream().distinct().collect(Collectors.toList());
    if (distinct.size() == 1) {
        HpoTermId4LoincTest hpoTermId4LoincTest = annotationForLoinc.loincInterpretationToHPO(distinct.get(0));
        if (hpoTermId4LoincTest == null)
            throw new UnrecognizedCodeException();
        return hpoTermId4LoincTest;
    } else {
        throw new AmbiguousResultsFoundException();
    }
}

Example 3 with HpoTermId4LoincTest

use of org.monarchinitiative.loinc2hpo.loinc.HpoTermId4LoincTest 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 4 with HpoTermId4LoincTest

use of org.monarchinitiative.loinc2hpo.loinc.HpoTermId4LoincTest 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;
}

Example 5 with HpoTermId4LoincTest

use of org.monarchinitiative.loinc2hpo.loinc.HpoTermId4LoincTest in project loinc2hpo by monarch-initiative.

the class CurrentAnnotationController method populateTables.

private void populateTables() {
    if (model == null) {
        logger.error("model is null.");
        return;
    }
    this.currentAnnotation = model.getCurrentAnnotation();
    LoincEntry currentLoincEntry = model.getLoincEntryMap().get(currentAnnotation.getLoincId());
    annotationTitle.setText(String.format("Annotations for Loinc: %s[%s]", currentLoincEntry.getLOINC_Number(), currentLoincEntry.getLongName()));
    internalCodeAnnotations.clear();
    currentAnnotation.getCandidateHpoTerms().entrySet().stream().filter(p -> p.getKey().getSystem().equals(Loinc2HPOCodedValue.CODESYSTEM)).map(p -> new Annotation(p.getKey(), p.getValue())).forEach(internalCodeAnnotations::add);
    externalCodeAnnotations.clear();
    currentAnnotation.getCandidateHpoTerms().entrySet().stream().filter(p -> !p.getKey().getSystem().equals(Loinc2HPOCodedValue.CODESYSTEM)).map(p -> new Annotation(p.getKey(), p.getValue())).forEach(externalCodeAnnotations::add);
    interpretationCodeAnnotations.clear();
    for (Map.Entry<Code, Code> entry : CodeSystemConvertor.getCodeConversionMap().entrySet()) {
        logger.debug("key: " + entry.getKey() + "\nvalue: " + entry.getValue());
        HpoTermId4LoincTest result = currentAnnotation.loincInterpretationToHPO(entry.getValue());
        logger.debug("result is null? " + (result == null));
        if (result != null) {
            Annotation annotation = new Annotation(entry.getKey(), result);
            interpretationCodeAnnotations.add(annotation);
            logger.debug("interpretationCodeAnnotations size: " + interpretationCodeAnnotations.size());
        }
    }
    logger.debug("internalTableview is null: " + (internalTableview == null));
    logger.debug("internalCodeAnnotations is null: " + (internalTableview == null));
    logger.debug("internal annotation size: " + internalCodeAnnotations.size());
    internalCodeAnnotations.forEach(logger::info);
    logger.trace("exit initInternalTableview()");
}