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Example 1 with ImmutableTermId

use of com.github.phenomics.ontolib.ontology.data.ImmutableTermId 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;
}
Also used : LocalDateTime(java.time.LocalDateTime) HashMap(java.util.HashMap) LinkedHashMap(java.util.LinkedHashMap) LinkedHashMap(java.util.LinkedHashMap) HpoTermId4LoincTest(org.monarchinitiative.loinc2hpo.loinc.HpoTermId4LoincTest) LoincScale(org.monarchinitiative.loinc2hpo.loinc.LoincScale) TermPrefix(com.github.phenomics.ontolib.ontology.data.TermPrefix) ImmutableTermPrefix(com.github.phenomics.ontolib.ontology.data.ImmutableTermPrefix) UniversalLoinc2HPOAnnotation(org.monarchinitiative.loinc2hpo.loinc.UniversalLoinc2HPOAnnotation) LoincId(org.monarchinitiative.loinc2hpo.loinc.LoincId) MalformedLoincCodeException(org.monarchinitiative.loinc2hpo.exception.MalformedLoincCodeException) Code(org.monarchinitiative.loinc2hpo.codesystems.Code) HpoTerm(com.github.phenomics.ontolib.formats.hpo.HpoTerm) ImmutableTermId(com.github.phenomics.ontolib.ontology.data.ImmutableTermId) ImmutableTermPrefix(com.github.phenomics.ontolib.ontology.data.ImmutableTermPrefix)

Example 2 with ImmutableTermId

use of com.github.phenomics.ontolib.ontology.data.ImmutableTermId in project loinc2hpo by monarch-initiative.

the class FromFile method getHpoTermId.

TermId getHpoTermId(String termString) throws MalformedHpoTermIdException {
    logger.trace("getHpoTermId=" + termString);
    if (termString.equalsIgnoreCase("NA"))
        return null;
    int i = termString.indexOf(":");
    if (i != 2)
        throw new MalformedHpoTermIdException("Malformed HPO String: " + termString);
    TermId id = new ImmutableTermId(HPPREFIX, termString.substring(3));
    if (ontology.getTermMap().containsKey(id))
        return id;
    else
        throw new MalformedHpoTermIdException("Could not find id " + termString);
}
Also used : MalformedHpoTermIdException(org.monarchinitiative.loinc2hpo.exception.MalformedHpoTermIdException) ImmutableTermId(com.github.phenomics.ontolib.ontology.data.ImmutableTermId) TermId(com.github.phenomics.ontolib.ontology.data.TermId) ImmutableTermId(com.github.phenomics.ontolib.ontology.data.ImmutableTermId)

Example 3 with ImmutableTermId

use of com.github.phenomics.ontolib.ontology.data.ImmutableTermId in project loinc2hpo by monarch-initiative.

the class WriteToFile method convertToTermID.

private static TermId convertToTermID(String record) {
    TermPrefix prefix = new ImmutableTermPrefix("HP");
    if (!record.startsWith(prefix.getValue()) || record.length() <= 3) {
        logger.error("Non HPO termId is detected from TSV");
        return null;
    }
    String id = record.substring(3);
    return new ImmutableTermId(prefix, id);
}
Also used : TermPrefix(com.github.phenomics.ontolib.ontology.data.TermPrefix) ImmutableTermPrefix(com.github.phenomics.ontolib.ontology.data.ImmutableTermPrefix) ImmutableTermId(com.github.phenomics.ontolib.ontology.data.ImmutableTermId) ImmutableTermPrefix(com.github.phenomics.ontolib.ontology.data.ImmutableTermPrefix)

Aggregations

ImmutableTermId (com.github.phenomics.ontolib.ontology.data.ImmutableTermId)3 ImmutableTermPrefix (com.github.phenomics.ontolib.ontology.data.ImmutableTermPrefix)2 TermPrefix (com.github.phenomics.ontolib.ontology.data.TermPrefix)2 HpoTerm (com.github.phenomics.ontolib.formats.hpo.HpoTerm)1 TermId (com.github.phenomics.ontolib.ontology.data.TermId)1 LocalDateTime (java.time.LocalDateTime)1 HashMap (java.util.HashMap)1 LinkedHashMap (java.util.LinkedHashMap)1 Code (org.monarchinitiative.loinc2hpo.codesystems.Code)1 MalformedHpoTermIdException (org.monarchinitiative.loinc2hpo.exception.MalformedHpoTermIdException)1 MalformedLoincCodeException (org.monarchinitiative.loinc2hpo.exception.MalformedLoincCodeException)1 HpoTermId4LoincTest (org.monarchinitiative.loinc2hpo.loinc.HpoTermId4LoincTest)1 LoincId (org.monarchinitiative.loinc2hpo.loinc.LoincId)1 LoincScale (org.monarchinitiative.loinc2hpo.loinc.LoincScale)1 UniversalLoinc2HPOAnnotation (org.monarchinitiative.loinc2hpo.loinc.UniversalLoinc2HPOAnnotation)1