@Override public <T> PatientData<T> getData(String name) { return this.patient.getData(name); }
/** * Prompts retrieval of rejected {@link VocabularyTerm gene} objects from {@link #patient}. * * @return {@link AdapterBuilder self} */ AdapterBuilder withRejectedGenes() { final PatientData<Gene> genes = this.patient.getData(GENES); this.rejectedGenes = extractRejectedGenes(genes); return this; }
@Override public void writeJSON(Patient patient, JSONObject json, Collection<String> selectedFieldNames) { if (selectedFieldNames != null && !selectedFieldNames.contains(DATA_NAME)) { return; } PatientData<String> lifeStatusData = patient.getData(DATA_NAME); if (lifeStatusData == null) { if (selectedFieldNames != null && selectedFieldNames.contains(DATA_NAME)) { json.put(DATA_NAME, ALIVE); } return; } json.put(DATA_NAME, lifeStatusData.getValue()); }
private static String gender(Patient patient) { String rawSex = patient.<ImmutablePair<String, String>>getData("sex").get(0).getRight(); if (rawSex.toUpperCase().equals("M")) { return ApiConfiguration.JSON_PATIENT_GENDER_MALE; } if (rawSex.toUpperCase().equals("F")) { return ApiConfiguration.JSON_PATIENT_GENDER_FEMALE; } return ApiConfiguration.JSON_PATIENT_GENDER_OTHER; }
@Override public void writeJSON(Patient patient, JSONObject json, Collection<String> selectedFieldNames) { if (selectedFieldNames != null && !selectedFieldNames.contains(DIAGNOSIS_PROPERTY)) { return; } PatientData<Disorder> data = patient.getData(getName()); json.put(JSON_KEY_CLINICAL_DIAGNOSIS, diseasesToJSON(data)); }
@Override public void writeJSON(Patient patient, JSONObject json, Collection<String> selectedFieldNames) { if (selectedFieldNames != null && !selectedFieldNames.contains(EXTERNAL_IDENTIFIER_PROPERTY_NAME)) { return; } PatientData<String> patientData = patient.<String>getData(DATA_NAME); if (patientData != null && patientData.isNamed()) { Iterator<Entry<String, String>> values = patientData.dictionaryIterator(); while (values.hasNext()) { Entry<String, String> datum = values.next(); json.put(datum.getKey(), datum.getValue()); } } }
/** * Sets present and absent {@link VocabularyTerm} vocabulary terms from {@link #patient}. */ private void setTerms() { final Set<? extends Feature> features = this.patient.getFeatures(); final PatientData<List<VocabularyTerm>> qualifiers = this.patient.getData(GLOBAL_QUALIFIERS); final Map<String, Set<VocabularyTerm>> terms = extractTerms(features, qualifiers); this.presentTerms = terms.get(PRESENT_TERMS); this.absentTerms = terms.get(ABSENT_TERMS); }
@Override public void writeJSON(Patient patient, JSONObject json, Collection<String> selectedFieldNames) { if (selectedFieldNames != null && !selectedFieldNames.contains(DIAGNOSIS_PROPERTY)) { return; } PatientData<Disorder> data = patient.getData(getName()); json.put(JSON_KEY_CLINICAL_DIAGNOSIS, diseasesToJSON(data)); }
@Override public Collection<String> getNotificationEmailsForPatient(Patient patient) { List<String> result = new ArrayList<>(); if (patient != null) { PatientData<ContactInfo> data = patient.getData("contact"); if (data != null && data.size() > 0) { for (ContactInfo contact : data) { result.addAll(contact.getEmails()); } } } return result; } }
@Override public void writeJSON(Patient patient, JSONObject json, Collection<String> selectedFieldNames) { if (!isFieldIncluded(selectedFieldNames, DISORDER_PROPERTIES)) { return; } PatientData<Disorder> data = patient.getData(getName()); json.put(JSON_KEY_DISORDERS, diseasesToJSON(data, selectedFieldNames)); }
@Override public void save(Patient patient, DocumentModelBridge doc) { BaseObject data = ((XWikiDocument) doc).getXObject(Patient.CLASS_REFERENCE); if (data == null) { throw new NullPointerException(ERROR_MESSAGE_NO_PATIENT_CLASS); } String gender = patient.<String>getData(DATA_NAME).getValue(); data.setStringValue(INTERNAL_PROPERTY_NAME, gender); }
@Override public void save(Patient patient, DocumentModelBridge doc) { BaseObject data = ((XWikiDocument) doc).getXObject(Patient.CLASS_REFERENCE); if (data == null) { throw new NullPointerException(ERROR_MESSAGE_NO_PATIENT_CLASS); } PatientData<String> lifeStatus = patient.getData(DATA_NAME); data.setStringValue(DATA_NAME, lifeStatus.getValue()); }
@Override public void writeJSON(Patient patient, JSONObject json, Collection<String> selectedFieldNames) { if (!isFieldIncluded(selectedFieldNames, DISORDER_PROPERTIES)) { return; } PatientData<Disorder> data = patient.getData(getName()); json.put(JSON_KEY_DISORDERS, diseasesToJSON(data, selectedFieldNames)); }
@Override public void writeJSON(@Nonnull final Patient patient, @Nonnull final JSONObject json) { final PatientData<Pair<String, String>> identifiers = patient.getData(IDENTIFIERS_STRING); final JSONArray eidsJSON = (identifiers != null && identifiers.isIndexed() && identifiers.size() > 0) ? toJSON(identifiers) : null; json.putOpt(IDENTIFIERS_STRING, eidsJSON); }
@Override public void writeJSON(Patient patient, JSONObject json, Collection<String> selectedFieldNames) { if (selectedFieldNames != null && !isFieldSuffixIncluded(selectedFieldNames, PHENOTYPE_POSITIVE_PROPERTY)) { return; } PatientData<Feature> data = patient.getData(getName()); json.put(JSON_KEY_FEATURES, featuresToJSON(data, selectedFieldNames)); json.put(JSON_KEY_NON_STANDARD_FEATURES, nonStandardFeaturesToJSON(data, selectedFieldNames)); }
@Override public void writeJSON(Patient patient, JSONObject json, Collection<String> selectedFieldNames) { if (selectedFieldNames != null && !isFieldSuffixIncluded(selectedFieldNames, PHENOTYPE_POSITIVE_PROPERTY)) { return; } PatientData<Feature> data = patient.getData(getName()); json.put(JSON_KEY_FEATURES, featuresToJSON(data, selectedFieldNames)); json.put(JSON_KEY_NON_STANDARD_FEATURES, nonStandardFeaturesToJSON(data, selectedFieldNames)); }
@Override public void save(Patient patient, DocumentModelBridge doc) { BaseObject data = ((XWikiDocument) doc).getXObject(Patient.CLASS_REFERENCE); if (data == null) { throw new NullPointerException(ERROR_MESSAGE_NO_PATIENT_CLASS); } PatientData<String> identifiers = patient.<String>getData(DATA_NAME); if (!identifiers.isNamed()) { return; } String externalId = identifiers.get(EXTERNAL_IDENTIFIER_PROPERTY_NAME); data.setStringValue(EXTERNAL_IDENTIFIER_PROPERTY_NAME, externalId); }
private void readDetails(Patient patient) { this.genes = this.getGenes(patient); this.phenotypes = new DefaultPhenotypesMap(patient); PatientData<List<SolrVocabularyTerm>> globalControllers = patient.getData("global-qualifiers"); this.ageOfOnset = this.getAgeOfOnset(globalControllers); this.modeOfInheritance = this.getModeOfInheritance(globalControllers); }
@Override public void save(Patient patient, DocumentModelBridge doc) { PatientData<Integer> data = patient.getData(getName()); if (data == null || !data.isNamed()) { return; } XWikiContext context = this.xcontext.get(); BaseObject o = ((XWikiDocument) doc).getXObject(getXClassReference(), true, context); for (String property : getProperties()) { o.set(PREFIX + property, data.get(property), context); } }
@Override public void save(Patient patient, DocumentModelBridge doc) { PatientData<Integer> data = patient.getData(getName()); if (data == null || !data.isNamed()) { return; } XWikiContext context = this.xcontext.get(); BaseObject o = ((XWikiDocument) doc).getXObject(getXClassReference(), true, context); for (String property : getProperties()) { o.set(property, data.get(property), context); } }