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

Example 1 with LoincEntry

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

the class ObservationDownloader method iteratorHapiFHIRServer.

public static void iteratorHapiFHIRServer() {
    // printObservationInfo();
    // printPatientInfo();
    // BufferedReader bufferedReader = new BufferedReader(new FileReader(""));
    // find20CompleteRecordOfEachType();
    String path = null;
    HashMap<String, StringBuilder> completeObservations = new HashMap<>();
    completeObservations.put("Qn", new StringBuilder());
    completeObservations.put("Ord", new StringBuilder());
    completeObservations.put("Nom", new StringBuilder());
    completeObservations.put("Nar", new StringBuilder());
    completeObservations.put("OrdQn", new StringBuilder());
    completeObservations.put("unkown", new StringBuilder());
    HashMap<String, Integer> countComplete = new HashMap<>();
    countComplete.put("Qn", 0);
    countComplete.put("Ord", 0);
    countComplete.put("Nom", 0);
    countComplete.put("Nar", 0);
    countComplete.put("OrdQn", 0);
    countComplete.put("unknown", 0);
    HashMap<String, StringBuilder> accetableObservations = new HashMap<>();
    accetableObservations.put("Qn", new StringBuilder());
    accetableObservations.put("Ord", new StringBuilder());
    accetableObservations.put("Nom", new StringBuilder());
    accetableObservations.put("Nar", new StringBuilder());
    accetableObservations.put("OrdQn", new StringBuilder());
    accetableObservations.put("unknown", new StringBuilder());
    HashMap<String, Integer> countAccetable = new HashMap<>();
    countAccetable.put("Qn", 0);
    countAccetable.put("Ord", 0);
    countAccetable.put("Nom", 0);
    countAccetable.put("Nar", 0);
    countAccetable.put("OrdQn", 0);
    countAccetable.put("unknown", 0);
    JFileChooser chooser = new JFileChooser();
    int returnVal = chooser.showOpenDialog(null);
    if (returnVal == JFileChooser.APPROVE_OPTION) {
        path = chooser.getSelectedFile().getAbsolutePath();
        System.out.println(path);
        Map<LoincId, LoincEntry> loincEntryMap = LoincEntry.getLoincEntryList(path);
        System.out.println("size of loinc table: " + loincEntryMap.size());
        for (LoincEntry loincEntry : loincEntryMap.values()) {
            if (countComplete.containsKey(loincEntry.getScale()) && countComplete.get(loincEntry.getScale()) < 50) {
                try {
                    List<Observation> results = ObservationDownloader.retrieveObservation(loincEntry.getLOINC_Number().toString());
                    if (results != null && !results.isEmpty()) {
                        for (Observation observation : results) {
                            if (isComplte(observation)) {
                                String aCompleteRecord = jsonParser.setPrettyPrint(true).encodeResourceToString(observation);
                                if (completeObservations.containsKey(loincEntry.getScale())) {
                                    completeObservations.get(loincEntry.getScale()).append(aCompleteRecord);
                                    completeObservations.get(loincEntry.getScale()).append("\n\n");
                                    completeObservations.get(loincEntry.getScale()).append(Character.toString((char) 12));
                                    countComplete.put(loincEntry.getScale(), countComplete.get(loincEntry.getScale()) + 1);
                                } else {
                                    completeObservations.get("unknown").append(aCompleteRecord);
                                    completeObservations.get("unknown").append("\n\n");
                                    completeObservations.get("unknown").append(Character.toString((char) 12));
                                    countComplete.put("unknown", countAccetable.get("unknown") + 1);
                                }
                                continue;
                            }
                            if (isAcceptable(observation)) {
                                String aAcceptableRecord = jsonParser.setPrettyPrint(true).encodeResourceToString(observation);
                                if (accetableObservations.containsKey(loincEntry.getScale()) && countAccetable.get(loincEntry.getScale()) < 50) {
                                    accetableObservations.get(loincEntry.getScale()).append(aAcceptableRecord);
                                    accetableObservations.get(loincEntry.getScale()).append("\n\n");
                                    accetableObservations.get(loincEntry.getScale()).append(Character.toString((char) 12));
                                    countAccetable.put(loincEntry.getScale(), countAccetable.get(loincEntry.getScale()) + 1);
                                } else if (countAccetable.get("unknown") < 50) {
                                    accetableObservations.get("unknown").append(aAcceptableRecord);
                                    accetableObservations.get("unknown").append("\n\n");
                                    accetableObservations.get("unknown").append(Character.toString((char) 12));
                                    countAccetable.put("unknown", countAccetable.get("unknown") + 1);
                                }
                            }
                        }
                    }
                } catch (Exception e) {
                    continue;
                }
            }
        }
    }
    for (String scale : completeObservations.keySet()) {
        if (!completeObservations.get(scale).toString().isEmpty()) {
            WriteToFile.writeToFile(completeObservations.get(scale).toString(), scale + "_complteObservations.txt");
        } else {
            System.out.println("No complete observations were found for loinc scale type: " + scale);
        }
    }
    for (String scale : accetableObservations.keySet()) {
        if (!accetableObservations.get(scale).toString().isEmpty()) {
            WriteToFile.writeToFile(accetableObservations.get(scale).toString(), scale + "_acceptableObservations.txt");
        } else {
            System.out.println("No acceptable observations were found for loinc scale type: " + scale);
        }
    }
}

Example 2 with LoincEntry

use of org.monarchinitiative.loinc2hpo.loinc.LoincEntry 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()");
}