Examples with AnnotatorResponse ubic.basecode.ontology.ncbo.AnnotatorResponse used on opensource projects

Example 1 with AnnotatorResponse

use of ubic.basecode.ontology.ncbo.AnnotatorResponse in project Gemma by PavlidisLab.

the class ExternalDatabaseEvidenceImporterAbstractCLI method findWithAnnotator.

// step 3
private boolean findWithAnnotator(String meshOrOmimId, String keywordSearchAnnotator, String externalDatabase, boolean modifySearch, Collection<OntologyTerm> onParents, String child) throws Exception {
    String usedChild = "";
    if (child == null) {
        usedChild = null;
    }
    if (onParents != null) {
        for (OntologyTerm o : onParents) {
            boolean found = this.findWithAnnotator(o.getLabel(), keywordSearchAnnotator, externalDatabase, modifySearch, null, meshOrOmimId);
            if (found) {
                return true;
            }
        }
        return false;
    }
    String searchTerm = keywordSearchAnnotator.toLowerCase();
    Collection<AnnotatorResponse> annotatorResponses = null;
    String key = meshOrOmimId;
    // we are not dealing with an omim identifier, gwas using this case for example
    if (key == null) {
        key = keywordSearchAnnotator;
    }
    if (modifySearch) {
        searchTerm = ExternalDatabaseEvidenceImporterAbstractCLI.removeSpecificKeywords(keywordSearchAnnotator.toLowerCase());
    }
    if (!descriptionToIgnore.contains(searchTerm)) {
        // we already know the answer for this term
        if (cacheAnswerFromAnnotator.containsKey(searchTerm)) {
            return false;
        }
        // search with the annotator and filter result to take out obsolete terms given
        try {
            annotatorResponses = this.removeNotExistAndObsolete(AnnotatorClient.findTerm(searchTerm));
        } catch (SocketException e1) {
            Thread.sleep(10000);
            try {
                annotatorResponses = this.removeNotExistAndObsolete(AnnotatorClient.findTerm(searchTerm));
            } catch (SocketException e2) {
                Thread.sleep(10000);
                try {
                    annotatorResponses = this.removeNotExistAndObsolete(AnnotatorClient.findTerm(searchTerm));
                } catch (SocketException e3) {
                    AbstractCLI.log.error("connection problem");
                    return false;
                }
            }
        }
        cacheAnswerFromAnnotator.put(searchTerm, annotatorResponses);
        if (annotatorResponses != null && !annotatorResponses.isEmpty()) {
            AnnotatorResponse annotatorResponse = annotatorResponses.iterator().next();
            String condition = annotatorResponse.findCondition(modifySearch);
            if (condition != null) {
                OntologyTerm on = this.findOntologyTermExistAndNotObsolote(annotatorResponse.getValueUri());
                if (on != null) {
                    searchTerm = AnnotatorClient.removeSpecialCharacters(searchTerm).replaceAll("\\+", " ");
                    if (modifySearch) {
                        searchTerm = searchTerm + "   (" + keywordSearchAnnotator + ")";
                    }
                    String lineToWrite = key + "\t" + on.getUri() + "\t" + on.getLabel() + "\t" + searchTerm + "\t" + usedChild + "\t" + condition + "\t" + externalDatabase + "\n";
                    outMappingFoundBuffer.add(lineToWrite);
                    return true;
                }
            }
        }
    }
    logRequestAnnotator.write(AnnotatorClient.removeSpecialCharacters(searchTerm).replaceAll("\\+", " ") + "   (" + keywordSearchAnnotator + ")\t");
    if (annotatorResponses != null && !annotatorResponses.isEmpty()) {
        for (AnnotatorResponse ar : annotatorResponses) {
            logRequestAnnotator.write(ar.getTxtMatched() + ";   ");
        }
    }
    logRequestAnnotator.write("\n");
    logRequestAnnotator.flush();
    return false;
}