Example #1
0
 /** Force a refresh of all names assigned to graph nodes. */
 @SuppressWarnings("unchecked")
 void refreshNodeNames(boolean showCode, boolean abbreviate) {
   for (Iterator<Tuple> tuples = getNodes().tuples(); tuples.hasNext(); ) {
     Tuple t = tuples.next();
     ResolvedConceptReference rcr = (ResolvedConceptReference) t.get("RCR");
     if (rcr != null) {
       String code = showCode ? rcr.getConceptCode() : null;
       String desc =
           rcr.getEntityDescription() != null ? rcr.getEntityDescription().getContent() : null;
       t.set("name", getNodeName(code, desc, abbreviate, "\n"));
     }
   }
 }
Example #2
0
  /*
   * (non-Javadoc)
   *
   * @see prefuse.data.Graph#addNode()
   */
  public Node addNode(ResolvedConceptReference rcr, boolean showCode) {
    // Limit length for nodes other than the focus item
    // to allow more items in same horizontal space.
    String code = showCode ? rcr.getConceptCode() : null;
    String desc =
        rcr.getEntityDescription() != null ? rcr.getEntityDescription().getContent() : null;
    String nodeName = getNodeName(code, desc, false, "\n");

    if (allNodes.containsKey(nodeName)) {
      return allNodes.get(nodeName);
    } else {
      Node newNode = addNode();

      newNode.setString("name", nodeName);
      newNode.set("RCR", rcr);
      allNodes.put(nodeName, newNode);
      return newNode;
    }
  }
Example #3
0
  public static List searchEVS(
      String term,
      String dtsVocab,
      String retired,
      String sSearchInEVS,
      String sUISearchType,
      String sMetaSource,
      int sMetaLimit)
      throws Exception {

    String algorithm;
    String altNameType;
    String CCode;
    String prefName = "";
    Boolean isRetired = new Boolean(false);
    Boolean bTrue = new Boolean(true);
    Boolean bFalse = new Boolean(false);
    boolean isMetaCodeSearch = false;
    Boolean codeFoundInThesaurus = new Boolean(false);
    String source = "";
    String definition = "";
    List vCon = new ArrayList();
    String sDefDefault = "No value exists.";
    String sDef = "";
    String sDefSrc = "";
    // List vCon = null;
    List vMetaDefs = new ArrayList();
    // List vMetaDefs = null;

    if (dtsVocab.equals("Thesaurus/Metathesaurus")
        || dtsVocab.equals("")
        || dtsVocab.equals("NCI Thesaurus")
        || dtsVocab.equals("NCI_Thesaurus")) {
      dtsVocab = "NCI Thesaurus";
      altNameType = "NCI_CONCEPT_CODE";
    }
    // for search Meta by (LOINC) code
    else if (dtsVocab.equals("Metathesaurus") || sSearchInEVS.equals("Code")) {
      dtsVocab = "NCI_Thesaurus";
      altNameType = "NCI_CONCEPT_CODE";
      isMetaCodeSearch = true;
      sUISearchType = "term";
    }
    // for Meta searches only (no Thes search), like in getSuperConcepts Meta
    else if (dtsVocab.equals("NCI Metathesaurus")) {
      altNameType = "UMLS_CUI";
      isMetaCodeSearch = false;
      sUISearchType = "term";
    } else altNameType = "";

    LexEVSApplicationService evsService =
        (LexEVSApplicationService)
            ApplicationServiceProvider.getApplicationService("EvsServiceInfo");

    /*  if (!sSearchInEVS.equals("Concept Code") || term.equals("")) {*/
    Pattern pattern = Pattern.compile("^C\\d{2,8}");
    Matcher matcher = pattern.matcher(term);

    algorithm = getAlgorithm(term);
    term = cleanTerm(term);
    int totalReturnCount = 0;

    try {
      if (retired.equals(
          "Include")) // do this if all concepts, including retired, should be included
      isRetired = new Boolean(false);
      else {

        try {

          ResolvedConceptReferenceList rcrl =
              searchPrefTerm(evsService, dtsVocab, term, sMetaLimit, algorithm);
          if (rcrl != null && rcrl.getResolvedConceptReferenceCount() > 0)
            isRetired = (Boolean) (!rcrl.getResolvedConceptReference(0).getEntity().isIsActive());

        } catch (Exception ex) {
          ex.printStackTrace();
        }
      }

      if (isRetired.equals(bFalse)) {
        ResolvedConceptReferenceList concepts = null;
        // CCode = term;
        int codesSize = 0;
        try {
          if (sSearchInEVS.equals("Concept Code") || matcher.matches())
            concepts = searchConceptCode(evsService, dtsVocab, term, sMetaLimit);
          else concepts = searchPrefTerm(evsService, dtsVocab, term, sMetaLimit, algorithm);

          codesSize = concepts.getResolvedConceptReferenceCount();

        } catch (Exception ex) {
          System.out.println("Error do_EVSSearch get concept: " + ex.toString());
        }

        if (concepts != null && codesSize > 0) {

          codeFoundInThesaurus = new Boolean(true);

          prefName = concepts.getResolvedConceptReference(0).getEntityDescription().getContent();

          concepts = new ResolvedConceptReferenceList();
          try {
            concepts = searchPrefTerm(evsService, dtsVocab, prefName, sMetaLimit, algorithm);
            codesSize = concepts.getResolvedConceptReferenceCount();
          } catch (Exception ex) {
            // ex.printStackTrace();
            System.out.println("Error do_EVSSearch DescLogic: " + ex.toString());
          }
          if (concepts != null) {
            ResolvedConceptReference rcr = new ResolvedConceptReference();
            for (int i = 0; i < codesSize; i++) {
              rcr = concepts.getResolvedConceptReference(i);
              prefName = rcr.getEntityDescription().getContent();
              CCode = rcr.getConceptCode();

              Definition[] defs = rcr.getEntity().getDefinition();
              if (defs == null) defs = new Definition[0];
              sDef = sDefDefault; // "No Value Exists.";
              sDefSrc = "";

              for (int k = 0; k < defs.length; k++) {

                Definition def = defs[k];

                if (def != null) {
                  if (def.getIsPreferred() != null) {
                    sDef = def.getValue().getContent();
                    if (def.getSourceCount() > 0)
                      sDefSrc = def.getSource(0).getContent(); // get def source
                  }
                }
              }

              EVSBean conBean = new EVSBean();
              conBean.setCode(CCode);
              conBean.setDefinition(sDef);
              conBean.setDictionary(dtsVocab);
              conBean.setName(prefName);
              conBean.setSource(sDefSrc);
              conBean.setType(altNameType);
              vCon.add(conBean);
              totalReturnCount++;

              if (totalReturnCount >= sMetaLimit) return vCon;
            }
          }
        }
      }

    } catch (Exception ex) {
      System.out.println("Error do_EVSSearch Concept code: " + ex.toString());
    }

    // Search Meta
    int length = 0;
    length = term.length();
    ResolvedConceptReferenceList concepts = null;
    if (sSearchInEVS.equals("Concept Code"))
      concepts = searchConceptCode(evsService, "NCI Metathesaurus", term, sMetaLimit);
    else if (!sSearchInEVS.equals("Concept Code"))
      concepts = searchPrefTerm(evsService, "NCI Metathesaurus", term, sMetaLimit, algorithm);

    if (concepts != null) {
      ResolvedConceptReference rcr = new ResolvedConceptReference();
      for (int i = 0; i < concepts.getResolvedConceptReferenceCount(); i++) {
        if (totalReturnCount >= sMetaLimit) break;
        rcr = concepts.getResolvedConceptReference(i);
        prefName = rcr.getEntityDescription().getContent();
        CCode = rcr.getConceptCode();

        Definition[] defs = rcr.getEntity().getDefinition();
        if (defs == null) defs = new Definition[0];
        sDef = sDefDefault; // "No Value Exists.";
        sDefSrc = "";

        for (int k = 0; k < defs.length; k++) {

          Definition def = defs[k];

          if (def != null) {
            sDef = def.getValue().getContent();
            if (def.getSourceCount() > 0) sDefSrc = def.getSource(0).getContent(); // get def source
          }

          EVSBean conBean = new EVSBean();
          conBean.setCode(CCode);
          conBean.setDefinition(sDef);
          conBean.setDictionary("NCI Metathesaurus");
          conBean.setName(prefName);
          conBean.setSource(sDefSrc);
          conBean.setType("UMLS_CUI");
          vCon.add(conBean);
          totalReturnCount++;
          if (totalReturnCount >= sMetaLimit) break;
        }
      }
    }

    evsService = null;
    System.out.println(vCon.size());
    return vCon;
  }