@Test
  public void getTreeSharedRoot() {
    ResolvedConceptReferenceList list1 = new ResolvedConceptReferenceList();
    ResolvedConceptReferenceList list2 = new ResolvedConceptReferenceList();

    AssociatedConcept as1 = this.createResolvedConceptReference("a");
    AssociatedConcept at1 = this.createResolvedConceptReference("b");
    this.addAssociatedConcept(as1, at1);

    AssociatedConcept as2 = this.createResolvedConceptReference("a");
    AssociatedConcept at2 = this.createResolvedConceptReference("c");
    this.addAssociatedConcept(as2, at2);

    list1.addResolvedConceptReference(as1);
    list2.addResolvedConceptReference(as2);
    KeyedGraph g1 = new KeyedGraph(list1);
    KeyedGraph g2 = new KeyedGraph(list2);

    KeyedGraph unionedGraph = g1.union(g2);

    ResolvedConceptReferenceList returnList = unionedGraph.toResolvedConceptReferenceList();
    assertEquals(1, returnList.getResolvedConceptReferenceCount());

    assertEquals("a", returnList.getResolvedConceptReference(0).getCode());

    assertEquals(
        2,
        returnList
            .getResolvedConceptReference(0)
            .getSourceOf()
            .getAssociation(0)
            .getAssociatedConcepts()
            .getAssociatedConceptCount());
  }
Exemple #2
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  private static ResolvedConceptReferenceList searchConceptCode(
      LexEVSApplicationService evsService, String dtsVocab, String CCode, int sMetaLimit) {

    ResolvedConceptReferenceList concepts = new ResolvedConceptReferenceList();

    int codesSize = 0;
    try {
      CodedNodeSet metaNodes = evsService.getNodeSet(dtsVocab, null, null);

      ConceptReferenceList crefs =
          ConvenienceMethods.createConceptReferenceList(new String[] {CCode}, dtsVocab);
      metaNodes = metaNodes.restrictToCodes(crefs);

      metaNodes.restrictToStatus(ActiveOption.ACTIVE_ONLY, null);

      concepts =
          metaNodes.resolveToList(
              null, // Sorts used to sort results (null means sort by match score)
              null, // PropertyNames to resolve (null resolves all)
              null, // PropertyTypess to resolve (null resolves all)
              sMetaLimit // cap the number of results returned (-1 resolves all)
              );

      codesSize = concepts.getResolvedConceptReferenceCount();

    } catch (Exception ex) {
      System.out.println("Error do_EVSSearch get concept: " + ex.toString());
    }
    return concepts;
  }
 /*
  * (non-Javadoc)
  *
  * @see
  * org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator
  * #next(int)
  */
 public ResolvedConceptReferenceList next(int maxToReturn)
     throws LBResourceUnavailableException, LBInvocationException {
   ResolvedConceptReferenceList returnList = new ResolvedConceptReferenceList();
   while (returnList.getResolvedConceptReferenceCount() < maxToReturn) {
     ResolvedConceptReference ref = getNextFromList();
     if (ref == null) {
       return returnList;
     } else {
       returnList.addResolvedConceptReference(ref);
     }
   }
   return returnList;
 }
Exemple #4
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  private static ResolvedConceptReferenceList searchPrefTerm(
      LexEVSApplicationService evsService,
      String dtsVocab,
      String prefName,
      int sMetaLimit,
      String algorithm) {

    ResolvedConceptReferenceList concepts = new ResolvedConceptReferenceList();
    int codesSize = 0;
    try {
      CodedNodeSet metaNodes = evsService.getNodeSet(dtsVocab, null, null);

      metaNodes =
          metaNodes.restrictToMatchingDesignations(
              prefName, // the text to match
              CodedNodeSet.SearchDesignationOption
                  .ALL, // whether to search all designation, only Preferred or only Non-Preferred
              algorithm, // the match algorithm to use
              null); // the language to match (null matches all)

      metaNodes = metaNodes.restrictToStatus(ActiveOption.ACTIVE_ONLY, null);

      concepts =
          metaNodes.resolveToList(
              null, // Sorts used to sort results (null means sort by match score)
              null, // PropertyNames to resolve (null resolves all)
              new CodedNodeSet.PropertyType[] {
                PropertyType.DEFINITION, PropertyType.PRESENTATION
              }, // PropertyTypess to resolve (null resolves all)
              sMetaLimit // cap the number of results returned (-1 resolves all)
              );
      codesSize = concepts.getResolvedConceptReferenceCount();
    } catch (Exception ex) {
      // ex.printStackTrace();
      System.out.println("Error do_EVSSearch DescLogic: " + ex.toString());
    }

    return concepts;
  }
Exemple #5
0
  public static String getEVSCode(String prefName, String dtsVocab) {
    LexEVSApplicationService evsService = null;

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

    } catch (Exception e) {
      throw new RuntimeException(e);
    }

    if (dtsVocab == null) dtsVocab = "";
    String CCode = "";
    if (dtsVocab.equals("Thesaurus/Metathesaurus")
        || dtsVocab.equals("")
        || dtsVocab.equals("NCI Thesaurus")
        || dtsVocab.equals("NCI_Thesaurus")) dtsVocab = "NCI_Thesaurus";
    ResolvedConceptReferenceList codes2 = null;
    int codesSize = 0;

    try {
      CodedNodeSet metaNodes = evsService.getNodeSet("NCI MetaThesaurus", null, null);

      metaNodes =
          metaNodes.restrictToMatchingDesignations(
              prefName, // the text to match
              CodedNodeSet.SearchDesignationOption
                  .PREFERRED_ONLY, // whether to search all designation, only Preferred or only
                                   // Non-Preferred
              "exactMatch", // the match algorithm to use
              null); // the language to match (null matches all)

      metaNodes = metaNodes.restrictToStatus(ActiveOption.ACTIVE_ONLY, null);

      codes2 =
          metaNodes.resolveToList(
              null, // Sorts used to sort results (null means sort by match score)
              null, // PropertyNames to resolve (null resolves all)
              new CodedNodeSet.PropertyType[] {
                PropertyType.DEFINITION, PropertyType.PRESENTATION
              }, // PropertyTypess to resolve (null resolves all)  //PropertyTypess to resolve (null
                 // resolves all)
              10 // cap the number of results returned (-1 resolves all)
              );
      codesSize = codes2.getResolvedConceptReferenceCount();

    } catch (Exception ex) {
      System.err.println("Error do_getEVSCode:resolveToList: " + ex.toString());
      ex.printStackTrace();
    }

    if (codes2 != null) {
      ResolvedConceptReference conceptReference = new ResolvedConceptReference();
      // logger.debug("Got "+codesSize+" results for the do_getEVSCode search using prefName and
      // exactMatch");
      for (int i = 0; i < codesSize; i++) {
        conceptReference = (ResolvedConceptReference) codes2.getResolvedConceptReference(i);
        CCode = (String) conceptReference.getConceptCode();
      }
    }

    evsService = null;
    return CCode;
  }
Exemple #6
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;
  }