/**
* Resolve the Iterator
*
* @param iterator
* @param maxToReturn
* @param code
* @return
*/
public Vector<Entity> resolveIterator(
ResolvedConceptReferencesIterator iterator, int maxToReturn, String code) {
Vector<Entity> v = new Vector<Entity>();
if (iterator == null) {
_logger.warn("No match.");
return v;
}
try {
int iteration = 0;
while (iterator.hasNext()) {
iteration++;
iterator = iterator.scroll(maxToReturn);
ResolvedConceptReferenceList rcrl = iterator.getNext();
ResolvedConceptReference[] rcra = rcrl.getResolvedConceptReference();
for (int i = 0; i < rcra.length; i++) {
ResolvedConceptReference rcr = rcra[i];
Entity ce = rcr.getReferencedEntry();
if (code == null) {
v.add(ce);
} else {
if (ce.getEntityCode().compareTo(code) != 0) v.add(ce);
}
}
}
} catch (Exception e) {
_logger.warn(e.getMessage());
}
return v;
}
@Override
public DirectoryResult<T> execute(String state, int start, int maxResults) {
ResolvedConceptReferencesIterator iterator;
try {
iterator =
searchExtension.search(
state, toCodingSchemeReference(this.codeSystemVersions), MatchAlgorithm.LUCENE);
} catch (LBParameterException e) {
throw new RuntimeException(e);
}
ResolvedConceptReferenceList list;
boolean atEnd;
try {
list = iterator.get(start, start + maxResults);
atEnd = iterator.numberRemaining() <= start + maxResults;
} catch (Exception e) {
throw new RuntimeException(e);
}
List<T> returnList = new ArrayList<T>();
for (ResolvedConceptReference ref : list.getResolvedConceptReference()) {
returnList.add(this.doTransform(ref));
}
return new DirectoryResult<T>(returnList, atEnd);
}
/*
* (non-Javadoc)
*
* @see
* org.LexGrid.LexBIG.Utility.Iterators.EntityListIterator#numberRemaining()
*/
public int numberRemaining() throws LBResourceUnavailableException {
int number = 0;
for (ResolvedConceptReferencesIterator itr : _iterators) {
number += itr.numberRemaining();
}
return number;
}
@Test
public void testGetTargetCodesToNodeList() throws Exception {
LexBIGService lbs = ServiceHolder.instance().getLexBIGService();
CodedNodeGraph mappingGraph = lbs.getNodeGraph(MAPPING_SCHEME_URI, null, null);
CodedNodeSet cns =
mappingGraph.restrictToTargetCodeSystem(PARTS_SCHEME).toNodeList(null, false, true, 0, -1);
ResolvedConceptReferencesIterator itr = cns.resolve(null, null, null);
int count = 0;
Set<String> foundCodes = new HashSet<String>();
while (itr.hasNext()) {
count++;
foundCodes.add(itr.next().getCode());
}
assertEquals(3, foundCodes.size());
assertTrue(foundCodes.contains("R0001"));
assertTrue(foundCodes.contains("E0001"));
assertTrue(foundCodes.contains("P0001"));
}
/*
* (non-Javadoc)
*
* @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
*/
public int compare(
ResolvedConceptReferencesIterator itr1, ResolvedConceptReferencesIterator itr2) {
try {
return itr2.numberRemaining() - itr1.numberRemaining();
} catch (LBResourceUnavailableException e) {
throw new RuntimeException(e);
}
}
/** Removes the empty iterators. */
private void removeEmptyIterators() {
List<ResolvedConceptReferencesIterator> newList =
new ArrayList<ResolvedConceptReferencesIterator>();
for (ResolvedConceptReferencesIterator itr : _iterators) {
try {
if (itr.hasNext()) {
newList.add(itr);
}
} catch (LBResourceUnavailableException e) {
throw new RuntimeException(e);
}
}
_iterators = newList;
}
public void testNextInt() {
try {
LexBIGService lbs = ServiceHolder.instance().getLexBIGService();
CodedNodeSet cns = lbs.getCodingSchemeConcepts("NCI Thesaurus", null);
cns = cns.restrictToMatchingDesignations("heart", null, "startsWith", null);
ResolvedConceptReferencesIterator rcrl = cns.resolve(null, null, null, null, false);
ResolvedConceptReferenceList list1 = rcrl.next(10);
ResolvedConceptReferenceList list2 = rcrl.next(10);
assertFalse(compareResolvedConceptReferenceList(list1, list2));
} catch (Exception e) {
fail("Exception Thrown: " + e.getMessage());
e.printStackTrace();
}
}
/**
* Gets the next from list.
*
* @return the next from list
*/
private ResolvedConceptReference getNextFromList() {
try {
while (hasNext()) {
int iterator = _currentIterator % _iterators.size();
ResolvedConceptReferencesIterator itr = _iterators.get(iterator);
if (itr.hasNext()) {
_currentIterator++;
return itr.next();
} else {
_currentIterator++;
}
}
return null;
} catch (Exception e) {
throw new RuntimeException(e);
}
}
/**
* Get concept Entity by code
*
* @param codingScheme
* @param code
* @return
*/
public ResolvedConceptReference getConceptByCode(String codingScheme, String code) {
CodedNodeSet cns = null;
ResolvedConceptReferencesIterator iterator = null;
try {
LexBIGService lbSvc = RemoteServerUtil.createLexBIGService();
cns = lbSvc.getCodingSchemeConcepts(codingScheme, null);
ConceptReferenceList crefs = createConceptReferenceList(new String[] {code}, codingScheme);
cns.restrictToCodes(crefs);
iterator = cns.resolve(null, null, null);
if (iterator.numberRemaining() > 0) {
ResolvedConceptReference ref = (ResolvedConceptReference) iterator.next();
return ref;
}
} catch (LBException e) {
_logger.info("Error: " + e.getMessage());
}
return null;
}
public void run() throws LBException {
ValueSetDefinition vsd = Util.promptForValueSetDefinition(message);
if (vsd != null) {
AbsoluteCodingSchemeVersionReferenceList acsvList = null;
Util.displayMessage("Now select Code System to use to resolve Value Set Definition");
CodingSchemeSummary css = Util.promptForCodeSystem();
if (css != null) {
acsvList = new AbsoluteCodingSchemeVersionReferenceList();
acsvList.addAbsoluteCodingSchemeVersionReference(
Constructors.createAbsoluteCodingSchemeVersionReference(
css.getCodingSchemeURI(), css.getRepresentsVersion()));
}
LexEVSValueSetDefinitionServices vsdServ =
LexEVSValueSetDefinitionServicesImpl.defaultInstance();
ResolvedValueSetDefinition rVSD = null;
try {
rVSD =
vsdServ.resolveValueSetDefinition(
new URI(vsd.getValueSetDefinitionURI()), null, acsvList, null, null);
} catch (URISyntaxException e) {
e.printStackTrace();
}
if (rVSD != null) {
Util.displayMessage(
"Member of Value Set Definition (" + vsd.getValueSetDefinitionURI() + ") are :");
ResolvedConceptReferencesIterator conceptItr = rVSD.getResolvedConceptReferenceIterator();
while (conceptItr.hasNext()) {
ResolvedConceptReference concept = conceptItr.next();
Util.displayMessage("Concept code : " + concept.getCode());
Util.displayMessage("\tCoding Scheme Name...: " + concept.getCodingSchemeName());
Util.displayMessage("\tCoding Scheme URI....: " + concept.getCodingSchemeURI());
Util.displayMessage("\tCoding Scheme Version: " + concept.getCodingSchemeVersion());
}
} else {
Util.displayMessage(
"No members found for Value Set Definition : '" + vsd.getValueSetDefinitionURI() + "'");
}
}
}
public void testNext() {
try {
LexBIGService lbs = ServiceHolder.instance().getLexBIGService();
CodedNodeSet cns = lbs.getCodingSchemeConcepts("NCI Thesaurus", null);
cns = cns.restrictToMatchingDesignations("heart", null, "startsWith", null);
ResolvedConceptReferencesIterator rcrl = cns.resolve(null, null, null, null, false);
String conceptCode = null;
while (rcrl.hasNext()) {
ResolvedConceptReference ref = rcrl.next();
String currentCode = ref.getConceptCode();
assertFalse(currentCode.equals(conceptCode));
conceptCode = currentCode;
}
} catch (Exception e) {
fail("Exception Thrown: " + e.getMessage());
e.printStackTrace();
}
}
/*
* (non-Javadoc)
*
* @see org.LexGrid.LexBIG.Utility.Iterators.EntityListIterator#release()
*/
public void release() throws LBResourceUnavailableException {
for (ResolvedConceptReferencesIterator itr : _iterators) {
itr.release();
}
}