/**
* Instantiates a new Iterator. Be sure that any desired restrictions have already been placed on
* the CodedNodeSets before passing into this constructor
*
* @param codedNodeSets the coded node sets
* @param sortOptions the sort options
* @param filterOptions the filter options
* @param restrictToProperties the restrict to properties
* @param restrictToPropertyTypes the restrict to property types
* @param resolve the resolve
* @throws LBException the LB exception
*/
public QuickUnionIterator(
Vector<CodedNodeSet> codedNodeSets,
SortOptionList sortOptions,
LocalNameList filterOptions,
LocalNameList restrictToProperties,
PropertyType[] restrictToPropertyTypes,
boolean resolve)
throws LBException {
for (CodedNodeSet cns : codedNodeSets) {
// KLO 012310
if (cns != null) {
try {
ResolvedConceptReferencesIterator iterator =
cns.resolve(
sortOptions,
filterOptions,
restrictToProperties,
restrictToPropertyTypes,
resolve);
if (iterator != null) {
_iterators.add(iterator);
}
} catch (Exception ex) {
_logger.error("QuickUnionIterator constructor - cns.resolve throws exception???");
// ex.printStackTrace();
System.out.println(
"WARNING: QuickUnionIteratorWrapper constructor - cns.resolve throws exception???");
}
}
}
Collections.sort(_iterators, new IteratorSizeComparator());
}
/** The Class MappingUtils. */
public class MappingUtils {
private static Logger _logger = Logger.getLogger(MappingUtils.class);
private String serviceUrl = null;
private LexBIGService lbSvc = null;
public MappingUtils(LexBIGService lbSvc) {
this.lbSvc = lbSvc;
}
public void setServiceUrl(String serviceUrl) {
this.serviceUrl = serviceUrl;
}
public List<MappingSortOption> createMappingSortOption(int sortBy) {
List<MappingSortOption> list = new ArrayList<MappingSortOption>();
MappingSortOption option = null;
QualifierSortOption qualifierOption = null;
switch (sortBy) {
case 1:
option = new MappingSortOption(MappingSortOptionName.SOURCE_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.SOURCE_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
qualifierOption = new QualifierSortOption(Direction.ASC, "rel");
list.add(qualifierOption);
qualifierOption = new QualifierSortOption(Direction.DESC, "score");
list.add(qualifierOption);
option = new MappingSortOption(MappingSortOptionName.TARGET_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.TARGET_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
break;
case 2:
option =
new MappingSortOption(MappingSortOptionName.SOURCE_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
option = new MappingSortOption(MappingSortOptionName.SOURCE_CODE, Direction.ASC);
list.add(option);
qualifierOption = new QualifierSortOption(Direction.ASC, "rel");
list.add(qualifierOption);
qualifierOption = new QualifierSortOption(Direction.DESC, "score");
list.add(qualifierOption);
option = new MappingSortOption(MappingSortOptionName.TARGET_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.TARGET_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
break;
// to be modified
case 3:
option =
new MappingSortOption(MappingSortOptionName.SOURCE_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
option = new MappingSortOption(MappingSortOptionName.SOURCE_CODE, Direction.ASC);
list.add(option);
qualifierOption = new QualifierSortOption(Direction.ASC, "rel");
list.add(qualifierOption);
qualifierOption = new QualifierSortOption(Direction.DESC, "score");
list.add(qualifierOption);
option = new MappingSortOption(MappingSortOptionName.TARGET_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.TARGET_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
break;
case 4:
qualifierOption = new QualifierSortOption(Direction.ASC, "rel");
list.add(qualifierOption);
qualifierOption = new QualifierSortOption(Direction.DESC, "score");
list.add(qualifierOption);
option = new MappingSortOption(MappingSortOptionName.SOURCE_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.SOURCE_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
option = new MappingSortOption(MappingSortOptionName.TARGET_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.TARGET_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
break;
case 5:
qualifierOption = new QualifierSortOption(Direction.DESC, "score");
list.add(qualifierOption);
option = new MappingSortOption(MappingSortOptionName.SOURCE_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.SOURCE_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
qualifierOption = new QualifierSortOption(Direction.ASC, "rel");
list.add(qualifierOption);
option = new MappingSortOption(MappingSortOptionName.TARGET_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.TARGET_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
break;
case 6:
option = new MappingSortOption(MappingSortOptionName.TARGET_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.TARGET_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
option = new MappingSortOption(MappingSortOptionName.SOURCE_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.SOURCE_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
qualifierOption = new QualifierSortOption(Direction.ASC, "rel");
list.add(qualifierOption);
qualifierOption = new QualifierSortOption(Direction.DESC, "score");
list.add(qualifierOption);
break;
case 7:
option =
new MappingSortOption(MappingSortOptionName.TARGET_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
option = new MappingSortOption(MappingSortOptionName.TARGET_CODE, Direction.ASC);
list.add(option);
option = new MappingSortOption(MappingSortOptionName.SOURCE_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.SOURCE_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
qualifierOption = new QualifierSortOption(Direction.ASC, "rel");
list.add(qualifierOption);
qualifierOption = new QualifierSortOption(Direction.DESC, "score");
list.add(qualifierOption);
break;
// to be modified
case 8:
// option = new MappingSortOption(MappingSortOptionName.TARGET_NAMESPACE, Direction.ASC);
// list.add(option);
option =
new MappingSortOption(MappingSortOptionName.TARGET_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
option = new MappingSortOption(MappingSortOptionName.TARGET_CODE, Direction.ASC);
list.add(option);
option = new MappingSortOption(MappingSortOptionName.SOURCE_CODE, Direction.ASC);
list.add(option);
option =
new MappingSortOption(MappingSortOptionName.SOURCE_ENTITY_DESCRIPTION, Direction.ASC);
list.add(option);
qualifierOption = new QualifierSortOption(Direction.ASC, "rel");
list.add(qualifierOption);
qualifierOption = new QualifierSortOption(Direction.DESC, "score");
list.add(qualifierOption);
break;
default:
return createMappingSortOption(1);
}
return list;
}
public ResolvedConceptReferencesIterator getMappingDataIterator(String scheme, String version) {
return getMappingDataIterator(scheme, version, MappingData.COL_SOURCE_CODE);
}
public ResolvedConceptReferencesIterator getMappingDataIterator(
String scheme, String version, int sortBy) {
List<MappingSortOption> sortOptionList = createMappingSortOption(sortBy);
return getMappingDataIterator(scheme, version, sortOptionList);
}
public ResolvedConceptReferencesIterator getMappingDataIterator(
String scheme, String version, List<MappingSortOption> sortOptionList) {
CodingSchemeVersionOrTag versionOrTag = new CodingSchemeVersionOrTag();
if (version != null) {
versionOrTag.setVersion(version);
}
String relationsContainerName = null;
try {
CodingScheme cs = lbSvc.resolveCodingScheme(scheme, versionOrTag);
if (cs == null) return null;
java.util.Enumeration<? extends Relations> relations = cs.enumerateRelations();
while (relations.hasMoreElements()) {
Relations relation = (Relations) relations.nextElement();
Boolean isMapping = relation.getIsMapping();
if (isMapping != null && isMapping.equals(Boolean.TRUE)) {
relationsContainerName = relation.getContainerName();
break;
}
}
if (relationsContainerName == null) {
return null;
}
MappingExtension mappingExtension =
(MappingExtension) lbSvc.getGenericExtension("MappingExtension");
ResolvedConceptReferencesIterator itr =
mappingExtension.resolveMapping(
scheme, versionOrTag, relationsContainerName, sortOptionList);
return itr;
} catch (Exception ex) {
ex.printStackTrace();
}
return null;
}
public NameAndValueList getMappingAssociationNames(String scheme, String version) {
CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
if (version != null) {
csvt.setVersion(version);
}
NameAndValueList navList = new NameAndValueList();
try {
CodingScheme cs = lbSvc.resolveCodingScheme(scheme, csvt);
Relations[] relations = cs.getRelations();
for (int i = 0; i < relations.length; i++) {
Relations relation = relations[i];
Boolean isMapping = relation.isIsMapping();
if (isMapping != null && isMapping.equals(Boolean.TRUE)) {
AssociationPredicate[] associationPredicates = relation.getAssociationPredicate();
for (int j = 0; j < associationPredicates.length; j++) {
AssociationPredicate associationPredicate = associationPredicates[j];
String name = associationPredicate.getAssociationName();
NameAndValue vNameAndValue = new NameAndValue();
vNameAndValue.setName(name);
navList.addNameAndValue(vNameAndValue);
}
return navList;
} else {
return null;
}
}
} catch (Exception ex) {
ex.printStackTrace();
}
return null;
}
public Vector getMappingCodingSchemesEntityParticipatesIn(String code, String namespace) {
Vector v = new Vector();
try {
MappingExtension mappingExtension =
(MappingExtension) lbSvc.getGenericExtension("MappingExtension");
AbsoluteCodingSchemeVersionReferenceList mappingSchemes =
mappingExtension.getMappingCodingSchemesEntityParticipatesIn(code, namespace);
// output is all of the mapping ontologies that this code participates in.
for (AbsoluteCodingSchemeVersionReference ref :
mappingSchemes.getAbsoluteCodingSchemeVersionReference()) {
v.add(ref.getCodingSchemeURN() + "|" + ref.getCodingSchemeVersion());
}
} catch (Exception ex) {
ex.printStackTrace();
}
return v;
}
}
/**
* The Class QuickUnionIterator. Provides Union-like resolving of CodedNodeSets without the Union
* performance penalty. This Iterator assumes that all restrictions have been placed on the
* CodedNodeSets BEFORE being passed into this Iterator.
*/
public class QuickUnionIterator implements ResolvedConceptReferencesIterator {
private static Logger _logger = Logger.getLogger(QuickUnionIterator.class);
/** The Constant serialVersionUID. */
private static final long serialVersionUID = 6285970594380754741L;
/** The current iterator. */
private int _currentIterator = 0;
/** The iterators. */
private List<ResolvedConceptReferencesIterator> _iterators =
new ArrayList<ResolvedConceptReferencesIterator>();
/**
* Instantiates a new Iterator. Be sure that any desired restrictions have already been placed on
* the CodedNodeSets before passing into this constructor
*
* @param codedNodeSets the coded node sets
* @param sortOptions the sort options
* @param filterOptions the filter options
* @param restrictToProperties the restrict to properties
* @param restrictToPropertyTypes the restrict to property types
* @param resolve the resolve
* @throws LBException the LB exception
*/
public QuickUnionIterator(
Vector<CodedNodeSet> codedNodeSets,
SortOptionList sortOptions,
LocalNameList filterOptions,
LocalNameList restrictToProperties,
PropertyType[] restrictToPropertyTypes,
boolean resolve)
throws LBException {
for (CodedNodeSet cns : codedNodeSets) {
// KLO 012310
if (cns != null) {
try {
ResolvedConceptReferencesIterator iterator =
cns.resolve(
sortOptions,
filterOptions,
restrictToProperties,
restrictToPropertyTypes,
resolve);
if (iterator != null) {
_iterators.add(iterator);
}
} catch (Exception ex) {
_logger.error("QuickUnionIterator constructor - cns.resolve throws exception???");
// ex.printStackTrace();
System.out.println(
"WARNING: QuickUnionIteratorWrapper constructor - cns.resolve throws exception???");
}
}
}
Collections.sort(_iterators, new IteratorSizeComparator());
}
/*
* (non-Javadoc)
*
* @see
* org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator
* #get(int, int)
*/
public ResolvedConceptReferenceList get(int start, int end)
throws LBResourceUnavailableException, LBInvocationException, LBParameterException {
throw new UnsupportedOperationException();
}
/*
* (non-Javadoc)
*
* @see
* org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator
* #getNext()
*/
public ResolvedConceptReferenceList getNext() {
throw new UnsupportedOperationException();
}
/*
* (non-Javadoc)
*
* @see
* org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator
* #next()
*/
public ResolvedConceptReference next()
throws LBResourceUnavailableException, LBInvocationException {
return next(1).getResolvedConceptReference(0);
}
/*
* (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;
}
/*
* (non-Javadoc)
*
* @see
* org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator
* #scroll(int)
*/
public ResolvedConceptReferencesIterator scroll(int maxToReturn)
throws LBResourceUnavailableException, LBInvocationException {
throw new UnsupportedOperationException();
}
/*
* (non-Javadoc)
*
* @see org.LexGrid.LexBIG.Utility.Iterators.EntityListIterator#hasNext()
*/
public boolean hasNext() throws LBResourceUnavailableException {
removeEmptyIterators();
return _iterators.size() > 0;
}
/** 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;
}
/*
* (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;
}
/*
* (non-Javadoc)
*
* @see org.LexGrid.LexBIG.Utility.Iterators.EntityListIterator#release()
*/
public void release() throws LBResourceUnavailableException {
for (ResolvedConceptReferencesIterator itr : _iterators) {
itr.release();
}
}
/**
* 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);
}
}
/** The Class IteratorSizeComparator. */
private static class IteratorSizeComparator
implements java.io.Serializable, Comparator<ResolvedConceptReferencesIterator> {
/*
* (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);
}
}
}
}