@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"));
}
/**
* Test map synonymto preferred names.
*
* @throws LBException the LB exception
*/
public void testMapSynonymtoPreferredNames() throws LBException {
CodedNodeSet cns =
ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(THES_SCHEME, null);
cns =
cns.restrictToMatchingDesignations(
"skeleton", SearchDesignationOption.ALL, "exactMatch", null);
ResolvedConceptReference[] rcr =
cns.resolveToList(null, null, null, 0).getResolvedConceptReference();
assertTrue(rcr.length == 2);
boolean found = false;
for (int i = 0; i < rcr.length; i++) {
if (rcr[i].getConceptCode().equals("C12788")) {
found = true;
assertTrue(rcr[i].getReferencedEntry().getPropertyCount() == 5);
assertTrue(
rcr[i]
.getReferencedEntry()
.getEntityDescription()
.getContent()
.equals("Skeletal System"));
}
}
assertTrue(found);
}
/**
* 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());
}
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;
}
public void testT1_FNC_02() throws LBException {
CodedNodeSet cns =
ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(THES_SCHEME, null);
cns.restrictToCodes(
Constructors.createConceptReferenceList(
new String[] {"Vallecula", "Palate", "Hard_Palate"}, THES_SCHEME));
// this test is really lacking... but here is how you subset. You can
// serialize however
// you want from here...
assertTrue(cns.resolveToList(null, null, null, 0).getResolvedConceptReference().length == 3);
}
/**
* Test retrieve most recent versionof concept.
*
* @throws LBException the LB exception
*/
public void testRetrieveMostRecentVersionofConcept() throws LBException {
// not providing a version number gets you the PRODUCTION (which can be assumed to be the latest
// good version)
CodedNodeSet cns =
ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(THES_SCHEME, null);
cns =
cns.restrictToCodes(
Constructors.createConceptReferenceList(new String[] {"C12223"}, THES_SCHEME));
assertTrue(cns.resolveToList(null, null, null, 0).getResolvedConceptReference().length == 1);
}
@Test
public void testT1_FNC_16() throws LBException {
CodedNodeSet cns =
ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(AUTO_SCHEME, null);
cns = cns.restrictToStatus(null, new String[] {"Retired"});
ResolvedConceptReference[] rcr =
cns.resolveToList(null, null, null, 0).getResolvedConceptReference();
assertTrue(rcr.length == 1);
assertTrue(rcr[0].getConceptCode().equals("73"));
}
/**
* Test limit returned values.
*
* @throws LBException the LB exception
*/
public void testLimitReturnedValues() throws LBException {
CodedNodeSet cns =
ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(THES_SCHEME, null);
cns =
cns.restrictToMatchingDesignations(
"heaart", SearchDesignationOption.ALL, "DoubleMetaphoneLuceneQuery", null);
ResolvedConceptReference[] rcr =
cns.resolveToList(null, null, null, 1).getResolvedConceptReference();
assertTrue(rcr.length == 1);
}
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();
}
}
/**
* 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 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();
}
}
/**
* Return Iterator for codedNodeGraph
*
* @param cng
* @param graphFocus
* @param resolveForward
* @param resolveBackward
* @param resolveAssociationDepth
* @param maxToReturn
* @return
*/
public ResolvedConceptReferencesIterator codedNodeGraph2CodedNodeSetIterator(
CodedNodeGraph cng,
ConceptReference graphFocus,
boolean resolveForward,
boolean resolveBackward,
int resolveAssociationDepth,
int maxToReturn) {
CodedNodeSet cns = null;
try {
cns =
cng.toNodeList(
graphFocus, resolveForward, resolveBackward, resolveAssociationDepth, maxToReturn);
if (cns == null) return null;
return cns.resolve(null, null, null);
} catch (Exception ex) {
_logger.warn(ex.getMessage());
}
return null;
}
public void testT1_FNC_17() throws LBException {
CodedNodeSet cns =
ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(THES_SCHEME, null);
cns =
cns.restrictToMatchingDesignations(
"heaart", SearchDesignationOption.ALL, "DoubleMetaphoneLuceneQuery", null);
ResolvedConceptReference[] rcr =
cns.resolveToList(null, null, null, 0).getResolvedConceptReference();
// should have found the concept code C48589 - "Base of the Heart"
boolean found = false;
for (int i = 0; i < rcr.length; i++) {
if (rcr[i].getConceptCode().equals("Base_of_the_Heart")) {
found = true;
}
}
assertTrue(found);
}
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;
}
/**
* Testfor current or obsolete conceptb.
*
* @throws LBException the LB exception
*/
public void testforCurrentOrObsoleteConceptb() throws LBException {
// same as above, but this time, using the new methods (that aren't deprecated)
CodedNodeSet cns =
ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(THES_SCHEME, null);
cns = cns.restrictToStatus(ActiveOption.ACTIVE_ONLY, null);
cns =
cns.restrictToCodes(
Constructors.createConceptReferenceList(new String[] {"C38389"}, THES_SCHEME));
ResolvedConceptReference[] rcr =
cns.resolveToList(null, null, null, 0).getResolvedConceptReference();
assertTrue("1", rcr.length == 0);
cns = ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(THES_SCHEME, null);
cns = cns.restrictToStatus(ActiveOption.ALL, null);
cns =
cns.restrictToCodes(
Constructors.createConceptReferenceList(new String[] {"C38389"}, THES_SCHEME));
rcr = cns.resolveToList(null, null, null, 0).getResolvedConceptReference();
assertTrue("2", rcr.length == 1);
// same test again - no status restriction
cns = ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(THES_SCHEME, null);
cns =
cns.restrictToCodes(
Constructors.createConceptReferenceList(new String[] {"C38389"}, THES_SCHEME));
rcr = cns.resolveToList(null, null, null, 0).getResolvedConceptReference();
assertTrue("3", rcr.length == 1);
// add a status restriction
cns = ServiceHolder.instance().getLexBIGService().getCodingSchemeConcepts(THES_SCHEME, null);
cns =
cns.restrictToMatchingDesignations(
"Sex Not Known", SearchDesignationOption.ALL, "exactMatch", null);
cns = cns.restrictToStatus(ActiveOption.INACTIVE_ONLY, null);
rcr = cns.resolveToList(null, null, null, 0).getResolvedConceptReference();
assertTrue("4", rcr.length == 1);
assertFalse("6", rcr[0].getReferencedEntry().getIsActive().booleanValue());
}
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;
}