/**
* Test coding scheme restriction search.
*
* @throws Exception the exception
*/
public void testCodingSchemeRestrictionSearch() throws Exception {
LexBIGServiceMetadata md = ServiceHolder.instance().getLexBIGService().getServiceMetadata();
md = md.restrictToValue("English", "LuceneQuery");
MetadataProperty[] result = md.resolve().getMetadataProperty();
HashSet<String> temp = new HashSet<String>();
for (int i = 0; i < result.length; i++) {
temp.add(result[i].getCodingSchemeURI() + ":" + result[i].getCodingSchemeVersion());
}
// should contain this
assertTrue(temp.contains(THES_URN + ":" + THES_METADATA_VERSION));
// now do the restriction, and retest.
md = ServiceHolder.instance().getLexBIGService().getServiceMetadata();
md = md.restrictToValue("English", "LuceneQuery");
md =
md.restrictToCodingScheme(
Constructors.createAbsoluteCodingSchemeVersionReference(
THES_URN, THES_METADATA_VERSION));
result = md.resolve().getMetadataProperty();
temp = new HashSet<String>();
for (int i = 0; i < result.length; i++) {
temp.add(result[i].getCodingSchemeURI() + ":" + result[i].getCodingSchemeVersion());
}
// should be more than 1 unique code system.
assertTrue(temp.size() >= 1);
// should contain this
assertTrue(temp.contains(THES_URN + ":" + THES_METADATA_VERSION));
}
public void testT1_FNC_11() throws LBException {
// in LexBig, a role is just an association, so this is traversing
// associations.
CodedNodeGraph cng =
ServiceHolder.instance().getLexBIGService().getNodeGraph(THES_SCHEME, null, null);
cng.restrictToAssociations(
Constructors.createNameAndValueList(new String[] {"subClassOf"}), null);
// role "Anatomy_Kind"
ResolvedConceptReference[] rcr =
cng.resolveAsList(
Constructors.createConceptReference("Anatomy_Kind", THES_SCHEME),
false,
true,
1,
1,
null,
null,
null,
0)
.getResolvedConceptReference();
// check for some source (down) codes that I know should be there.
assertTrue(rcr.length == 1);
assertTrue(rcr[0].getConceptCode().equals("Anatomy_Kind"));
Association[] a = rcr[0].getTargetOf().getAssociation();
assertTrue(contains(a, "subClassOf", "Anatomic_Structure_System_or_Substance"));
// go down one more level from one of the codes.
ConvenienceMethods cm = new ConvenienceMethods(ServiceHolder.instance().getLexBIGService());
a =
new Association[] {
cm.getAssociationForwardOneLevel(
"Anatomic_Structure_System_or_Substance",
"roles",
"subClassOf",
THES_SCHEME,
null,
false,
null)
};
contains(a, "subClassOf", "C13018");
contains(a, "subClassOf", "Body_Fluid_or_Substance");
}
/**
* Primary entry point for the program.
*
* @throws Exception
*/
public void run(String[] args) throws Exception {
synchronized (ResourceManager.instance()) {
// Parse the command line ...
CommandLine cl = null;
Options options = getCommandOptions();
try {
cl = new BasicParser().parse(options, args);
} catch (ParseException e) {
Util.displayCommandOptions(
"TagScheme",
options,
"TagScheme -u \"urn:oid:2.16.840.1.113883.3.26.1.1\" -v \"05.09e\" -t \"TEST\"",
e);
Util.displayMessage(Util.getPromptForSchemeHelp());
return;
}
// Interpret provided values ...
String urn = cl.getOptionValue("u");
String ver = cl.getOptionValue("v");
String tag = cl.getOptionValue("t").trim();
CodingSchemeSummary css = null;
// Find in list of registered vocabularies ...
if (urn != null && ver != null) {
urn = urn.trim();
ver = ver.trim();
LexBIGService lbs = LexBIGServiceImpl.defaultInstance();
Enumeration<? extends CodingSchemeRendering> schemes =
lbs.getSupportedCodingSchemes().enumerateCodingSchemeRendering();
while (schemes.hasMoreElements() && css == null) {
CodingSchemeSummary summary = schemes.nextElement().getCodingSchemeSummary();
if (urn.equalsIgnoreCase(summary.getCodingSchemeURI())
&& ver.equalsIgnoreCase(summary.getRepresentsVersion())) css = summary;
}
}
// Found it? If not, prompt...
if (css == null) {
if (urn != null || ver != null) {
Util.displayMessage("No matching coding scheme was found for the given URN or version.");
Util.displayMessage("");
}
css = Util.promptForCodeSystem();
if (css == null) return;
}
// Continue and perform the action ...
Util.displayTaggedMessage("A matching coding scheme was found ...");
LexBIGServiceManager lbsm =
LexBIGServiceImpl.defaultInstance().getServiceManager(new Object());
lbsm.setVersionTag(Constructors.createAbsoluteCodingSchemeVersionReference(css), tag);
Util.displayTaggedMessage("Request complete");
}
}
/**
* 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());
}
/**
* Test list coding schemes.
*
* @throws Exception the exception
*/
public void testListCodingSchemes() throws Exception {
LexBIGServiceMetadata md = ServiceHolder.instance().getLexBIGService().getServiceMetadata();
AbsoluteCodingSchemeVersionReference[] acsvrl =
md.listCodingSchemes().getAbsoluteCodingSchemeVersionReference();
assertTrue(acsvrl.length >= 1);
assertTrue(
contains(
acsvrl,
Constructors.createAbsoluteCodingSchemeVersionReference(
THES_URN, THES_METADATA_VERSION)));
}
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 container restriction search.
*
* @throws Exception the exception
*/
public void testContainerRestrictionSearch() throws Exception {
LexBIGServiceMetadata md = ServiceHolder.instance().getLexBIGService().getServiceMetadata();
md = md.restrictToValue("OWL-FULL", "LuceneQuery");
md =
md.restrictToCodingScheme(
Constructors.createAbsoluteCodingSchemeVersionReference(
THES_URN, THES_METADATA_VERSION));
MetadataProperty[] result = md.resolve().getMetadataProperty();
assertTrue(result.length >= 1);
assertTrue(contains(result, THES_URN, THES_METADATA_VERSION, "format", "OWL-FULL"));
}
/**
* 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);
}
private Set<CodingSchemeReference> toCodingSchemeReference(
Iterable<NameOrURI> codeSystemVersions) {
Set<CodingSchemeReference> returnSet = new HashSet<CodingSchemeReference>();
for (NameOrURI version : codeSystemVersions) {
NameVersionPair pair = this.versionNameConverter.fromCts2VersionName(version.getName());
CodingSchemeReference ref = new CodingSchemeReference();
ref.setCodingScheme(pair.getName());
ref.setVersionOrTag(
Constructors.createCodingSchemeVersionOrTagFromVersion(pair.getVersion()));
returnSet.add(ref);
}
return returnSet;
}
/**
* Test value restriction.
*
* @throws Exception the exception
*/
public void testValueRestriction() throws Exception {
LexBIGServiceMetadata md = ServiceHolder.instance().getLexBIGService().getServiceMetadata();
md =
md.restrictToCodingScheme(
Constructors.createAbsoluteCodingSchemeVersionReference(
THES_URN, THES_METADATA_VERSION));
md = md.restrictToValue(".*core.*", "RegExp");
MetadataProperty[] result = md.resolve().getMetadataProperty();
assertTrue(result.length >= 2);
assertTrue(
contains(
result,
THES_URN,
THES_METADATA_VERSION,
"homepage",
"http://ncicb.nci.nih.gov/core/EVS"));
}
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() + "'");
}
}
}