private ValidationResult verifyCodeInCodeSystem(
CodeSystem cs, String system, String code, String display) throws Exception {
ConceptDefinitionComponent cc = findCodeInConcept(cs.getConcept(), code);
if (cc == null)
if (cs.getContent().equals(CodeSystem.CodeSystemContentMode.COMPLETE))
return new ValidationResult(
IssueSeverity.ERROR, "Unknown Code " + code + " in " + cs.getUrl());
else if (!cs.getContent().equals(CodeSystem.CodeSystemContentMode.NOTPRESENT))
return new ValidationResult(
IssueSeverity.WARNING,
"Unknown Code " + code + " in partial code list of " + cs.getUrl());
else
return verifyCodeExternal(
null, new Coding().setSystem(system).setCode(code).setDisplay(display), false);
//
// return new ValidationResult(IssueSeverity.WARNING, "A definition was found for
// "+cs.getUrl()+", but it has no codes in the definition");
// return new ValidationResult(IssueSeverity.ERROR, "Unknown Code "+code+" in
// "+cs.getUrl());
if (display == null) return new ValidationResult(cc);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
if (cc.hasDisplay()) {
b.append(cc.getDisplay());
if (display.equalsIgnoreCase(cc.getDisplay())) return new ValidationResult(cc);
}
for (ConceptDefinitionDesignationComponent ds : cc.getDesignation()) {
b.append(ds.getValue());
if (display.equalsIgnoreCase(ds.getValue())) return new ValidationResult(cc);
}
return new ValidationResult(
IssueSeverity.WARNING,
"Display Name for " + code + " must be one of '" + b.toString() + "'",
cc);
}
@Test
public void testStoreCodeSystemInvalidCyclicLoop() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id =
myCodeSystemDao.create(codeSystem, new ServletRequestDetails()).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parent = new TermConcept();
parent.setCodeSystem(cs);
parent.setCode("parent");
cs.getConcepts().add(parent);
TermConcept child = new TermConcept();
child.setCodeSystem(cs);
child.setCode("child");
parent.addChild(child, RelationshipTypeEnum.ISA);
child.addChild(parent, RelationshipTypeEnum.ISA);
try {
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://foo", cs);
fail();
} catch (InvalidRequestException e) {
assertEquals("CodeSystem contains circular reference around code parent", e.getMessage());
}
}
private IIdType createCodeSystem() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id =
myCodeSystemDao.create(codeSystem, new ServletRequestDetails()).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA");
cs.getConcepts().add(parentA);
TermConcept childAA = new TermConcept(cs, "childAA");
parentA.addChild(childAA, RelationshipTypeEnum.ISA);
TermConcept childAAA = new TermConcept(cs, "childAAA");
childAA.addChild(childAAA, RelationshipTypeEnum.ISA);
TermConcept childAAB = new TermConcept(cs, "childAAB");
childAA.addChild(childAAB, RelationshipTypeEnum.ISA);
TermConcept childAB = new TermConcept(cs, "childAB");
parentA.addChild(childAB, RelationshipTypeEnum.ISA);
TermConcept parentB = new TermConcept(cs, "ParentB");
cs.getConcepts().add(parentB);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://foo", cs);
return id;
}
private String cacheValue(CodeSystem cs) throws IOException {
CodeSystem csid = new CodeSystem();
csid.setId(cs.getId());
csid.setVersion(cs.getVersion());
csid.setContent(cs.getContent());
csid.setHierarchyMeaning(CodeSystemHierarchyMeaning.GROUPEDBY);
for (ConceptDefinitionComponent cc : cs.getConcept())
csid.getConcept().add(processCSConcept(cc));
JsonParser parser = new JsonParser();
parser.setOutputStyle(OutputStyle.NORMAL);
ByteArrayOutputStream b = new ByteArrayOutputStream();
parser.compose(b, csid);
b.close();
return new String(b.toByteArray(), Charsets.UTF_8);
}
@Test
public void testCreateDuplicateCodeSystemUri() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id =
myCodeSystemDao.create(codeSystem, new ServletRequestDetails()).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, cs);
// Update
cs = new TermCodeSystemVersion();
TermConcept parentA = new TermConcept(cs, "ParentA");
cs.getConcepts().add(parentA);
id = myCodeSystemDao.update(codeSystem, new ServletRequestDetails()).getId().toUnqualified();
table = myResourceTableDao.findOne(id.getIdPartAsLong());
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, cs);
// Try to update to a different resource
codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
id = myCodeSystemDao.create(codeSystem, new ServletRequestDetails()).getId().toUnqualified();
table = myResourceTableDao.findOne(id.getIdPartAsLong());
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
try {
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, cs);
fail();
} catch (UnprocessableEntityException e) {
assertThat(
e.getMessage(),
containsString(
"Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
}
}
@Override
public boolean supportsSystem(String system) throws TerminologyServiceException {
if (codeSystems.containsKey(system)) return true;
else if (nonSupportedCodeSystems.contains(system)) return false;
else if (system.startsWith("http://example.org")
|| system.startsWith("http://acme.com")
|| system.startsWith("http://hl7.org/fhir/valueset-")
|| system.startsWith("urn:oid:")) return false;
else {
if (noTerminologyServer) return false;
if (bndCodeSystems == null) {
try {
log("Terminology server: Check for supported code systems for " + system);
bndCodeSystems =
txServer.fetchFeed(
txServer.getAddress()
+ "/CodeSystem?content=not-present&_summary=true&_count=1000");
} catch (Exception e) {
if (canRunWithoutTerminology) {
noTerminologyServer = true;
log("==============!! Running without terminology server !!==============");
return false;
} else throw new TerminologyServiceException(e);
}
}
if (bndCodeSystems != null) {
for (BundleEntryComponent be : bndCodeSystems.getEntry()) {
CodeSystem cs = (CodeSystem) be.getResource();
if (!codeSystems.containsKey(cs.getUrl())) {
codeSystems.put(cs.getUrl(), null);
}
}
}
if (codeSystems.containsKey(system)) return true;
}
nonSupportedCodeSystems.add(system);
return false;
}
private String gen(Section section, CodeSystem cs, ValueSet vs) {
String bn = getPNameForUri(cs.getUrl());
if (!bn.startsWith("<")) {
section.triple(bn + ".system", "a", "fhir:CodeSystem");
if (cs.hasVersion()) section.triple(bn + ".system", "fhir:version", literal(cs.getVersion()));
if (vs.hasName()) section.label(bn + ".system", vs.getName());
if (vs.hasDescription())
section.comment(
bn + ".system",
vs.getDescription()
.replace("value set", "code system")
.replace("Value Set", "Code System")
.replace("Value set", "Code system"));
if (vs.hasCopyright())
section.triple(bn + ".system", "dc:rights", literal(vs.getCopyright()));
if (vs.hasDate()) section.triple(bn + ".system", "dc:date", literal(vs.getDate().toString()));
section.triple(bn, "a", "fhir:Concept");
gen(section, bn, bn, cs.getConcept());
}
return bn;
}