@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;
}
@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/"));
}
}
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);
}