Examples with System org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System used on opensource projects

Example 71 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project cqf-ruler by DBCG.

the class CodeSystemUpdateProvider method performCodeSystemUpdate.

public OperationOutcome performCodeSystemUpdate(List<ValueSet> valueSets) {
    OperationOutcome response = new OperationOutcome();
    List<String> codeSystems = new ArrayList<>();
    // Possible for this to run out of memory with really large ValueSets and
    // CodeSystems.
    Map<String, Set<String>> codesBySystem = new HashMap<>();
    for (ValueSet vs : valueSets) {
        if (vs.hasCompose() && vs.getCompose().hasInclude()) {
            for (ValueSet.ConceptSetComponent csc : vs.getCompose().getInclude()) {
                if (!csc.hasSystem() || !csc.hasConcept()) {
                    continue;
                }
                String system = csc.getSystem();
                if (!codesBySystem.containsKey(system)) {
                    codesBySystem.put(system, new HashSet<>());
                }
                Set<String> codes = codesBySystem.get(system);
                codes.addAll(csc.getConcept().stream().map(ValueSet.ConceptReferenceComponent::getCode).collect(Collectors.toList()));
            }
        }
    }
    for (Map.Entry<String, Set<String>> entry : codesBySystem.entrySet()) {
        String system = entry.getKey();
        CodeSystem codeSystem = getCodeSystemByUrl(system);
        updateCodeSystem(codeSystem.setUrl(system), getUnionDistinctCodes(entry.getValue(), codeSystem));
        codeSystems.add(codeSystem.getUrl());
    }
    if (codeSystems.size() > 0) {
        return buildIssue(response, "information", "informational", "Successfully updated the following CodeSystems: " + String.join(", ", codeSystems));
    } else {
        return buildIssue(response, "information", "informational", "No code systems were updated");
    }
}

Example 72 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project cqf-ruler by DBCG.

the class CodeSystemUpdateProvider method updateCodeSystems.

/**
 * Update existing {@link CodeSystem CodeSystems} with the codes in all
 * {@link ValueSet ValueSet} resources.
 * System level CodeSystem update operation
 *
 * @return FHIR {@link OperationOutcome OperationOutcome} detailing the success
 *         or failure of the
 *         operation
 */
@Description(shortDefinition = "$updateCodeSystems", value = "Update existing CodeSystems with the codes in all ValueSet resources. System level CodeSystem update operation", example = "$updateCodeSystems")
@Operation(name = "$updateCodeSystems", idempotent = true)
public OperationOutcome updateCodeSystems() {
    IBundleProvider valuesets = this.myValueSetDaoDSTU3.search(SearchParameterMap.newSynchronous());
    List<ValueSet> valueSets = valuesets.getAllResources().stream().map(x -> (ValueSet) x).collect(Collectors.toList());
    OperationOutcome outcome = this.performCodeSystemUpdate(valueSets);
    OperationOutcome response = new OperationOutcome();
    if (outcome.hasIssue()) {
        for (OperationOutcome.OperationOutcomeIssueComponent issue : outcome.getIssue()) {
            response.addIssue(issue);
        }
    }
    return response;
}

Example 73 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project cqf-ruler by DBCG.

the class JpaTerminologyProvider method expand.

@Override
public Iterable<Code> expand(ValueSetInfo valueSet) throws ResourceNotFoundException {
    // This could possibly be refactored into a single call to the underlying HAPI
    // Terminology service. Need to think through that..,
    IBaseResource vs;
    if (hasUrlId(valueSet)) {
        if (hasVersion(valueSet) || hasVersionedCodeSystem(valueSet)) {
            throw new UnsupportedOperationException(String.format("Could not expand value set %s; version and code system bindings are not supported at this time.", valueSet.getId()));
        }
        IBundleProvider bundleProvider = search(getClass("ValueSet"), Searches.byUrl(valueSet.getId()), myRequestDetails);
        List<IBaseResource> valueSets = bundleProvider.getAllResources();
        if (valueSets.isEmpty()) {
            throw new IllegalArgumentException(String.format("Could not resolve value set %s.", valueSet.getId()));
        } else if (valueSets.size() == 1) {
            vs = valueSets.get(0);
        } else {
            throw new IllegalArgumentException("Found more than 1 ValueSet with url: " + valueSet.getId());
        }
    } else {
        vs = read(Ids.newId(this.myTerminologySvc.getFhirContext(), "ValueSet", valueSet.getId()), myRequestDetails);
        if (vs == null) {
            throw new IllegalArgumentException(String.format("Could not resolve value set %s.", valueSet.getId()));
        }
    }
    // relies heavily on reflection.
    switch(vs.getStructureFhirVersionEnum()) {
        case DSTU3:
            return getCodes((org.hl7.fhir.dstu3.model.ValueSet) vs);
        case R4:
            return getCodes((org.hl7.fhir.r4.model.ValueSet) vs);
        case R5:
            return getCodes((org.hl7.fhir.r5.model.ValueSet) vs);
        default:
            throw new IllegalArgumentException(String.format("expand does not support FHIR version %s", vs.getStructureFhirVersionEnum().getFhirVersionString()));
    }
}

Example 74 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project BridgeServer2 by Sage-Bionetworks.

the class CRCControllerTest method procedureWrongIdentifier.

@Test(expectedExceptions = BadRequestException.class, expectedExceptionsMessageRegExp = "Could not find Bridge user ID.")
public void procedureWrongIdentifier() throws Exception {
    when(mockRequest.getHeader(AUTHORIZATION)).thenReturn(AUTHORIZATION_HEADER_VALUE);
    when(mockAccountService.authenticate(any(), any())).thenReturn(account);
    when(mockAccountService.getAccount(ACCOUNT_ID)).thenReturn(Optional.of(account));
    Identifier identifier = new Identifier();
    identifier.setSystem("wrong-system");
    identifier.setValue(TEST_USER_ID);
    ProcedureRequest procedure = new ProcedureRequest();
    procedure.addIdentifier(identifier);
    String json = FHIR_CONTEXT.newJsonParser().encodeResourceToString(procedure);
    mockRequestBody(mockRequest, json);
    controller.postProcedureRequest();
}

Example 75 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project BridgeServer2 by Sage-Bionetworks.

the class CRCControllerTest method operationWrongIdentifier.

@Test(expectedExceptions = BadRequestException.class, expectedExceptionsMessageRegExp = "Could not find Bridge user ID.")
public void operationWrongIdentifier() throws Exception {
    when(mockRequest.getHeader(AUTHORIZATION)).thenReturn(AUTHORIZATION_HEADER_VALUE);
    when(mockAccountService.authenticate(any(), any())).thenReturn(account);
    when(mockAccountService.getAccount(ACCOUNT_ID)).thenReturn(Optional.of(account));
    Identifier identifier = new Identifier();
    identifier.setSystem("wrong-system");
    identifier.setValue(TEST_USER_ID);
    Observation observation = new Observation();
    observation.addIdentifier(identifier);
    String json = FHIR_CONTEXT.newJsonParser().encodeResourceToString(observation);
    mockRequestBody(mockRequest, json);
    controller.postObservation();
}