Search in sources :

Example 6 with OperationOutcome

use of org.hl7.fhir.r5.model.OperationOutcome 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;
}
Also used : IIdType(org.hl7.fhir.instance.model.api.IIdType) IdParam(ca.uhn.fhir.rest.annotation.IdParam) IBundleProvider(ca.uhn.fhir.rest.api.server.IBundleProvider) Coding(org.hl7.fhir.dstu3.model.Coding) IdType(org.hl7.fhir.dstu3.model.IdType) Description(ca.uhn.fhir.model.api.annotation.Description) Autowired(org.springframework.beans.factory.annotation.Autowired) HashMap(java.util.HashMap) CodeableConcept(org.hl7.fhir.dstu3.model.CodeableConcept) Operation(ca.uhn.fhir.rest.annotation.Operation) Enumerations(org.hl7.fhir.dstu3.model.Enumerations) CodeSystem(org.hl7.fhir.dstu3.model.CodeSystem) Ids(org.opencds.cqf.ruler.utility.Ids) ArrayList(java.util.ArrayList) OperationProvider(org.opencds.cqf.ruler.api.OperationProvider) HashSet(java.util.HashSet) IFhirResourceDaoValueSet(ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet) Map(java.util.Map) OperationOutcome(org.hl7.fhir.dstu3.model.OperationOutcome) SearchParameterMap(ca.uhn.fhir.jpa.searchparam.SearchParameterMap) Set(java.util.Set) UriParam(ca.uhn.fhir.rest.param.UriParam) UUID(java.util.UUID) Collectors(java.util.stream.Collectors) List(java.util.List) IFhirResourceDaoCodeSystem(ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem) Collections(java.util.Collections) ValueSet(org.hl7.fhir.dstu3.model.ValueSet) OperationOutcome(org.hl7.fhir.dstu3.model.OperationOutcome) IBundleProvider(ca.uhn.fhir.rest.api.server.IBundleProvider) IFhirResourceDaoValueSet(ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet) ValueSet(org.hl7.fhir.dstu3.model.ValueSet) Description(ca.uhn.fhir.model.api.annotation.Description) Operation(ca.uhn.fhir.rest.annotation.Operation)

Example 7 with OperationOutcome

use of org.hl7.fhir.r5.model.OperationOutcome in project cqf-ruler by DBCG.

the class CacheValueSetsProvider method cacheValuesets.

/**
 * Using basic authentication this {@link Operation Operation} will update
 * any {@link ValueSet Valueset} listed given the {@link Endpoint Endpoint}
 * provided.
 * Any Valuesets that require expansion will be expanded.
 *
 * @param details    the {@link RequestDetails RequestDetails}
 * @param endpointId the {@link Endpoint Endpoint} id
 * @param valuesets  the {@link StringAndListParam list} of {@link ValueSet
 *                   Valueset} ids
 * @param userName   the userName
 * @param password   the password
 * @return the {@link OperationOutcome OperationOutcome} or the resulting
 *         {@link Bundle Bundle}
 */
@Description(shortDefinition = "$cache-valuesets", value = "Using basic authentication this Operation will update any Valueset listed given the Endpoint provided. Any Valuesets that require expansion will be expanded.", example = "Endpoint/example-id/$cache-valuesets?valuesets=valuesetId1&valuesets=valuesetId2&user=user&password=password")
@Operation(name = "cache-valuesets", idempotent = true, type = Endpoint.class)
public Resource cacheValuesets(RequestDetails details, @IdParam IdType endpointId, @OperationParam(name = "valuesets") StringAndListParam valuesets, @OperationParam(name = "user") String userName, @OperationParam(name = "pass") String password) {
    Endpoint endpoint = null;
    try {
        endpoint = this.endpointDao.read(endpointId);
        if (endpoint == null) {
            return createErrorOutcome("Could not find Endpoint/" + endpointId);
        }
    } catch (Exception e) {
        return createErrorOutcome("Could not find Endpoint/" + endpointId + "\n" + e);
    }
    IGenericClient client = Clients.forEndpoint(ourCtx, endpoint);
    if (userName != null || password != null) {
        if (userName == null) {
            return createErrorOutcome("Password was provided, but not a user name.");
        } else if (password == null) {
            return createErrorOutcome("User name was provided, but not a password.");
        }
        BasicAuthInterceptor basicAuth = new BasicAuthInterceptor(userName, password);
        client.registerInterceptor(basicAuth);
    // TODO - more advanced security like bearer tokens, etc...
    }
    try {
        Bundle bundleToPost = new Bundle();
        for (StringOrListParam params : valuesets.getValuesAsQueryTokens()) {
            for (StringParam valuesetId : params.getValuesAsQueryTokens()) {
                bundleToPost.addEntry().setRequest(new Bundle.BundleEntryRequestComponent().setMethod(Bundle.HTTPVerb.PUT).setUrl("ValueSet/" + valuesetId.getValue())).setResource(resolveValueSet(client, valuesetId.getValue()));
            }
        }
        return (Resource) systemDao.transaction(details, bundleToPost);
    } catch (Exception e) {
        return createErrorOutcome(e.getMessage());
    }
}
Also used : Endpoint(org.hl7.fhir.r4.model.Endpoint) BasicAuthInterceptor(ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor) IGenericClient(ca.uhn.fhir.rest.client.api.IGenericClient) Bundle(org.hl7.fhir.r4.model.Bundle) Resource(org.hl7.fhir.r4.model.Resource) StringParam(ca.uhn.fhir.rest.param.StringParam) StringOrListParam(ca.uhn.fhir.rest.param.StringOrListParam) Description(ca.uhn.fhir.model.api.annotation.Description) Operation(ca.uhn.fhir.rest.annotation.Operation)

Example 8 with OperationOutcome

use of org.hl7.fhir.r5.model.OperationOutcome in project cqf-ruler by DBCG.

the class CacheValueSetsProviderIT method validateOutcome.

private void validateOutcome(Resource outcomeResource, String detailMessage) {
    assertTrue(outcomeResource instanceof OperationOutcome);
    OperationOutcome outcome = (OperationOutcome) outcomeResource;
    for (OperationOutcomeIssueComponent issue : outcome.getIssue()) {
        assertEquals(OperationOutcome.IssueSeverity.ERROR, issue.getSeverity());
        assertTrue(issue.getDetails().getCodingFirstRep().getDisplay().startsWith(detailMessage));
    }
}
Also used : OperationOutcomeIssueComponent(org.hl7.fhir.dstu3.model.OperationOutcome.OperationOutcomeIssueComponent) OperationOutcome(org.hl7.fhir.dstu3.model.OperationOutcome)

Example 9 with OperationOutcome

use of org.hl7.fhir.r5.model.OperationOutcome in project cqf-ruler by DBCG.

the class CodeSystemProviderIT method testDSTU3UpdateCodeSystems.

@Test
@Order(5)
public void testDSTU3UpdateCodeSystems() throws IOException {
    log.info("Beginning Test DSTU3 Update Code Systems");
    assertEquals(0, performCodeSystemSearchByUrl(cptUrl).size());
    File[] valuesets = new File(CodeSystemProviderIT.class.getResource("valueset").getPath()).listFiles();
    for (File file : valuesets) {
        if (file.isFile() && FilenameUtils.getExtension(file.getPath()).equals("json")) {
            BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
            String resourceString = reader.lines().collect(Collectors.joining(System.lineSeparator()));
            reader.close();
            loadResource("json", resourceString);
        } else if (file.isFile() && FilenameUtils.getExtension(file.getPath()).equals("xml")) {
            BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
            String resourceString = reader.lines().collect(Collectors.joining(System.lineSeparator()));
            reader.close();
            loadResource("xml", resourceString);
        }
    }
    OperationOutcome outcome = codeSystemUpdateProvider.updateCodeSystems();
    for (OperationOutcomeIssueComponent issue : outcome.getIssue()) {
        assertEquals(OperationOutcome.IssueSeverity.INFORMATION, issue.getSeverity());
        assertTrue(issue.getDetails().getText().startsWith("Successfully updated the following CodeSystems: "));
        assertTrue(issue.getDetails().getText().contains("cpt"));
        assertTrue(issue.getDetails().getText().contains("icd-10"));
        assertTrue(issue.getDetails().getText().contains("sct"));
        assertTrue(issue.getDetails().getText().contains("rxnorm"));
    }
    assertEquals(1, performCodeSystemSearchByUrl(icd10).size());
    assertEquals(1, performCodeSystemSearchByUrl(rxNormUrl).size());
    assertEquals(1, performCodeSystemSearchByUrl(snomedSctUrl).size());
    assertEquals(1, performCodeSystemSearchByUrl(cptUrl).size());
    log.info("Finished Test DSTU3 Update Code Systems");
}
Also used : InputStreamReader(java.io.InputStreamReader) OperationOutcomeIssueComponent(org.hl7.fhir.dstu3.model.OperationOutcome.OperationOutcomeIssueComponent) OperationOutcome(org.hl7.fhir.dstu3.model.OperationOutcome) BufferedReader(java.io.BufferedReader) File(java.io.File) FileInputStream(java.io.FileInputStream) Order(org.junit.jupiter.api.Order) TestMethodOrder(org.junit.jupiter.api.TestMethodOrder) RestIntegrationTest(org.opencds.cqf.ruler.test.RestIntegrationTest) Test(org.junit.jupiter.api.Test) SpringBootTest(org.springframework.boot.test.context.SpringBootTest)

Example 10 with OperationOutcome

use of org.hl7.fhir.r5.model.OperationOutcome in project cqf-ruler by DBCG.

the class CacheValueSetsProviderIT method validateOutcome.

private void validateOutcome(Resource outcomeResource, String detailMessage) {
    assertTrue(outcomeResource instanceof OperationOutcome);
    OperationOutcome outcome = (OperationOutcome) outcomeResource;
    for (OperationOutcomeIssueComponent issue : outcome.getIssue()) {
        assertEquals(OperationOutcome.IssueSeverity.ERROR, issue.getSeverity());
        assertTrue(issue.getDetails().getCodingFirstRep().getDisplay().startsWith(detailMessage));
    }
}
Also used : OperationOutcomeIssueComponent(org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent) OperationOutcome(org.hl7.fhir.r4.model.OperationOutcome)

Aggregations

Test (org.junit.Test)214 MockHttpServletResponse (org.springframework.mock.web.MockHttpServletResponse)181 OperationOutcome (org.hl7.fhir.r4.model.OperationOutcome)161 OperationOutcome (org.hl7.fhir.dstu3.model.OperationOutcome)144 Test (org.junit.jupiter.api.Test)42 BaseFhirIntegrationTest (org.openmrs.module.fhir2.BaseFhirIntegrationTest)31 IOException (java.io.IOException)26 IBaseOperationOutcome (org.hl7.fhir.instance.model.api.IBaseOperationOutcome)24 OperationOutcomeIssueComponent (org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent)23 MethodOutcome (ca.uhn.fhir.rest.api.MethodOutcome)22 OperationOutcome (org.hl7.fhir.r5.model.OperationOutcome)20 IdType (org.hl7.fhir.dstu3.model.IdType)17 IdType (org.hl7.fhir.r4.model.IdType)17 CodeableConcept (org.hl7.fhir.dstu3.model.CodeableConcept)15 SpringBootTest (org.springframework.boot.test.context.SpringBootTest)15 URISyntaxException (java.net.URISyntaxException)13 GET (javax.ws.rs.GET)12 Path (javax.ws.rs.Path)12 Produces (javax.ws.rs.Produces)12 Header (org.apache.http.Header)11