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ResourceProviderR4Test.java
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ResourceProviderR4Test.java
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package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.PreferReturnEnum;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.client.apache.ResourceEntity;
import ca.uhn.fhir.rest.client.api.IClientInterceptor;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
import ca.uhn.fhir.rest.gclient.ICriterion;
import ca.uhn.fhir.rest.gclient.NumberClientParam;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.NumberParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.util.ClasspathUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.http.NameValuePair;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpDelete;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPatch;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.entity.ByteArrayEntity;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.apache.http.message.BasicNameValuePair;
import org.apache.http.util.EntityUtils;
import org.hamcrest.Matchers;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Attachment;
import org.hl7.fhir.r4.model.AuditEvent;
import org.hl7.fhir.r4.model.BaseResource;
import org.hl7.fhir.r4.model.Basic;
import org.hl7.fhir.r4.model.Binary;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
import org.hl7.fhir.r4.model.Bundle.SearchEntryMode;
import org.hl7.fhir.r4.model.CarePlan;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.Coverage;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.DecimalType;
import org.hl7.fhir.r4.model.Device;
import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.DocumentManifest;
import org.hl7.fhir.r4.model.DocumentReference;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Encounter.EncounterLocationComponent;
import org.hl7.fhir.r4.model.Encounter.EncounterStatus;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.ImagingStudy;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Location;
import org.hl7.fhir.r4.model.Media;
import org.hl7.fhir.r4.model.Medication;
import org.hl7.fhir.r4.model.MedicationAdministration;
import org.hl7.fhir.r4.model.MedicationRequest;
import org.hl7.fhir.r4.model.Meta;
import org.hl7.fhir.r4.model.MolecularSequence;
import org.hl7.fhir.r4.model.Narrative;
import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Observation.ObservationComponentComponent;
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Period;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Procedure;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Questionnaire;
import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.r4.model.QuestionnaireResponse;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.SearchParameter;
import org.hl7.fhir.r4.model.ServiceRequest;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.Subscription;
import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
import org.hl7.fhir.r4.model.UnsignedIntType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.junit.jupiter.params.provider.ValueSource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.util.AopTestUtils;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.math.BigDecimal;
import java.net.InetSocketAddress;
import java.net.Socket;
import java.net.SocketTimeoutException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import static ca.uhn.fhir.jpa.config.r4.FhirContextR4Config.DEFAULT_PRESERVE_VERSION_REFS;
import static ca.uhn.fhir.jpa.util.TestUtil.sleepOneClick;
import static ca.uhn.fhir.rest.param.BaseParamWithPrefix.MSG_PREFIX_INVALID_FORMAT;
import static ca.uhn.fhir.test.utilities.CustomMatchersUtil.assertDoesNotContainAnyOf;
import static ca.uhn.fhir.util.TestUtil.sleepAtLeast;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsInRelativeOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.emptyString;
import static org.hamcrest.Matchers.endsWith;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.lessThan;
import static org.hamcrest.Matchers.lessThanOrEqualTo;
import static org.hamcrest.Matchers.matchesPattern;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.startsWith;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@SuppressWarnings("Duplicates")
public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
public static final int LARGE_NUMBER = 77;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4Test.class);
private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
private CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
@Autowired
private ISearchDao mySearchEntityDao;
@Override
@AfterEach
public void after() throws Exception {
super.after();
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
myDaoConfig.setCountSearchResultsUpTo(new DaoConfig().getCountSearchResultsUpTo());
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
myDaoConfig.setAdvancedHSearchIndexing(new DaoConfig().isAdvancedHSearchIndexing());
myModelConfig.setIndexOnContainedResources(new ModelConfig().isIndexOnContainedResources());
mySearchCoordinatorSvcRaw.setLoadingThrottleForUnitTests(null);
mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(QueryParameterUtils.DEFAULT_SYNC_SIZE);
mySearchCoordinatorSvcRaw.setNeverUseLocalSearchForUnitTests(false);
mySearchCoordinatorSvcRaw.cancelAllActiveSearches();
myDaoConfig.getModelConfig().setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
myClient.unregisterInterceptor(myCapturingInterceptor);
myDaoConfig.setUpdateWithHistoryRewriteEnabled(false);
myDaoConfig.setPreserveRequestIdInResourceBody(false);
}
@BeforeEach
@Override
public void before() throws Exception {
super.before();
myFhirContext.setParserErrorHandler(new StrictErrorHandler());
myFhirContext.getParserOptions().setDontStripVersionsFromReferencesAtPaths(DEFAULT_PRESERVE_VERSION_REFS);
myDaoConfig.setAllowMultipleDelete(true);
myClient.registerInterceptor(myCapturingInterceptor);
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
}
@Test
public void testParameterWithNoValueThrowsError_InvalidChainOnCustomSearch() throws IOException {
SearchParameter searchParameter = new SearchParameter();
searchParameter.addBase("BodyStructure").addBase("Procedure");
searchParameter.setCode("focalAccess");
searchParameter.setType(Enumerations.SearchParamType.REFERENCE);
searchParameter.setExpression("Procedure.extension('Procedure#focalAccess')");
searchParameter.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
myClient.create().resource(searchParameter).execute();
mySearchParamRegistry.forceRefresh();
HttpGet get = new HttpGet(ourServerBase + "/Procedure?focalAccess.a%20ne%20e");
try (CloseableHttpResponse resp = ourHttpClient.execute(get)) {
String output = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
assertThat(output, containsString("Invalid parameter chain: focalAccess.a ne e"));
assertEquals(400, resp.getStatusLine().getStatusCode());
}
}
@Test
public void createResourceSearchParameter_withExpressionMetaSecurity_succeeds(){
SearchParameter searchParameter = new SearchParameter();
searchParameter.setId("resource-security");
searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
searchParameter.setName("Security");
searchParameter.setCode("_security");
searchParameter.addBase("Patient").addBase("Account");
searchParameter.setType(Enumerations.SearchParamType.TOKEN);
searchParameter.setExpression("meta.security");
IIdType id = myClient.update().resource(searchParameter).execute().getId().toUnqualifiedVersionless();
assertNotNull(id);
assertEquals("resource-security", id.getIdPart());
}
@Test
public void createSearchParameter_with2Expressions_succeeds(){
SearchParameter searchParameter = new SearchParameter();
searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
searchParameter.setCode("myGender");
searchParameter.addBase("Patient").addBase("Person");
searchParameter.setType(Enumerations.SearchParamType.TOKEN);
searchParameter.setExpression("Patient.gender|Person.gender");
MethodOutcome result= myClient.create().resource(searchParameter).execute();
assertEquals(true, result.getCreated());
}
@Test
public void testParameterWithNoValueThrowsError_InvalidRootParam() throws IOException {
SearchParameter searchParameter = new SearchParameter();
searchParameter.addBase("BodyStructure").addBase("Procedure");
searchParameter.setCode("focalAccess");
searchParameter.setType(Enumerations.SearchParamType.REFERENCE);
searchParameter.setExpression("Procedure.extension('Procedure#focalAccess')");
searchParameter.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
myClient.create().resource(searchParameter).execute();
mySearchParamRegistry.forceRefresh();
HttpGet get = new HttpGet(ourServerBase + "/Procedure?a");
try (CloseableHttpResponse resp = ourHttpClient.execute(get)) {
String output = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
assertThat(output, containsString("Unknown search parameter "a""));
assertEquals(400, resp.getStatusLine().getStatusCode());
}
}
@Test
public void testSearchForTokenValueOnlyUsesValueHash() {
myCaptureQueriesListener.clear();
myClient
.loadPage()
.byUrl(ourServerBase + "/Practitioner?identifier=" + UrlUtil.escapeUrlParam("ABC|,DEF"))
.andReturnBundle(Bundle.class)
.execute();
myCaptureQueriesListener.logSelectQueries();
}
@Test
public void testSearchWithContainsLowerCase() {
myDaoConfig.setAllowContainsSearches(true);
Patient pt1 = new Patient();
pt1.addName().setFamily("Elizabeth");
String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
Patient pt2 = new Patient();
pt2.addName().setFamily("fghijk");
String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
Patient pt3 = new Patient();
pt3.addName().setFamily("zzzzz");
myPatientDao.create(pt3).getId().toUnqualifiedVersionless().getValue();
Bundle output = myClient
.search()
.forResource("Patient")
.where(Patient.NAME.contains().value("ZAB"))
.returnBundle(Bundle.class)
.execute();
List<String> ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
assertThat(ids, containsInAnyOrder(pt1id));
output = myClient
.search()
.forResource("Patient")
.where(Patient.NAME.contains().value("zab"))
.returnBundle(Bundle.class)
.execute();
ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
assertThat(ids, containsInAnyOrder(pt1id));
}
@Test
public void testSearchWithPercentSign() {
myDaoConfig.setAllowContainsSearches(true);
Patient pt1 = new Patient();
pt1.addName().setFamily("Smith%");
String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
Bundle output = myClient
.search()
.forResource("Patient")
.where(Patient.NAME.contains().value("Smith%"))
.returnBundle(Bundle.class)
.execute();
List<String> ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
assertThat(ids, containsInAnyOrder(pt1id));
Patient pt2 = new Patient();
pt2.addName().setFamily("Sm%ith");
String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
output = myClient
.search()
.forResource("Patient")
.where(Patient.NAME.contains().value("Sm%ith"))
.returnBundle(Bundle.class)
.execute();
ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
assertThat(ids, containsInAnyOrder(pt2id));
}
@Test
public void testSearchWithDateInvalid() throws IOException {
HttpGet get = new HttpGet(ourServerBase + "/Condition?onset-date=junk");
try (CloseableHttpResponse resp = ourHttpClient.execute(get)) {
String output = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
assertThat(output, containsString(MSG_PREFIX_INVALID_FORMAT + ""junk""));
assertEquals(400, resp.getStatusLine().getStatusCode());
}
get = new HttpGet(ourServerBase + "/Condition?onset-date=ge");
try (CloseableHttpResponse resp = ourHttpClient.execute(get)) {
String output = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
assertThat(output, containsString(MSG_PREFIX_INVALID_FORMAT + ""ge""));
assertEquals(400, resp.getStatusLine().getStatusCode());
}
get = new HttpGet(ourServerBase + "/Condition?onset-date=" + UrlUtil.escapeUrlParam(">"));
try (CloseableHttpResponse resp = ourHttpClient.execute(get)) {
String output = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
assertThat(output, containsString(MSG_PREFIX_INVALID_FORMAT + "">""));
assertEquals(400, resp.getStatusLine().getStatusCode());
}
}
@Test
public void testSearchWithSlashes() {
myDaoConfig.setSearchPreFetchThresholds(Lists.newArrayList(10, 50, 10000));
Procedure procedure = new Procedure();
procedure.setStatus(Procedure.ProcedureStatus.COMPLETED);
String procedureId = myClient.create().resource(procedure).execute().getId().toUnqualifiedVersionless().getValue();
DocumentReference dr = new DocumentReference();
dr.addContent().getAttachment().setContentType("application/vnd.mfer");
String drId = myClient.create().resource(dr).execute().getId().toUnqualifiedVersionless().getValue();
for (int i = 0; i < 60; i++) {
Observation obs = new Observation();
obs.addPartOf().setReference(procedureId);
obs.addDerivedFrom().setReference(drId);
myClient.create().resource(obs).execute();
}
ourLog.info("Starting search");
Bundle response = myClient
.search()
.byUrl("Observation?part-of=" + procedureId + "&derived-from:DocumentReference.contenttype=application/vnd.mfer&_total=accurate&_count=2")
.returnBundle(Bundle.class)
.execute();
int obsCount = 0;
int pageCount = 0;
while (response != null) {
obsCount += response.getEntry().size();
pageCount++;
if (response.getLink("next") != null) {
response = myClient.loadPage().next(response).execute();
} else {
response = null;
}
ourLog.info("Have loaded {} pages and {} reources", pageCount, obsCount);
}
assertEquals(60, obsCount);
assertEquals(30, pageCount);
}
@Test
public void testManualPagingLinkOffsetDoesntReturnBeyondEnd() {
myDaoConfig.setSearchPreFetchThresholds(Lists.newArrayList(10, 1000));
for (int i = 0; i < 50; i++) {
Organization o = new Organization();
o.setId("O" + i);
o.setName("O" + i);
myClient.update().resource(o).execute().getId().toUnqualifiedVersionless();
}
Bundle output = myClient
.search()
.forResource("Organization")
.count(3)
.returnBundle(Bundle.class)
.execute();
assertNull(output.getTotalElement().getValue());
output = myClient
.search()
.forResource("Organization")
.count(3)
.totalMode(SearchTotalModeEnum.ACCURATE)
.returnBundle(Bundle.class)
.execute();
assertNotNull(output.getTotalElement().getValue());
String linkNext = output.getLink("next").getUrl();
linkNext = linkNext.replaceAll("_getpagesoffset=[0-9]+", "_getpagesoffset=3300");
assertThat(linkNext, containsString("_getpagesoffset=3300"));
Bundle nextPageBundle = myClient.loadPage().byUrl(linkNext).andReturnBundle(Bundle.class).execute();
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(nextPageBundle));
assertEquals(null, nextPageBundle.getLink("next"));
}
@Test
public void testSearchLinksWorkWithIncludes() {
for (int i = 0; i < 5; i++) {
Organization o = new Organization();
o.setId("O" + i);
o.setName("O" + i);
IIdType oid = myClient.update().resource(o).execute().getId().toUnqualifiedVersionless();
Patient p = new Patient();
p.setId("P" + i);
p.getManagingOrganization().setReference(oid.getValue());
myClient.update().resource(p).execute();
}
Bundle output = myClient
.search()
.forResource("Patient")
.include(IBaseResource.INCLUDE_ALL)
.count(3)
.returnBundle(Bundle.class)
.execute();
List<String> ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
ourLog.info("Ids: {}", ids);
assertEquals(6, output.getEntry().size());
assertNotNull(output.getLink("next"));
// Page 2
output = myClient
.loadPage()
.next(output)
.execute();
ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
ourLog.info("Ids: {}", ids);
assertEquals(4, output.getEntry().size());
assertNull(output.getLink("next"));
}
@Test
public void testSearchWithDeepChain() throws IOException {
SearchParameter sp = new SearchParameter();
sp.addBase("Patient");
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.setCode("extpatorg");
sp.setName("extpatorg");
sp.setExpression("Patient.extension('http:https://patext').value.as(Reference)");
myClient.create().resource(sp).execute();
sp = new SearchParameter();
sp.addBase("Organization");
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.setCode("extorgorg");
sp.setName("extorgorg");
sp.setExpression("Organization.extension('http:https://orgext').value.as(Reference)");
myClient.create().resource(sp).execute();
mySearchParamRegistry.forceRefresh();
Organization grandParent = new Organization();
grandParent.setName("GRANDPARENT");
IIdType grandParentId = myClient.create().resource(grandParent).execute().getId().toUnqualifiedVersionless();
Organization parent = new Organization();
parent.setName("PARENT");
parent.getPartOf().setReference(grandParentId.getValue());
parent.addExtension("http:https://orgext", new Reference().setReference(grandParentId.getValue()));
IIdType parentId = myClient.create().resource(parent).execute().getId().toUnqualifiedVersionless();
Organization org = new Organization();
org.setName("ORGANIZATION");
org.getPartOf().setReference(parentId.getValue());
org.addExtension("http:https://orgext", new Reference().setReference(parentId.getValue()));
IIdType orgId = myClient.create().resource(org).execute().getId().toUnqualifiedVersionless();
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
myCaptureQueriesListener.clear();
Patient p = new Patient();
p.getManagingOrganization().setReference(orgId.getValue());
p.addExtension("http:https://patext", new Reference().setReference(orgId.getValue()));
String pid = myClient.create().resource(p).execute().getId().toUnqualified().getValue();
List<String> idValues;
// Regular search param
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient?organization=" + orgId.getValue());
assertThat(idValues, contains(pid));
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient?organization.name=ORGANIZATION");
assertThat(idValues, contains(pid));
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient?organization.partof.name=PARENT");
assertThat(idValues, contains(pid));
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient?organization.partof.partof.name=GRANDPARENT");
assertThat(idValues, contains(pid));
// Search param on extension
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient?extpatorg=" + orgId.getValue());
assertThat(idValues, contains(pid));
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient?extpatorg.name=ORGANIZATION");
assertThat(idValues, contains(pid));
myCaptureQueriesListener.clear();
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient?extpatorg.extorgorg.name=PARENT");
myCaptureQueriesListener.logSelectQueries();
assertThat(idValues, contains(pid));
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient?extpatorg.extorgorg.extorgorg.name=GRANDPARENT");
assertThat(idValues, contains(pid));
}
@Test
public void testSearchFetchPageBeyondEnd() {
for (int i = 0; i < 10; i++) {
Organization o = new Organization();
o.setId("O" + i);
o.setName("O" + i);
IIdType oid = myClient.update().resource(o).execute().getId().toUnqualifiedVersionless();
}
Bundle output = myClient
.search()
.forResource("Organization")
.count(3)
.returnBundle(Bundle.class)
.execute();
String nextPageUrl = output.getLink("next").getUrl();
String url = nextPageUrl.replace("_getpagesoffset=3", "_getpagesoffset=999");
ourLog.info("Going to request URL: {}", url);
output = myClient
.loadPage()
.byUrl(url)
.andReturnBundle(Bundle.class)
.execute();
assertEquals(0, output.getEntry().size());
}
@Test
public void testDeleteConditional() {
Patient p = new Patient();
p.addName().setFamily("FAM").addGiven("GIV");
IIdType id = myPatientDao.create(p).getId();
myClient.read().resource("Patient").withId(id.toUnqualifiedVersionless()).execute();
myClient
.delete()
.resourceConditionalByUrl("Patient?family=FAM&given=giv")
.execute();
try {
myClient.read().resource("Patient").withId(id.toUnqualifiedVersionless()).execute();
fail();
} catch (ResourceGoneException e) {
// good
}
}
@Test
public void testResourceGoneIncludesVersion() {
Patient p = new Patient();
p.addName().setFamily("FAM").addGiven("GIV");
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
myClient
.delete()
.resourceById(id)
.execute();
CapturingInterceptor captureInterceptor = new CapturingInterceptor();
myClient.registerInterceptor(captureInterceptor);
try {
myClient.read().resource("Patient").withId(id.toUnqualifiedVersionless()).execute();
fail();
} catch (ResourceGoneException e) {
// good
}
List<String> locationHeader = captureInterceptor.getLastResponse().getHeaders(Constants.HEADER_LOCATION);
assertEquals(1, locationHeader.size());
assertThat(locationHeader.get(0), containsString(id.getValue() + "/_history/2"));
}
@Test
public void testUpdateWithNoBody() throws IOException {
HttpPut httpPost = new HttpPut(ourServerBase + "/Patient/AAA");
try (CloseableHttpResponse status = ourHttpClient.execute(httpPost)) {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(status.getStatusLine().toString());
ourLog.info(responseContent);
assertEquals(400, status.getStatusLine().getStatusCode());
assertThat(responseContent, containsString("No body was supplied in request"));
}
}
@Test
public void testCreateWithNoBody() throws IOException {
HttpPost httpPost = new HttpPost(ourServerBase + "/Patient");
try (CloseableHttpResponse status = ourHttpClient.execute(httpPost)) {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(status.getStatusLine().toString());
ourLog.info(responseContent);
assertEquals(400, status.getStatusLine().getStatusCode());
assertThat(responseContent, containsString("No body was supplied in request"));
}
}
@Test
public void testCreateWithClientAssignedId() throws IOException {
// Create with client assigned ID
Patient p = new Patient();
p.setActive(true);
p.setId("AAA");
String encoded = myFhirContext.newJsonParser().encodeResourceToString(p);
HttpPut httpPut = new HttpPut(ourServerBase + "/Patient/AAA");
httpPut.setEntity(new StringEntity(encoded, ContentType.parse("application/json+fhir")));
try (CloseableHttpResponse status = ourHttpClient.execute(httpPut)) {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(status.getStatusLine().toString());
ourLog.info(responseContent);
assertEquals(201, status.getStatusLine().getStatusCode());
assertThat(responseContent, containsString("true"));
}
// Delete
HttpDelete httpDelete = new HttpDelete(ourServerBase + "/Patient/AAA");
try (CloseableHttpResponse status = ourHttpClient.execute(httpDelete)) {
assertEquals(200, status.getStatusLine().getStatusCode());
}
// Create it again
p = new Patient();
p.setActive(true);
p.setId("AAA");
encoded = myFhirContext.newJsonParser().encodeResourceToString(p);
httpPut = new HttpPut(ourServerBase + "/Patient/AAA");
httpPut.setEntity(new StringEntity(encoded, ContentType.parse("application/json+fhir")));
try (CloseableHttpResponse status = ourHttpClient.execute(httpPut)) {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(status.getStatusLine().toString());
ourLog.info(responseContent);
assertEquals(201, status.getStatusLine().getStatusCode());
assertThat(responseContent, containsString("true"));
}
}
@BeforeEach
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
mySearchCoordinatorSvcRaw = AopTestUtils.getTargetObject(mySearchCoordinatorSvc);
}
private void checkParamMissing(String paramName) throws IOException {
HttpGet get = new HttpGet(ourServerBase + "/Observation?" + paramName + ":missing=false");
CloseableHttpResponse resp = ourHttpClient.execute(get);
resp.getEntity().getContent().close();
assertEquals(200, resp.getStatusLine().getStatusCode());
}
private ArrayList<IBaseResource> genResourcesOfType(Bundle theRes, Class<? extends IBaseResource> theClass) {
ArrayList<IBaseResource> retVal = new ArrayList<>();
for (BundleEntryComponent next : theRes.getEntry()) {
if (next.getResource() != null) {
if (theClass.isAssignableFrom(next.getResource().getClass())) {
retVal.add(next.getResource());
}
}
}
return retVal;
}
/**
* See #484
*/
@Test
public void saveAndRetrieveBasicResource() throws IOException {
String input = IOUtils.toString(getClass().getResourceAsStream("/basic-stu3.xml"), StandardCharsets.UTF_8);
String respString = myClient.transaction().withBundle(input).prettyPrint().execute();
ourLog.info(respString);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, respString);
IdType id = new IdType(bundle.getEntry().get(0).getResponse().getLocation());
Basic basic = myClient.read().resource(Basic.class).withId(id).execute();
List<Extension> exts = basic.getExtensionsByUrl("http:https://localhost:1080/hapi-fhir-jpaserver-example/baseDstu2/StructureDefinition/DateID");
assertEquals(1, exts.size());
}
private List<String> searchAndReturnUnqualifiedIdValues(String theUri) throws IOException {
List<String> ids;
HttpGet get = new HttpGet(theUri);
ourLog.info("About to perform search for: {}", theUri);
try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
ids = toUnqualifiedIdValues(bundle);
}
return ids;
}
private List<String> searchAndReturnUnqualifiedVersionlessIdValues(String uri) throws IOException {
List<String> ids;
HttpGet get = new HttpGet(uri);
try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
ids = toUnqualifiedVersionlessIdValues(bundle);
ourLog.info("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
}
return ids;
}
@Test
@Disabled
public void test() throws IOException {
HttpGet get = new HttpGet(ourServerBase + "/QuestionnaireResponse?_count=50&status=completed&questionnaire=ARIncenterAbsRecord&_lastUpdated=%3E" + UrlUtil.escapeUrlParam("=2018-01-01") + "&context.organization=O3435");
ourLog.info("*** MAKING QUERY");
ourHttpClient.execute(get);
System.exit(0);
}
@Test
public void testBundleCreate() throws Exception {
IGenericClient client = myClient;
String resBody = IOUtils.toString(ResourceProviderR4Test.class.getResource("/r4/document-father.json"), StandardCharsets.UTF_8);
IIdType id = client.create().resource(resBody).execute().getId();
ourLog.info("Created: {}", id);
Bundle bundle = client.read().resource(Bundle.class).withId(id).execute();
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
}
@Test
public void testBundleCreateWithTypeTransaction() throws Exception {
IGenericClient client = myClient;
String resBody = IOUtils.toString(ResourceProviderR4Test.class.getResource("/r4/document-father.json"), StandardCharsets.UTF_8);
resBody = resBody.replace("\"type\": \"document\"", "\"type\": \"transaction\"");
try {
client.create().resource(resBody).execute();
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Unable to store a Bundle resource on this server with a Bundle.type value of: transaction. Note that if you are trying to perform a FHIR transaction or batch operation you should POST the Bundle resource to the Base URL of the server, not to the /Bundle endpoint."));
}
}
@Test
public void testCodeSearch() {
Subscription subs = new Subscription();
subs.setStatus(SubscriptionStatus.ACTIVE);
subs.getChannel().setType(SubscriptionChannelType.WEBSOCKET);
subs.setCriteria("Observation?");
IIdType id = myClient.create().resource(subs).execute().getId().toUnqualifiedVersionless();
//@formatter:off
Bundle resp = myClient
.search()
.forResource(Subscription.class)
.where(Subscription.TYPE.exactly().code(SubscriptionChannelType.WEBSOCKET.toCode()))
.and(Subscription.STATUS.exactly().code(SubscriptionStatus.ACTIVE.toCode()))
.returnBundle(Bundle.class)
.execute();
//@formatter:off
assertThat(toUnqualifiedVersionlessIds(resp), contains(id));
//@formatter:off
resp = myClient
.search()
.forResource(Subscription.class)
.where(Subscription.TYPE.exactly().systemAndCode(SubscriptionChannelType.WEBSOCKET.getSystem(), SubscriptionChannelType.WEBSOCKET.toCode()))
.and(Subscription.STATUS.exactly().systemAndCode(SubscriptionStatus.ACTIVE.getSystem(), SubscriptionStatus.ACTIVE.toCode()))
.returnBundle(Bundle.class)
.execute();
//@formatter:off
assertThat(toUnqualifiedVersionlessIds(resp), contains(id));
//@formatter:off
resp = myClient
.search()
.forResource(Subscription.class)
.where(Subscription.TYPE.exactly().systemAndCode(SubscriptionChannelType.WEBSOCKET.getSystem(), SubscriptionChannelType.WEBSOCKET.toCode()))
.and(Subscription.STATUS.exactly().systemAndCode("foo", SubscriptionStatus.ACTIVE.toCode()))
.returnBundle(Bundle.class)
.execute();
//@formatter:off
assertThat(toUnqualifiedVersionlessIds(resp), empty());
}
@Test
public void testCreateAndReadBackResourceWithContainedReferenceToContainer() {
myFhirContext.setParserErrorHandler(new StrictErrorHandler());
String input = "{\n" +
" \"resourceType\": \"Organization\",\n" +
" \"id\": \"1\",\n" +
" \"meta\": {\n" +
" \"tag\": [\n" +
" {\n" +
" \"system\": \"https://blah.org/deployment\",\n" +
" \"code\": \"e69414dd-b5c2-462d-bcfd-9d04d6b16596\",\n" +
" \"display\": \"DEPLOYMENT\"\n" +
" },\n" +
" {\n" +
" \"system\": \"https://blah.org/region\",\n" +
" \"code\": \"b47d7a5b-b159-4bed-a8f8-3258e6603adb\",\n" +
" \"display\": \"REGION\"\n" +
" },\n" +
" {\n" +
" \"system\": \"https://blah.org/provider\",\n" +
" \"code\": \"28c30004-0333-40cf-9e7f-3f9e080930bd\",\n" +
" \"display\": \"PROVIDER\"\n" +