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Fix missing qualifier search for reference search parameters (#6306) 

* Fix missing qualifier search for reference search parameter. Reuse tests and run them for both indexing enabled and disabled.

* Fix edge case where the search parameter has multiple paths. Add a test. Fix some of the compile warnings in a test class.

* Fix test setup.
This commit is contained in:
Martha Mitran 2024-09-24 16:46:38 -07:00 committed by GitHub
parent 4aea94ccb6
commit 20d3e6bb25
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4 changed files with 631 additions and 643 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6305-search-missing-qualifier-does-not-work-reference-parameters.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 6305
title: "Previously, when having StorageSettings#getIndexMissingFields() == IndexEnabledEnum.DISABLED (default value)
and attempting to search with the missing qualifier against a resource type with multiple search parameters of type reference,
the returned results would be incorrect. This has been fixed."

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java
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@ -800,14 +800,19 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
subquery.addCustomColumns(1);
subquery.addFromTable(getTable());
String resourceType = theParams.getResourceTablePredicateBuilder().getResourceType();
RuntimeSearchParam paramDefinition =
mySearchParamRegistry.getRuntimeSearchParam(resourceType, theParams.getParamName());
List<String> pathList = paramDefinition.getPathsSplitForResourceType(resourceType);
Condition subQueryCondition = ComboCondition.and(
BinaryCondition.equalTo(
getResourceIdColumn(),
theParams.getResourceTablePredicateBuilder().getResourceIdColumn()),
BinaryCondition.equalTo(
getResourceTypeColumn(),
generatePlaceholder(
theParams.getResourceTablePredicateBuilder().getResourceType())));
BinaryCondition.equalTo(getResourceTypeColumn(), generatePlaceholder(resourceType)),
ComboCondition.or(pathList.stream()
.map(path -> BinaryCondition.equalTo(getColumnSourcePath(), generatePlaceholder(path)))
.toArray(BinaryCondition[]::new)));
subquery.addCondition(subQueryCondition);

963
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchMissingTest.java
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292
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
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@ -217,7 +217,7 @@ import static org.mockito.Mockito.when;
public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4Test.class);
private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
private CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
private final CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
@Autowired
private ISearchDao mySearchEntityDao;
@ -413,15 +413,15 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient pt1 = new Patient();
pt1.addName().setFamily("Elizabeth");
String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
String pt1id = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless().getValue();
Patient pt2 = new Patient();
pt2.addName().setFamily("fghijk");
String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
String pt2id = myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless().getValue();
Patient pt3 = new Patient();
pt3.addName().setFamily("zzzzz");
myPatientDao.create(pt3).getId().toUnqualifiedVersionless().getValue();
myPatientDao.create(pt3, mySrd).getId().toUnqualifiedVersionless().getValue();
Bundle output = myClient
@ -450,7 +450,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient pt1 = new Patient();
pt1.addName().setFamily("Smith%");
String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
String pt1id = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless().getValue();
Bundle output = myClient
.search()
@ -463,7 +463,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient pt2 = new Patient();
pt2.addName().setFamily("Sm%ith");
String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
String pt2id = myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless().getValue();
output = myClient
.search()
@ -740,7 +740,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient p = new Patient();
p.addName().setFamily("FAM").addGiven("GIV");
IIdType id = myPatientDao.create(p).getId();
IIdType id = myPatientDao.create(p, mySrd).getId();
myClient.read().resource("Patient").withId(id.toUnqualifiedVersionless()).execute();
@ -763,7 +763,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient p = new Patient();
p.addName().setFamily("FAM").addGiven("GIV");
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
myClient
.delete()
@ -1025,57 +1025,58 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
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" +
" }\n" +
" ]\n" +
" },\n" +
" \"contained\": [\n" +
" {\n" +
" \"resourceType\": \"Location\",\n" +
" \"id\": \"2\",\n" +
" \"position\": {\n" +
" \"longitude\": 51.443238301454289,\n" +
" \"latitude\": 7.34196905697293\n" +
" },\n" +
" \"managingOrganization\": {\n" +
" \"reference\": \"#\"\n" +
" }\n" +
" }\n" +
" ],\n" +
" \"type\": [\n" +
" {\n" +
" \"coding\": [\n" +
" {\n" +
" \"system\": \"https://blah.org/fmc/OrganizationType\",\n" +
" \"code\": \"CLINIC\",\n" +
" \"display\": \"Clinic\"\n" +
" }\n" +
" ]\n" +
" }\n" +
" ],\n" +
" \"name\": \"testOrg\"\n" +
"}";
String input = """
{
"resourceType": "Organization",
"id": "1",
"meta": {
"tag": [
{
"system": "https://blah.org/deployment",
"code": "e69414dd-b5c2-462d-bcfd-9d04d6b16596",
"display": "DEPLOYMENT"
},
{
"system": "https://blah.org/region",
"code": "b47d7a5b-b159-4bed-a8f8-3258e6603adb",
"display": "REGION"
},
{
"system": "https://blah.org/provider",
"code": "28c30004-0333-40cf-9e7f-3f9e080930bd",
"display": "PROVIDER"
}
]
},
"contained": [
{
"resourceType": "Location",
"id": "2",
"position": {
"longitude": 51.443238301454289,
"latitude": 7.34196905697293
},
"managingOrganization": {
"reference": "#"
}
}
],
"type": [
{
"coding": [
{
"system": "https://blah.org/fmc/OrganizationType",
"code": "CLINIC",
"display": "Clinic"
}
]
}
],
"name": "testOrg"
}""";
Organization org = myFhirContext.newJsonParser().parseResource(Organization.class, input);
IIdType id = myOrganizationDao.create(org).getId();
IIdType id = myOrganizationDao.create(org, mySrd).getId();
org = myOrganizationDao.read(id);
String output = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(org);
@ -1095,9 +1096,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
List<IBaseResource> outcome = myClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
runInTransaction(() -> {
assertEquals(100, myResourceTableDao.count());
});
runInTransaction(() -> assertEquals(100, myResourceTableDao.count()));
Bundle found = myClient
.search()
@ -1306,7 +1305,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
@Test
public void testCreateQuestionnaireResponseWithValidation() throws IOException {
public void testCreateQuestionnaireResponseWithValidation() {
CodeSystem cs = new CodeSystem();
cs.setUrl("http://cs");
cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
@ -1906,8 +1905,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
* Try it with a raw socket call. The Apache client won't let us use the unescaped "|" in the URL but we want to make sure that works too..
*/
Socket sock = new Socket();
sock.setSoTimeout(3000);
try {
try (sock) {
sock.setSoTimeout(3000);
sock.connect(new InetSocketAddress("localhost", myPort));
sock.getOutputStream().write(("DELETE /fhir/context/Patient?identifier=http://ghh.org/patient|" + methodName + " HTTP/1.1\n").getBytes(StandardCharsets.UTF_8));
sock.getOutputStream().write("Host: localhost\n".getBytes(StandardCharsets.UTF_8));
@ -1915,7 +1914,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
BufferedReader socketInput = new BufferedReader(new InputStreamReader(sock.getInputStream()));
// String response = "";
StringBuilder b = new StringBuilder();
char[] buf = new char[1000];
while (socketInput.read(buf) != -1) {
@ -1925,9 +1923,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
ourLog.debug("Resp: {}", resp);
} catch (SocketTimeoutException e) {
e.printStackTrace();
} finally {
sock.close();
ourLog.debug(e.getMessage(), e);
}
Thread.sleep(1000);
@ -2398,7 +2394,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
assertThat(idValues).as(idValues.toString()).hasSize(10);
idValues = searchAndReturnUnqualifiedIdValues(myServerBase + "/_history?_at=gt" + InstantDt.withCurrentTime().getYear());
assertThat(idValues).hasSize(0);
assertThat(idValues).isEmpty();
}
@ -2427,7 +2423,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myMemoryCacheService.invalidateCaches(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID);
}
Bundle history = myClient.history().onInstance(id.getValue()).andReturnBundle(Bundle.class).execute();
Bundle history = myClient.history().onInstance(id.getValue()).returnBundle(Bundle.class).execute();
assertEquals(1, history.getEntry().size());
BundleEntryComponent historyEntry0 = history.getEntry().get(0);
// validate entry.fullUrl
@ -2476,7 +2472,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myMemoryCacheService.invalidateCaches(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID);
}
Bundle history = myClient.history().onInstance(id.getValue()).andReturnBundle(Bundle.class).execute();
Bundle history = myClient.history().onInstance(id.getValue()).returnBundle(Bundle.class).execute();
assertEquals(1, history.getEntry().size());
BundleEntryComponent historyEntry0 = history.getEntry().get(0);
// validate entry.fullUrl
@ -2508,7 +2504,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
ourLog.info("Res ID: {}", id);
Bundle history = myClient.history().onInstance(id.getValue()).andReturnBundle(Bundle.class).prettyPrint().summaryMode(SummaryEnum.DATA).execute();
Bundle history = myClient.history().onInstance(id.getValue()).returnBundle(Bundle.class).prettyPrint().summaryMode(SummaryEnum.DATA).execute();
assertThat(history.getEntry()).hasSize(3);
assertEquals(id.withVersion("3").getValue(), history.getEntry().get(0).getResource().getId());
assertThat(((Patient) history.getEntry().get(0).getResource()).getName()).hasSize(1);
@ -2746,7 +2742,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
int total = 20;
Organization org = new Organization();
org.setName("ORG");
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
Coding tagCode = new Coding();
tagCode.setCode("test");
@ -2757,7 +2753,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.addTag(tagCode);
t.setStatus(Task.TaskStatus.REQUESTED);
t.getOwner().setReference(orgId.getValue());
myTaskDao.create(t);
myTaskDao.create(t, mySrd);
}
HashSet<String> ids = new HashSet<>();
@ -2835,12 +2831,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
if (orgCount > 0) {
Organization org = new Organization();
org.setName("ORG");
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
orgCount--;
t.getOwner().setReference(orgId.getValue());
}
myTaskDao.create(t);
myTaskDao.create(t, mySrd);
}
}
@ -2909,12 +2905,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
if (orgCount > 0) {
Organization org = new Organization();
org.setName("ORG");
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
orgCount--;
t.getOwner().setReference(orgId.getValue());
}
myTaskDao.create(t);
myTaskDao.create(t, mySrd);
}
}
@ -2961,13 +2957,13 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
public void testIncludeCountDoesntIncludeIncludes() {
Organization org = new Organization();
org.setName("ORG");
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
for (int i = 0; i < 10; i++) {
Patient pt = new Patient();
pt.getManagingOrganization().setReference(orgId.getValue());
pt.addName().setFamily("FAM" + i);
myPatientDao.create(pt);
myPatientDao.create(pt, mySrd);
}
Bundle bundle = myClient
@ -3168,7 +3164,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
assertEquals("2", newPt.getIdElement().getVersionIdPart());
assertEquals(false, newPt.getActive());
assertFalse(newPt.getActive());
}
@Test
@ -3196,7 +3192,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
assertEquals("1", newPt.getIdElement().getVersionIdPart());
assertEquals(true, newPt.getActive());
assertTrue(newPt.getActive());
}
@Test
@ -3226,7 +3222,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
assertEquals("2", newPt.getIdElement().getVersionIdPart());
assertEquals(false, newPt.getActive());
assertFalse(newPt.getActive());
}
@Test
@ -3255,7 +3251,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
assertEquals("2", newPt.getIdElement().getVersionIdPart());
assertEquals(false, newPt.getActive());
assertFalse(newPt.getActive());
}
@Test
@ -3323,12 +3319,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
{
Bundle returned = myClient.search().forResource(Patient.class).encodedXml().returnBundle(Bundle.class).execute();
assertThat(returned.getEntry().size()).isGreaterThan(1);
assertThat(returned.getEntry()).hasSizeGreaterThan(1);
assertEquals(BundleType.SEARCHSET, returned.getType());
}
{
Bundle returned = myClient.search().forResource(Patient.class).encodedJson().returnBundle(Bundle.class).execute();
assertThat(returned.getEntry().size()).isGreaterThan(1);
assertThat(returned.getEntry()).hasSizeGreaterThan(1);
}
}
@ -3350,7 +3346,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
});
Bundle bundle = myClient.history().onServer().andReturnBundle(Bundle.class).execute();
Bundle bundle = myClient.history().onServer().returnBundle(Bundle.class).execute();
assertEquals(1, bundle.getTotal());
assertThat(bundle.getEntry()).hasSize(1);
assertEquals(id2.getIdPart(), bundle.getEntry().get(0).getResource().getIdElement().getIdPart());
@ -3507,15 +3503,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
assertThat(text).doesNotContain("\"B\"");
assertThat(text).doesNotContain("\"B1\"");
}
// HttpGet read = new HttpGet(ourServerBase + "/Observation?patient=P5000000302&_sort:desc=code&code:in=http://fkcfhir.org/fhir/vs/ccdacapddialysisorder");
// try (CloseableHttpResponse response = ourHttpClient.execute(read)) {
// String text = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
// ourLog.info(text);
// assertEquals(Constants.STATUS_HTTP_200_OK, response.getStatusLine().getStatusCode());
// assertThat(text).doesNotContain("\"text\",\"type\"");
// }
}
@Test
@ -3873,9 +3860,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
p.addName().setFamily(methodName + "1");
IIdType pid1 = myClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
Thread.sleep(10);
long time1 = System.currentTimeMillis();
Thread.sleep(10);
Patient p2 = new Patient();
p2.addName().setFamily(methodName + "2");
@ -4064,9 +4049,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
public void testSearchLastUpdatedParamRp() throws InterruptedException {
String methodName = "testSearchLastUpdatedParamRp";
int sleep = 100;
Thread.sleep(sleep);
DateTimeType beforeAny = new DateTimeType(new Date(), TemporalPrecisionEnum.MILLI);
IIdType id1a;
{
@ -4083,9 +4065,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
id1b = myClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
}
Thread.sleep(1100);
DateTimeType beforeR2 = new DateTimeType(new Date(), TemporalPrecisionEnum.MILLI);
Thread.sleep(1100);
IIdType id2;
{
@ -4249,13 +4229,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
matches = bundle.getEntry().size();
assertThat(matches).isGreaterThan(0);
assertThat(matches).isPositive();
}
@Test
public void testSearchReturnsSearchDate() throws Exception {
Date before = new Date();
Thread.sleep(1);
//@formatter:off
Bundle found = myClient
@ -4266,7 +4245,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.execute();
//@formatter:on
Thread.sleep(1);
Date after = new Date();
InstantType updated = found.getMeta().getLastUpdatedElement();
@ -4300,7 +4278,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4313,7 +4291,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4326,7 +4304,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4339,24 +4317,24 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
// > 1m
String uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt1|http://unitsofmeasure.org|m");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(3);
//>= 100cm
uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt100|http://unitsofmeasure.org|cm");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(3);
//>= 10dm
uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt10|http://unitsofmeasure.org|dm");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(3);
}
@ -4381,7 +4359,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4392,7 +4370,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4403,7 +4381,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4414,7 +4392,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
String uri;
@ -4451,7 +4429,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4462,7 +4440,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4474,7 +4452,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
myCaptureQueriesListener.clear();
@ -4490,8 +4468,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
//-- check use normalized quantity table to search
String searchSql = myCaptureQueriesListener.getSelectQueries().get(0).getSql(true, true);
assertThat(searchSql).doesNotContain("HFJ_SPIDX_QUANTITY t0");
assertThat(searchSql).contains("HFJ_SPIDX_QUANTITY_NRML");
assertThat(searchSql).doesNotContain("HFJ_SPIDX_QUANTITY t0").contains("HFJ_SPIDX_QUANTITY_NRML");
}
@Test
@ -5044,7 +5021,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5056,7 +5033,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid2 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5068,7 +5045,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid3 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5080,7 +5057,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid4 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
String uri = myServerBase + "/Observation?_sort=code-value-quantity";
@ -5092,7 +5069,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
found = myFhirContext.newXmlParser().parseResource(Bundle.class, output);
}
ourLog.debug("Bundle: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
ourLog.debug("Bundle: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
List<IIdType> list = toUnqualifiedVersionlessIds(found);
assertThat(found.getEntry()).hasSize(4);
@ -5129,7 +5106,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5145,7 +5122,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid2 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5161,7 +5138,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid3 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5176,7 +5153,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
comp.setValue(new Quantity().setValue(250));
oid4 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
String uri = myServerBase + "/Observation?_sort=combo-code-value-quantity";
@ -5188,7 +5165,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
found = myFhirContext.newXmlParser().parseResource(Bundle.class, output);
}
ourLog.debug("Bundle: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
ourLog.debug("Bundle: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
List<IIdType> list = toUnqualifiedVersionlessIds(found);
assertThat(found.getEntry()).hasSize(4);
@ -5264,9 +5241,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
List<IIdType> list = toUnqualifiedVersionlessIds(found);
ourLog.info(methodName + " found: " + list.toString() + " - Wanted " + orgMissing + " but not " + orgNotMissing);
assertThat(list).doesNotContain(orgNotMissing);
assertThat(list).doesNotContain(deletedIdMissingTrue);
assertThat(list).contains(orgMissing);
assertThat(list).doesNotContain(orgNotMissing).doesNotContain(deletedIdMissingTrue).contains(orgMissing);
}
@Test
@ -5927,7 +5902,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
Date before = new Date();
Thread.sleep(100);
pt = new Patient();
pt.setId(id.getIdPart());
@ -6450,7 +6424,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
obs.setValue(new Quantity().setValueElement(new DecimalType(125.12)).setUnit("CM").setSystem(UcumServiceUtil.UCUM_CODESYSTEM_URL).setCode("cm"));
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
IIdType opid1 = myObservationDao.create(obs, mySrd).getId();
@ -6463,7 +6437,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
obs.setValue(new Quantity().setValueElement(new DecimalType(24.12)).setUnit("CM").setSystem(UcumServiceUtil.UCUM_CODESYSTEM_URL).setCode("cm"));
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
myObservationDao.update(obs, mySrd);
}
@ -6479,7 +6453,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -6492,7 +6466,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -6505,25 +6479,25 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
// > 1m
String uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt1|http://unitsofmeasure.org|m");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(2);
//>= 100cm
uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt100|http://unitsofmeasure.org|cm");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(2);
//>= 10dm
uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt10|http://unitsofmeasure.org|dm");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(2);
}
@ -6540,7 +6514,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
patient.setBirthDateElement(new DateType("2073"));
pid0 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Patient: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.debug("Patient: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info("pid0 " + pid0);
}
@ -6553,7 +6527,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
ourLog.debug("Patient: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
ourLog.debug("Patient: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
}
uri = myServerBase + "/Patient?_total=accurate&birthdate=gt2072-01-01";
@ -6564,7 +6538,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
ourLog.debug("Patient: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
ourLog.debug("Patient: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
}
}
@ -6995,9 +6969,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
&& theInput.IsEnforceRefOnType
&& theInput.IsEnforceRefOnWrite).isFalse();
} catch (InvalidRequestException ex) {
assertThat(ex.getMessage().contains(
"Invalid resource reference"
)).as(ex.getMessage()).isTrue();
assertThat(ex.getMessage()).as(ex.getMessage()).contains("Invalid resource reference");
} finally {
myStorageSettings.setEnforceReferentialIntegrityOnWrite(isEnforceRefOnWrite);
myStorageSettings.setEnforceReferenceTargetTypes(isEnforceRefTargetTypes);
@ -7331,9 +7303,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
patient.setBirthDate(cal.getTime());
}
return patient;
}, (isMissing) -> {
return doSearch(Patient.class, Patient.BIRTHDATE.isMissing(isMissing));
});
}, (isMissing) -> doSearch(Patient.class, Patient.BIRTHDATE.isMissing(isMissing)));
}
@ParameterizedTest
@ -7346,9 +7316,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
patient.setGender(AdministrativeGender.FEMALE);
}
return patient;
}, isMissing -> {
return doSearch(Patient.class, Patient.GENDER.isMissing(isMissing));
});
}, isMissing -> doSearch(Patient.class, Patient.GENDER.isMissing(isMissing)));
}
@ParameterizedTest
@ -7364,9 +7332,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
patient.setGeneralPractitioner(Collections.singletonList(new Reference(practitionerId)));
}
return patient;
}, isMissing -> {
return doSearch(Patient.class, Patient.GENERAL_PRACTITIONER.isMissing(isMissing));
});
}, isMissing -> doSearch(Patient.class, Patient.GENERAL_PRACTITIONER.isMissing(isMissing)));
}
@ParameterizedTest
@ -7409,9 +7375,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
sp.setUrl("http://example.com");
}
return sp;
}, isMissing -> {
return doSearch(SearchParameter.class, SearchParameter.URL.isMissing(isMissing));
});
}, isMissing -> doSearch(SearchParameter.class, SearchParameter.URL.isMissing(isMissing)));
}
@ParameterizedTest
@ -7424,9 +7388,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
obs.setValue(new Quantity(3));
}
return obs;
}, isMissing -> {
return doSearch(Observation.class, Observation.VALUE_QUANTITY.isMissing(isMissing));
});
}, isMissing -> doSearch(Observation.class, Observation.VALUE_QUANTITY.isMissing(isMissing)));
}
@ParameterizedTest
@ -7457,7 +7419,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Y doTask(X theInput);
}
private static class MissingSearchTestParameters {
public static class MissingSearchTestParameters {
/**
* The setting for IndexMissingFields
*/