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Mergeback of rel_6_8 (#5146) 

* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* Rename file to force IT mode

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
This commit is contained in:
Tadgh 2023-07-30 15:28:26 -07:00 committed by GitHub
parent 2b91f0a232
commit 5eda18f500
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24 changed files with 533 additions and 86 deletions
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53
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlPathTokenizer.java
View File

@ -19,18 +19,45 @@
*/
package ca.uhn.fhir.util;
import java.util.StringTokenizer;
import ca.uhn.fhir.i18n.Msg;
import org.apache.commons.lang3.ArrayUtils;
import java.util.ArrayList;
import java.util.List;
import java.util.NoSuchElementException;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class UrlPathTokenizer {
private final StringTokenizer myTok;
private String[] tokens;
private int curPos;
public UrlPathTokenizer(String theRequestPath) {
myTok = new StringTokenizer(theRequestPath, "/");
if (theRequestPath == null) {
theRequestPath = "";
}
tokens = removeBlanksAndSanitize(theRequestPath.split("/"));
curPos = 0;
}
public boolean hasMoreTokens() {
return myTok.hasMoreTokens();
return curPos < tokens.length;
}
public int countTokens() {
return tokens.length;
}
/**
* Returns the next token without updating the current position.
* Will throw NoSuchElementException if there are no more tokens.
*/
public String peek() {
if (!hasMoreTokens()) {
throw new NoSuchElementException(Msg.code(2420) + "Attempt to retrieve URL token out of bounds");
}
return tokens[curPos];
}
/**
@ -43,6 +70,22 @@ public class UrlPathTokenizer {
* @see UrlUtil#unescape(String)
*/
public String nextTokenUnescapedAndSanitized() {
return UrlUtil.sanitizeUrlPart(UrlUtil.unescape(myTok.nextToken()));
String token = peek();
curPos++;
return token;
}
/**
* Given an array of Strings, this method will return all the non-blank entries in that
* array, after running sanitizeUrlPart() and unescape() on them.
*/
private static String[] removeBlanksAndSanitize(String[] theInput) {
List<String> output = new ArrayList<>();
for (String s : theInput) {
if (!isBlank(s)) {
output.add(UrlUtil.sanitizeUrlPart(UrlUtil.unescape(s)));
}
}
return output.toArray(ArrayUtils.EMPTY_STRING_ARRAY);
}
}

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5117-fix-no-match-mdm-score-included-in-total-score.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: fix
issue: 5117
title: "Previously, all MDM field scores, including `NO_MATCH`es, were included in the final total MDM score. This has
now been fixed so that only `MATCH`ed fields are included in the total MDM score."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5119-consent-removing-all-resources-suppresses-next-link-in-bundle.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 5119
jira: SMILE-7090
title: "Previously, when the consent service would remove all resources to be returned, the response bundle would
not provide the previous/next link(s). This has been corrected."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5126-hfj_res_ver_prov-might-cause-migration-error-on-db-that-automatically-indexes-the-primary-key.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 5126
title: "Previously, updating from Hapi-fhir 6.6.0 to 6.8.0 would cause migration error, it is now fixed."

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -126,8 +126,13 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.withColumns("RES_VER_PID")
.failureAllowed();
// drop the index for any database that has RES_PID column already indexed from previous migrations
version.onTable("HFJ_RES_VER_PROV")
.addIndex("20230510.2", "IDX_RESVERPROV_RES_PID")
.dropIndex("20230510.2", "FK_RESVERPROV_RES_PID")
.failureAllowed();
version.onTable("HFJ_RES_VER_PROV")
.addIndex("20230510.3", "IDX_RESVERPROV_RES_PID")
.unique(false)
.withColumns("RES_PID");

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java
View File

@ -336,8 +336,13 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
String dirName = "package";
NpmPackage.NpmPackageFolder packageFolder = npmPackage.getFolders().get(dirName);
for (Map.Entry<String, List<String>> nextTypeToFiles :
packageFolder.getTypes().entrySet()) {
Map<String, List<String>> packageFolderTypes = null;
try {
packageFolderTypes = packageFolder.getTypes();
} catch (IOException e) {
throw new InternalErrorException(Msg.code(2371) + e);
}
for (Map.Entry<String, List<String>> nextTypeToFiles : packageFolderTypes.entrySet()) {
String nextType = nextTypeToFiles.getKey();
for (String nextFile : nextTypeToFiles.getValue()) {

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/loader/PackageResourceParsingSvc.java
View File

@ -49,8 +49,13 @@ public class PackageResourceParsingSvc {
return Collections.emptyList();
}
ArrayList<IBaseResource> resources = new ArrayList<>();
List<String> filesForType =
thePkg.getFolders().get("package").getTypes().get(theType);
List<String> filesForType = null;
try {
filesForType = thePkg.getFolders().get("package").getTypes().get(theType);
} catch (IOException e) {
throw new InternalErrorException(
Msg.code(2370) + "Cannot install resource of type " + theType + ": Could not get types", e);
}
if (filesForType != null) {
for (String file : filesForType) {
try {

32
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/interceptor/ForceOffsetSearchModeInterceptorTest.java
View File

@ -15,6 +15,7 @@ import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.emptyOrNullString;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
@ -125,6 +126,36 @@ public class ForceOffsetSearchModeInterceptorTest extends BaseResourceProviderR4
}
@Test
public void testPagingNextLink_whenAllResourcesHaveBeenReturned_willNotBePresent(){
myServer.setDefaultPageSize(5);
for (int i = 0; i < 10; i++) {
createPatient(withId("A" + i), withActiveTrue());
}
Bundle outcome = myClient
.search()
.forResource("Patient")
.where(Patient.ACTIVE.exactly().code("true"))
.returnBundle(Bundle.class)
.execute();
assertThat(outcome.getEntry(), hasSize(5));
Bundle secondPageBundle = myClient.loadPage().next(outcome).execute();
assertThat(secondPageBundle.getEntry(), hasSize(5));
Bundle thirdPageBundle = myClient.loadPage().next(secondPageBundle).execute();
assertThat(thirdPageBundle.getEntry(), hasSize(0));
assertNull(thirdPageBundle.getLink("next"), () -> thirdPageBundle.getLink("next").getUrl());
}
@Test
public void testSearch_WithExplicitCount() {
@ -179,7 +210,6 @@ public class ForceOffsetSearchModeInterceptorTest extends BaseResourceProviderR4
assertEquals(1, myCaptureQueriesListener.countCommits());
assertEquals(0, myCaptureQueriesListener.countRollbacks());
assertThat(outcome.getLink(Constants.LINK_NEXT).getUrl(), containsString("Patient?_count=7&_offset=14&active=true"));
assertThat(outcome.getLink(Constants.LINK_PREVIOUS).getUrl(), containsString("Patient?_count=7&_offset=0&active=true"));
}

50
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ConsentInterceptorResourceProviderR4Test.java → hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ConsentInterceptorResourceProviderR4IT.java
View File

@ -84,9 +84,9 @@ import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
public class ConsentInterceptorResourceProviderR4Test extends BaseResourceProviderR4Test {
public class ConsentInterceptorResourceProviderR4IT extends BaseResourceProviderR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(ConsentInterceptorResourceProviderR4Test.class);
private static final Logger ourLog = LoggerFactory.getLogger(ConsentInterceptorResourceProviderR4IT.class);
private List<String> myObservationIds;
private List<String> myPatientIds;
private List<String> myObservationIdsOddOnly;
@ -745,6 +745,42 @@ public class ConsentInterceptorResourceProviderR4Test extends BaseResourceProvid
}
@Test
public void testPaging_whenResourceViewingIsRejected_responseBundleWillHaveNextLink(){
// given
create50Observations();
myConsentInterceptor = new ConsentInterceptor(new ConsentSvcRejectWillSeeResource());
myServer.getRestfulServer().getInterceptorService().registerInterceptor(myConsentInterceptor);
// when
Bundle results = myClient.search().forResource(Observation.class).count(10).returnBundle(Bundle.class).execute();
assertThat(results.getEntry(), hasSize(0));
// then
String nextUrl = BundleUtil.getLinkUrlOfType(myFhirContext, results, "next");
assertThat(nextUrl, containsString("_getpagesoffset=10"));
}
@Test
public void testPaging_whenResourceViewingIsRejected_secondPageWillHavePreviousLink(){
// given
create50Observations();
myConsentInterceptor = new ConsentInterceptor(new ConsentSvcRejectWillSeeResource());
myServer.getRestfulServer().getInterceptorService().registerInterceptor(myConsentInterceptor);
// when
Bundle results = myClient.search().forResource(Observation.class).count(10).returnBundle(Bundle.class).execute();
Bundle nextResults = myClient.loadPage().next(results).execute();
// then
String previous = BundleUtil.getLinkUrlOfType(myFhirContext, nextResults, "previous");
assertThat(previous, containsString("_getpagesoffset=0"));
}
private void createPatientAndOrg() {
myPatientIds = new ArrayList<>();
@ -1062,5 +1098,15 @@ public class ConsentInterceptorResourceProviderR4Test extends BaseResourceProvid
}
private static class ConsentSvcRejectWillSeeResource implements IConsentService {
@Override
public ConsentOutcome willSeeResource(RequestDetails theRequestDetails, IBaseResource theResource, IConsentContextServices theContextServices) {
if("Bundle".equals(theResource.fhirType())){
return new ConsentOutcome(ConsentOperationStatusEnum.PROCEED);
}
return new ConsentOutcome(ConsentOperationStatusEnum.REJECT);
}
}
}

8
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
View File

@ -2482,12 +2482,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
"Patient/A/_history/1"
));
history = myClient
.loadPage()
.next(history)
.execute();
assertEquals(0, history.getEntry().size());
// we got them all
assertNull(history.getLink("next"));
/*
* Try with a date offset

2
hapi-fhir-server-cds-hooks/src/test/java/ca/uhn/hapi/fhir/cdshooks/svc/CdsHooksContextBooterTest.java
View File

@ -28,7 +28,7 @@ class CdsHooksContextBooterTest {
@Test
void validateJsonThrowsExceptionWhenInputIsInvalid() {
// setup
final String expected = "Invalid JSON: Unrecognized token 'abc': was expecting (JSON String, Number, Array, Object or token 'null', 'true' or 'false')\n" +
final String expected = "HAPI-2378: Invalid JSON: Unrecognized token 'abc': was expecting (JSON String, Number, Array, Object or token 'null', 'true' or 'false')\n" +
" at [Source: (String)\"abc\"; line: 1, column: 4]";
// execute
final UnprocessableEntityException actual = assertThrows(UnprocessableEntityException.class, () -> myFixture.validateJson("abc"));

4
hapi-fhir-server-cds-hooks/src/test/java/ca/uhn/hapi/fhir/cdshooks/svc/prefetch/CdsPrefetchFhirClientSvcTest.java
View File

@ -93,7 +93,7 @@ class CdsPrefetchFhirClientSvcTest {
IBaseResource srq = myCdsPrefetchFhirClientSvc.resourceFromUrl(cdsServiceRequestJson, "1234");
fail("should throw, no resource present");
} catch (InvalidRequestException e) {
assertEquals("Unable to translate url 1234 into a resource or a bundle.", e.getMessage());
assertEquals("HAPI-2384: Unable to translate url 1234 into a resource or a bundle.", e.getMessage());
}
}
@ -106,7 +106,7 @@ class CdsPrefetchFhirClientSvcTest {
IBaseResource srq = myCdsPrefetchFhirClientSvc.resourceFromUrl(cdsServiceRequestJson, "/1234");
fail("should throw, no resource present");
} catch (InvalidRequestException e) {
assertEquals("Failed to resolve /1234. Url does not start with a resource type.", e.getMessage());
assertEquals("HAPI-2383: Failed to resolve /1234. Url does not start with a resource type.", e.getMessage());
}
}
}

10
hapi-fhir-server-cds-hooks/src/test/java/ca/uhn/hapi/fhir/cdshooks/svc/prefetch/PrefetchTemplateUtilTest.java
View File

@ -36,7 +36,7 @@ class PrefetchTemplateUtilTest {
PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
fail();
} catch (InvalidRequestException e) {
assertEquals("Either request context was empty or it did not provide a value for key <userId>. Please make sure you are including a context with valid keys.", e.getMessage());
assertEquals("HAPI-2375: Either request context was empty or it did not provide a value for key <userId>. Please make sure you are including a context with valid keys.", e.getMessage());
}
}
@ -50,7 +50,7 @@ class PrefetchTemplateUtilTest {
PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
fail();
} catch (InvalidRequestException e) {
assertEquals("Either request context was empty or it did not provide a value for key <userId>. Please make sure you are including a context with valid keys.", e.getMessage());
assertEquals("HAPI-2375: Either request context was empty or it did not provide a value for key <userId>. Please make sure you are including a context with valid keys.", e.getMessage());
}
}
@ -63,7 +63,7 @@ class PrefetchTemplateUtilTest {
PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
fail();
} catch (InvalidRequestException e) {
assertEquals("Request context did not provide a value for key <draftOrders>. Available keys in context are: [patientId]", e.getMessage());
assertEquals("HAPI-2372: Request context did not provide a value for key <draftOrders>. Available keys in context are: [patientId]", e.getMessage());
}
}
@ -119,7 +119,7 @@ class PrefetchTemplateUtilTest {
PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
fail("substituteTemplate call was successful with a null context field.");
} catch (InvalidRequestException e) {
assertEquals("Request context did not provide for resource(s) matching template. ResourceType missing is: ServiceRequest", e.getMessage());
assertEquals("HAPI-2373: Request context did not provide for resource(s) matching template. ResourceType missing is: ServiceRequest", e.getMessage());
}
}
@ -134,7 +134,7 @@ class PrefetchTemplateUtilTest {
PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
fail();
} catch (InvalidRequestException e) {
assertEquals("Request context did not provide valid " + fhirContextR4.getVersion().getVersion() + " Bundle resource for template key <draftOrders>" , e.getMessage());
assertEquals("HAPI-2374: Request context did not provide valid " + fhirContextR4.getVersion().getVersion() + " Bundle resource for template key <draftOrders>", e.getMessage());
}
}

2
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvc.java
View File

@ -151,13 +151,13 @@ public class MdmResourceMatcherSvc {
fieldComparator.getName(),
matchEvaluation.score,
vector);
score += matchEvaluation.score;
} else {
ourLog.trace(
"No match: Matcher {} did not match (score: {}).",
fieldComparator.getName(),
matchEvaluation.score);
}
score += matchEvaluation.score;
appliedRuleCount += 1;
}

15
hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvcR4Test.java
View File

@ -57,4 +57,19 @@ public class MdmResourceMatcherSvcR4Test extends BaseMdmRulesR4Test {
patient3.addName().addGiven("Henry");
assertMatchResult(MdmMatchResultEnum.NO_MATCH, 0L, 0.0, false, false, myMdmResourceMatcherSvc.getMatchResult(myJohn, patient3));
}
@Test
public void testScoreOnlySummedWhenMatchFieldMatches() {
MdmMatchOutcome outcome = myMdmResourceMatcherSvc.getMatchResult(myJohn, myJohny);
assertMatchResult(MdmMatchResultEnum.POSSIBLE_MATCH, 1L, 0.816, false, false, outcome);
myJohn.addName().setFamily("Smith");
myJohny.addName().setFamily("htims");
outcome = myMdmResourceMatcherSvc.getMatchResult(myJohn, myJohny);
assertMatchResult(MdmMatchResultEnum.POSSIBLE_MATCH, 1L, 0.816, false, false, outcome);
myJohny.addName().setFamily("Smith");
outcome = myMdmResourceMatcherSvc.getMatchResult(myJohn, myJohny);
assertMatchResult(MdmMatchResultEnum.MATCH, 3L, 1.816, false, false, outcome);
}
}

78
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/ResponseBundleBuilder.java
View File

@ -234,6 +234,7 @@ public class ResponseBundleBuilder {
theResponseBundleRequest.includes,
RestfulServerUtils.prettyPrintResponse(server, theResponseBundleRequest.requestDetails),
theResponseBundleRequest.bundleType);
retval.setSelf(theResponseBundleRequest.linkSelf);
if (bundleProvider.getCurrentPageOffset() != null) {
@ -264,21 +265,22 @@ public class ResponseBundleBuilder {
// Paging without caching
// We're doing offset pages
int requestedToReturn = theResponsePage.numToReturn;
if (server.getPagingProvider() == null && pageRequest.offset != null) {
// There is no paging provider at all, so assume we're querying up to all the results we need every time
if (pageRequest.offset != null) {
requestedToReturn += pageRequest.offset;
}
if (theResponsePage.numTotalResults == null || requestedToReturn < theResponsePage.numTotalResults) {
if (!theResponsePage.resourceList.isEmpty()) {
retval.setNext(RestfulServerUtils.createOffsetPagingLink(
retval,
theResponseBundleRequest.requestDetails.getRequestPath(),
theResponseBundleRequest.requestDetails.getTenantId(),
ObjectUtils.defaultIfNull(pageRequest.offset, 0) + theResponsePage.numToReturn,
theResponsePage.numToReturn,
theResponseBundleRequest.getRequestParameters()));
}
retval.setNext(RestfulServerUtils.createOffsetPagingLink(
retval,
theResponseBundleRequest.requestDetails.getRequestPath(),
theResponseBundleRequest.requestDetails.getTenantId(),
ObjectUtils.defaultIfNull(pageRequest.offset, 0) + theResponsePage.numToReturn,
theResponsePage.numToReturn,
theResponseBundleRequest.getRequestParameters()));
}
if (pageRequest.offset != null && pageRequest.offset > 0) {
int start = Math.max(0, pageRequest.offset - theResponsePage.pageSize);
retval.setPrev(RestfulServerUtils.createOffsetPagingLink(
@ -289,6 +291,7 @@ public class ResponseBundleBuilder {
theResponsePage.pageSize,
theResponseBundleRequest.getRequestParameters()));
}
} else if (StringUtils.isNotBlank(bundleProvider.getCurrentPageId())) {
// We're doing named pages
final String uuid = bundleProvider.getUuid();
@ -300,6 +303,7 @@ public class ResponseBundleBuilder {
bundleProvider.getNextPageId(),
theResponseBundleRequest.getRequestParameters()));
}
if (StringUtils.isNotBlank(bundleProvider.getPreviousPageId())) {
retval.setPrev(RestfulServerUtils.createPagingLink(
retval,
@ -308,37 +312,33 @@ public class ResponseBundleBuilder {
bundleProvider.getPreviousPageId(),
theResponseBundleRequest.getRequestParameters()));
}
} else if (theResponsePage.searchId != null) {
/*
* We're doing offset pages - Note that we only return paging links if we actually
* included some results in the response. We do this to avoid situations where
* people have faked the offset number to some huge number to avoid them getting
* back paging links that don't make sense.
*/
if (theResponsePage.size() > 0) {
if (theResponsePage.numTotalResults == null
|| theResponseBundleRequest.offset + theResponsePage.numToReturn
< theResponsePage.numTotalResults) {
retval.setNext((RestfulServerUtils.createPagingLink(
retval,
theResponseBundleRequest.requestDetails,
theResponsePage.searchId,
theResponseBundleRequest.offset + theResponsePage.numToReturn,
theResponsePage.numToReturn,
theResponseBundleRequest.getRequestParameters())));
}
if (theResponseBundleRequest.offset > 0) {
int start = Math.max(0, theResponseBundleRequest.offset - theResponsePage.pageSize);
retval.setPrev(RestfulServerUtils.createPagingLink(
retval,
theResponseBundleRequest.requestDetails,
theResponsePage.searchId,
start,
theResponsePage.pageSize,
theResponseBundleRequest.getRequestParameters()));
}
if (theResponsePage.numTotalResults == null
|| theResponseBundleRequest.offset + theResponsePage.numToReturn
< theResponsePage.numTotalResults) {
retval.setNext((RestfulServerUtils.createPagingLink(
retval,
theResponseBundleRequest.requestDetails,
theResponsePage.searchId,
theResponseBundleRequest.offset + theResponsePage.numToReturn,
theResponsePage.numToReturn,
theResponseBundleRequest.getRequestParameters())));
}
if (theResponseBundleRequest.offset > 0) {
int start = Math.max(0, theResponseBundleRequest.offset - theResponsePage.pageSize);
retval.setPrev(RestfulServerUtils.createPagingLink(
retval,
theResponseBundleRequest.requestDetails,
theResponsePage.searchId,
start,
theResponsePage.pageSize,
theResponseBundleRequest.getRequestParameters()));
}
}
return retval;
}

46
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/tenant/UrlBaseTenantIdentificationStrategy.java
View File

@ -22,10 +22,10 @@ package ca.uhn.fhir.rest.server.tenant;
import ca.uhn.fhir.i18n.HapiLocalizer;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.UrlPathTokenizer;
import org.apache.commons.lang3.Validate;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -51,12 +51,41 @@ public class UrlBaseTenantIdentificationStrategy implements ITenantIdentificatio
@Override
public void extractTenant(UrlPathTokenizer theUrlPathTokenizer, RequestDetails theRequestDetails) {
String tenantId = null;
if (theUrlPathTokenizer.hasMoreTokens()) {
tenantId = defaultIfBlank(theUrlPathTokenizer.nextTokenUnescapedAndSanitized(), null);
ourLog.trace("Found tenant ID {} in request string", tenantId);
theRequestDetails.setTenantId(tenantId);
boolean isSystemRequest = (theRequestDetails instanceof SystemRequestDetails);
// If we were given no partition for a system request, use DEFAULT:
if (!theUrlPathTokenizer.hasMoreTokens()) {
if (isSystemRequest) {
tenantId = "DEFAULT";
theRequestDetails.setTenantId(tenantId);
ourLog.trace("No tenant ID found for system request; using DEFAULT.");
}
}
// We were given at least one URL token:
else {
// peek() won't consume this token:
tenantId = defaultIfBlank(theUrlPathTokenizer.peek(), null);
// If it's "metadata" or starts with "$", use DEFAULT partition and don't consume this token:
if (tenantId != null && (tenantId.equals("metadata") || tenantId.startsWith("$"))) {
tenantId = "DEFAULT";
theRequestDetails.setTenantId(tenantId);
ourLog.trace("No tenant ID found for metadata or system request; using DEFAULT.");
}
// It isn't metadata or $, so assume that this first token is the partition name and consume it:
else {
tenantId = defaultIfBlank(theUrlPathTokenizer.nextTokenUnescapedAndSanitized(), null);
if (tenantId != null) {
theRequestDetails.setTenantId(tenantId);
ourLog.trace("Found tenant ID {} in request string", tenantId);
}
}
}
// If we get to this point without a tenant, it's an invalid request:
if (tenantId == null) {
HapiLocalizer localizer =
theRequestDetails.getServer().getFhirContext().getLocalizer();
@ -67,7 +96,10 @@ public class UrlBaseTenantIdentificationStrategy implements ITenantIdentificatio
@Override
public String massageServerBaseUrl(String theFhirServerBase, RequestDetails theRequestDetails) {
Validate.notNull(theRequestDetails.getTenantId(), "theTenantId is not populated on this request");
return theFhirServerBase + '/' + theRequestDetails.getTenantId();
String result = theFhirServerBase;
if (theRequestDetails.getTenantId() != null) {
result += "/" + theRequestDetails.getTenantId();
}
return result;
}
}

2
hapi-fhir-storage/src/test/java/ca/uhn/fhir/rest/server/method/ResponseBundleBuilderTest.java
View File

@ -435,8 +435,8 @@ class ResponseBundleBuilderTest {
private void setCanStoreSearchResults(boolean theCanStoreSearchResults) {
when(myServer.canStoreSearchResults()).thenReturn(theCanStoreSearchResults);
when(myServer.getPagingProvider()).thenReturn(myPagingProvider);
if (theCanStoreSearchResults) {
when(myServer.getPagingProvider()).thenReturn(myPagingProvider);
if (myLimit == null) {
when(myPagingProvider.getDefaultPageSize()).thenReturn(DEFAULT_PAGE_SIZE);
} else {

8
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/interceptor/ConsentInterceptorTest.java
View File

@ -2,14 +2,11 @@ package ca.uhn.fhir.rest.server.interceptor;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.param.StringParam;
@ -53,7 +50,6 @@ import javax.servlet.ReadListener;
import javax.servlet.ServletInputStream;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.EOFException;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
@ -64,18 +60,14 @@ import java.util.List;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.doThrow;
import static org.mockito.Mockito.reset;
import static org.mockito.Mockito.timeout;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.verifyNoMoreInteractions;
import static org.mockito.Mockito.when;
import static org.mockito.Mockito.withSettings;
@ExtendWith(MockitoExtension.class)
public class ConsentInterceptorTest {

78
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/UrlPathTokenizerTest.java Normal file
View File

@ -0,0 +1,78 @@
package ca.uhn.fhir.util;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class UrlPathTokenizerTest {
@Test
void urlPathTokenizer_withValidPath_tokenizesCorrectly() {
UrlPathTokenizer tokenizer = new UrlPathTokenizer("/root/subdir/subsubdir/file.html");
assertTrue(tokenizer.hasMoreTokens());
assertEquals(4, tokenizer.countTokens());
assertEquals("root", tokenizer.nextTokenUnescapedAndSanitized());
assertEquals("subdir", tokenizer.nextTokenUnescapedAndSanitized());
assertEquals("subsubdir", tokenizer.nextTokenUnescapedAndSanitized());
assertEquals("file.html", tokenizer.nextTokenUnescapedAndSanitized());
assertFalse(tokenizer.hasMoreTokens());
}
@ParameterizedTest
@ValueSource(strings = {
"", // actually empty
"///////", // effectively empty
"// / / / / " // effectively empty with extraneous whitespace
})
void urlPathTokenizer_withEmptyPath_returnsEmpty(String thePath) {
UrlPathTokenizer tokenizer = new UrlPathTokenizer(thePath);
assertEquals(0, tokenizer.countTokens());
}
@Test
void urlPathTokenizer_withNullPath_returnsEmpty() {
UrlPathTokenizer tokenizer = new UrlPathTokenizer(null);
assertEquals(0, tokenizer.countTokens());
}
@Test
void urlPathTokenizer_withSinglePathElement_returnsSingleToken() {
UrlPathTokenizer tokenizer = new UrlPathTokenizer("hello");
assertTrue(tokenizer.hasMoreTokens());
assertEquals("hello", tokenizer.nextTokenUnescapedAndSanitized());
}
@Test
void urlPathTokenizer_withEscapedPath_shouldUnescape() {
UrlPathTokenizer tokenizer = new UrlPathTokenizer("Homer%20Simpson");
assertTrue(tokenizer.hasMoreTokens());
assertEquals("Homer Simpson", tokenizer.nextTokenUnescapedAndSanitized());
tokenizer = new UrlPathTokenizer("hack%2Fslash");
assertTrue(tokenizer.hasMoreTokens());
assertEquals("hack/slash", tokenizer.nextTokenUnescapedAndSanitized());
}
@Test
void urlPathTokenizer_peek_shouldNotConsumeTokens() {
UrlPathTokenizer tokenizer = new UrlPathTokenizer("this/that");
assertEquals(2, tokenizer.countTokens());
tokenizer.peek();
assertEquals(2, tokenizer.countTokens());
}
@Test
void urlPathTokenizer_withSuspiciousCharacters_sanitizesCorrectly() {
UrlPathTokenizer tokenizer = new UrlPathTokenizer("<DROP TABLE USERS>");
assertTrue(tokenizer.hasMoreTokens());
assertEquals("&lt;DROP TABLE USERS&gt;", tokenizer.nextTokenUnescapedAndSanitized());
tokenizer = new UrlPathTokenizer("'\n\r\"");
assertTrue(tokenizer.hasMoreTokens());
assertEquals("&apos;&#10;&#13;&quot;", tokenizer.nextTokenUnescapedAndSanitized());
}
}

5
hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/ctx/HapiWorkerContext.java
View File

@ -321,6 +321,11 @@ public final class HapiWorkerContext extends I18nBase implements IWorkerContext
throw new UnsupportedOperationException(Msg.code(234));
}
@Override
public <T extends Resource> T fetchResourceRaw(Class<T> class_, String uri) {
return fetchResource(class_, uri);
}
@Override
public <T extends org.hl7.fhir.r5.model.Resource> T fetchResource(Class<T> theClass, String theUri) {
if (myValidationSupport == null || theUri == null) {

173
hapi-fhir-test-utilities/src/test/java/ca/uhn/fhir/rest/server/tenant/UrlBaseTenantIdentificationStrategyTest.java Normal file
View File

@ -0,0 +1,173 @@
package ca.uhn.fhir.rest.server.tenant;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.HapiLocalizer;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.UrlPathTokenizer;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class UrlBaseTenantIdentificationStrategyTest {
private final static String BASE_URL = "http://localhost:8888";
@Mock
private RequestDetails myRequestDetails;
private static SystemRequestDetails ourSystemRequestDetails;
@Mock
private IRestfulServerDefaults myRestfulServerDefaults;
@Mock
private FhirContext myFHIRContext;
@Mock
private HapiLocalizer myHapiLocalizer;
private static UrlBaseTenantIdentificationStrategy ourTenantStrategy;
private UrlPathTokenizer myUrlTokenizer;
@BeforeAll
static void setup() {
ourSystemRequestDetails = new SystemRequestDetails();
ourTenantStrategy = new UrlBaseTenantIdentificationStrategy();
}
@Test
void massageBaseUrl_givenBaseUrlAndTenant_shouldApplyTenant() {
//given a tenant id of TENANT1
when(myRequestDetails.getTenantId()).thenReturn("TENANT1");
//when we massage the server base url
String actual = ourTenantStrategy.massageServerBaseUrl(BASE_URL, myRequestDetails);
//then we should see /TENANT1 in the url
assertEquals(BASE_URL + "/TENANT1", actual);
}
@Test
void massageBaseUrl_givenBaseUrlAndNullTenant_shouldReturnBaseUrl() {
//given a null tenant id
when(myRequestDetails.getTenantId()).thenReturn(null);
//when we massage our base url
String actual = ourTenantStrategy.massageServerBaseUrl(BASE_URL, myRequestDetails);
//then nothing should happen
assertEquals(BASE_URL, actual);
}
@Test
void extractTenant_givenNormalRequestAndExplicitTenant_shouldUseTenant() {
//given a Patient request on MYTENANT
myUrlTokenizer = new UrlPathTokenizer("MYTENANT/Patient");
//when we extract the tenant identifier
ourTenantStrategy.extractTenant(myUrlTokenizer, myRequestDetails);
//then we should see MYTENANT
verify(myRequestDetails, times(1)).setTenantId("MYTENANT");
}
@Test
void extractTenant_givenSystemRequestWithNoTenant_shouldUseDefault() {
//given any request that starts with $ and no given partition name
myUrlTokenizer = new UrlPathTokenizer("$partition-management-create-partition");
//when we try to extract the tenant id
ourTenantStrategy.extractTenant(myUrlTokenizer, ourSystemRequestDetails);
//then we should see that it defaulted to the DEFAULT partition
assertEquals("DEFAULT", ourSystemRequestDetails.getTenantId());
}
@Test
void extractTenant_givenSystemRequestWithExplicitTenant_shouldUseTenant() {
//given a request that starts with $ on a named partition
myUrlTokenizer = new UrlPathTokenizer("MYTENANT/$partition-management-create-partition");
//when we extract the tenant from the request
ourTenantStrategy.extractTenant(myUrlTokenizer, ourSystemRequestDetails);
//then we should see MYTENANT
assertEquals("MYTENANT", ourSystemRequestDetails.getTenantId());
}
@Test
void extractTenant_givenMetadataRequestWithNoTenant_shouldUseDefault() {
//given a metadata request with no specified partition name
myUrlTokenizer = new UrlPathTokenizer("metadata");
//when we try to extract the tenant from the request
ourTenantStrategy.extractTenant(myUrlTokenizer, myRequestDetails);
//then we should see that it defaulted to the DEFAULT partition
verify(myRequestDetails, times(1)).setTenantId("DEFAULT");
}
@Test
void extractTenant_givenMetadataRequestWithExplicitTenant_shouldUseTenant() {
//given a metadata request on a named partition
myUrlTokenizer = new UrlPathTokenizer("MYTENANT/metadata");
//when we extract the tenant id
ourTenantStrategy.extractTenant(myUrlTokenizer, myRequestDetails);
//then we should see MYTENANT
verify(myRequestDetails, times(1)).setTenantId("MYTENANT");
}
@Test
void extractTenant_givenPatientRequestAndNoTenant_shouldInterpretPatientAsPartition() {
//given a Patient request with no partition name specified
myUrlTokenizer = new UrlPathTokenizer("Patient");
//when we try to extract the tenant from the request
ourTenantStrategy.extractTenant(myUrlTokenizer, myRequestDetails);
//then we should see that it interpreted Patient as the partition name
verify(myRequestDetails, times(1)).setTenantId("Patient");
}
@Test
void extractTenant_givenEmptyURLNoPartition_shouldThrowException() {
//given an empty URL with no partition name
when(myRequestDetails.getServer()).thenReturn(myRestfulServerDefaults);
when(myRestfulServerDefaults.getFhirContext()).thenReturn(myFHIRContext);
when(myFHIRContext.getLocalizer()).thenReturn(myHapiLocalizer);
myUrlTokenizer = new UrlPathTokenizer("");
//when we try to extract the tenant from the request
InvalidRequestException ire = assertThrows(InvalidRequestException.class, () -> {
ourTenantStrategy.extractTenant(myUrlTokenizer, myRequestDetails);
});
//then we should see an exception thrown with HAPI-0307 in it
verify(myHapiLocalizer, times(1)).getMessage(RestfulServer.class, "rootRequest.multitenant");
assertTrue(ire.getMessage().contains("HAPI-0307"));
}
@Test
void extractTenant_givenSystemRequestWithEmptyUrl_shouldUseDefaultPartition() {
//given a system request with a blank url (is this even a valid test case?)
myUrlTokenizer = new UrlPathTokenizer("");
//when we try to extract the tenant id
ourTenantStrategy.extractTenant(myUrlTokenizer, ourSystemRequestDetails);
//then we should see that it defaulted to the DEFAULT partition
assertEquals("DEFAULT", ourSystemRequestDetails.getTenantId());
}
}

11
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/VersionSpecificWorkerContextWrapper.java
View File

@ -376,6 +376,11 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
return null;
}
@Override
public <T extends Resource> T fetchResourceRaw(Class<T> class_, String uri) {
return fetchResource(class_, uri);
}
@Override
public <T extends Resource> T fetchResource(Class<T> class_, String uri) {
@ -443,8 +448,10 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
}
@Override
public List<StructureDefinition> fetchTypeDefinitions(String n) {
throw new UnsupportedOperationException(Msg.code(2329));
public List<StructureDefinition> fetchTypeDefinitions(String typeName) {
List<StructureDefinition> allStructures = new ArrayList<>(allStructures());
allStructures.removeIf(sd -> !sd.hasType() || !sd.getType().equals(typeName));
return allStructures;
}
@Override

2
pom.xml
View File

@ -897,7 +897,7 @@
</licenses>
<properties>
<fhir_core_version>6.0.15</fhir_core_version>
<fhir_core_version>6.0.22</fhir_core_version>
<spotless_version>2.37.0</spotless_version>
<ucum_version>1.0.3</ucum_version>
<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>