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hapi-fhir
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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
jamesagnew 2019-09-09 15:02:55 -04:00
parent 362c658f9a 7e41951508
commit 95e75d0a7d
22 changed files with 117 additions and 34 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TestUtil.java
View File

@ -182,4 +182,13 @@ public class TestUtil {
return defaultString(theString).replace("\r", "");
}
/**
* <b>THIS IS FOR UNIT TESTS ONLY - DO NOT CALL THIS METHOD FROM USER CODE</b>
* <p>
* Strip \r chars from a string to account for line ending platform differences
*/
public static String stripWhitespace(String theString) {
return stripReturns(theString).replace(" ", "");
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
View File

@ -52,7 +52,7 @@ public class TermValueSetConceptDesignation implements Serializable {
@JoinColumn(name = "VALUESET_CONCEPT_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_CONCEPT_PID"))
private TermValueSetConcept myConcept;
@ManyToOne()
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VSCD_VS_PID"))
private TermValueSet myValueSet;

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/GraphQLR4ProviderTest.java → hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/JpaGraphQLR4ProviderTest.java
View File

@ -44,9 +44,11 @@ import static org.hamcrest.Matchers.startsWith;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
public class GraphQLR4ProviderTest {
public class JpaGraphQLR4ProviderTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(GraphQLR4ProviderTest.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JpaGraphQLR4ProviderTest.class);
public static final String DATA_PREFIX = "{\"data\": ";
public static final String DATA_SUFFIX = "}";
private static CloseableHttpClient ourClient;
private static FhirContext ourCtx = FhirContext.forR4();
private static int ourPort;
@ -67,14 +69,14 @@ public class GraphQLR4ProviderTest {
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"name\":[{\n" +
" \"family\":\"FAMILY\",\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
" },{\n" +
" \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(responseContent));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
} finally {
@ -93,12 +95,12 @@ public class GraphQLR4ProviderTest {
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"name\":[{\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
" \"family\":\"FAMILY\"\n" +
" }]\n" +
"}"), TestUtil.stripReturns(responseContent));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
} finally {
@ -117,7 +119,7 @@ public class GraphQLR4ProviderTest {
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"Patient\":{\n" +
" \"name\":[{\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
@ -126,7 +128,7 @@ public class GraphQLR4ProviderTest {
" \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
" }]\n" +
" }\n" +
"}"), TestUtil.stripReturns(responseContent));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
} finally {
@ -145,7 +147,7 @@ public class GraphQLR4ProviderTest {
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"PatientList\":[{\n" +
" \"name\":[{\n" +
" \"family\":\"pet\",\n" +
@ -158,7 +160,7 @@ public class GraphQLR4ProviderTest {
" \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
" }]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(responseContent));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
} finally {

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/GraphQLProviderDstu3Test.java
View File

@ -5,8 +5,8 @@ import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -14,6 +14,8 @@ import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_PREFIX;
import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_SUFFIX;
import static org.junit.Assert.assertEquals;
public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {
@ -30,14 +32,14 @@ public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {
try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX +"{\n" +
" \"name\":[{\n" +
" \"family\":\"FAM\",\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
" },{\n" +
" \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(resp));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
}
}
@ -52,7 +54,7 @@ public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {
try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX +"{\n" +
" \"PatientList\":[{\n" +
" \"name\":[{\n" +
" \"family\":\"FAM\",\n" +
@ -65,7 +67,7 @@ public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {
" \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
" }]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(resp));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
}
}

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLProviderR4Test.java
View File

@ -14,6 +14,8 @@ import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_PREFIX;
import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_SUFFIX;
import static org.junit.Assert.assertEquals;
public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
@ -30,14 +32,14 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"name\":[{\n" +
" \"family\":\"FAM\",\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
" },{\n" +
" \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(resp));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
}
}
@ -52,7 +54,7 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"PatientList\":[{\n" +
" \"name\":[{\n" +
" \"family\":\"FAM\",\n" +
@ -65,7 +67,7 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
" \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
" }]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(resp));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
}
}

10
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropForeignKeyTask.java
View File

@ -34,14 +34,14 @@ public class DropForeignKeyTask extends BaseTableTask<DropForeignKeyTask> {
private static final Logger ourLog = LoggerFactory.getLogger(DropForeignKeyTask.class);
private String myConstraintName;
private String myForeignTableName;
private String myParentTableName;
public void setConstraintName(String theConstraintName) {
myConstraintName = theConstraintName;
}
public void setForeignTableName(String theForeignTableName) {
myForeignTableName = theForeignTableName;
public void setParentTableName(String theParentTableName) {
myParentTableName = theParentTableName;
}
@Override
@ -49,13 +49,13 @@ public class DropForeignKeyTask extends BaseTableTask<DropForeignKeyTask> {
super.validate();
Validate.isTrue(isNotBlank(myConstraintName));
Validate.isTrue(isNotBlank(myForeignTableName));
Validate.isTrue(isNotBlank(myParentTableName));
}
@Override
public void execute() throws SQLException {
Set<String> existing = JdbcUtils.getForeignKeys(getConnectionProperties(), getTableName(), myForeignTableName);
Set<String> existing = JdbcUtils.getForeignKeys(getConnectionProperties(), myParentTableName, getTableName());
if (!existing.contains(myConstraintName)) {
ourLog.info("Don't have constraint named {} - No action performed", myConstraintName);
return;

6
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/BaseMigrationTasks.java
View File

@ -249,13 +249,13 @@ public class BaseMigrationTasks<T extends Enum> {
/**
*
* @param theFkName the name of the foreign key
* @param theForeignTableName the name of the table that imports the foreign key (I know it's a confusing name, but that's what java.sql.DatabaseMetaData calls it)
* @param theParentTableName the name of the table that exports the foreign key
*/
public void dropForeignKey(String theFkName, String theForeignTableName) {
public void dropForeignKey(String theFkName, String theParentTableName) {
DropForeignKeyTask task = new DropForeignKeyTask();
task.setConstraintName(theFkName);
task.setForeignTableName(theForeignTableName);
task.setTableName(getTableName());
task.setParentTableName(theParentTableName);
addTask(task);
}

4
hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/DropForeignKeyTaskTest.java
View File

@ -20,8 +20,8 @@ public class DropForeignKeyTaskTest extends BaseTest {
assertThat(JdbcUtils.getForeignKeys(getConnectionProperties(), "PARENT", "CHILD"), hasSize(1));
DropForeignKeyTask task = new DropForeignKeyTask();
task.setTableName("PARENT");
task.setForeignTableName("CHILD");
task.setTableName("CHILD");
task.setParentTableName("PARENT");
task.setConstraintName("FK_MOM");
getMigrator().addTask(task);

5
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java
View File

@ -877,6 +877,11 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
return false;
}
@Override
public ValueSet resolveValueSet(Object appContext, String url) {
return null;
}
}
private static <T extends Enum<?>> String extractSystem(Enumeration<T> theBoundCode) {

6
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
View File

@ -848,7 +848,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
@SuppressWarnings("WeakerAccess")
protected void handleRequest(RequestTypeEnum theRequestType, HttpServletRequest theRequest, HttpServletResponse theResponse) throws ServletException, IOException {
String fhirServerBase;
ServletRequestDetails requestDetails = new ServletRequestDetails(getInterceptorService());
ServletRequestDetails requestDetails = newRequestDetails();
requestDetails.setServer(this);
requestDetails.setRequestType(theRequestType);
requestDetails.setServletRequest(theRequest);
@ -1095,6 +1095,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
}
}
protected ServletRequestDetails newRequestDetails() {
return new ServletRequestDetails(getInterceptorService());
}
protected void addRequestIdToResponse(ServletRequestDetails theRequestDetails, String theRequestId) {
theRequestDetails.getResponse().addHeader(Constants.HEADER_REQUEST_ID, theRequestId);
}

12
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/ctx/HapiWorkerContext.java
View File

@ -336,6 +336,18 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
expandedValueSet = new ValueSetExpansionOutcome(expansion);
}
/*
* We'll just accept all mimetypes, since this is pretty much impossible to exhaustively
* validate.
*/
if (theVs != null && "http://hl7.org/fhir/ValueSet/mimetypes".equals(theVs.getUrl())) {
ConceptDefinitionComponent definition = new ConceptDefinitionComponent();
definition.setCode(wantCode);
definition.setDisplay(wantCode);
ValidationResult retVal = new ValidationResult(definition);
return retVal;
}
if (expandedValueSet == null) {
expandedValueSet = expand(theVs, null);
}

5
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/HapiWorkerContext.java
View File

@ -389,6 +389,11 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
throw new UnsupportedOperationException();
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public List<String> getTypeNames() {
throw new UnsupportedOperationException();

6
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/GraphQLEngineTest.java
View File

@ -66,7 +66,8 @@ public class GraphQLEngineTest {
engine.setGraphQL(Parser.parse("{valueQuantity{value,unit}}"));
engine.execute();
ObjectValue output = engine.getOutput();
GraphQLResponse output = engine.getOutput();
output.setWriteWrapper(false);
StringBuilder outputBuilder = new StringBuilder();
output.write(outputBuilder, 0, "\n");
@ -100,7 +101,8 @@ public class GraphQLEngineTest {
engine.setServices(createStorageServices());
engine.execute();
ObjectValue output = engine.getOutput();
GraphQLResponse output = engine.getOutput();
output.setWriteWrapper(false);
StringBuilder outputBuilder = new StringBuilder();
output.write(outputBuilder, 0, "\n");

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

@ -438,4 +438,9 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
throw new UnsupportedOperationException();
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
}

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidator.java
View File

@ -339,6 +339,11 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
throw new UnsupportedOperationException();
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition p) throws FHIRException {
// nothing yet

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/instance/hapi/validation/FhirInstanceValidator.java
View File

@ -522,6 +522,11 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public Parameters getExpansionParameters() {
return myExpansionProfile;

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/FhirInstanceValidator.java
View File

@ -669,6 +669,11 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
return convertValidationResult(result);
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
}
private static class ResourceKey {

6
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/SnapshotGeneratingValidationSupport.java
View File

@ -145,6 +145,12 @@ public class SnapshotGeneratingValidationSupport implements IValidationSupport {
public boolean prependLinks() {
return false;
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
}
}

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/FhirInstanceValidator.java
View File

@ -282,6 +282,11 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
// nothing yet
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public org.hl7.fhir.r5.model.Parameters getExpansionParameters() {
return myExpansionProfile;

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/SnapshotGeneratingValidationSupport.java
View File

@ -131,6 +131,11 @@ public class SnapshotGeneratingValidationSupport implements IValidationSupport {
return null;
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public BindingResolution resolveBinding(StructureDefinition def, String url, String path) throws FHIRException {
return null;

2
pom.xml
View File

@ -562,7 +562,7 @@
<properties>
<fhir_core_version>4.0.2-SNAPSHOT</fhir_core_version>
<fhir_core_version>4.0.8-SNAPSHOT</fhir_core_version>
<ucum_version>1.0.2</ucum_version>
<!-- configure timestamp in MANIFEST.MF for maven-war-provider -->

4
src/changes/changes.xml
View File

@ -117,6 +117,10 @@
the RequestValidatingInterceptor, but not including any HAPI FHIR security interceptors)
could be bypassed if a Content Type was not included.
</action>
<action type="fix">
The GraphQL provider did not wrap the respone in a "data" element as described in the FHIR
specification. This has been corrected.
</action>
</release>
<release version="4.0.1" date="2019-09-03" description="Igloo (Point Release)">
<action type="fix">