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hapi-fhir
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Fix case sensitivity issue

This commit is contained in:
James Agnew 2018-12-13 08:31:35 -05:00
parent 8d195aedf0
commit 11b8304cb4
5 changed files with 76 additions and 17 deletions
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4
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
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@ -53,8 +53,8 @@ public class FhirTerser {
if (theChildDefinition == null)
return null;
if (theCurrentList == null || theCurrentList.isEmpty())
return new ArrayList<String>(Arrays.asList(theChildDefinition.getElementName()));
List<String> newList = new ArrayList<String>(theCurrentList);
return new ArrayList<>(Arrays.asList(theChildDefinition.getElementName()));
List<String> newList = new ArrayList<>(theCurrentList);
newList.add(theChildDefinition.getElementName());
return newList;
}

55
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInterceptorR4Test.java
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@ -10,6 +10,8 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.interceptor.IServerOperationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
import ca.uhn.fhir.rest.server.interceptor.ServerOperationInterceptorAdapter;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
@ -17,15 +19,13 @@ import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.hamcrest.Matchers;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Test;
@ -38,6 +38,7 @@ import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.stream.Collectors;
import static org.hamcrest.Matchers.in;
import static org.hamcrest.Matchers.startsWith;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.any;
@ -236,6 +237,32 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
}
@Test
public void testCreateReflexResourceTheHardWay() throws IOException, ServletException {
ServerOperationInterceptorAdapter interceptor = new ReflexInterceptor();
ourRestServer.registerInterceptor(interceptor);
try {
Patient p = new Patient();
p.setActive(true);
IIdType pid = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
Bundle observations = ourClient
.search()
.forResource("Observation")
.where(Observation.SUBJECT.hasId(pid))
.returnBundle(Bundle.class)
.execute();
assertEquals(1, observations.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(observations));
} finally {
ourRestServer.unregisterInterceptor(interceptor);
}
}
@Test
public void testCreateResourceWithVersionedReference() throws IOException, ServletException {
String methodName = "testCreateResourceWithVersionedReference";
@ -353,6 +380,26 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
}
}
public class ReflexInterceptor extends ServerOperationInterceptorAdapter {
@Override
public void resourceCreated(RequestDetails theRequest, IBaseResource theResource) {
if (theResource instanceof Patient) {
((ServletRequestDetails) theRequest).getServletRequest().setAttribute("CREATED_PATIENT", theResource);
}
}
@Override
public void processingCompletedNormally(ServletRequestDetails theRequestDetails) {
Patient createdPatient = (Patient) theRequestDetails.getServletRequest().getAttribute("CREATED_PATIENT");
if (createdPatient != null) {
Observation observation = new Observation();
observation.setSubject(new Reference(createdPatient.getId()));
ourClient.create().resource(observation).execute();
}
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

28
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -53,7 +53,7 @@ public class JdbcUtils {
DatabaseMetaData metadata;
try {
metadata = connection.getMetaData();
ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), theTableName, false, true);
ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), false, true);
Set<String> indexNames = new HashSet<>();
while (indexes.next()) {
@ -81,7 +81,7 @@ public class JdbcUtils {
DatabaseMetaData metadata;
try {
metadata = connection.getMetaData();
ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), theTableName, false, false);
ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), false, false);
while (indexes.next()) {
String indexName = indexes.getString("INDEX_NAME");
@ -112,7 +112,7 @@ public class JdbcUtils {
metadata = connection.getMetaData();
String catalog = connection.getCatalog();
String schema = connection.getSchema();
ResultSet indexes = metadata.getColumns(catalog, schema, theTableName, null);
ResultSet indexes = metadata.getColumns(catalog, schema, massageIdentifier(metadata, theTableName), null);
while (indexes.next()) {
@ -165,7 +165,7 @@ public class JdbcUtils {
DatabaseMetaData metadata;
try {
metadata = connection.getMetaData();
ResultSet indexes = metadata.getCrossReference(connection.getCatalog(), connection.getSchema(), theTableName, connection.getCatalog(), connection.getSchema(), theForeignTable);
ResultSet indexes = metadata.getCrossReference(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theForeignTable));
Set<String> columnNames = new HashSet<>();
while (indexes.next()) {
@ -201,7 +201,7 @@ public class JdbcUtils {
DatabaseMetaData metadata;
try {
metadata = connection.getMetaData();
ResultSet indexes = metadata.getColumns(connection.getCatalog(), connection.getSchema(), theTableName, null);
ResultSet indexes = metadata.getColumns(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), null);
Set<String> columnNames = new HashSet<>();
while (indexes.next()) {
@ -253,7 +253,7 @@ public class JdbcUtils {
}
}
return sequenceNames;
} catch (SQLException e ) {
} catch (SQLException e) {
throw new InternalErrorException(e);
}
});
@ -298,7 +298,7 @@ public class JdbcUtils {
DatabaseMetaData metadata;
try {
metadata = connection.getMetaData();
ResultSet tables = metadata.getColumns(connection.getCatalog(), connection.getSchema(), theTableName, theColumnName);
ResultSet tables = metadata.getColumns(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), null);
while (tables.next()) {
String tableName = toUpperCase(tables.getString("TABLE_NAME"), Locale.US);
@ -325,4 +325,14 @@ public class JdbcUtils {
});
}
}
private static String massageIdentifier(DatabaseMetaData theMetadata, String theCatalog) throws SQLException {
String retVal = theCatalog;
if (theMetadata.storesLowerCaseIdentifiers()) {
retVal = retVal.toLowerCase();
} else {
retVal = retVal.toUpperCase();
}
return retVal;
}
}

2
pom.xml
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@ -518,7 +518,7 @@
<jaxb_api_version>2.3.0</jaxb_api_version>
<jaxb_core_version>2.3.0</jaxb_core_version>
<jersey_version>2.25.1</jersey_version>
<jetty_version>9.4.12.v20180830</jetty_version>
<jetty_version>9.4.14.v20181114</jetty_version>
<jsr305_version>3.0.2</jsr305_version>
<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
<hibernate_version>5.3.6.Final</hibernate_version>

4
src/changes/changes.xml
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@ -98,9 +98,11 @@
or authorizing the contents of the response.
</action>
<action type="add">
JPA Migrator tool enhancements:
An invalid SQL syntax issue has been fixed when running the CLI JPA Migrator tool against
Oracle or SQL Server. In addition, when using the "Dry Run" option, all generated SQL
statements will be logged at the end of the run.
statements will be logged at the end of the run. Also, a case sensitivity issue when running against
some Postgres databases has been corrected.
</action>
<action type="add">
In the JPA server, when performing a chained reference search on a search parameter with