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Merge branch 'master' into tinder-for-non-java

This commit is contained in:
Bill Denton 2016-12-06 11:29:04 -08:00
parent 1452a29a09 e8fad33042
commit 1ba2680acc
8 changed files with 146 additions and 38 deletions
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20
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IContextValidationSupport.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.context.support;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* 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.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.List;
import org.hl7.fhir.instance.model.api.IBaseResource;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/fluentpath/FluentPathExecutionException.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.fluentpath;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* 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.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
/**

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/fluentpath/IFluentPath.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.fluentpath;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* 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.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.List;
import org.hl7.fhir.instance.model.api.IBase;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/LenientErrorHandler.java
View File

@ -61,7 +61,7 @@ public class LenientErrorHandler implements IParserErrorHandler {
@Override
public void incorrectJsonType(IParseLocation theLocation, String theElementName, ValueType theExpected, ValueType theFound) {
if (myLogErrors) {
ourLog.warn("Found incorrect type for element {} - Expected {} and found {}", theElementName, theExpected.name(), theFound.name());
ourLog.warn("Found incorrect type for element {} - Expected {} and found {}", new Object[]{theElementName, theExpected.name(), theFound.name()});
}
}

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/CorsInterceptor.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.interceptor;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* 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.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.io.IOException;
import javax.servlet.http.HttpServletRequest;

75
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ExampleDataUploader.java
View File

@ -245,7 +245,7 @@ public class ExampleDataUploader extends BaseCommand {
iter.remove();
}
}
List<IBaseResource> subResourceList = new ArrayList<IBaseResource>();
while (resources.size() > 0) {
@ -253,7 +253,7 @@ public class ExampleDataUploader extends BaseCommand {
subResourceList.add(nextAddedResource);
Set<String> checkedTargets = new HashSet<String>();
for (int i = 0; i < subResourceList.size(); i++) {
IBaseResource nextCandidateSource = subResourceList.get(i);
for (ResourceReferenceInfo nextRef : ctx.newTerser().getAllResourceReferences(nextCandidateSource)) {
@ -276,7 +276,7 @@ public class ExampleDataUploader extends BaseCommand {
boolean found = false;
for (int j = 0; j < resources.size(); j++) {
String candidateTarget = resources.get(j).getIdElement().getValue();
String candidateTarget = resources.get(j).getIdElement().getValue();
if (isNotBlank(nextTarget) && nextTarget.equals(candidateTarget)) {
ourLog.info("Reflexively adding resource {} to bundle as it is a reference target", nextTarget);
subResourceList.add(resources.remove(j));
@ -287,7 +287,6 @@ public class ExampleDataUploader extends BaseCommand {
}
}
if (subResourceList.size() < 10 && resources.size() > 0) {
subResourceList.add(resources.remove(0));
continue;
@ -357,8 +356,8 @@ public class ExampleDataUploader extends BaseCommand {
Entry next = iterator.next();
// DataElement have giant IDs that seem invalid, need to investigate this..
if ("Subscription".equals(next.getResource().getResourceName()) || "DataElement".equals(next.getResource().getResourceName()) || "OperationOutcome".equals(next.getResource().getResourceName())
|| "OperationDefinition".equals(next.getResource().getResourceName())) {
if ("Subscription".equals(next.getResource().getResourceName()) || "DataElement".equals(next.getResource().getResourceName())
|| "OperationOutcome".equals(next.getResource().getResourceName()) || "OperationDefinition".equals(next.getResource().getResourceName())) {
ourLog.info("Skipping " + next.getResource().getResourceName() + " example");
iterator.remove();
} else {
@ -399,7 +398,7 @@ public class ExampleDataUploader extends BaseCommand {
// }
nextRef.getResourceReference().setResource(null);
String value = nextRef.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue();
if (isNotBlank(value)) {
if (!qualIds.contains(value) && !nextRef.getResourceReference().getReferenceElement().isLocal()) {
ourLog.info("Discarding unknown reference: {}", value);
@ -437,8 +436,8 @@ public class ExampleDataUploader extends BaseCommand {
BundleEntryComponent next = iterator.next();
// DataElement have giant IDs that seem invalid, need to investigate this..
if ("Subscription".equals(next.getResource().getResourceType()) || "DataElement".equals(next.getResource().getResourceType()) || "OperationOutcome".equals(next.getResource().getResourceType())
|| "OperationDefinition".equals(next.getResource().getResourceType())) {
if ("Subscription".equals(next.getResource().getResourceType()) || "DataElement".equals(next.getResource().getResourceType())
|| "OperationOutcome".equals(next.getResource().getResourceType()) || "OperationDefinition".equals(next.getResource().getResourceType())) {
ourLog.info("Skipping " + next.getResource().getResourceType() + " example");
iterator.remove();
} else {
@ -479,7 +478,7 @@ public class ExampleDataUploader extends BaseCommand {
// }
nextRef.getResourceReference().setResource(null);
String value = nextRef.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue();
if (isNotBlank(value)) {
if (!qualIds.contains(value) && !nextRef.getResourceReference().getReferenceElement().isLocal()) {
ourLog.info("Discarding unknown reference: {}", value);
@ -659,37 +658,41 @@ public class ExampleDataUploader extends BaseCommand {
private void downloadFileFromInternet(CloseableHttpResponse result, File localFile) throws IOException {
FileOutputStream buffer = FileUtils.openOutputStream(localFile);
try {
long maxLength = result.getEntity().getContentLength();
long nextLog = -1;
// ByteArrayOutputStream buffer = new ByteArrayOutputStream();
int nRead;
byte[] data = new byte[16384];
while ((nRead = result.getEntity().getContent().read(data, 0, data.length)) != -1) {
buffer.write(data, 0, nRead);
long fileSize = FileUtils.sizeOf(localFile);
if (fileSize > nextLog) {
System.err.print("\r" + Ansi.ansi().eraseLine());
System.err.print(FileUtils.byteCountToDisplaySize(fileSize));
if (maxLength > 0) {
System.err.print(" [");
int stars = (int) (50.0f * ((float) fileSize / (float) maxLength));
for (int i = 0; i < stars; i++) {
System.err.print("*");
long maxLength = result.getEntity().getContentLength();
long nextLog = -1;
// ByteArrayOutputStream buffer = new ByteArrayOutputStream();
int nRead;
byte[] data = new byte[16384];
while ((nRead = result.getEntity().getContent().read(data, 0, data.length)) != -1) {
buffer.write(data, 0, nRead);
long fileSize = FileUtils.sizeOf(localFile);
if (fileSize > nextLog) {
System.err.print("\r" + Ansi.ansi().eraseLine());
System.err.print(FileUtils.byteCountToDisplaySize(fileSize));
if (maxLength > 0) {
System.err.print(" [");
int stars = (int) (50.0f * ((float) fileSize / (float) maxLength));
for (int i = 0; i < stars; i++) {
System.err.print("*");
}
for (int i = stars; i < 50; i++) {
System.err.print(" ");
}
System.err.print("]");
}
for (int i = stars; i < 50; i++) {
System.err.print(" ");
}
System.err.print("]");
System.err.flush();
nextLog += 100000;
}
System.err.flush();
nextLog += 100000;
}
}
buffer.flush();
buffer.flush();
System.err.println();
System.err.flush();
System.err.println();
System.err.flush();
} finally {
IOUtils.closeQuietly(buffer);
}
}
}

12
hapi-fhir-osgi-core/pom.xml
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@ -82,6 +82,18 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<excludes>
<exclude>**/ca/uhn/fhir/rest/server/interceptor/CorsInterceptor.java</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<executions>

15
src/changes/changes.xml
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@ -7,7 +7,16 @@
</properties>
<body>
<release version="2.2" date="TBD">
<action type="fix">
<!--<action type="add">
Bump the version of a few dependencies to the
latest versions (dependent HAPI modules listed in brackets):
<![CDATA[
<ul>
<li>spring (JPA): 4.3.1 -&gt; 4.3.4</li>
</ul>
]]>
</action>-->
<action type="fix">
Fix issue in AuthorizationIntetceptor where
transactions are blocked even when they
should not be
@ -66,6 +75,10 @@
external references (and therefore can't be loaded
by the server). Thanks to Hannes Ulrich for reporting!
</action>
<action type="fix">
HAPI FHIR CLI failed to delete a file when uploading
example resources while running under Windows.
</action>
</release>
<release version="2.1" date="2016-11-11">
<action type="add">