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Remove dependency on StAX for XML parsing in DSTU2 Xhtml type

This commit is contained in:
James Agnew 2017-10-16 17:22:50 -04:00
parent a782bd7630
commit 175f9dfc5a
9 changed files with 168 additions and 87 deletions
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19
hapi-fhir-android/pom.xml
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@ -35,6 +35,25 @@
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
<exclusion>
<groupId>org.codehaus.woodstox</groupId>
<artifactId>woodstox-core-asl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>

2
hapi-fhir-android/src/test/java/ca/uhn/fhir/android/BuiltJarDstu2ShadeIT.java
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@ -9,6 +9,7 @@ import java.util.zip.ZipFile;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.filefilter.WildcardFileFilter;
import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
@ -21,6 +22,7 @@ public class BuiltJarDstu2ShadeIT {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BuiltJarDstu2ShadeIT.class);
@Test
@Ignore
public void testParserXml() throws Exception {
FhirContext ctx = FhirContext.forDstu2();

16
hapi-fhir-android/src/test/java/ca/uhn/fhir/android/client/GenericClientDstu3IT.java
View File

@ -7,7 +7,6 @@ import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.Date;
import org.apache.http.client.ClientProtocolException;
import org.hl7.fhir.dstu3.model.*;
import org.junit.*;
import org.mockito.ArgumentCaptor;
@ -82,6 +81,7 @@ public class GenericClientDstu3IT {
* TODO: narratives don't work without stax
*/
@Test
@Ignore
public void testBinaryCreateWithFhirContentType() throws Exception {
IParser p = ourCtx.newXmlParser();
@ -142,7 +142,7 @@ public class GenericClientDstu3IT {
.returnBundle(Bundle.class)
.execute();
assertEquals("http://example.com/fhir/Patient", capt.getAllValues().get(idx).url().toString());
assertEquals("http://example.com/fhir/Patient?_format=json", capt.getAllValues().get(idx).url().toString());
idx++;
}
@ -177,12 +177,12 @@ public class GenericClientDstu3IT {
Request request = capt.getAllValues().get(0);
ourLog.info(request.headers().toString());
assertEquals("http://example.com/fhir/Binary", request.url().toString());
assertEquals("http://example.com/fhir/Binary?_format=json", request.url().toString());
validateUserAgent(capt);
assertEquals(Constants.CT_FHIR_XML_NEW + ";charset=utf-8", request.body().contentType().toString().toLowerCase().replace(" ", ""));
assertEquals(Constants.HEADER_ACCEPT_VALUE_XML_NON_LEGACY, request.header("Accept"));
assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourCtx.newXmlParser().parseResource(Binary.class, extractBodyAsString(capt)).getContent());
assertEquals(Constants.CT_FHIR_JSON_NEW + ";charset=utf-8", request.body().contentType().toString().toLowerCase().replace(" ", ""));
assertEquals(Constants.HEADER_ACCEPT_VALUE_JSON_NON_LEGACY, request.header("Accept"));
assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourCtx.newJsonParser().parseResource(Binary.class, extractBodyAsString(capt)).getContent());
}
@ -257,11 +257,11 @@ public class GenericClientDstu3IT {
assertNotNull(outcome.getResource());
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">FINAL VALUE</div>", ((Patient) outcome.getResource()).getText().getDivAsString());
assertEquals("http://example.com/fhir/Patient", capt.getAllValues().get(0).url().toString());
assertEquals("http://example.com/fhir/Patient?_format=json", capt.getAllValues().get(0).url().toString());
}
private ArgumentCaptor<Request> prepareClientForSearchResponse() throws IOException, ClientProtocolException {
private ArgumentCaptor<Request> prepareClientForSearchResponse() throws IOException {
final String respString = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
myHttpResponse = new Response.Builder()
.request(myRequest)

113
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/XhtmlDt.java
View File

@ -20,29 +20,28 @@ package ca.uhn.fhir.model.primitive;
* #L%
*/
import java.io.StringReader;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;
import javax.xml.stream.FactoryConfigurationError;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLEventWriter;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.events.XMLEvent;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.model.api.BasePrimitive;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
import ca.uhn.fhir.model.api.annotation.SimpleSetter;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.util.XmlUtil;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* Note that as of HAPI FHIR 3.1.0, this method no longer uses
* the StAX XMLEvent type as the XML representation, and uses a
* String instead. If you need to work with XML as StAX events, you
* can use the {@link XmlUtil#parse(String)} and {@link XmlUtil#encode(List)}
* methods to do so.
*/
@DatatypeDef(name = "xhtml")
public class XhtmlDt extends BasePrimitive<List<XMLEvent>> {
public class XhtmlDt extends BasePrimitive<String> {
private static final String DECL_XMLNS = " xmlns=\"http://www.w3.org/1999/xhtml\"";
private static final String DIV_OPEN_FIRST = "<div" + DECL_XMLNS + ">";
public static final String DIV_OPEN_FIRST = "<div" + DECL_XMLNS + ">";
private static final long serialVersionUID = 1L;
/**
@ -54,7 +53,7 @@ public class XhtmlDt extends BasePrimitive<List<XMLEvent>> {
/**
* Constructor which accepts a string code
*
*
* @see #setValueAsString(String) for a description of how this value is applied
*/
@SimpleSetter()
@ -63,29 +62,12 @@ public class XhtmlDt extends BasePrimitive<List<XMLEvent>> {
}
@Override
protected String encode(List<XMLEvent> theValue) {
try {
StringWriter w = new StringWriter();
XMLEventWriter ew = XmlUtil.createXmlFragmentWriter(w);
for (XMLEvent next : getValue()) {
if (next.isCharacters()) {
ew.add(next);
} else {
ew.add(next);
}
}
ew.close();
return w.toString();
} catch (XMLStreamException e) {
throw new DataFormatException("Problem with the contained XML events", e);
} catch (FactoryConfigurationError e) {
throw new ConfigurationException(e);
}
protected String encode(String theValue) {
return theValue;
}
public boolean hasContent() {
return getValue() != null && getValue().size() > 0;
return isNotBlank(getValue());
}
@Override
@ -94,40 +76,37 @@ public class XhtmlDt extends BasePrimitive<List<XMLEvent>> {
}
@Override
protected List<XMLEvent> parse(String theValue) {
String val = theValue.trim();
if (!val.startsWith("<")) {
val = DIV_OPEN_FIRST + val + "</div>";
}
boolean hasProcessingInstruction = val.startsWith("<?");
if (hasProcessingInstruction && val.endsWith("?>")) {
return null;
protected String parse(String theValue) {
if (XmlUtil.isStaxPresent()) {
// for validation
XmlUtil.parse(theValue);
}
return theValue;
}
try {
ArrayList<XMLEvent> value = new ArrayList<XMLEvent>();
StringReader reader = new StringReader(val);
XMLEventReader er = XmlUtil.createXmlReader(reader);
boolean first = true;
while (er.hasNext()) {
XMLEvent next = er.nextEvent();
if (first) {
first = false;
continue;
}
if (er.hasNext()) {
// don't add the last event
value.add(next);
}
}
return value;
} catch (XMLStreamException e) {
throw new DataFormatException("String does not appear to be valid XML/XHTML (error is \"" + e.getMessage() + "\"): " + theValue, e);
} catch (FactoryConfigurationError e) {
throw new ConfigurationException(e);
}
/**
* Note that as of HAPI FHIR 3.1.0, this method no longer uses
* the StAX XMLEvent type as the XML representation, and uses a
* String instead. If you need to work with XML as StAX events, you
* can use the {@link XmlUtil#parse(String)} and {@link XmlUtil#encode(List)}
* methods to do so.
*/
@Override
public String getValue() {
return super.getValue();
}
/**
* Note that as of HAPI FHIR 3.1.0, this method no longer uses
* the StAX XMLEvent type as the XML representation, and uses a
* String instead. If you need to work with XML as StAX events, you
* can use the {@link XmlUtil#parse(String)} and {@link XmlUtil#encode(List)}
* methods to do so.
*/
@Override
public BasePrimitive<String> setValue(String theValue) throws DataFormatException {
return super.setValue(theValue);
}
/**
@ -157,7 +136,7 @@ public class XhtmlDt extends BasePrimitive<List<XMLEvent>> {
if (value.charAt(0) != '<') {
value = DIV_OPEN_FIRST + value + "</div>";
}
boolean hasProcessingInstruction = value.startsWith("<?");
int firstTagIndex = value.indexOf("<", hasProcessingInstruction ? 1 : 0);
if (firstTagIndex != -1) {

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
View File

@ -1559,7 +1559,8 @@ class ParserState<T> {
if (theEvent.isEndElement()) {
if (myDepth == 0) {
myDt.setValue(myEvents);
String eventsAsString = XmlUtil.encode(myEvents);
myDt.setValue(eventsAsString);
doPop();
}
}

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
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@ -24,6 +24,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.Reader;
import java.io.StringReader;
import java.io.Writer;
import java.util.*;
@ -605,13 +606,16 @@ public class XmlParser extends BaseParser /* implements IParser */ {
}
}
private void encodeXhtml(XhtmlDt theDt, XMLStreamWriter theEventWriter) throws XMLStreamException {
if (theDt == null || theDt.getValue() == null) {
return;
}
List<XMLEvent> events = XmlUtil.parse(theDt.getValue());
boolean firstElement = true;
for (XMLEvent event : theDt.getValue()) {
for (XMLEvent event : events) {
switch (event.getEventType()) {
case XMLStreamConstants.ATTRIBUTE:
Attribute attr = (Attribute) event;

77
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/XmlUtil.java
View File

@ -20,12 +20,13 @@ package ca.uhn.fhir.util;
* #L%
*/
import java.io.*;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import java.util.*;
import javax.xml.stream.*;
import javax.xml.stream.events.XMLEvent;
import ca.uhn.fhir.model.primitive.XhtmlDt;
import ca.uhn.fhir.parser.DataFormatException;
import org.apache.commons.lang3.StringEscapeUtils;
import org.codehaus.stax2.XMLOutputFactory2;
import org.codehaus.stax2.io.EscapingWriterFactory;
@ -37,6 +38,8 @@ import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.util.jar.DependencyLogFactory;
import ca.uhn.fhir.util.jar.IDependencyLog;
import static org.apache.commons.lang3.StringUtils.isBlank;
/**
* Utility methods for working with the StAX API.
*
@ -1507,6 +1510,74 @@ public class XmlUtil {
VALID_ENTITY_NAMES = Collections.unmodifiableMap(validEntityNames);
}
/**
* Parses an XML string into a set of StAX events
*/
public static List<XMLEvent> parse(String theValue) {
if (isBlank(theValue)) {
return Collections.emptyList();
}
String val = theValue.trim();
if (!val.startsWith("<")) {
val = XhtmlDt.DIV_OPEN_FIRST + val + "</div>";
}
boolean hasProcessingInstruction = val.startsWith("<?");
if (hasProcessingInstruction && val.endsWith("?>")) {
return null;
}
try {
ArrayList<XMLEvent> value = new ArrayList<>();
StringReader reader = new StringReader(val);
XMLEventReader er = XmlUtil.createXmlReader(reader);
boolean first = true;
while (er.hasNext()) {
XMLEvent next = er.nextEvent();
if (first) {
first = false;
continue;
}
if (er.hasNext()) {
// don't add the last event
value.add(next);
}
}
return value;
} catch (XMLStreamException e) {
throw new DataFormatException("String does not appear to be valid XML/XHTML (error is \"" + e.getMessage() + "\"): " + theValue, e);
} catch (FactoryConfigurationError e) {
throw new ConfigurationException(e);
}
}
/**
* Encode a set of StAX events into a String
*/
public static String encode(List<XMLEvent> theEvents) {
try {
StringWriter w = new StringWriter();
XMLEventWriter ew = XmlUtil.createXmlFragmentWriter(w);
for (XMLEvent next : theEvents) {
if (next.isCharacters()) {
ew.add(next);
} else {
ew.add(next);
}
}
ew.close();
return w.toString();
} catch (XMLStreamException e) {
throw new DataFormatException("Problem with the contained XML events", e);
} catch (FactoryConfigurationError e) {
throw new ConfigurationException(e);
}
}
private static XMLOutputFactory createOutputFactory() throws FactoryConfigurationError {
try {
// Detect if we're running with the Android lib, and force repackaged Woodstox to be used

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -50,10 +50,7 @@ import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.OperationOutcomeUtil;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.*;
import com.google.common.base.Charsets;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Sets;
@ -2043,7 +2040,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
StringBuilder b = new StringBuilder();
if (theResource instanceof IResource) {
IResource resource = (IResource) theResource;
List<XMLEvent> xmlEvents = resource.getText().getDiv().getValue();
List<XMLEvent> xmlEvents = XmlUtil.parse(resource.getText().getDiv().getValue());
if (xmlEvents != null) {
for (XMLEvent next : xmlEvents) {
if (next.isCharacters()) {
@ -2056,8 +2053,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
IDomainResource resource = (IDomainResource) theResource;
try {
String divAsString = resource.getText().getDivAsString();
XhtmlDt xhtml = new XhtmlDt(divAsString);
List<XMLEvent> xmlEvents = xhtml.getValue();
List<XMLEvent> xmlEvents = XmlUtil.parse(divAsString);
if (xmlEvents != null) {
for (XMLEvent next : xmlEvents) {
if (next.isCharacters()) {

9
src/changes/changes.xml
View File

@ -87,6 +87,15 @@
hapi-fhir-base module, as they were also duplicated in the
hapi-fhir-utilities module.
</action>
<action type="add">
The DSTU2 XhtmlDt type has been modified so that it no longer uses
the StAX XMLEvent type as its internal model, and instead simply uses
a String. New methods called "parse" and "encode" have been added
to HAPI FHIR's XmlUtil class, which can be used to convert
between a String and an XML representatio. This should allow
HAPI FHIR to run in environments where StAX is not available, such
as Android phones.
</action>
</release>
<release version="3.0.0" date="2017-09-27">
<action type="add">