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Resources containing entities which are not valid in basic XML (e.g. 

§) will have those
				entities converted to their equivalent
unicode characters when resources are encoded, since FHIR does
				not allow extended entities in resource
instances.
This commit is contained in:
James Agnew 2014-09-22 16:44:59 -04:00
parent c214f7fe19
commit 5c0ccaab9a
6 changed files with 55 additions and 41 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
hapi-fhir-base/src/changes/changes.xml
View File

@ -37,10 +37,6 @@
HAPI now runs successfully on Servlet 2.5 containers (such as Tomcat 6). Thanks to
Bernard Gitaadji for reporting and diagnosing the issue!
</action>
<action type="fix">
XHTML (in narratives) containing escapable characters (e.g. &lt; or &quot;) will now always have those characters
escaped properly in encoded messages.
</action>
<action type="fix">
Summary (in the bundle entry) is now encoded by the XML and JSON parsers if supplied. Thanks to David Hay of
Orion Health for reporting this!
@ -50,6 +46,15 @@
which meant that the profile did not correctly validate. Thanks to Bill de Beaubien of Systems Made Simple
for reporting this!
</action>
<action type="fix">
XHTML (in narratives) containing escapable characters (e.g. &lt; or &quot;) will now always have those characters
escaped properly in encoded messages.
</action>
<action type="fix">
Resources containing entities which are not valid in basic XML (e.g. &amp;sect;) will have those
entities converted to their equivalent unicode characters when resources are encoded, since FHIR does
not allow extended entities in resource instances.
</action>
</release>
<release version="0.6" date="2014-Sep-08" description="This release brings a number of new features and bug fixes!">
<!--

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/XhtmlDt.java
View File

@ -73,6 +73,10 @@ public class XhtmlDt extends BasePrimitive<List<XMLEvent>> {
* <b>Formatting note:</b> The text will be trimmed {@link String#trim()}. If the text does not start with an HTML tag (generally this would be a div tag), a div tag will be automatically placed
* surrounding the text.
* </p>
* <p>
* Also note that if the parsed text contains any entities (&foo;) which are not a part of the entities defined in core XML (e.g. &sect; which
* is valid in XHTML 1.0 but not in XML 1.0) they will be parsed and converted to their equivalent unicode character.
* </p>
*/
@Override
public void setValueAsString(String theValue) throws DataFormatException {

12
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/XmlUtil.java
View File

@ -167,18 +167,18 @@ public class XmlUtil {
public Object resolveEntity(String thePublicID, String theSystemID, String theBaseURI, String theNamespace) throws XMLStreamException {
if (thePublicID == null && theSystemID == null) {
if (theNamespace != null && VALID_ENTITY_NAMES.containsKey(theNamespace)) {
return IOUtils.toInputStream(Character.toString((char)VALID_ENTITY_NAMES.get(theNamespace).intValue()));
return new String(Character.toChars(VALID_ENTITY_NAMES.get(theNamespace)));
}
}
return null;
}
};
inputFactory.setProperty(WstxInputFactory.IS_REPLACING_ENTITY_REFERENCES, false);
// inputFactory.setProperty(WstxInputFactory.IS_SUPPORTING_EXTERNAL_ENTITIES, false);
// inputFactory.setProperty(WstxInputFactory.IS_VALIDATING, false);
// inputFactory.setProperty(WstxInputProperties.P_TREAT_CHAR_REFS_AS_ENTS, true);
// inputFactory.setProperty(WstxInputProperties.P_UNDECLARED_ENTITY_RESOLVER, xmlResolver);
// In the following two lines, you can uncomment the first and comment the second to disable
// automatic parsing of extended entities, e.g. &sect;
// inputFactory.setProperty(WstxInputFactory.IS_REPLACING_ENTITY_REFERENCES, false);
inputFactory.setProperty(WstxInputProperties.P_UNDECLARED_ENTITY_RESOLVER, xmlResolver);
XMLEventReader er = inputFactory.createXMLEventReader(reader);
return er;

3
hapi-fhir-base/src/test/java/ca/uhn/fhir/model/primitive/XhtmlDtTest.java
View File

@ -59,7 +59,8 @@ public class XhtmlDtTest {
x.setValueAsString(input);
// <div>Sect: § uuml: ü Ü</div>
assertEquals("<div>Sect: &sect; uuml: &uuml; &Uuml;</div>", x.getValueAsString());
// <div>Sect: &sect; uuml: &uuml; &Uuml;</div>
assertEquals("<div>Sect: § uuml: ü Ü</div>", x.getValueAsString());
}

2
hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java
View File

@ -464,7 +464,7 @@ public class JsonParserTest {
JSON expected = JSONSerializer.toJSON(msg.trim());
JSON actual = JSONSerializer.toJSON(encoded.trim());
String exp = expected.toString().replace("\\r\\n", "\\n");
String exp = expected.toString().replace("\\r\\n", "\\n").replace("&sect;", "§");
String act = actual.toString().replace("\\r\\n","\\n");
ourLog.info("Expected: {}", exp);

62
hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/XmlParserTest.java
View File

@ -70,14 +70,14 @@ public class XmlParserTest {
@Test
public void testEncodeProfile() {
Profile p = new Profile();
p.getStructureFirstRep().getElementFirstRep().getDefinition().getBinding().setReference(new ResourceReferenceDt("ValudSet/123"));
String encoded = ourCtx.newXmlParser().encodeResourceToString(p);
ourLog.info(encoded);
}
@Test
public void testEncodeBinaryResource() {
@ -137,7 +137,7 @@ public class XmlParserTest {
List<String> strings = new ArrayList<String>();
strings.addAll(Arrays.asList("<published>", pub.getValueAsString(), "</published>"));
strings.add("<category term=\"http://hl7.org/fhir/tag/message\" label=\"Message\" scheme=\"http://hl7.org/fhir/tag\"/>");
strings.addAll(Arrays.asList("<entry>", "<id>1</id>", "</Patient>","<summary type=\"xhtml\">", "<div", "</entry>"));
strings.addAll(Arrays.asList("<entry>", "<id>1</id>", "</Patient>", "<summary type=\"xhtml\">", "<div", "</entry>"));
strings.addAll(Arrays.asList("<entry>", "<id>2</id>", "<link rel=\"alternate\" href=\"http://foo/bar\"/>", "<link rel=\"search\" href=\"http://foo/bar/search\"/>", "</entry>"));
strings.addAll(Arrays.asList("<at:deleted-entry", "ref=\"Patient/3", "/>"));
assertThat(bundleString, StringContainsInOrder.stringContainsInOrder(strings));
@ -183,26 +183,27 @@ public class XmlParserTest {
@Test
public void testEncodeEscapedChars() {
Patient p = new Patient();
p.addName().addFamily("and <>&ü");
String enc = ourCtx.newXmlParser().encodeResourceToString(p);
ourLog.info(enc);
p = ourCtx.newXmlParser().parseResource(Patient.class, enc);
assertEquals("and <>&ü", p.getNameFirstRep().getFamilyFirstRep().getValue());
p = ourCtx.newXmlParser().parseResource(Patient.class, "<Patient xmlns=\"http://hl7.org/fhir\"><name><family value=\"quot &quot;\"/></name></Patient>");
assertEquals("quot \"", p.getNameFirstRep().getFamilyFirstRep().getValue());
// Unescaped entities are swallowed
p = ourCtx.newXmlParser().parseResource(Patient.class, "<Patient xmlns=\"http://hl7.org/fhir\"><name><family value=\"uuml &uuml;\"/></name></Patient>");
assertEquals("uuml ", p.getNameFirstRep().getFamilyFirstRep().getValue());
}
@Test
public void testEncodeEscapedExtendedChars() {
Patient p = ourCtx.newXmlParser().parseResource(Patient.class, "<Patient xmlns=\"http://hl7.org/fhir\"><name><family value=\"uuml &uuml;\"/></name></Patient>");
assertEquals("uuml ü", p.getNameFirstRep().getFamilyFirstRep().getValue());
}
@Test
public void testEncodeContainedAndIncludedResources() {
@ -322,11 +323,11 @@ public class XmlParserTest {
p.addIdentifier("foo", "bar");
p.getText().setStatus(NarrativeStatusEnum.GENERATED);
p.getText().setDiv("<div>hello</div>");
Bundle b = new Bundle();
b.getTotalResults().setValue(123);
b.addEntry().setResource(p);
String out = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
ourLog.info(out);
assertThat(out, containsString("<div xmlns=\"http://www.w3.org/1999/xhtml\">hello</div>"));
@ -335,10 +336,9 @@ public class XmlParserTest {
out = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
ourLog.info(out);
assertThat(out, containsString("<xhtml:div xmlns:xhtml=\"http://www.w3.org/1999/xhtml\">hello</xhtml:div>"));
}
@Test
public void testEncodePrettyPrint() throws DataFormatException {
@ -762,7 +762,9 @@ public class XmlParserTest {
String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
assertThat(enc, containsString("<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension></extension>"));
assertThat(
enc,
containsString("<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension></extension>"));
assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
}
@ -802,12 +804,12 @@ public class XmlParserTest {
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resB);
ourLog.info(encoded);
assertThat(encoded, stringContainsInOrder(Arrays.asList("<contained>", "<Observation", "</Observation>", "</contained>")));
assertThat(encoded, not(stringContainsInOrder(Arrays.asList("<contained>", "<Observation", "</Observation>", "<Obser", "</contained>"))));
}
@Test
public void testNestedContainedResources() {
@ -943,7 +945,7 @@ public class XmlParserTest {
ValueSet resource = (ValueSet) entry.getResource();
assertEquals("LOINC Codes for Cholesterol", resource.getName().getValue());
String exp = summaryText.trim();
exp = exp.replace("\"LOINC", "&quot;LOINC");
exp = exp.replace("terol\"", "terol&quot;");
@ -957,7 +959,8 @@ public class XmlParserTest {
assertEquals("256a5231-a2bb-49bd-9fea-f349d428b70d", resource.getId().getIdPart());
msg = msg.replace("<link href=\"http://hl7.org/implement/standards/fhir/valueset/256a5231-a2bb-49bd-9fea-f349d428b70d\" rel=\"self\"/>", "<link href=\"http://hl7.org/implement/standards/fhir/valueset/256a5231-a2bb-49bd-9fea-f349d428b70d/_history/12345\" rel=\"self\"/>");
msg = msg.replace("<link href=\"http://hl7.org/implement/standards/fhir/valueset/256a5231-a2bb-49bd-9fea-f349d428b70d\" rel=\"self\"/>",
"<link href=\"http://hl7.org/implement/standards/fhir/valueset/256a5231-a2bb-49bd-9fea-f349d428b70d/_history/12345\" rel=\"self\"/>");
entry = p.parseBundle(msg).getEntries().get(0);
resource = (ValueSet) entry.getResource();
assertEquals("256a5231-a2bb-49bd-9fea-f349d428b70d", resource.getId().getIdPart());
@ -965,7 +968,7 @@ public class XmlParserTest {
assertEquals("12345", ((IdDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.VERSION_ID)).getVersionIdPart());
assertThat(entry.getSummary().getValueAsString(), containsString("LOINC Codes for Cholesterol"));
}
@SuppressWarnings("deprecation")
@ -1092,9 +1095,10 @@ public class XmlParserTest {
@Test
public void testParseQuery() {
String msg = "<Query xmlns=\"http://hl7.org/fhir\">\n" + " <text>\n" + " <status value=\"generated\"/>\n" + " <div xmlns=\"http://www.w3.org/1999/xhtml\">[Put rendering here]</div>\n" + " </text>\n" + "\n"
+ " <!-- this is an extermely simple query - a request to execute the query 'example' on the\n" + " responder -->\n" + " <identifier value=\"urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376\"/>\n" + " <parameter url=\"http://hl7.org/fhir/query#_query\">\n"
+ " <valueString value=\"example\"/>\n" + " </parameter>\n" + "</Query>";
String msg = "<Query xmlns=\"http://hl7.org/fhir\">\n" + " <text>\n" + " <status value=\"generated\"/>\n" + " <div xmlns=\"http://www.w3.org/1999/xhtml\">[Put rendering here]</div>\n"
+ " </text>\n" + "\n" + " <!-- this is an extermely simple query - a request to execute the query 'example' on the\n" + " responder -->\n"
+ " <identifier value=\"urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376\"/>\n" + " <parameter url=\"http://hl7.org/fhir/query#_query\">\n" + " <valueString value=\"example\"/>\n"
+ " </parameter>\n" + "</Query>";
Query query = ourCtx.newXmlParser().parseResource(Query.class, msg);
assertEquals("urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376", query.getIdentifier().getValueAsString());