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* fix bug not recognising some content as xml or json

This commit is contained in:
Grahame Grieve 2020-10-29 13:59:45 +11:00
parent 944be1cfba
commit 14cc22f9a2
2 changed files with 77 additions and 3 deletions
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78
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
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@ -29,6 +29,10 @@ import java.util.UUID;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.convertors.VersionConvertorAdvisor50;
import org.hl7.fhir.convertors.VersionConvertor_10_30;
@ -56,6 +60,7 @@ import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.elementmodel.ParserBase.ValidationPolicy;
import org.hl7.fhir.r5.elementmodel.ObjectConverter;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
@ -98,9 +103,11 @@ import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.turtle.Turtle;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
@ -111,6 +118,7 @@ import org.hl7.fhir.validation.cli.model.ScanOutputItem;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageInstaller;
import org.hl7.fhir.validation.cli.utils.*;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;
@ -538,7 +546,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
throw new FHIRException("Unable to fetch content from "+src+" ("+errors.toString()+")");
}
FhirFormat fmt = checkIsResource(cnt, src);
FhirFormat fmt = checkFormat(cnt, src);
if (fmt != null) {
Map<String, byte[]> res = new HashMap<String, byte[]>();
res.put(Utilities.changeFileExt(src, "."+fmt.getExtension()), cnt);
@ -809,33 +817,99 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
this.noInvariantChecks = value;
}
private FhirFormat checkFormat(byte[] cnt, String filename) {
System.out.println(" ..Detect format for "+filename);
try {
JsonTrackingParser.parseJson(cnt);
return FhirFormat.JSON;
} catch (Exception e) {
if (debug) {
System.out.println("Not JSON: "+e.getMessage());
}
}
try {
parseXml(cnt);
return FhirFormat.XML;
} catch (Exception e) {
if (debug) {
System.out.println("Not XML: "+e.getMessage());
}
}
try {
new Turtle().parse(TextFile.bytesToString(cnt));
return FhirFormat.TURTLE;
} catch (Exception e) {
if (debug) {
System.out.println("Not Turtle: "+e.getMessage());
}
}
try {
new StructureMapUtilities(context, null, null).parse(TextFile.bytesToString(cnt), null);
return FhirFormat.TEXT;
} catch (Exception e) {
if (debug) {
System.out.println("Not Text: "+e.getMessage());
}
}
if (debug)
System.out.println(" .. not a resource: "+filename);
return null;
}
private FhirFormat checkIsResource(byte[] cnt, String filename) {
System.out.println(" ..Detect format for "+filename);
try {
Manager.parse(context, new ByteArrayInputStream(cnt), FhirFormat.JSON);
return FhirFormat.JSON;
} catch (Exception e) {
if (debug) {
System.out.println("Not JSON: "+e.getMessage());
}
}
try {
Manager.parse(context, new ByteArrayInputStream(cnt),FhirFormat.XML);
parseXml(cnt);
return FhirFormat.XML;
} catch (Exception e) {
if (debug) {
System.out.println("Not XML: "+e.getMessage());
}
}
try {
Manager.parse(context, new ByteArrayInputStream(cnt),FhirFormat.TURTLE);
return FhirFormat.TURTLE;
} catch (Exception e) {
if (debug) {
System.out.println("Not Turtle: "+e.getMessage());
}
}
try {
new StructureMapUtilities(context, null, null).parse(TextFile.bytesToString(cnt), null);
return FhirFormat.TEXT;
} catch (Exception e) {
if (debug) {
System.out.println("Not Text: "+e.getMessage());
}
}
if (debug)
System.out.println(" .. not a resource: "+filename);
return null;
}
private Document parseXml(byte[] cnt) throws ParserConfigurationException, SAXException, IOException {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
// xxe protection
factory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
factory.setFeature("http://xml.org/sax/features/external-general-entities", false);
factory.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
factory.setXIncludeAware(false);
factory.setExpandEntityReferences(false);
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
return builder.parse(new ByteArrayInputStream(cnt));
}
private FhirFormat checkIsResource(String path) throws IOException {
String ext = Utilities.getFileExtension(path);
if (Utilities.existsInList(ext, "xml"))

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationEngineTests.java
View File

@ -90,7 +90,7 @@ public class ValidationEngineTests {
}
if (!org.hl7.fhir.validation.tests.utilities.TestUtilities.silent)
System.out.println("Test102: Validate patient-example.xml in v1.0.2 version");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, "41.0.2");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, "1.0.2");
ve.setNoInvariantChecks(true);
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "patient102.xml"), null);
if (!TestUtilities.silent)