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Merge pull request #1443 from hapifhir/do-20230921-shc-validation-service 

SHC Validation
This commit is contained in:
Grahame Grieve 2023-10-04 06:01:07 +03:00 committed by GitHub
parent d6eb345692 2a6538cd02
commit 7698ee4b7f
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
10 changed files with 147 additions and 124 deletions
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6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/FmlParser.java
View File

@ -50,9 +50,9 @@ public class FmlParser extends ParserBase {
ByteArrayInputStream stream = new ByteArrayInputStream(content);
String text = TextFile.streamToString(stream);
List<ValidatedFragment> result = new ArrayList<>();
ValidatedFragment ctxt = new ValidatedFragment("focus", "fml", content);
ctxt.setElement(parse(ctxt.getErrors(), text));
result.add(ctxt);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "fml", content, false);
focusFragment.setElement(parse(focusFragment.getErrors(), text));
result.add(focusFragment);
return result;
}

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
View File

@ -123,7 +123,7 @@ public class JsonParser extends ParserBase {
public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
// long start = System.currentTimeMillis();
byte[] content = TextFile.streamToBytes(inStream);
ValidatedFragment ctxt = new ValidatedFragment("focus", "json", content);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "json", content, false);
ByteArrayInputStream stream = new ByteArrayInputStream(content);
@ -135,17 +135,17 @@ public class JsonParser extends ParserBase {
try {
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true);
} catch (Exception e) {
logError(ctxt.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1,context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1,context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
}
} else {
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true);
}
if (obj != null) {
ctxt.setElement(parse(ctxt.getErrors(), obj));
focusFragment.setElement(parse(focusFragment.getErrors(), obj));
}
List<ValidatedFragment> res = new ArrayList<>();
res.add(ctxt);
res.add(focusFragment);
// long t =System.currentTimeMillis()-start;
// System.out.println("json parser: "+(t)+"ms, "+(content.length/1024)+"kb "+(t == 0 ? "" : " @ "+(content.length / t)+"kb/s"));

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/SHCParser.java
View File

@ -83,7 +83,7 @@ public class SHCParser extends ParserBase {
byte[] content = TextFile.streamToBytes(inStream);
ByteArrayInputStream stream = new ByteArrayInputStream(content);
List<ValidatedFragment> res = new ArrayList<>();
ValidatedFragment shc = new ValidatedFragment("shc", "txt", content);
ValidatedFragment shc = new ValidatedFragment("shc", "txt", content, false);
res.add(shc);
String src = TextFile.streamToString(stream).trim();
@ -121,7 +121,7 @@ public class SHCParser extends ParserBase {
return res;
}
ValidatedFragment bnd = new ValidatedFragment("payload", "json", jwt.payloadSrc);
ValidatedFragment bnd = new ValidatedFragment("payload", "json", jwt.payloadSrc, true);
res.add(bnd);
checkNamedProperties(shc.getErrors(), jwt.getPayload(), prefix+"payload", "iss", "nbf", "vc");
checkProperty(shc.getErrors(), jwt.getPayload(), prefix+"payload", "iss", true, "String");

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/SHLParser.java
View File

@ -280,7 +280,7 @@ public class SHLParser extends ParserBase {
}
private ValidatedFragment addNamedElement(List<ValidatedFragment> res, String name, String type, byte[] content) {
ValidatedFragment result = new ValidatedFragment(name, type, content);
ValidatedFragment result = new ValidatedFragment(name, type, content, true);
res.add(result);
return result;
}

66
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/TurtleParser.java
View File

@ -2,34 +2,34 @@ package org.hl7.fhir.r5.elementmodel;
import java.io.ByteArrayInputStream;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
@ -83,7 +83,7 @@ public class TurtleParser extends ParserBase {
@Override
public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
byte[] content = TextFile.streamToBytes(inStream);
ValidatedFragment ctxt = new ValidatedFragment("focus", "ttl", content);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "ttl", content, false);
ByteArrayInputStream stream = new ByteArrayInputStream(content);
Turtle src = new Turtle();
@ -91,16 +91,16 @@ public class TurtleParser extends ParserBase {
try {
src.parse(TextFile.streamToString(stream));
} catch (Exception e) {
logError(ctxt.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1, "(document)", IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_TURTLE_, e.getMessage()), IssueSeverity.FATAL);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1, "(document)", IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_TURTLE_, e.getMessage()), IssueSeverity.FATAL);
return null;
}
ctxt.setElement(parse(ctxt.getErrors(), src));
focusFragment.setElement(parse(focusFragment.getErrors(), src));
} else {
src.parse(TextFile.streamToString(stream));
ctxt.setElement(parse(ctxt.getErrors(), src));
focusFragment.setElement(parse(focusFragment.getErrors(), src));
}
List<ValidatedFragment> res = new ArrayList<>();
res.add(ctxt);
res.add(focusFragment);
return res;
}

56
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ValidatedFragment.java
View File

@ -3,63 +3,55 @@ package org.hl7.fhir.r5.elementmodel;
import java.util.ArrayList;
import java.util.List;
import lombok.Getter;
import lombok.Setter;
import org.hl7.fhir.utilities.validation.ValidationMessage;
public class ValidatedFragment {
@Getter
private String name;
@Getter @Setter
private String elementPath;
@Getter
private String extension;
@Getter @Setter
private Element element;
@Getter @Setter
private byte[] content;
@Getter
private final boolean isDerivedContent;
public final static String FOCUS_NAME = "focus";
@Getter
private List<ValidationMessage> errors = new ArrayList<>();
public ValidatedFragment(String name, String extension, Element element, byte[] content) {
public ValidatedFragment(String name, String extension, Element element, byte[] content, boolean isDerivedContent) {
super();
this.name = name;
this.element = element;
this.content = content;
this.extension = extension;
this.isDerivedContent = isDerivedContent;
}
public ValidatedFragment(String name, String extension, byte[] content) {
public ValidatedFragment(String name, String extension, byte[] content, boolean isDerivedContent) {
super();
this.name = name;
this.content = content;
this.extension = extension;
this.isDerivedContent = isDerivedContent;
}
public String getName() {
return name;
}
public Element getElement() {
return element;
}
public byte[] getContent() {
return content;
}
public List<ValidationMessage> getErrors() {
return errors;
}
public void setElement(Element element) {
this.element = element;
}
public String getFilename() {
return name+"."+extension;
}
public String getElementPath() {
return elementPath;
}
public void setElementPath(String elementPath) {
this.elementPath = elementPath;
}
public String path() {
return elementPath == null ? name : elementPath;
}

58
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/VerticalBarParser.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r5.elementmodel;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
@ -465,7 +465,7 @@ public class VerticalBarParser extends ParserBase {
while (!reader.isFinished()) // && (getOptions().getSegmentLimit() == 0 || getOptions().getSegmentLimit() > message.getSegments().size()))
readSegment(message, reader);
List<ValidatedFragment> res = new ArrayList<>();
res.add(new ValidatedFragment("focus", "hl7", message, content));
res.add(new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "hl7", message, content, false));
return res;
}

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
View File

@ -117,7 +117,7 @@ public class XmlParser extends ParserBase {
public List<ValidatedFragment> parse(InputStream inStream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
byte[] content = TextFile.streamToBytes(inStream);
ValidatedFragment context = new ValidatedFragment("focus", "xml", content);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "xml", content, false);
ByteArrayInputStream stream = new ByteArrayInputStream(content);
Document doc = null;
@ -137,7 +137,7 @@ public class XmlParser extends ParserBase {
// if we can, we'll inspect the header/encoding ourselves
stream.mark(1024);
version = checkHeader(context.getErrors(), stream);
version = checkHeader(focusFragment.getErrors(), stream);
stream.reset();
// use a slower parser that keeps location data
@ -171,17 +171,17 @@ public class XmlParser extends ParserBase {
if (e.getMessage().contains("lineNumber:") && e.getMessage().contains("columnNumber:")) {
int line = Utilities.parseInt(extractVal(e.getMessage(), "lineNumber"), 0);
int col = Utilities.parseInt(extractVal(e.getMessage(), "columnNumber"), 0);
logError(context.getErrors(), ValidationMessage.NO_RULE_DATE, line, col, "(xml)", IssueType.INVALID, e.getMessage().substring(e.getMessage().lastIndexOf(";")+1).trim(), IssueSeverity.FATAL);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, line, col, "(xml)", IssueType.INVALID, e.getMessage().substring(e.getMessage().lastIndexOf(";")+1).trim(), IssueSeverity.FATAL);
} else {
logError(context.getErrors(), ValidationMessage.NO_RULE_DATE, 0, 0, "(xml)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, 0, 0, "(xml)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
}
doc = null;
}
if (doc != null) {
context.setElement(parse(context.getErrors(), doc));
focusFragment.setElement(parse(focusFragment.getErrors(), doc));
}
List<ValidatedFragment> res = new ArrayList<>();
res.add(context);
res.add(focusFragment);
return res;
}

13
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -32,12 +32,8 @@ import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContextManager;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.context.SystemOutLoggingService;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.*;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.elementmodel.ObjectConverter;
import org.hl7.fhir.r5.elementmodel.ParserBase;
import org.hl7.fhir.r5.elementmodel.SHCParser;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
@ -635,6 +631,13 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
return results.getEntryFirstRep().getResource();
}
public List<ValidatedFragment> validateAsFragments(byte[] source, FhirFormat cntType, List<String> profiles, List<ValidationMessage> messages) throws FHIRException, IOException, EOperationOutcome {
InstanceValidator validator = getValidator(cntType);
validator.validate(null, messages, new ByteArrayInputStream(source), cntType, asSdList(profiles));
return validator.validatedContent;
}
public OperationOutcome validate(byte[] source, FhirFormat cntType, List<String> profiles, List<ValidationMessage> messages) throws FHIRException, IOException, EOperationOutcome {
InstanceValidator validator = getValidator(cntType);

46
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
View File

@ -29,6 +29,7 @@ import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.LanguageUtils;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.elementmodel.ValidatedFragment;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Bundle;
@ -61,10 +62,7 @@ import org.hl7.fhir.utilities.i18n.XLIFFProducer;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.IgLoader;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.ValidationRecord;
import org.hl7.fhir.validation.ValidatorUtils;
import org.hl7.fhir.validation.*;
import org.hl7.fhir.validation.ValidatorUtils.SourceFile;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.model.FileInfo;
@ -114,13 +112,43 @@ public class ValidationService {
ValidationResponse response = new ValidationResponse().setSessionId(sessionId);
for (FileInfo fp : request.getFilesToValidate()) {
for (FileInfo fileToValidate : request.getFilesToValidate()) {
if (fileToValidate.getFileType() == null) {
Manager.FhirFormat format = ResourceChecker.checkIsResource(validator.getContext(),
false,
fileToValidate.getFileContent().getBytes(),
fileToValidate.getFileName(),
false);
fileToValidate.setFileType(format.getExtension());
}
List<ValidationMessage> messages = new ArrayList<>();
validator.validate(fp.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fp.getFileType()),
List<ValidatedFragment> validatedFragments = validator.validateAsFragments(fileToValidate.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fileToValidate.getFileType()),
request.getCliContext().getProfiles(), messages);
ValidationOutcome outcome = new ValidationOutcome().setFileInfo(fp);
messages.forEach(outcome::addMessage);
response.addOutcome(outcome);
if (validatedFragments.size() == 1 && !validatedFragments.get(0).isDerivedContent()) {
ValidatedFragment validatedFragment = validatedFragments.get(0);
ValidationOutcome outcome = new ValidationOutcome();
FileInfo fileInfo = new FileInfo(
fileToValidate.getFileName(),
new String(validatedFragment.getContent()),
validatedFragment.getExtension());
outcome.setMessages(validatedFragment.getErrors());
outcome.setFileInfo(fileInfo);
response.addOutcome(outcome);
} else {
for (ValidatedFragment validatedFragment : validatedFragments) {
ValidationOutcome outcome = new ValidationOutcome();
FileInfo fileInfo = new FileInfo(
validatedFragment.getFilename(),
new String(validatedFragment.getContent()),
validatedFragment.getExtension());
outcome.setMessages(validatedFragment.getErrors());
outcome.setFileInfo(fileInfo);
response.addOutcome(outcome);
}
}
}
System.out.println(" Max Memory: "+Runtime.getRuntime().maxMemory());
return response;