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

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
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@ -123,7 +123,7 @@ public class JsonParser extends ParserBase {
public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException { public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
// long start = System.currentTimeMillis(); // long start = System.currentTimeMillis();
byte[] content = TextFile.streamToBytes(inStream); 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); ByteArrayInputStream stream = new ByteArrayInputStream(content);
@ -135,17 +135,17 @@ public class JsonParser extends ParserBase {
try { try {
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true); obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true);
} catch (Exception e) { } 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 { } else {
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true); obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true);
} }
if (obj != null) { if (obj != null) {
ctxt.setElement(parse(ctxt.getErrors(), obj)); focusFragment.setElement(parse(focusFragment.getErrors(), obj));
} }
List<ValidatedFragment> res = new ArrayList<>(); List<ValidatedFragment> res = new ArrayList<>();
res.add(ctxt); res.add(focusFragment);
// long t =System.currentTimeMillis()-start; // long t =System.currentTimeMillis()-start;
// System.out.println("json parser: "+(t)+"ms, "+(content.length/1024)+"kb "+(t == 0 ? "" : " @ "+(content.length / t)+"kb/s")); // 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
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@ -83,7 +83,7 @@ public class SHCParser extends ParserBase {
byte[] content = TextFile.streamToBytes(inStream); byte[] content = TextFile.streamToBytes(inStream);
ByteArrayInputStream stream = new ByteArrayInputStream(content); ByteArrayInputStream stream = new ByteArrayInputStream(content);
List<ValidatedFragment> res = new ArrayList<>(); List<ValidatedFragment> res = new ArrayList<>();
ValidatedFragment shc = new ValidatedFragment("shc", "txt", content); ValidatedFragment shc = new ValidatedFragment("shc", "txt", content, false);
res.add(shc); res.add(shc);
String src = TextFile.streamToString(stream).trim(); String src = TextFile.streamToString(stream).trim();
@ -121,7 +121,7 @@ public class SHCParser extends ParserBase {
return res; return res;
} }
ValidatedFragment bnd = new ValidatedFragment("payload", "json", jwt.payloadSrc); ValidatedFragment bnd = new ValidatedFragment("payload", "json", jwt.payloadSrc, true);
res.add(bnd); res.add(bnd);
checkNamedProperties(shc.getErrors(), jwt.getPayload(), prefix+"payload", "iss", "nbf", "vc"); checkNamedProperties(shc.getErrors(), jwt.getPayload(), prefix+"payload", "iss", "nbf", "vc");
checkProperty(shc.getErrors(), jwt.getPayload(), prefix+"payload", "iss", true, "String"); 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
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@ -280,7 +280,7 @@ public class SHLParser extends ParserBase {
} }
private ValidatedFragment addNamedElement(List<ValidatedFragment> res, String name, String type, byte[] content) { 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); res.add(result);
return result; return result;
} }

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/TurtleParser.java
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@ -83,7 +83,7 @@ public class TurtleParser extends ParserBase {
@Override @Override
public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException { public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
byte[] content = TextFile.streamToBytes(inStream); 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); ByteArrayInputStream stream = new ByteArrayInputStream(content);
Turtle src = new Turtle(); Turtle src = new Turtle();
@ -91,16 +91,16 @@ public class TurtleParser extends ParserBase {
try { try {
src.parse(TextFile.streamToString(stream)); src.parse(TextFile.streamToString(stream));
} catch (Exception e) { } 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; return null;
} }
ctxt.setElement(parse(ctxt.getErrors(), src)); focusFragment.setElement(parse(focusFragment.getErrors(), src));
} else { } else {
src.parse(TextFile.streamToString(stream)); src.parse(TextFile.streamToString(stream));
ctxt.setElement(parse(ctxt.getErrors(), src)); focusFragment.setElement(parse(focusFragment.getErrors(), src));
} }
List<ValidatedFragment> res = new ArrayList<>(); List<ValidatedFragment> res = new ArrayList<>();
res.add(ctxt); res.add(focusFragment);
return res; return res;
} }

54
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ValidatedFragment.java
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@ -3,63 +3,55 @@ package org.hl7.fhir.r5.elementmodel;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import lombok.Getter;
import lombok.Setter;
import org.hl7.fhir.utilities.validation.ValidationMessage; import org.hl7.fhir.utilities.validation.ValidationMessage;
public class ValidatedFragment { public class ValidatedFragment {
@Getter
private String name; private String name;
@Getter @Setter
private String elementPath; private String elementPath;
@Getter
private String extension; private String extension;
@Getter @Setter
private Element element; private Element element;
@Getter @Setter
private byte[] content; private byte[] content;
@Getter
private final boolean isDerivedContent;
public final static String FOCUS_NAME = "focus";
@Getter
private List<ValidationMessage> errors = new ArrayList<>(); 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(); super();
this.name = name; this.name = name;
this.element = element; this.element = element;
this.content = content; this.content = content;
this.extension = extension; 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(); super();
this.name = name; this.name = name;
this.content = content; this.content = content;
this.extension = extension; 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() { public String getFilename() {
return name+"."+extension; return name+"."+extension;
} }
public String getElementPath() {
return elementPath;
}
public void setElementPath(String elementPath) {
this.elementPath = elementPath;
}
public String path() { public String path() {
return elementPath == null ? name : elementPath; return elementPath == null ? name : elementPath;
} }

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/VerticalBarParser.java
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@ -465,7 +465,7 @@ public class VerticalBarParser extends ParserBase {
while (!reader.isFinished()) // && (getOptions().getSegmentLimit() == 0 || getOptions().getSegmentLimit() > message.getSegments().size())) while (!reader.isFinished()) // && (getOptions().getSegmentLimit() == 0 || getOptions().getSegmentLimit() > message.getSegments().size()))
readSegment(message, reader); readSegment(message, reader);
List<ValidatedFragment> res = new ArrayList<>(); 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; return res;
} }

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
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@ -117,7 +117,7 @@ public class XmlParser extends ParserBase {
public List<ValidatedFragment> parse(InputStream inStream) throws FHIRFormatError, DefinitionException, FHIRException, IOException { public List<ValidatedFragment> parse(InputStream inStream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
byte[] content = TextFile.streamToBytes(inStream); 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); ByteArrayInputStream stream = new ByteArrayInputStream(content);
Document doc = null; Document doc = null;
@ -137,7 +137,7 @@ public class XmlParser extends ParserBase {
// if we can, we'll inspect the header/encoding ourselves // if we can, we'll inspect the header/encoding ourselves
stream.mark(1024); stream.mark(1024);
version = checkHeader(context.getErrors(), stream); version = checkHeader(focusFragment.getErrors(), stream);
stream.reset(); stream.reset();
// use a slower parser that keeps location data // 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:")) { if (e.getMessage().contains("lineNumber:") && e.getMessage().contains("columnNumber:")) {
int line = Utilities.parseInt(extractVal(e.getMessage(), "lineNumber"), 0); int line = Utilities.parseInt(extractVal(e.getMessage(), "lineNumber"), 0);
int col = Utilities.parseInt(extractVal(e.getMessage(), "columnNumber"), 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 { } 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; doc = null;
} }
if (doc != null) { if (doc != null) {
context.setElement(parse(context.getErrors(), doc)); focusFragment.setElement(parse(focusFragment.getErrors(), doc));
} }
List<ValidatedFragment> res = new ArrayList<>(); List<ValidatedFragment> res = new ArrayList<>();
res.add(context); res.add(focusFragment);
return res; return res;
} }

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

44
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
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@ -29,6 +29,7 @@ import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.LanguageUtils; import org.hl7.fhir.r5.elementmodel.LanguageUtils;
import org.hl7.fhir.r5.elementmodel.Manager; import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat; 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;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Bundle; 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.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage; import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage; import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.IgLoader; import org.hl7.fhir.validation.*;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.ValidationRecord;
import org.hl7.fhir.validation.ValidatorUtils;
import org.hl7.fhir.validation.ValidatorUtils.SourceFile; import org.hl7.fhir.validation.ValidatorUtils.SourceFile;
import org.hl7.fhir.validation.cli.model.CliContext; import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.model.FileInfo; import org.hl7.fhir.validation.cli.model.FileInfo;
@ -114,13 +112,43 @@ public class ValidationService {
ValidationResponse response = new ValidationResponse().setSessionId(sessionId); 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<>(); 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); request.getCliContext().getProfiles(), messages);
ValidationOutcome outcome = new ValidationOutcome().setFileInfo(fp);
messages.forEach(outcome::addMessage); 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); 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()); System.out.println(" Max Memory: "+Runtime.getRuntime().maxMemory());
return response; return response;