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Include validation of local files #1647

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Include validation of local files #1647

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c42befd
Extend context to look for local files on a resolve()
bvdh Apr 17, 2024
6e50279
Added a dir test
bvdh Apr 30, 2024
1911b8f
Merge remote-tracking branch 'upstream/master' into include-local-files
bvdh May 22, 2024
f105798
resolveReference of different FHIRversions than 4.0
bvdh Jun 3, 2024
8f3928d
Merge remote-tracking branch 'upstream/master' into include-local-files
bvdh Jun 3, 2024
c4cc740
Fixed error from merge in checkReference
bvdh Jun 3, 2024
1c1edc8
Runnning test case
bvdh Jun 3, 2024
c714ff9
Fixed a error in the test and implementation
bvdh Jun 3, 2024
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2 changes: 1 addition & 1 deletion org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ObjectConverter.java
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Expand Up @@ -73,7 +73,7 @@ public Element convert(Resource ig) throws IOException, FHIRException {
ByteArrayInputStream bi = new ByteArrayInputStream(bs.toByteArray());
List<ValidatedFragment> list = new JsonParser(context).parse(bi);
if (list.size() != 1) {
throw new FHIRException("Unable to convert because the source contains multieple resources");
throw new FHIRException("Unable to convert because the source contains multiple resources");
}
return list.get(0).getElement();
}
Expand Down
10 changes: 7 additions & 3 deletions org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/IgLoader.java
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Expand Up @@ -800,10 +800,13 @@ else if (fn.endsWith(".txt") || fn.endsWith(".map") || fn.endsWith(".fml"))
r = VersionConvertorFactory_30_50.convertResource(res);
} else if (fhirVersion.startsWith("4.0")) {
org.hl7.fhir.r4.model.Resource res;
String str = new String( content );
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
res = new org.hl7.fhir.r4.formats.XmlParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.r4.formats.JsonParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json")) {
// res = new org.hl7.fhir.r4.formats.JsonParser().parse(new ByteArrayInputStream(content));
res = new org.hl7.fhir.r4.formats.JsonParser().parse(str);
}
else if (fn.endsWith(".txt") || fn.endsWith(".map") || fn.endsWith(".fml"))
res = new org.hl7.fhir.r4.utils.StructureMapUtilities(org.hl7.fhir.r4.context.SimpleWorkerContext.fromNothing()).parse(new String(content), fn);
else
Expand Down Expand Up @@ -861,8 +864,9 @@ private void log(String s) {
}

@Override
public void load(Content cnt) throws FHIRException, IOException {
public Resource load(Content cnt) throws FHIRException, IOException {
Resource res = loadResourceByVersion(version, cnt.getFocus().getBytes(), cnt.getExampleFileName());
context.cacheResource(res);
return res;
}
}
37 changes: 21 additions & 16 deletions org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
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Expand Up @@ -19,7 +19,6 @@
import java.util.Locale;
import java.util.Map;
import java.util.Set;
import java.util.UUID;

import org.fhir.ucum.UcumEssenceService;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_50;
Expand Down Expand Up @@ -71,12 +70,9 @@
import org.hl7.fhir.r5.utils.validation.IResourceValidator;
import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor;
import org.hl7.fhir.r5.utils.validation.IValidatorResourceFetcher;
import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.AdditionalBindingPurpose;
import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.CodedContentValidationAction;
import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
import org.hl7.fhir.r5.utils.validation.constants.BindingKind;
import org.hl7.fhir.r5.utils.validation.constants.CheckDisplayOption;
import org.hl7.fhir.r5.utils.validation.constants.CodedContentValidationPolicy;
import org.hl7.fhir.r5.utils.validation.constants.ContainedReferenceValidationPolicy;
import org.hl7.fhir.r5.utils.validation.constants.IdStatus;
import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
Expand Down Expand Up @@ -107,6 +103,7 @@
import org.hl7.fhir.validation.cli.utils.ValidationLevel;
import org.hl7.fhir.validation.instance.BasePolicyAdvisorForFullValidation;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.validation.instance.R5EvaluationContext;
import org.hl7.fhir.validation.instance.utils.ValidationContext;
import org.hl7.fhir.utilities.ByteProvider;
import org.xml.sax.SAXException;
Expand Down Expand Up @@ -192,7 +189,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP

public interface IValidationEngineLoader {

void load(Content cnt) throws FHIRException, IOException;
Resource load(Content cnt) throws FHIRException, IOException;

}

Expand Down Expand Up @@ -558,7 +555,7 @@ public void loadProfile(String src) throws FHIRException, IOException {
// testing entry point
public OperationOutcome validate(FhirFormat format, InputStream stream, List<String> profiles) throws FHIRException, IOException, EOperationOutcome {
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
InstanceValidator validator = getValidator(format);
InstanceValidator validator = getValidator(format );
validator.validate(null, messages, stream, format, asSdList(profiles));
return ValidatorUtils.messagesToOutcome(messages, context, fhirPathEngine);
}
Expand Down Expand Up @@ -600,7 +597,7 @@ public Resource validate(List<String> sources, List<String> profiles, List<Sourc
} else if (!first && delay != 0) {
Thread.sleep(delay);
}

// round one: try to read them all natively
// Ignore if it fails.The purpose of this is to make dependencies
// available for other resources to depend on. if it fails to load, there'll be an error if there's
Expand All @@ -610,7 +607,9 @@ public Resource validate(List<String> sources, List<String> profiles, List<Sourc
ref.setCnt(igLoader.loadContent(ref.getRef(), "validate", false, first));
if (loader != null && ref.getCnt() != null) {
try {
loader.load(ref.getCnt());
Resource res = loader.load(ref.getCnt());
ref.setResourceType( res.getResourceType() );
ref.setId( res.getIdElement().getIdPart() );
} catch (Throwable t) {
if (debug) {
System.out.println("Error during round 1 scanning: "+t.getMessage());
Expand All @@ -619,15 +618,17 @@ public Resource validate(List<String> sources, List<String> profiles, List<Sourc
}
}
}


R5EvaluationContext r5EvaluationContext = new R5EvaluationContext(context, refs);

for (SourceFile ref : refs) {
if ((ref.isProcess() || all) && ref.getCnt() != null) {
TimeTracker.Session tts = context.clock().start("validation");
context.clock().milestone();
System.out.println(" Validate " + ref.getRef());

try {
OperationOutcome outcome = validate(ref.getRef(), ref.getCnt().getFocus(), ref.getCnt().getCntType(), profiles, record);
OperationOutcome outcome = validate( ref.getRef(), ref.getCnt().getFocus(), ref.getCnt().getCntType(), profiles, record, r5EvaluationContext );
ToolingExtensions.addStringExtension(outcome, ToolingExtensions.EXT_OO_FILE, ref.getRef());
System.out.println(" " + context.clock().milestone());
results.addEntry().setResource(outcome);
Expand All @@ -648,25 +649,25 @@ public Resource validate(List<String> sources, List<String> profiles, List<Sourc


public ValidatedFragments validateAsFragments(byte[] source, FhirFormat cntType, List<String> profiles, List<ValidationMessage> messages) throws FHIRException, IOException, EOperationOutcome {
InstanceValidator validator = getValidator(cntType);
InstanceValidator validator = getValidator(cntType );
validator.validate(null, messages, new ByteArrayInputStream(source), cntType, asSdList(profiles));
return new ValidatedFragments(validator.validatedContent,
ValidationTime.fromTimeTracker(validator.timeTracker));
}

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 );

validator.validate(null, messages, new ByteArrayInputStream(source), cntType, asSdList(profiles));
return ValidatorUtils.messagesToOutcome(messages, context, fhirPathEngine);
}

public OperationOutcome validate(String location, ByteProvider source, FhirFormat cntType, List<String> profiles, List<ValidationRecord> record) throws FHIRException, IOException, EOperationOutcome, SAXException {
public OperationOutcome validate(String location, ByteProvider source, FhirFormat cntType, List<String> profiles, List<ValidationRecord> record, R5EvaluationContext r5EvaluationContext) throws FHIRException, IOException, EOperationOutcome, SAXException {
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
if (doNative) {
SchemaValidator.validateSchema(location, cntType, messages);
}
InstanceValidator validator = getValidator(cntType);
InstanceValidator validator = getValidator( cntType, r5EvaluationContext );
validator.validate(null, messages, new ByteArrayInputStream(source.getBytes()), cntType, asSdList(profiles));
if (showTimes) {
System.out.println(location + ": " + validator.reportTimes());
Expand Down Expand Up @@ -812,7 +813,7 @@ public void convert(String source, String output) throws FHIRException, IOExcept

public String evaluateFhirPath(String source, String expression) throws FHIRException, IOException {
Content cnt = igLoader.loadContent(source, "validate", false, true);
FHIRPathEngine fpe = this.getValidator(null).getFHIRPathEngine();
FHIRPathEngine fpe = this.getValidator(null ).getFHIRPathEngine();
Element e = Manager.parseSingle(context, new ByteArrayInputStream(cnt.getFocus().getBytes()), cnt.getCntType());
ExpressionNode exp = fpe.parse(expression);
return fpe.evaluateToString(new ValidationContext(context, e), e, e, e, exp);
Expand Down Expand Up @@ -849,7 +850,11 @@ public void dropResource(String type, String id) {
}

public InstanceValidator getValidator(FhirFormat format) throws FHIRException, IOException {
InstanceValidator validator = new InstanceValidator(context, null, null);
return getValidator( format, new R5EvaluationContext() );
}

public InstanceValidator getValidator(FhirFormat format, R5EvaluationContext evaluationContext) throws FHIRException, IOException {
InstanceValidator validator = new InstanceValidator(context, evaluationContext, null);
context.getTxClientManager().setUsage("validation");
validator.setHintAboutNonMustSupport(hintAboutNonMustSupport);
validator.setAnyExtensionsAllowed(anyExtensionsAllowed);
Expand Down
14 changes: 13 additions & 1 deletion org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidatorUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.fhirpath.FHIRPathEngine;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.ResourceType;
import org.hl7.fhir.r5.renderers.RendererFactory;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
Expand All @@ -49,7 +50,9 @@ public static class SourceFile {
private long date;
private boolean process;
private Content cnt;

private ResourceType resourceType;
private String id;

public boolean isProcess() {
return process;
}
Expand All @@ -72,6 +75,15 @@ public void setCnt(Content cnt) {
public boolean isKnownToBeMissing () {
return date == 0; // File::lastModified() returns 0 if the file is missing
}

public void setResourceType(ResourceType resourceType ){
this.resourceType = resourceType;
}
public ResourceType getResourceType(){return this.resourceType;}
public void setId( String id ){
this.id = id;
}
public String getId(){return this.id;}
}

protected static void grabNatives(Map<String, ByteProvider> source, Map<String, ByteProvider> binaries, String prefix) {
Expand Down
2 changes: 1 addition & 1 deletion org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/tasks/ScanTask.java
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Expand Up @@ -39,7 +39,7 @@ public void printHelp(PrintStream out) {

@Override
public void executeTask(ValidationService validationService, ValidationEngine validationEngine, CliContext cliContext, String[] args, TimeTracker tt, TimeTracker.Session tts) throws Exception {
Scanner validationScanner = new Scanner(validationEngine.getContext(), validationEngine.getValidator(null), validationEngine.getIgLoader(), validationEngine.getFhirPathEngine());
Scanner validationScanner = new Scanner(validationEngine.getContext(), validationEngine.getValidator(null ), validationEngine.getIgLoader(), validationEngine.getFhirPathEngine());
validationScanner.validateScan(cliContext.getOutput(), cliContext.getSources());
}

Expand Down
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