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Hack fix for wrong R3 invariant, Improved Terminology Performance Tracking

This commit is contained in:
Grahame Grieve 2021-09-01 09:59:23 +10:00
parent 66fb0893ad
commit 7d7280078f
1 changed files with 31 additions and 15 deletions
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46
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -128,6 +128,7 @@ import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.renderers.DataRenderer;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.utils.FHIRLexer.FHIRLexerException;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
@ -192,16 +193,17 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private static final String EXECUTED_CONSTRAINT_LIST = "validator.executed.invariant.list";
private static final String EXECUTION_ID = "validator.execution.id";
private static final String HTML_FRAGMENT_REGEX = "[a-zA-Z]\\w*(((\\s+)(\\S)*)*)";
private static final boolean STACK_TRACE = false;
private class ValidatorHostServices implements IEvaluationContext {
@Override
public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
public List<Base> resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
ValidatorHostContext c = (ValidatorHostContext) appContext;
if (externalHostServices != null)
return externalHostServices.resolveConstant(c.getAppContext(), name, beforeContext);
else
return null;
return new ArrayList<Base>();
}
@Override
@ -819,11 +821,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private boolean checkCode(List<ValidationMessage> errors, Element element, String path, String code, String system, String display, boolean checkDisplay, NodeStack stack) throws TerminologyServiceException {
long t = System.nanoTime();
boolean ss = context.supportsSystem(system);
timeTracker.tx(t);
timeTracker.tx(t, "ss "+system);
if (ss) {
t = System.nanoTime();
ValidationResult s = checkCodeOnServer(stack, code, system, display, checkDisplay);
timeTracker.tx(t);
timeTracker.tx(t, "vc "+system+"#"+code+" '"+display+"'");
if (s == null)
return true;
if (s.isOk()) {
@ -1113,10 +1115,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
checkBindings(errors, path, element, stack, valueset, nextCoding);
}
}
timeTracker.tx(t);
timeTracker.tx(t, "vc "+DataRenderer.display(context, cc));
}
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODEABLECONCEPT, e.getMessage());
}
}
@ -1238,10 +1241,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
}
timeTracker.tx(t);
timeTracker.tx(t, DataRenderer.display(context, cc));
}
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODEABLECONCEPT, e.getMessage());
}
// special case: if the logical model has both CodeableConcept and Coding mappings, we'll also check the first coding.
@ -1286,7 +1290,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
removeTrackedMessagesForLocation(errors, element, path);
}
timeTracker.tx(t);
timeTracker.tx(t, "vc "+system+"#"+code+" '"+display+"'");
if (vr != null && !vr.isOk()) {
if (vr.IsNoService())
txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_BINDING_NOSERVER);
@ -1317,6 +1321,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODING1, e.getMessage());
}
}
@ -1328,6 +1333,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODING2, e.getMessage(), e.toString());
}
}
@ -1410,7 +1416,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
long t = System.nanoTime();
ValidationResult vr = checkCodeOnServer(stack, valueset, cc, false);
timeTracker.tx(t);
timeTracker.tx(t, "vc "+cc.toString());
if (!vr.isOk()) {
if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure())
txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_7, describeReference(maxVSUrl), valueset.getUrl(), vr.getMessage());
@ -1418,6 +1424,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_8, describeReference(maxVSUrl), valueset.getUrl(), ccSummary(cc));
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODEABLECONCEPT_MAX, e.getMessage());
}
}
@ -1429,7 +1436,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
long t = System.nanoTime();
ValidationResult vr = checkCodeOnServer(stack, valueset, c, true);
timeTracker.tx(t);
timeTracker.tx(t, "vc "+c.getSystem()+"#"+c.getCode()+" '"+c.getDisplay()+"'");
if (!vr.isOk()) {
if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure())
txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_9, describeReference(maxVSUrl), valueset.getUrl(), vr.getMessage());
@ -1437,6 +1444,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_10, describeReference(maxVSUrl), valueset.getUrl(), c.getSystem(), c.getCode());
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODEABLECONCEPT_MAX, e.getMessage());
}
}
@ -1448,7 +1456,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
long t = System.nanoTime();
ValidationResult vr = checkCodeOnServer(stack, valueset, value, new ValidationOptions(stack.getWorkingLang()));
timeTracker.tx(t);
timeTracker.tx(t, "vc "+value);
if (!vr.isOk()) {
if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure())
txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_9, describeReference(maxVSUrl), valueset.getUrl(), vr.getMessage());
@ -1456,6 +1464,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_11, describeReference(maxVSUrl), valueset.getUrl(), "), and a code from this value set is required) (code = " + value + "), (error = " + vr.getMessage() + ")");
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODEABLECONCEPT_MAX, e.getMessage());
}
}
@ -1505,7 +1514,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (binding.getStrength() != BindingStrength.EXAMPLE) {
vr = checkCodeOnServer(stack, valueset, c, true);
}
timeTracker.tx(t);
timeTracker.tx(t, "vc "+c.getSystem()+"#"+c.getCode()+" '"+c.getDisplay()+"'");
if (binding.getStrength() == BindingStrength.REQUIRED) {
removeTrackedMessagesForLocation(errors, element, path);
}
@ -1541,6 +1550,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODING1, e.getMessage());
}
}
@ -1552,6 +1562,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODING2, e.getMessage(), e.toString());
}
}
@ -2458,7 +2469,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
ValidationOptions options = new ValidationOptions(stack.getWorkingLang()).guessSystem();
vr = checkCodeOnServer(stack, vs, value, options);
}
timeTracker.tx(t);
timeTracker.tx(t, "vc "+value+"");
if (binding.getStrength() == BindingStrength.REQUIRED) {
removeTrackedMessagesForLocation(errors, element, path);
}
@ -2562,6 +2573,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else {
fetchError = context.formatMessage(I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_UNKNOWN_URL_SCHEME, url); }
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
fetchError = context.formatMessage(I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_URL_ERROR, url, e.getMessage());
}
}
@ -2632,6 +2644,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
ext = fetcher.fetch(this, hostContext.getAppContext(), ref);
} catch (IOException e) {
if (STACK_TRACE) e.printStackTrace();
throw new FHIRException(e);
}
if (ext != null) {
@ -3058,6 +3071,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
expr = fpe.parse(fp);
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
throw new FHIRException(context.formatMessage(I18nConstants.DISCRIMINATOR_BAD_PATH, e.getMessage(), fp), e);
}
long t2 = System.nanoTime();
@ -3160,7 +3174,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
return context.fetchCodeSystem(system);
} finally {
timeTracker.tx(t);
timeTracker.tx(t, "cs "+system);
}
}
@ -3637,6 +3651,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
n = fpe.parse(fixExpr(expression.toString(), null));
} catch (FHIRLexerException e) {
if (STACK_TRACE) e.printStackTrace();
throw new FHIRException(context.formatMessage(I18nConstants.PROBLEM_PROCESSING_EXPRESSION__IN_PROFILE__PATH__, expression, profile.getUrl(), path, e.getMessage()));
}
timeTracker.fpe(t);
@ -3667,7 +3682,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
timeTracker.fpe(t);
msg = fpe.forLog();
} catch (Exception ex) {
ex.printStackTrace();
if (STACK_TRACE) ex.printStackTrace();
throw new FHIRException(context.formatMessage(I18nConstants.PROBLEM_EVALUATING_SLICING_EXPRESSION_FOR_ELEMENT_IN_PROFILE__PATH__FHIRPATH___, profile.getUrl(), path, n, ex.getMessage()));
}
return ok;
@ -3997,6 +4012,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
sd = (StructureDefinition) fetcher.fetchCanonicalResource(this, profile.primitiveValue());
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, profile.primitiveValue(), e.getMessage());
}
if (sd != null) {
@ -5344,7 +5360,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return "(reference = '#') or reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))";
}
if ("reference.startsWith('#').not() or (reference.substring(1).trace('url') in %resource.contained.id.trace('ids'))".equals(expr)) {
return "(reference = '#') or reference.startsWith('#').not() or (reference.substring(1).trace('url') in %resource.contained.id.trace('ids'))";
return "(reference = '#') or reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))";
}
if ("".equals(expr))
return "";