package org.hl7.fhir.dstu2016may.validation;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.dstu2016may.formats.FormatUtilities;
import org.hl7.fhir.dstu2016may.metamodel.Element;
import org.hl7.fhir.dstu2016may.metamodel.Element.SpecialElement;
import org.hl7.fhir.dstu2016may.metamodel.JsonParser;
import org.hl7.fhir.dstu2016may.metamodel.Manager;
import org.hl7.fhir.dstu2016may.metamodel.Manager.FhirFormat;
import org.hl7.fhir.dstu2016may.metamodel.ParserBase;
import org.hl7.fhir.dstu2016may.metamodel.ParserBase.ValidationPolicy;
import org.hl7.fhir.dstu2016may.metamodel.XmlParser;
import org.hl7.fhir.dstu2016may.model.Address;
import org.hl7.fhir.dstu2016may.model.Attachment;
import org.hl7.fhir.dstu2016may.model.Bundle;
import org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu2016may.model.CodeSystem;
import org.hl7.fhir.dstu2016may.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu2016may.model.CodeableConcept;
import org.hl7.fhir.dstu2016may.model.Coding;
import org.hl7.fhir.dstu2016may.model.ContactPoint;
import org.hl7.fhir.dstu2016may.model.DateType;
import org.hl7.fhir.dstu2016may.model.DomainResource;
import org.hl7.fhir.dstu2016may.model.ElementDefinition;
import org.hl7.fhir.dstu2016may.model.ElementDefinition.ConstraintSeverity;
import org.hl7.fhir.dstu2016may.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.dstu2016may.model.ElementDefinition.ElementDefinitionConstraintComponent;
import org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.dstu2016may.model.Enumerations.BindingStrength;
import org.hl7.fhir.dstu2016may.model.ExpressionNode;
import org.hl7.fhir.dstu2016may.model.Extension;
import org.hl7.fhir.dstu2016may.model.HumanName;
import org.hl7.fhir.dstu2016may.model.Identifier;
import org.hl7.fhir.dstu2016may.model.IntegerType;
import org.hl7.fhir.dstu2016may.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.dstu2016may.model.OperationOutcome.IssueType;
import org.hl7.fhir.dstu2016may.model.Period;
import org.hl7.fhir.dstu2016may.model.Quantity;
import org.hl7.fhir.dstu2016may.model.Questionnaire;
import org.hl7.fhir.dstu2016may.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.dstu2016may.model.Questionnaire.QuestionnaireItemOptionComponent;
import org.hl7.fhir.dstu2016may.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.dstu2016may.model.Range;
import org.hl7.fhir.dstu2016may.model.Ratio;
import org.hl7.fhir.dstu2016may.model.Reference;
import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.dstu2016may.model.SampledData;
import org.hl7.fhir.dstu2016may.model.StringType;
import org.hl7.fhir.dstu2016may.model.StructureDefinition;
import org.hl7.fhir.dstu2016may.model.StructureDefinition.ExtensionContext;
import org.hl7.fhir.dstu2016may.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.dstu2016may.model.StructureDefinition.StructureDefinitionSnapshotComponent;
import org.hl7.fhir.dstu2016may.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.dstu2016may.model.TimeType;
import org.hl7.fhir.dstu2016may.model.Timing;
import org.hl7.fhir.dstu2016may.model.Type;
import org.hl7.fhir.dstu2016may.model.UriType;
import org.hl7.fhir.dstu2016may.model.ValueSet;
import org.hl7.fhir.dstu2016may.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.dstu2016may.utils.FHIRPathEngine;
import org.hl7.fhir.dstu2016may.utils.IWorkerContext;
import org.hl7.fhir.dstu2016may.utils.IWorkerContext.ValidationResult;
import org.hl7.fhir.dstu2016may.utils.ProfileUtilities;
import org.hl7.fhir.dstu2016may.validation.ValidationMessage.Source;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.NodeType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import com.google.gson.JsonObject;
import ca.uhn.fhir.util.ObjectUtil;
/*
* todo:
* check urn's don't start oid: or uuid:
*/
public class InstanceValidator extends BaseValidator implements IResourceValidator {
private boolean anyExtensionsAllowed;
private BestPracticeWarningLevel bpWarnings;
// configuration items
private CheckDisplayOption checkDisplay;
private IWorkerContext context;
private FHIRPathEngine fpe;
private List<String> extensionDomains = new ArrayList<String>();
private IdStatus resourceIdRule;
// used during the build process to keep the overall volume of messages down
private boolean suppressLoincSnomedMessages;
private Bundle logical;
// time tracking
private long overall = 0;
private long txTime = 0;
private long sdTime = 0;
private long loadTime = 0;
private long fpeTime = 0;
public InstanceValidator(IWorkerContext theContext) {
super();
this.context = theContext;
fpe = new FHIRPathEngine(context);
source = Source.InstanceValidator;
}
private boolean allowUnknownExtension(String url) {
if (url.contains("example.org") || url.contains("acme.com") || url.contains("nema.org"))
return true;
for (String s : extensionDomains)
if (url.startsWith(s))
return true;
return anyExtensionsAllowed;
}
private void bpCheck(List<ValidationMessage> errors, IssueType invalid, int line, int col, String literalPath, boolean test, String message) {
if (bpWarnings != null) {
switch (bpWarnings) {
case Error:
rule(errors, invalid, line, col, literalPath, test, message);
break;
case Warning:
warning(errors, invalid, line, col, literalPath, test, message);
break;
case Hint:
hint(errors, invalid, line, col, literalPath, test, message);
break;
default: // do nothing
}
}
}
@Override
public void validate(List<ValidationMessage> errors, InputStream stream, FhirFormat format) throws Exception {
validate(errors, stream, format, (StructureDefinition) null);
}
@Override
public void validate(List<ValidationMessage> errors, InputStream stream, FhirFormat format, String profile) throws Exception {
long t = System.nanoTime();
StructureDefinition p = context.fetchResource(StructureDefinition.class, profile);
sdTime = sdTime + (System.nanoTime() - t);
if (p == null)
throw new DefinitionException("StructureDefinition '" + profile + "' not found");
validate(errors, stream, format, p);
}
@Override
public void validate(List<ValidationMessage> errors, InputStream stream, FhirFormat format, StructureDefinition profile) throws Exception {
ParserBase parser = Manager.makeParser(context, format);
parser.setupValidation(ValidationPolicy.EVERYTHING, errors);
long t = System.nanoTime();
Element e = parser.parse(stream);
loadTime = System.nanoTime() - t;
if (e != null)
validate(errors, e, profile);
}
@Override
public void validate(List<ValidationMessage> errors, Resource resource) throws Exception {
validate(errors, resource, (StructureDefinition) null);
}
@Override
public void validate(List<ValidationMessage> errors, Resource resource, String profile) throws Exception {
long t = System.nanoTime();
StructureDefinition p = context.fetchResource(StructureDefinition.class, profile);
sdTime = sdTime + (System.nanoTime() - t);
if (p == null)
throw new DefinitionException("StructureDefinition '" + profile + "' not found");
validate(errors, resource, p);
}
@Override
public void validate(List<ValidationMessage> errors, Resource resource, StructureDefinition profile) throws Exception {
throw new Exception("Not done yet");
// ParserBase parser = new ObjectParser(context);
// parser.setupValidation(ValidationPolicy.EVERYTHING, errors);
// long t = System.nanoTime();
// Element e = parser.parse(resource);
// loadTime = System.nanoTime() - t;
// validate(errors, e, profile);
}
@Override
public void validate(List<ValidationMessage> errors, Element element) throws Exception {
validate(errors, element, (StructureDefinition) null);
}
@Override
public void validate(List<ValidationMessage> errors, org.w3c.dom.Element element) throws Exception {
validate(errors, element, (StructureDefinition) null);
}
@Override
public void validate(List<ValidationMessage> errors, Element element, String profile) throws Exception {
long t = System.nanoTime();
StructureDefinition p = context.fetchResource(StructureDefinition.class, profile);
sdTime = sdTime + (System.nanoTime() - t);
if (p == null)
throw new DefinitionException("StructureDefinition '" + profile + "' not found");
validate(errors, element, p);
}
@Override
public void validate(List<ValidationMessage> errors, org.w3c.dom.Element element, String profile) throws Exception {
long t = System.nanoTime();
StructureDefinition p = context.fetchResource(StructureDefinition.class, profile);
sdTime = sdTime + (System.nanoTime() - t);
if (p == null)
throw new DefinitionException("StructureDefinition '" + profile + "' not found");
validate(errors, element, p);
}
@Override
public void validate(List<ValidationMessage> errors, org.w3c.dom.Element element, StructureDefinition profile) throws Exception {
XmlParser parser = new XmlParser(context);
parser.setupValidation(ValidationPolicy.EVERYTHING, errors);
long t = System.nanoTime();
Element e = parser.parse(element);
loadTime = System.nanoTime() - t;
validate(errors, e, profile);
}
@Override
public void validate(List<ValidationMessage> errors, Document document) throws Exception {
validate(errors, document, (StructureDefinition) null);
}
@Override
public void validate(List<ValidationMessage> errors, Document document, String profile) throws Exception {
long t = System.nanoTime();
StructureDefinition p = context.fetchResource(StructureDefinition.class, profile);
sdTime = sdTime + (System.nanoTime() - t);
if (p == null)
throw new DefinitionException("StructureDefinition '" + profile + "' not found");
validate(errors, document, p);
}
@Override
public void validate(List<ValidationMessage> errors, Document document, StructureDefinition profile) throws Exception {
XmlParser parser = new XmlParser(context);
parser.setupValidation(ValidationPolicy.EVERYTHING, errors);
long t = System.nanoTime();
Element e = parser.parse(document);
loadTime = System.nanoTime() - t;
validate(errors, e, profile);
}
@Override
public void validate(List<ValidationMessage> errors, JsonObject object) throws Exception {
// validate(errors, object, (StructureDefinition) null);
}
@Override
public void validate(List<ValidationMessage> errors, JsonObject object, String profile) throws Exception {
long t = System.nanoTime();
StructureDefinition p = context.fetchResource(StructureDefinition.class, profile);
sdTime = sdTime + (System.nanoTime() - t);
if (p == null)
throw new DefinitionException("StructureDefinition '" + profile + "' not found");
validate(errors, object, p);
}
@Override
public void validate(List<ValidationMessage> errors, JsonObject object, StructureDefinition profile) throws Exception {
JsonParser parser = new JsonParser(context);
parser.setupValidation(ValidationPolicy.EVERYTHING, errors);
long t = System.nanoTime();
Element e = parser.parse(object);
loadTime = System.nanoTime() - t;
validate(errors, e, profile);
}
@Override
public void validate(List<ValidationMessage> errors, Element element, StructureDefinition profile) throws Exception {
// this is the main entry point; all the other entry points end up here coming here...
long t = System.nanoTime();
validateResource(errors, element, element, profile, resourceIdRule, new NodeStack(element));
overall = System.nanoTime() - t;
}
private boolean check(String v1, String v2) {
return v1 == null ? Utilities.noString(v1) : v1.equals(v2);
}
private void checkAddress(List<ValidationMessage> errors, String path, Element focus, Address fixed) {
checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), "use");
checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), "text");
checkFixedValue(errors, path + ".city", focus.getNamedChild("city"), fixed.getCityElement(), "city");
checkFixedValue(errors, path + ".state", focus.getNamedChild("state"), fixed.getStateElement(), "state");
checkFixedValue(errors, path + ".country", focus.getNamedChild("country"), fixed.getCountryElement(), "country");
checkFixedValue(errors, path + ".zip", focus.getNamedChild("zip"), fixed.getPostalCodeElement(), "postalCode");
List<Element> lines = new ArrayList<Element>();
focus.getNamedChildren("line", lines);
if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, lines.size() == fixed.getLine().size(),
"Expected " + Integer.toString(fixed.getLine().size()) + " but found " + Integer.toString(lines.size()) + " line elements")) {
for (int i = 0; i < lines.size(); i++)
checkFixedValue(errors, path + ".coding", lines.get(i), fixed.getLine().get(i), "coding");
}
}
private void checkAttachment(List<ValidationMessage> errors, String path, Element focus, Attachment fixed) {
checkFixedValue(errors, path + ".contentType", focus.getNamedChild("contentType"), fixed.getContentTypeElement(), "contentType");
checkFixedValue(errors, path + ".language", focus.getNamedChild("language"), fixed.getLanguageElement(), "language");
checkFixedValue(errors, path + ".data", focus.getNamedChild("data"), fixed.getDataElement(), "data");
checkFixedValue(errors, path + ".url", focus.getNamedChild("url"), fixed.getUrlElement(), "url");
checkFixedValue(errors, path + ".size", focus.getNamedChild("size"), fixed.getSizeElement(), "size");
checkFixedValue(errors, path + ".hash", focus.getNamedChild("hash"), fixed.getHashElement(), "hash");
checkFixedValue(errors, path + ".title", focus.getNamedChild("title"), fixed.getTitleElement(), "title");
}
// public API
private boolean checkCode(List<ValidationMessage> errors, Element element, String path, String code, String system, String display) {
long t = System.nanoTime();
boolean ss = context.supportsSystem(system);
txTime = txTime + (System.nanoTime() - t);
if (ss) {
t = System.nanoTime();
ValidationResult s = context.validateCode(system, code, display);
txTime = txTime + (System.nanoTime() - t);
if (s == null || s.isOk())
return true;
if (s.getSeverity() == IssueSeverity.INFORMATION)
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage());
else if (s.getSeverity() == IssueSeverity.WARNING)
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage());
else
return rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage());
return true;
} else if (system.startsWith("http://hl7.org/fhir")) {
if (system.equals("http://hl7.org/fhir/sid/icd-10"))
return true; // else don't check ICD-10 (for now)
else {
CodeSystem cs = getCodeSystem(system);
if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, cs != null, "Unknown Code System " + system)) {
ConceptDefinitionComponent def = getCodeDefinition(cs, code);
if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, def != null, "Unknown Code (" + system + "#" + code + ")"))
return warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, display == null || display.equals(def.getDisplay()), "Display should be '" + def.getDisplay() + "'");
}
return false;
}
} else if (system.startsWith("http://loinc.org")) {
return true;
} else if (system.startsWith("http://unitsofmeasure.org")) {
return true;
} else
return true;
}
private void checkCodeableConcept(List<ValidationMessage> errors, String path, Element focus, CodeableConcept fixed) {
checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), "text");
List<Element> codings = new ArrayList<Element>();
focus.getNamedChildren("coding", codings);
if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() == fixed.getCoding().size(),
"Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size()) + " coding elements")) {
for (int i = 0; i < codings.size(); i++)
checkFixedValue(errors, path + ".coding", codings.get(i), fixed.getCoding().get(i), "coding");
}
}
private void checkCodeableConcept(List<ValidationMessage> errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext) {
if (theElementCntext != null && theElementCntext.hasBinding()) {
ElementDefinitionBindingComponent binding = theElementCntext.getBinding();
if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing (cc)")) {
if (binding.hasValueSet() && binding.getValueSet() instanceof Reference) {
ValueSet valueset = resolveBindingReference(profile, binding.getValueSet());
if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found")) {
try {
CodeableConcept cc = readAsCodeableConcept(element);
if (!cc.hasCoding()) {
if (binding.getStrength() == BindingStrength.REQUIRED)
rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code is required from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl());
else if (binding.getStrength() == BindingStrength.EXTENSIBLE)
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code should be provided from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl());
} else {
long t = System.nanoTime();
ValidationResult vr = context.validateCode(cc, valueset);
txTime = txTime + (System.nanoTime() - t);
if (!vr.isOk()) {
if (binding.getStrength() == BindingStrength.REQUIRED)
rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()+", and a code from this value set is required");
else if (binding.getStrength() == BindingStrength.EXTENSIBLE)
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code should come from this value set unless it has no suitable code");
else if (binding.getStrength() == BindingStrength.PREFERRED)
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is recommended to come from this value set");
}
}
} catch (Exception e) {
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating CodeableConcept");
}
}
} else if (binding.hasValueSet()) {
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked");
} else {
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked");
}
}
}
}
private CodeableConcept readAsCodeableConcept(Element element) {
CodeableConcept cc = new CodeableConcept();
List<Element> list = new ArrayList<Element>();
element.getNamedChildren("coding", list);
for (Element item : list)
cc.addCoding(readAsCoding(item));
cc.setText(element.getNamedChildValue("text"));
return cc;
}
private Coding readAsCoding(Element item) {
Coding c = new Coding();
c.setSystem(item.getNamedChildValue("system"));
c.setVersion(item.getNamedChildValue("version"));
c.setCode(item.getNamedChildValue("code"));
c.setDisplay(item.getNamedChildValue("display"));
return c;
}
private void checkCoding(List<ValidationMessage> errors, String path, Element focus, Coding fixed) {
checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), "system");
checkFixedValue(errors, path + ".code", focus.getNamedChild("code"), fixed.getCodeElement(), "code");
checkFixedValue(errors, path + ".display", focus.getNamedChild("display"), fixed.getDisplayElement(), "display");
checkFixedValue(errors, path + ".userSelected", focus.getNamedChild("userSelected"), fixed.getUserSelectedElement(), "userSelected");
}
private void checkCoding(List<ValidationMessage> errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, boolean inCodeableConcept) {
String code = element.getNamedChildValue("code");
String system = element.getNamedChildValue("system");
String display = element.getNamedChildValue("display");
rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, isAbsolute(system), "Coding.system must be an absolute reference, not a local reference");
if (system != null && code != null) {
if (checkCode(errors, element, path, code, system, display))
if (theElementCntext != null && theElementCntext.getBinding() != null) {
ElementDefinitionBindingComponent binding = theElementCntext.getBinding();
if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing")) {
if (binding.hasValueSet() && binding.getValueSet() instanceof Reference) {
ValueSet valueset = resolveBindingReference(profile, binding.getValueSet());
if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found")) {
try {
Coding c = readAsCoding(element);
long t = System.nanoTime();
ValidationResult vr = context.validateCode(c, valueset);
txTime = txTime + (System.nanoTime() - t);
if (!vr.isOk()) {
if (binding.getStrength() == BindingStrength.REQUIRED)
rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided is not in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is required from this value set");
else if (binding.getStrength() == BindingStrength.EXTENSIBLE)
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided is not in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code should come from this value set unless it has no suitable code");
else if (binding.getStrength() == BindingStrength.PREFERRED)
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided is not in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is recommended to come from this value set");
}
} catch (Exception e) {
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating CodeableConcept");
}
}
} else if (binding.hasValueSet()) {
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked");
} else if (!inCodeableConcept) {
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked");
}
}
}
}
}
private void checkContactPoint(List<ValidationMessage> errors, String path, Element focus, ContactPoint fixed) {
checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), "system");
checkFixedValue(errors, path + ".value", focus.getNamedChild("value"), fixed.getValueElement(), "value");
checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), "use");
checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), "period");
}
private void checkDeclaredProfiles(List<ValidationMessage> errors, Element resource, Element element, NodeStack stack) throws FHIRException {
Element meta = element.getNamedChild("meta");
if (meta != null) {
List<Element> profiles = new ArrayList<Element>();
meta.getNamedChildren("profile", profiles);
int i = 0;
for (Element profile : profiles) {
String ref = profile.primitiveValue();
String p = stack.addToLiteralPath("meta", "profile", ":" + Integer.toString(i));
if (rule(errors, IssueType.INVALID, element.line(), element.col(), p, !Utilities.noString(ref), "StructureDefinition reference invalid")) {
long t = System.nanoTime();
StructureDefinition pr = context.fetchResource(StructureDefinition.class, ref);
sdTime = sdTime + (System.nanoTime() - t);
if (warning(errors, IssueType.INVALID, element.line(), element.col(), p, pr != null, "StructureDefinition reference \"{0}\" could not be resolved", ref)) {
if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), p, pr.hasSnapshot(),
"StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided")) {
validateElement(errors, pr, pr.getSnapshot().getElement().get(0), null, null, resource, element, element.getName(), stack, false);
}
}
i++;
}
}
}
}
private StructureDefinition checkExtension(List<ValidationMessage> errors, String path, Element element, ElementDefinition def, StructureDefinition profile, NodeStack stack) {
String url = element.getNamedChildValue("url");
boolean isModifier = element.getName().equals("modifierExtension");
long t = System.nanoTime();
StructureDefinition ex = context.fetchResource(StructureDefinition.class, url);
sdTime = sdTime + (System.nanoTime() - t);
if (ex == null) {
if (!rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowUnknownExtension(url), "The extension " + url + " is unknown, and not allowed here"))
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowUnknownExtension(url), "Unknown extension " + url);
} else {
if (def.getIsModifier())
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", ex.getSnapshot().getElement().get(0).getIsModifier(),
"Extension modifier mismatch: the extension element is labelled as a modifier, but the underlying extension is not");
else
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", !ex.getSnapshot().getElement().get(0).getIsModifier(),
"Extension modifier mismatch: the extension element is not labelled as a modifier, but the underlying extension is");
// two questions
// 1. can this extension be used here?
checkExtensionContext(errors, element, /* path+"[url='"+url+"']", */ ex, stack, ex.getUrl());
if (isModifier)
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", ex.getSnapshot().getElement().get(0).getIsModifier(),
"The Extension '" + url + "' must be used as a modifierExtension");
else
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", !ex.getSnapshot().getElement().get(0).getIsModifier(),
"The Extension '" + url + "' must not be used as an extension (it's a modifierExtension)");
// 2. is the content of the extension valid?
}
return ex;
}
private boolean checkExtensionContext(List<ValidationMessage> errors, Element element, StructureDefinition definition, NodeStack stack, String extensionParent) {
String extUrl = definition.getUrl();
CommaSeparatedStringBuilder p = new CommaSeparatedStringBuilder();
for (String lp : stack.getLogicalPaths())
p.append(lp);
if (definition.getContextType() == ExtensionContext.DATATYPE) {
boolean ok = false;
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (StringType ct : definition.getContext()) {
b.append(ct.getValue());
if (ct.getValue().equals("*") || stack.getLogicalPaths().contains(ct.getValue() + ".extension"))
ok = true;
}
return rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), ok,
"The extension " + extUrl + " is not allowed to be used on the logical path set [" + p.toString() + "] (allowed: datatype=" + b.toString() + ")");
} else if (definition.getContextType() == ExtensionContext.EXTENSION) {
boolean ok = false;
for (StringType ct : definition.getContext())
if (ct.getValue().equals("*") || ct.getValue().equals(extensionParent))
ok = true;
return rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), ok,
"The extension " + extUrl + " is not allowed to be used with the extension '" + extensionParent + "'");
} else if (definition.getContextType() == ExtensionContext.RESOURCE) {
boolean ok = false;
// String simplePath = container.getPath();
// System.out.println(simplePath);
// if (effetive.endsWith(".extension") || simplePath.endsWith(".modifierExtension"))
// simplePath = simplePath.substring(0, simplePath.lastIndexOf('.'));
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (StringType ct : definition.getContext()) {
String c = ct.getValue();
b.append(c);
if (c.equals("*") || stack.getLogicalPaths().contains(c + ".extension") || (c.startsWith("@") && stack.getLogicalPaths().contains(c.substring(1) + ".extension")))
;
ok = true;
}
return rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), ok,
"The extension " + extUrl + " is not allowed to be used on the logical path set " + p.toString() + " (allowed: resource=" + b.toString() + ")");
} else
throw new Error("Unknown context type");
}
//
// private String simplifyPath(String path) {
// String s = path.replace("/f:", ".");
// while (s.contains("["))
// s = s.substring(0, s.indexOf("["))+s.substring(s.indexOf("]")+1);
// String[] parts = s.split("\\.");
// int i = 0;
// while (i < parts.length && !context.getProfiles().containsKey(parts[i].toLowerCase()))
// i++;
// if (i >= parts.length)
// throw new Error("Unable to process part "+path);
// int j = parts.length - 1;
// while (j > 0 && (parts[j].equals("extension") || parts[j].equals("modifierExtension")))
// j--;
// StringBuilder b = new StringBuilder();
// boolean first = true;
// for (int k = i; k <= j; k++) {
// if (k == j || !parts[k].equals(parts[k+1])) {
// if (first)
// first = false;
// else
// b.append(".");
// b.append(parts[k]);
// }
// }
// return b.toString();
// }
//
private void checkFixedValue(List<ValidationMessage> errors, String path, Element focus, org.hl7.fhir.dstu2016may.model.Element fixed, String propName) {
if (fixed == null && focus == null)
; // this is all good
else if (fixed == null && focus != null)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false, "Unexpected element " + focus.getName());
else if (fixed != null && focus == null)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false, "Mising element " + propName);
else {
String value = focus.primitiveValue();
if (fixed instanceof org.hl7.fhir.dstu2016may.model.BooleanType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.BooleanType) fixed).asStringValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.BooleanType) fixed).asStringValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.IntegerType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.IntegerType) fixed).asStringValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.IntegerType) fixed).asStringValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.DecimalType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.DecimalType) fixed).asStringValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.DecimalType) fixed).asStringValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.Base64BinaryType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.Base64BinaryType) fixed).asStringValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.Base64BinaryType) fixed).asStringValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.InstantType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.InstantType) fixed).getValue().toString(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.InstantType) fixed).asStringValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.StringType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.StringType) fixed).getValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.StringType) fixed).getValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.UriType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.UriType) fixed).getValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.UriType) fixed).getValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.DateType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.DateType) fixed).getValue().toString(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.DateType) fixed).getValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.DateTimeType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.DateTimeType) fixed).getValue().toString(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.DateTimeType) fixed).getValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.OidType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.OidType) fixed).getValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.OidType) fixed).getValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.UuidType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.UuidType) fixed).getValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.UuidType) fixed).getValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.CodeType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.CodeType) fixed).getValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.CodeType) fixed).getValue() + "'");
else if (fixed instanceof org.hl7.fhir.dstu2016may.model.IdType)
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.dstu2016may.model.IdType) fixed).getValue(), value),
"Value is '" + value + "' but must be '" + ((org.hl7.fhir.dstu2016may.model.IdType) fixed).getValue() + "'");
else if (fixed instanceof Quantity)
checkQuantity(errors, path, focus, (Quantity) fixed);
else if (fixed instanceof Address)
checkAddress(errors, path, focus, (Address) fixed);
else if (fixed instanceof ContactPoint)
checkContactPoint(errors, path, focus, (ContactPoint) fixed);
else if (fixed instanceof Attachment)
checkAttachment(errors, path, focus, (Attachment) fixed);
else if (fixed instanceof Identifier)
checkIdentifier(errors, path, focus, (Identifier) fixed);
else if (fixed instanceof Coding)
checkCoding(errors, path, focus, (Coding) fixed);
else if (fixed instanceof HumanName)
checkHumanName(errors, path, focus, (HumanName) fixed);
else if (fixed instanceof CodeableConcept)
checkCodeableConcept(errors, path, focus, (CodeableConcept) fixed);
else if (fixed instanceof Timing)
checkTiming(errors, path, focus, (Timing) fixed);
else if (fixed instanceof Period)
checkPeriod(errors, path, focus, (Period) fixed);
else if (fixed instanceof Range)
checkRange(errors, path, focus, (Range) fixed);
else if (fixed instanceof Ratio)
checkRatio(errors, path, focus, (Ratio) fixed);
else if (fixed instanceof SampledData)
checkSampledData(errors, path, focus, (SampledData) fixed);
else
rule(errors, IssueType.EXCEPTION, focus.line(), focus.col(), path, false, "Unhandled fixed value type " + fixed.getClass().getName());
List<Element> extensions = new ArrayList<Element>();
focus.getNamedChildren("extension", extensions);
if (fixed.getExtension().size() == 0) {
rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, extensions.size() == 0, "No extensions allowed");
} else if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, extensions.size() == fixed.getExtension().size(),
"Extensions count mismatch: expected " + Integer.toString(fixed.getExtension().size()) + " but found " + Integer.toString(extensions.size()))) {
for (Extension e : fixed.getExtension()) {
Element ex = getExtensionByUrl(extensions, e.getUrl());
if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, ex != null, "Extension count mismatch: unable to find extension: " + e.getUrl())) {
checkFixedValue(errors, path, ex.getNamedChild("extension").getNamedChild("value"), e.getValue(), "extension.value");
}
}
}
}
}
private void checkHumanName(List<ValidationMessage> errors, String path, Element focus, HumanName fixed) {
checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), "use");
checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), "text");
checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), "period");
List<Element> parts = new ArrayList<Element>();
focus.getNamedChildren("family", parts);
if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getFamily().size(),
"Expected " + Integer.toString(fixed.getFamily().size()) + " but found " + Integer.toString(parts.size()) + " family elements")) {
for (int i = 0; i < parts.size(); i++)
checkFixedValue(errors, path + ".family", parts.get(i), fixed.getFamily().get(i), "family");
}
focus.getNamedChildren("given", parts);
if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getGiven().size(),
"Expected " + Integer.toString(fixed.getGiven().size()) + " but found " + Integer.toString(parts.size()) + " given elements")) {
for (int i = 0; i < parts.size(); i++)
checkFixedValue(errors, path + ".given", parts.get(i), fixed.getGiven().get(i), "given");
}
focus.getNamedChildren("prefix", parts);
if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getPrefix().size(),
"Expected " + Integer.toString(fixed.getPrefix().size()) + " but found " + Integer.toString(parts.size()) + " prefix elements")) {
for (int i = 0; i < parts.size(); i++)
checkFixedValue(errors, path + ".prefix", parts.get(i), fixed.getPrefix().get(i), "prefix");
}
focus.getNamedChildren("suffix", parts);
if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getSuffix().size(),
"Expected " + Integer.toString(fixed.getSuffix().size()) + " but found " + Integer.toString(parts.size()) + " suffix elements")) {
for (int i = 0; i < parts.size(); i++)
checkFixedValue(errors, path + ".suffix", parts.get(i), fixed.getSuffix().get(i), "suffix");
}
}
private void checkIdentifier(List<ValidationMessage> errors, String path, Element element, ElementDefinition context) {
String system = element.getNamedChildValue("system");
rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, isAbsolute(system), "Identifier.system must be an absolute reference, not a local reference");
}
private void checkIdentifier(List<ValidationMessage> errors, String path, Element focus, Identifier fixed) {
checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), "use");
checkFixedValue(errors, path + ".type", focus.getNamedChild("type"), fixed.getType(), "type");
checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), "system");
checkFixedValue(errors, path + ".value", focus.getNamedChild("value"), fixed.getValueElement(), "value");
checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), "period");
checkFixedValue(errors, path + ".assigner", focus.getNamedChild("assigner"), fixed.getAssigner(), "assigner");
}
private void checkPeriod(List<ValidationMessage> errors, String path, Element focus, Period fixed) {
checkFixedValue(errors, path + ".start", focus.getNamedChild("start"), fixed.getStartElement(), "start");
checkFixedValue(errors, path + ".end", focus.getNamedChild("end"), fixed.getEndElement(), "end");
}
private void checkPrimitive(List<ValidationMessage> errors, String path, String type, ElementDefinition context, Element e, StructureDefinition profile) {
if (type.equals("boolean")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, "true".equals(e.primitiveValue()) || "false".equals(e.primitiveValue()), "boolean values must be 'true' or 'false'");
}
if (type.equals("uri")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, !e.primitiveValue().startsWith("oid:"), "URI values cannot start with oid:");
rule(errors, IssueType.INVALID, e.line(), e.col(), path, !e.primitiveValue().startsWith("uuid:"), "URI values cannot start with uuid:");
rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue().equals(e.primitiveValue().trim()), "URI values cannot have leading or trailing whitespace");
}
if (!type.equalsIgnoreCase("string") && e.hasPrimitiveValue()) {
if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().length() > 0, "@value cannot be empty")) {
warning(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().trim().equals(e.primitiveValue()), "value should not start or finish with whitespace");
}
}
if (type.equals("dateTime")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), "The value '" + e.primitiveValue() + "' does not have a valid year");
rule(errors, IssueType.INVALID, e.line(), e.col(), path,
e.primitiveValue()
.matches("-?[0-9]{4}(-(0[1-9]|1[0-2])(-(0[0-9]|[1-2][0-9]|3[0-1])(T([01][0-9]|2[0-3]):[0-5][0-9]:[0-5][0-9](\\.[0-9]+)?(Z|(\\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00))?)?)?)?"),
"Not a valid date time");
rule(errors, IssueType.INVALID, e.line(), e.col(), path, !hasTime(e.primitiveValue()) || hasTimeZone(e.primitiveValue()), "if a date has a time, it must have a timezone");
}
if (type.equals("instant")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path,
e.primitiveValue().matches("-?[0-9]{4}-(0[1-9]|1[0-2])-(0[0-9]|[1-2][0-9]|3[0-1])T([01][0-9]|2[0-3]):[0-5][0-9]:[0-5][0-9](\\.[0-9]+)?(Z|(\\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00))"),
"The instant '" + e.primitiveValue() + "' is not valid (by regex)");
rule(errors, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), "The value '" + e.primitiveValue() + "' does not have a valid year");
}
if (type.equals("code") && e.primitiveValue() != null) {
// Technically, a code is restricted to string which has at least one character and no leading or trailing whitespace, and where there is no whitespace
// other than single spaces in the contents
rule(errors, IssueType.INVALID, e.line(), e.col(), path, passesCodeWhitespaceRules(e.primitiveValue()), "The code '" + e.primitiveValue() + "' is not valid (whitespace rules)");
}
if (context.hasBinding() && e.primitiveValue() != null) {
checkPrimitiveBinding(errors, path, type, context, e, profile);
}
if (type.equals("xhtml")) {
XhtmlNode xhtml = e.getXhtml();
if (xhtml != null) { // if it is null, this is an error already noted in the parsers
// check that the namespace is there and correct.
String ns = xhtml.getNsDecl();
rule(errors, IssueType.INVALID, e.line(), e.col(), path, FormatUtilities.XHTML_NS.equals(ns), "Wrong namespace on the XHTML ('"+ns+"')");
// check that inner namespaces are all correct
checkInnerNS(errors, e, path, xhtml.getChildNodes());
rule(errors, IssueType.INVALID, e.line(), e.col(), path, "div".equals(xhtml.getName()), "Wrong name on the XHTML ('"+ns+"') - must start with div");
// check that no illegal elements and attributes have been used
checkInnerNames(errors, e, path, xhtml.getChildNodes());
}
}
// for nothing to check
}
private void checkInnerNames(List<ValidationMessage> errors, Element e, String path, List<XhtmlNode> list) {
for (XhtmlNode node : list) {
if (node.getNodeType() == NodeType.Element) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.existsInList(node.getName(),
"p", "br", "div", "h1", "h2", "h3", "h4", "h5", "h6", "a", "span", "b", "em", "i", "strong",
"small", "big", "tt", "small", "dfn", "q", "var", "abbr", "acronym", "cite", "blockquote", "hr", "address", "bdo", "kbd", "q", "sub", "sup",
"ul", "ol", "li", "dl", "dt", "dd", "pre", "table", "caption", "colgroup", "col", "thead", "tr", "tfoot", "tbody", "th", "td",
"code", "samp", "img", "map", "area"
), "Illegal element name in the XHTML ('"+node.getName()+"')");
for (String an : node.getAttributes().keySet()) {
boolean ok = an.startsWith("xmlns") || Utilities.existsInList(an,
"title", "style", "class", "id", "lang", "xml:lang", "dir", "accesskey", "tabindex",
// tables
"span", "width", "align", "valign", "char", "charoff", "abbr", "axis", "headers", "scope", "rowspan", "colspan") ||
Utilities.existsInList(node.getName()+"."+an, "a.href", "a.name", "img.src", "img.border", "div.xmlns", "blockquote.cite", "q.cite",
"a.charset", "a.type", "a.name", "a.href", "a.hreflang", "a.rel", "a.rev", "a.shape", "a.coords", "img.src",
"img.alt", "img.longdesc", "img.height", "img.width", "img.usemap", "img.ismap", "map.name", "area.shape",
"area.coords", "area.href", "area.nohref", "area.alt", "table.summary", "table.width", "table.border",
"table.frame", "table.rules", "table.cellspacing", "table.cellpadding", "pre.space"
);
if (!ok)
rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Illegal attribute name in the XHTML ('"+an+"' on '"+node.getName()+"')");
}
checkInnerNames(errors, e, path, node.getChildNodes());
}
}
}
private void checkInnerNS(List<ValidationMessage> errors, Element e, String path, List<XhtmlNode> list) {
for (XhtmlNode node : list) {
if (node.getNodeType() == NodeType.Element) {
String ns = node.getNsDecl();
rule(errors, IssueType.INVALID, e.line(), e.col(), path, ns == null || FormatUtilities.XHTML_NS.equals(ns), "Wrong namespace on the XHTML ('"+ns+"')");
checkInnerNS(errors, e, path, node.getChildNodes());
}
}
}
// note that we don't check the type here; it could be string, uri or code.
private void checkPrimitiveBinding(List<ValidationMessage> errors, String path, String type, ElementDefinition elementContext, Element element, StructureDefinition profile) {
if (!element.hasPrimitiveValue())
return;
String value = element.primitiveValue();
// System.out.println("check "+value+" in "+path);
// firstly, resolve the value set
ElementDefinitionBindingComponent binding = elementContext.getBinding();
if (binding.hasValueSet() && binding.getValueSet() instanceof Reference) {
ValueSet vs = resolveBindingReference(profile, binding.getValueSet());
if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, vs != null, "ValueSet {0} not found", describeReference(binding.getValueSet()))) {
long t = System.nanoTime();
ValidationResult vr = context.validateCode(null, value, null, vs);
txTime = txTime + (System.nanoTime() - t);
if (vr != null && !vr.isOk()) {
if (binding.getStrength() == BindingStrength.REQUIRED)
rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('"+value+"') is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code is required from this value set");
else if (binding.getStrength() == BindingStrength.EXTENSIBLE)
warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('"+value+"') is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code should come from this value set unless it has no suitable code");
else if (binding.getStrength() == BindingStrength.PREFERRED)
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('"+value+"') is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code is recommended to come from this value set");
}
}
} else
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, !type.equals("code"), "Binding has no source, so can't be checked");
}
private void checkQuantity(List<ValidationMessage> errors, String path, Element focus, Quantity fixed) {
checkFixedValue(errors, path + ".value", focus.getNamedChild("value"), fixed.getValueElement(), "value");
checkFixedValue(errors, path + ".comparator", focus.getNamedChild("comparator"), fixed.getComparatorElement(), "comparator");
checkFixedValue(errors, path + ".units", focus.getNamedChild("unit"), fixed.getUnitElement(), "units");
checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), "system");
checkFixedValue(errors, path + ".code", focus.getNamedChild("code"), fixed.getCodeElement(), "code");
}
// implementation
private void checkRange(List<ValidationMessage> errors, String path, Element focus, Range fixed) {
checkFixedValue(errors, path + ".low", focus.getNamedChild("low"), fixed.getLow(), "low");
checkFixedValue(errors, path + ".high", focus.getNamedChild("high"), fixed.getHigh(), "high");
}
private void checkRatio(List<ValidationMessage> errors, String path, Element focus, Ratio fixed) {
checkFixedValue(errors, path + ".numerator", focus.getNamedChild("numerator"), fixed.getNumerator(), "numerator");
checkFixedValue(errors, path + ".denominator", focus.getNamedChild("denominator"), fixed.getDenominator(), "denominator");
}
private void checkReference(List<ValidationMessage> errors, String path, Element element, StructureDefinition profile, ElementDefinition container, String parentType, NodeStack stack) {
String ref = element.getNamedChildValue("reference");
if (Utilities.noString(ref)) {
// todo - what should we do in this case?
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), "A Reference without an actual reference should have a display");
return;
}
Element we = resolve(ref, stack);
String ft;
if (we != null)
ft = we.getType();
else
ft = tryParse(ref);
if (hint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ft != null, "Unable to determine type of target resource")) {
boolean ok = false;
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (TypeRefComponent type : container.getType()) {
if (!ok && type.getCode().equals("Reference")) {
// we validate as much as we can. First, can we infer a type from the profile?
if (!type.hasProfile() || type.getProfile().get(0).getValue().equals("http://hl7.org/fhir/StructureDefinition/Resource"))
ok = true;
else {
String pr = type.getProfile().get(0).getValue();
String bt = getBaseType(profile, pr);
if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, bt != null, "Unable to resolve the profile reference '" + pr + "'")) {
b.append(bt);
ok = bt.equals(ft);
} else
ok = true; // suppress following check
}
}
if (!ok && type.getCode().equals("*")) {
ok = true; // can refer to anything
}
}
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ok, "Invalid Resource target type. Found " + ft + ", but expected one of (" + b.toString() + ")");
}
}
private String checkResourceType(String type) {
long t = System.nanoTime();
try {
if (context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + type) != null)
return type;
else
return null;
} finally {
sdTime = sdTime + (System.nanoTime() - t);
}
}
private void checkSampledData(List<ValidationMessage> errors, String path, Element focus, SampledData fixed) {
checkFixedValue(errors, path + ".origin", focus.getNamedChild("origin"), fixed.getOrigin(), "origin");
checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriodElement(), "period");
checkFixedValue(errors, path + ".factor", focus.getNamedChild("factor"), fixed.getFactorElement(), "factor");
checkFixedValue(errors, path + ".lowerLimit", focus.getNamedChild("lowerLimit"), fixed.getLowerLimitElement(), "lowerLimit");
checkFixedValue(errors, path + ".upperLimit", focus.getNamedChild("upperLimit"), fixed.getUpperLimitElement(), "upperLimit");
checkFixedValue(errors, path + ".dimensions", focus.getNamedChild("dimensions"), fixed.getDimensionsElement(), "dimensions");
checkFixedValue(errors, path + ".data", focus.getNamedChild("data"), fixed.getDataElement(), "data");
}
private void checkTiming(List<ValidationMessage> errors, String path, Element focus, Timing fixed) {
checkFixedValue(errors, path + ".repeat", focus.getNamedChild("repeat"), fixed.getRepeat(), "value");
List<Element> events = new ArrayList<Element>();
focus.getNamedChildren("event", events);
if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, events.size() == fixed.getEvent().size(),
"Expected " + Integer.toString(fixed.getEvent().size()) + " but found " + Integer.toString(events.size()) + " event elements")) {
for (int i = 0; i < events.size(); i++)
checkFixedValue(errors, path + ".event", events.get(i), fixed.getEvent().get(i), "event");
}
}
private boolean codeinExpansion(ValueSetExpansionContainsComponent cnt, String system, String code) {
for (ValueSetExpansionContainsComponent c : cnt.getContains()) {
if (code.equals(c.getCode()) && system.equals(c.getSystem().toString()))
return true;
if (codeinExpansion(c, system, code))
return true;
}
return false;
}
private boolean codeInExpansion(ValueSet vs, String system, String code) {
for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) {
if (code.equals(c.getCode()) && (system == null || system.equals(c.getSystem())))
return true;
if (codeinExpansion(c, system, code))
return true;
}
return false;
}
private String describeReference(Type reference) {
if (reference == null)
return "null";
if (reference instanceof UriType)
return ((UriType) reference).getValue();
if (reference instanceof Reference)
return ((Reference) reference).getReference();
return "??";
}
private String describeTypes(List<TypeRefComponent> types) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (TypeRefComponent t : types) {
b.append(t.getCode());
}
return b.toString();
}
private ElementDefinition findElement(StructureDefinition profile, String name) {
for (ElementDefinition c : profile.getSnapshot().getElement()) {
if (c.getPath().equals(name)) {
return c;
}
}
return null;
}
private String genFullUrl(String bundleBase, String entryBase, String type, String id) {
String base = Utilities.noString(entryBase) ? bundleBase : entryBase;
if (Utilities.noString(base)) {
return type + "/" + id;
} else if ("urn:uuid".equals(base) || "urn:oid".equals(base))
return base + id;
else
return Utilities.appendSlash(base) + type + "/" + id;
}
public BestPracticeWarningLevel getBasePracticeWarningLevel() {
return bpWarnings;
}
private String getBaseType(StructureDefinition profile, String pr) {
// if (pr.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
// // this just has to be a base type
// return pr.substring(40);
// } else {
StructureDefinition p = resolveProfile(profile, pr);
if (p == null)
return null;
else if (p.getKind() == StructureDefinitionKind.RESOURCE)
return p.getSnapshot().getElement().get(0).getPath();
else
return p.getSnapshot().getElement().get(0).getType().get(0).getCode();
// }
}
@Override
public CheckDisplayOption getCheckDisplay() {
return checkDisplay;
}
// private String findProfileTag(Element element) {
// String uri = null;
// List<Element> list = new ArrayList<Element>();
// element.getNamedChildren("category", list);
// for (Element c : list) {
// if ("http://hl7.org/fhir/tag/profile".equals(c.getAttribute("scheme"))) {
// uri = c.getAttribute("term");
// }
// }
// return uri;
// }
private ConceptDefinitionComponent getCodeDefinition(ConceptDefinitionComponent c, String code) {
if (code.equals(c.getCode()))
return c;
for (ConceptDefinitionComponent g : c.getConcept()) {
ConceptDefinitionComponent r = getCodeDefinition(g, code);
if (r != null)
return r;
}
return null;
}
private ConceptDefinitionComponent getCodeDefinition(CodeSystem cs, String code) {
for (ConceptDefinitionComponent c : cs.getConcept()) {
ConceptDefinitionComponent r = getCodeDefinition(c, code);
if (r != null)
return r;
}
return null;
}
private Element getContainedById(Element container, String id) {
List<Element> contained = new ArrayList<Element>();
container.getNamedChildren("contained", contained);
for (Element we : contained) {
if (id.equals(we.getNamedChildValue("id")))
return we;
}
return null;
}
public IWorkerContext getContext() {
return context;
}
private ElementDefinition getCriteriaForDiscriminator(String path, ElementDefinition ed, String discriminator, StructureDefinition profile) throws DefinitionException, org.hl7.fhir.exceptions.DefinitionException {
List<ElementDefinition> childDefinitions = ProfileUtilities.getChildMap(profile, ed);
List<ElementDefinition> snapshot = null;
int index;
if (childDefinitions.isEmpty()) {
// going to look at the type
if (ed.getType().size() == 0)
throw new DefinitionException("Error in profile for " + path + " no children, no type");
if (ed.getType().size() > 1)
throw new DefinitionException("Error in profile for " + path + " multiple types defined in slice discriminator");
StructureDefinition type;
if (ed.getType().get(0).hasProfile()) {
// need to do some special processing for reference here...
if (ed.getType().get(0).getCode().equals("Reference"))
discriminator = discriminator.substring(discriminator.indexOf(".")+1);
long t = System.nanoTime();
type = context.fetchResource(StructureDefinition.class, ed.getType().get(0).getProfile().get(0).getValue());
sdTime = sdTime + (System.nanoTime() - t);
} else {
long t = System.nanoTime();
type = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + ed.getType().get(0).getCode());
sdTime = sdTime + (System.nanoTime() - t);
}
snapshot = type.getSnapshot().getElement();
ed = snapshot.get(0);
index = 0;
} else {
snapshot = childDefinitions;
index = -1;
}
String originalPath = ed.getPath();
String goal = originalPath + "." + discriminator;
index++;
while (index < snapshot.size() && !snapshot.get(index).getPath().equals(originalPath)) {
if (snapshot.get(index).getPath().equals(goal))
return snapshot.get(index);
index++;
}
throw new Error("Unable to find discriminator definition for " + goal + " in " + discriminator + " at " + path);
}
private Element getExtensionByUrl(List<Element> extensions, String urlSimple) {
for (Element e : extensions) {
if (urlSimple.equals(e.getNamedChildValue("url")))
return e;
}
return null;
}
public List<String> getExtensionDomains() {
return extensionDomains;
}
private Element getFromBundle(Element bundle, String ref, String fullUrl) {
List<Element> entries = new ArrayList<Element>();
bundle.getNamedChildren("entry", entries);
for (Element we : entries) {
Element res = we.getNamedChild("resource");
if (res != null) {
String url = genFullUrl(bundle.getNamedChildValue("base"), we.getNamedChildValue("base"), res.getName(), res.getNamedChildValue("id"));
if (url.endsWith(ref))
return res;
}
}
return null;
}
private StructureDefinition getProfileForType(String type) {
if (logical != null)
for (BundleEntryComponent be : logical.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
if (sd.getId().equals(type))
return sd;
}
}
long t = System.nanoTime();
try {
return context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + type);
} finally {
sdTime = sdTime + (System.nanoTime() - t);
}
}
private Element getValueForDiscriminator(Element element, String discriminator, ElementDefinition criteria) {
// throw new Error("validation of slices not done yet");
return null;
}
private CodeSystem getCodeSystem(String system) {
long t = System.nanoTime();
try {
return context.fetchCodeSystem(system);
} finally {
txTime = txTime + (System.nanoTime() - t);
}
}
private boolean hasTime(String fmt) {
return fmt.contains("T");
}
private boolean hasTimeZone(String fmt) {
return fmt.length() > 10 && (fmt.substring(10).contains("-") || fmt.substring(10).contains("+") || fmt.substring(10).contains("Z"));
}
private boolean isAbsolute(String uri) {
return Utilities.noString(uri) || uri.startsWith("http:") || uri.startsWith("https:") || uri.startsWith("urn:uuid:") || uri.startsWith("urn:oid:") || uri.startsWith("urn:ietf:")
|| uri.startsWith("urn:iso:") || isValidFHIRUrn(uri);
}
private boolean isValidFHIRUrn(String uri) {
return (uri.equals("urn:x-fhir:uk:id:nhs-number"));
}
public boolean isAnyExtensionsAllowed() {
return anyExtensionsAllowed;
}
private boolean isParametersEntry(String path) {
String[] parts = path.split("\\.");
return parts.length > 2 && parts[parts.length - 1].equals("resource") && (parts[parts.length - 2].startsWith("parameter[") || parts[parts.length - 2].startsWith("part["));
}
private boolean isBundleEntry(String path) {
String[] parts = path.split("\\.");
return parts.length > 2 && parts[parts.length - 1].equals("resource") && parts[parts.length - 2].startsWith("entry[");
}
private boolean isPrimitiveType(String type) {
return type.equalsIgnoreCase("boolean") || type.equalsIgnoreCase("integer") || type.equalsIgnoreCase("string") || type.equalsIgnoreCase("decimal") || type.equalsIgnoreCase("uri")
|| type.equalsIgnoreCase("base64Binary") || type.equalsIgnoreCase("instant") || type.equalsIgnoreCase("date") || type.equalsIgnoreCase("uuid") || type.equalsIgnoreCase("id")
|| type.equalsIgnoreCase("xhtml") || type.equalsIgnoreCase("markdown") || type.equalsIgnoreCase("dateTime") || type.equalsIgnoreCase("time") || type.equalsIgnoreCase("code")
|| type.equalsIgnoreCase("oid") || type.equalsIgnoreCase("id");
}
public boolean isSuppressLoincSnomedMessages() {
return suppressLoincSnomedMessages;
}
private boolean nameMatches(String name, String tail) {
if (tail.endsWith("[x]"))
return name.startsWith(tail.substring(0, tail.length() - 3));
else
return (name.equals(tail));
}
// private String mergePath(String path1, String path2) {
// // path1 is xpath path
// // path2 is dotted path
// String[] parts = path2.split("\\.");
// StringBuilder b = new StringBuilder(path1);
// for (int i = 1; i < parts.length -1; i++)
// b.append("/f:"+parts[i]);
// return b.toString();
// }
private boolean passesCodeWhitespaceRules(String v) {
if (!v.trim().equals(v))
return false;
boolean lastWasSpace = true;
for (char c : v.toCharArray()) {
if (c == ' ') {
if (lastWasSpace)
return false;
else
lastWasSpace = true;
} else if (Character.isWhitespace(c))
return false;
else
lastWasSpace = false;
}
return true;
}
private Element resolve(String ref, NodeStack stack) {
if (ref.startsWith("#")) {
// work back through the contained list.
// really, there should only be one level for this (contained resources cannot contain
// contained resources), but we'll leave that to some other code to worry about
while (stack != null && stack.getElement() != null) {
if (stack.getElement().getProperty().isResource()) {
// ok, we'll try to find the contained reference
Element res = getContainedById(stack.getElement(), ref.substring(1));
if (res != null)
return res;
}
if (stack.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY) {
return null; // we don't try to resolve contained references across this boundary
}
stack = stack.parent;
}
return null;
} else {
// work back through the contained list - if any of them are bundles, try to resolve
// the resource in the bundle
String fullUrl = null; // we're going to try to work this out as we go up
while (stack != null && stack.getElement() != null) {
if (stack.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY) {
fullUrl = "test"; // we don't try to resolve contained references across this boundary
}
if ("Bundle".equals(stack.getElement().getType())) {
Element res = getFromBundle(stack.getElement(), ref, fullUrl);
return res;
}
stack = stack.parent;
}
// todo: consult the external host for resolution
return null;
}
}
private ValueSet resolveBindingReference(DomainResource ctxt, Type reference) {
if (reference instanceof UriType) {
long t = System.nanoTime();
ValueSet fr = context.fetchResource(ValueSet.class, ((UriType) reference).getValue().toString());
txTime = txTime + (System.nanoTime() - t);
return fr;
}
else if (reference instanceof Reference) {
String s = ((Reference) reference).getReference();
if (s.startsWith("#")) {
for (Resource c : ctxt.getContained()) {
if (c.getId().equals(s.substring(1)) && (c instanceof ValueSet))
return (ValueSet) c;
}
return null;
} else {
long t = System.nanoTime();
ValueSet fr = context.fetchResource(ValueSet.class, ((Reference) reference).getReference());
txTime = txTime + (System.nanoTime() - t);
return fr;
}
}
else
return null;
}
private Element resolveInBundle(List<Element> entries, String ref, String fullUrl, String type, String id) {
if (Utilities.isAbsoluteUrl(ref)) {
// if the reference is absolute, then you resolve by fullUrl. No other thinking is required.
for (Element entry : entries) {
String fu = entry.getNamedChildValue("fullUrl");
if (ref.equals(fu))
return entry;
}
return null;
} else {
// split into base, type, and id
String u = null;
if (fullUrl != null && fullUrl.endsWith(type+"/"+id))
// fullUrl = complex
u = fullUrl.substring((type+"/"+id).length())+ref;
String[] parts = ref.split("\\/");
if (parts.length >= 2) {
String t = parts[0];
String i = parts[1];
for (Element entry : entries) {
String fu = entry.getNamedChildValue("fullUrl");
if (u != null && fullUrl.equals(u))
return entry;
if (u == null) {
Element resource = entry.getNamedChild("resource");
String et = resource.getType();
String eid = resource.getNamedChildValue("id");
if (t.equals(et) && i.equals(eid))
return entry;
}
}
}
return null;
}
}
private ElementDefinition resolveNameReference(StructureDefinitionSnapshotComponent snapshot, String contentReference) {
for (ElementDefinition ed : snapshot.getElement())
if (contentReference.equals("#"+ed.getId()))
return ed;
return null;
}
private StructureDefinition resolveProfile(StructureDefinition profile, String pr) {
if (pr.startsWith("#")) {
for (Resource r : profile.getContained()) {
if (r.getId().equals(pr.substring(1)) && r instanceof StructureDefinition)
return (StructureDefinition) r;
}
return null;
} else {
long t = System.nanoTime();
StructureDefinition fr = context.fetchResource(StructureDefinition.class, pr);
sdTime = sdTime + (System.nanoTime() - t);
return fr;
}
}
private ElementDefinition resolveType(String type) {
if (logical != null)
for (BundleEntryComponent be : logical.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
if (sd.getId().equals(type))
return sd.getSnapshot().getElement().get(0);
}
}
String url = "http://hl7.org/fhir/StructureDefinition/" + type;
long t = System.nanoTime();
StructureDefinition sd = context.fetchResource(StructureDefinition.class, url);
sdTime = sdTime + (System.nanoTime() - t);
if (sd == null || !sd.hasSnapshot())
return null;
else
return sd.getSnapshot().getElement().get(0);
}
public void setAnyExtensionsAllowed(boolean anyExtensionsAllowed) {
this.anyExtensionsAllowed = anyExtensionsAllowed;
}
public void setBestPracticeWarningLevel(BestPracticeWarningLevel value) {
bpWarnings = value;
}
@Override
public void setCheckDisplay(CheckDisplayOption checkDisplay) {
this.checkDisplay = checkDisplay;
}
public void setSuppressLoincSnomedMessages(boolean suppressLoincSnomedMessages) {
this.suppressLoincSnomedMessages = suppressLoincSnomedMessages;
}
public IdStatus getResourceIdRule() {
return resourceIdRule;
}
public void setResourceIdRule(IdStatus resourceIdRule) {
this.resourceIdRule = resourceIdRule;
}
/**
*
* @param element
* - the candidate that might be in the slice
* @param path
* - for reporting any errors. the XPath for the element
* @param slice
* - the definition of how slicing is determined
* @param ed
* - the slice for which to test membership
* @return
* @throws DefinitionException
* @throws DefinitionException
* @throws Exception
*/
private boolean sliceMatches(Element element, String path, ElementDefinition slice, ElementDefinition ed, StructureDefinition profile) throws DefinitionException, DefinitionException {
if (!slice.getSlicing().hasDiscriminator())
return false; // cannot validate in this case
for (StringType s : slice.getSlicing().getDiscriminator()) {
String discriminator = s.getValue();
ElementDefinition criteria = getCriteriaForDiscriminator(path, ed, discriminator, profile);
if (discriminator.equals("url") && criteria.getPath().equals("Extension.url")) {
if (!element.getNamedChildValue("url").equals(((UriType) criteria.getFixed()).asStringValue()))
return false;
} else {
Element value = getValueForDiscriminator(element, discriminator, criteria);
if (!valueMatchesCriteria(value, criteria))
return false;
}
}
return true;
}
// we assume that the following things are true:
// the instance at root is valid against the schema and schematron
// the instance validator had no issues against the base resource profile
private void start(List<ValidationMessage> errors, Element resource, Element element, StructureDefinition profile, NodeStack stack) throws FHIRException, FHIRException {
// profile is valid, and matches the resource name
if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), profile.hasSnapshot(),
"StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided")) {
validateElement(errors, profile, profile.getSnapshot().getElement().get(0), null, null, resource, element, element.getName(), stack, false);
checkDeclaredProfiles(errors, resource, element, stack);
// specific known special validations
if (element.getType().equals("Bundle"))
validateBundle(errors, element, stack);
if (element.getType().equals("Observation"))
validateObservation(errors, element, stack);
if (element.getType().equals("QuestionnaireResponse"))
validateQuestionannaireResponse(errors, element, stack);
}
}
private void validateQuestionannaireResponse(List<ValidationMessage> errors, Element element, NodeStack stack) {
Element q = element.getNamedChild("questionnaire");
if (hint(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), q != null, "No questionnaire is identified, so no validation can be performed against the base questionnaire")) {
long t = System.nanoTime();
Questionnaire qsrc = context.fetchResource(Questionnaire.class, q.getNamedChildValue("reference"));
sdTime = sdTime + (System.nanoTime() - t);
if (warning(errors, IssueType.REQUIRED, q.line(), q.col(), stack.getLiteralPath(), qsrc != null, "The questionnaire could not be resolved, so no validation can be performed against the base questionnaire")) {
boolean inProgress = "in-progress".equals(element.getNamedChildValue("status"));
validateQuestionannaireResponseItems(qsrc, qsrc.getItem(), errors, element, stack, inProgress);
}
}
}
private void validateQuestionannaireResponseItem(Questionnaire qsrc, QuestionnaireItemComponent qItem, List<ValidationMessage> errors, Element element, NodeStack stack, boolean inProgress) {
String text = element.getNamedChildValue("text");
rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), Utilities.noString(text) || text.equals(qItem.getText()), "If text exists, it must match the questionnaire definition for linkId "+qItem.getLinkId());
List<Element> answers = new ArrayList<Element>();
element.getNamedChildren("answer", answers);
if (inProgress)
warning(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), (answers.size() > 0) || !qItem.getRequired(), "No response answer found for required item "+qItem.getLinkId());
else
rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), (answers.size() > 0) || !qItem.getRequired(), "No response answer found for required item "+qItem.getLinkId());
if (answers.size() > 1)
rule(errors, IssueType.INVALID, answers.get(1).line(), answers.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), "Only one response answer item with this linkId allowed");
for (Element answer : answers) {
NodeStack ns = stack.push(answer, -1, null, null);
switch (qItem.getType()) {
case GROUP:
rule(errors, IssueType.STRUCTURE, answer.line(), answer.col(), stack.getLiteralPath(), false, "Items of type group should not have answers");
break;
case DISPLAY: // nothing
break;
case BOOLEAN:
validateQuestionnaireResponseItemType(errors, answer, ns, "boolean");
break;
case DECIMAL:
validateQuestionnaireResponseItemType(errors, answer, ns, "decimal");
break;
case INTEGER:
validateQuestionnaireResponseItemType(errors, answer, ns, "integer");
break;
case DATE:
validateQuestionnaireResponseItemType(errors, answer, ns, "date");
break;
case DATETIME:
validateQuestionnaireResponseItemType(errors, answer, ns, "dateTime");
break;
case INSTANT:
validateQuestionnaireResponseItemType(errors, answer, ns, "instant");
break;
case TIME:
validateQuestionnaireResponseItemType(errors, answer, ns, "time");
break;
case STRING:
validateQuestionnaireResponseItemType(errors, answer, ns, "string");
break;
case TEXT:
validateQuestionnaireResponseItemType(errors, answer, ns, "text");
break;
case URL:
validateQuestionnaireResponseItemType(errors, answer, ns, "uri");
break;
case ATTACHMENT:
validateQuestionnaireResponseItemType(errors, answer, ns, "Attachment");
break;
case REFERENCE:
validateQuestionnaireResponseItemType(errors, answer, ns, "Reference");
break;
case QUANTITY:
if (validateQuestionnaireResponseItemType(errors, answer, ns, "Quantity").equals("Quantity"))
if (qItem.hasExtension("???"))
validateQuestionnaireResponseItemQuantity(errors, answer, ns);
break;
case CHOICE:
String itemType=validateQuestionnaireResponseItemType(errors, answer, ns, "Coding", "date", "time", "integer", "string");
if (itemType.equals("Coding")) validateAnswerCode(errors, answer, ns, qsrc, qItem, false);
else if (itemType.equals("date")) checkOption(errors, answer, ns, qsrc, qItem, "date");
else if (itemType.equals("time")) checkOption(errors, answer, ns, qsrc, qItem, "time");
else if (itemType.equals("integer")) checkOption(errors, answer, ns, qsrc, qItem, "integer");
else if (itemType.equals("string")) checkOption(errors, answer, ns, qsrc, qItem, "string");
break;
case OPENCHOICE:
itemType=validateQuestionnaireResponseItemType(errors, answer, ns, "Coding", "date", "time", "integer", "string");
if (itemType.equals("Coding")) validateAnswerCode(errors, answer, ns, qsrc, qItem, true);
else if (itemType.equals("date")) checkOption(errors, answer, ns, qsrc, qItem, "date");
else if (itemType.equals("time")) checkOption(errors, answer, ns, qsrc, qItem, "time");
else if (itemType.equals("integer")) checkOption(errors, answer, ns, qsrc, qItem, "integer");
else if (itemType.equals("string")) checkOption(errors, answer, ns, qsrc, qItem, "string", true);
break;
default:
break;
}
validateQuestionannaireResponseItems(qsrc, qItem.getItem(), errors, answer, stack, inProgress);
}
if (qItem.getType() == null) {
fail(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), false, "Definition for item "+qItem.getLinkId() + " does not contain a type");
} else if (qItem.getType() == QuestionnaireItemType.GROUP) {
validateQuestionannaireResponseItems(qsrc, qItem.getItem(), errors, element, stack, inProgress);
} else {
List<Element> items = new ArrayList<Element>();
element.getNamedChildren("item", items);
for (Element item : items) {
NodeStack ns = stack.push(item, -1, null, null);
rule(errors, IssueType.STRUCTURE, answers.get(0).line(), answers.get(0).col(), stack.getLiteralPath(), false, "Items not of type group should not have items - Item with linkId {0} of type {1} has {2} item(s)", qItem.getLinkId(), qItem.getType(), items.size());
}
}
}
private void validateQuestionannaireResponseItem(Questionnaire qsrc, QuestionnaireItemComponent qItem, List<ValidationMessage> errors, List<Element> elements, NodeStack stack, boolean inProgress) {
if (elements.size() > 1)
rule(errors, IssueType.INVALID, elements.get(1).line(), elements.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), "Only one response item with this linkId allowed");
for (Element element : elements) {
NodeStack ns = stack.push(element, -1, null, null);
validateQuestionannaireResponseItem(qsrc, qItem, errors, element, ns, inProgress);
}
}
private int getLinkIdIndex(List<QuestionnaireItemComponent> qItems, String linkId) {
for (int i = 0; i < qItems.size(); i++) {
if (linkId.equals(qItems.get(i).getLinkId()))
return i;
}
return -1;
}
private void validateQuestionannaireResponseItems(Questionnaire qsrc, List<QuestionnaireItemComponent> qItems, List<ValidationMessage> errors, Element element, NodeStack stack, boolean inProgress) {
List<Element> items = new ArrayList<Element>();
element.getNamedChildren("item", items);
// now, sort into stacks
Map<String, List<Element>> map = new HashMap<String, List<Element>>();
int lastIndex = -1;
for (Element item : items) {
String linkId = item.getNamedChildValue("linkId");
if (rule(errors, IssueType.REQUIRED, item.line(), item.col(), stack.getLiteralPath(), !Utilities.noString(linkId), "No LinkId, so can't be validated")) {
int index = getLinkIdIndex(qItems, linkId);
if (index == -1) {
QuestionnaireItemComponent qItem = findQuestionnaireItem(qsrc, linkId);
if (qItem != null) {
rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index > -1, "Structural Error: item is in the wrong place");
NodeStack ns = stack.push(item, -1, null, null);
validateQuestionannaireResponseItem(qsrc, qItem, errors, element, ns, inProgress);
}
else
rule(errors, IssueType.NOTFOUND, item.line(), item.col(), stack.getLiteralPath(), index > -1, "LinkId \""+linkId+"\" not found in questionnaire");
}
else
{
rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index >= lastIndex, "Structural Error: items are out of order");
lastIndex = index;
List<Element> mapItem = map.get(linkId);
if (mapItem == null) {
mapItem = new ArrayList<Element>();
map.put(linkId, mapItem);
}
mapItem.add(item);
}
}
}
// ok, now we have a list of known items, grouped by linkId. We"ve made an error for anything out of order
for (QuestionnaireItemComponent qItem : qItems) {
List<Element> mapItem = map.get(qItem.getLinkId());
if (mapItem != null)
validateQuestionannaireResponseItem(qsrc, qItem, errors, mapItem, stack, inProgress);
else
rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), !qItem.getRequired(), "No response found for required item "+qItem.getLinkId());
}
}
private void validateQuestionnaireResponseItemQuantity( List<ValidationMessage> errors, Element answer, NodeStack stack) {
}
private String validateQuestionnaireResponseItemType(List<ValidationMessage> errors, Element element, NodeStack stack, String... types) {
List<Element> values = new ArrayList<Element>();
element.getNamedChildrenWithWildcard("value[x]", values);
if (values.size() > 0) {
NodeStack ns = stack.push(values.get(0), -1, null, null);
CommaSeparatedStringBuilder l = new CommaSeparatedStringBuilder();
for (String s : types) {
l.append(s);
if (values.get(0).getName().equals("value"+Utilities.capitalize(s)))
return(s);
}
if (types.length == 1)
rule(errors, IssueType.STRUCTURE, values.get(0).line(), values.get(0).col(), ns.getLiteralPath(), false, "Answer value must be of type "+types[0]);
else
rule(errors, IssueType.STRUCTURE, values.get(0).line(), values.get(0).col(), ns.getLiteralPath(), false, "Answer value must be one of the types "+l.toString());
}
return null;
}
private QuestionnaireItemComponent findQuestionnaireItem(Questionnaire qSrc, String linkId) {
return findItem(qSrc.getItem(), linkId);
}
private QuestionnaireItemComponent findItem(List<QuestionnaireItemComponent> list, String linkId) {
for (QuestionnaireItemComponent item : list) {
if (linkId.equals(item.getLinkId()))
return item;
QuestionnaireItemComponent result = findItem(item.getItem(), linkId);
if (result != null)
return result;
}
return null;
}
/* private void validateAnswerCode(List<ValidationMessage> errors, Element value, NodeStack stack, List<Coding> optionList) {
String system = value.getNamedChildValue("system");
String code = value.getNamedChildValue("code");
boolean found = false;
for (Coding c : optionList) {
if (ObjectUtil.equals(c.getSystem(), system) && ObjectUtil.equals(c.getCode(), code)) {
found = true;
break;
}
}
rule(errors, IssueType.STRUCTURE, value.line(), value.col(), stack.getLiteralPath(), found, "The code "+system+"::"+code+" is not a valid option");
}*/
private void validateAnswerCode(List<ValidationMessage> errors, Element value, NodeStack stack, Questionnaire qSrc, Reference ref, boolean theOpenChoice) {
ValueSet vs = resolveBindingReference(qSrc, ref);
if (warning(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), vs != null, "ValueSet " + describeReference(ref) + " not found")) {
try {
Coding c = readAsCoding(value);
if (isBlank(c.getCode()) && isBlank(c.getSystem()) && isNotBlank(c.getDisplay())) {
if (theOpenChoice) {
return;
}
}
long t = System.nanoTime();
ValidationResult res = context.validateCode(c, vs);
txTime = txTime + (System.nanoTime() - t);
if (!res.isOk())
rule(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, "The value provided ("+c.getSystem()+"::"+c.getCode()+") is not in the options value set in the questionnaire");
} catch (Exception e) {
warning(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, "Error " + e.getMessage() + " validating Coding against Questionnaire Options");
}
}
}
private void validateAnswerCode( List<ValidationMessage> errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean theOpenChoice) {
Element v = answer.getNamedChild("valueCoding");
NodeStack ns = stack.push(v, -1, null, null);
if (qItem.getOption().size() > 0)
checkCodingOption(errors, answer, stack, qSrc, qItem, theOpenChoice);
// validateAnswerCode(errors, v, stack, qItem.getOption());
else if (qItem.hasOptions())
validateAnswerCode(errors, v, stack, qSrc, qItem.getOptions(), theOpenChoice);
else
hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate options because no option or options are provided");
}
private void checkOption( List<ValidationMessage> errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, String type) {
checkOption(errors, answer, stack, qSrc, qItem, type, false);
}
private void checkOption( List<ValidationMessage> errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, String type, boolean openChoice) {
if (type.equals("integer")) checkIntegerOption(errors, answer, stack, qSrc, qItem, openChoice);
else if (type.equals("date")) checkDateOption(errors, answer, stack, qSrc, qItem, openChoice);
else if (type.equals("time")) checkTimeOption(errors, answer, stack, qSrc, qItem, openChoice);
else if (type.equals("string")) checkStringOption(errors, answer, stack, qSrc, qItem, openChoice);
else if (type.equals("Coding")) checkCodingOption(errors, answer, stack, qSrc, qItem, openChoice);
}
private void checkIntegerOption( List<ValidationMessage> errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) {
Element v = answer.getNamedChild("valueInteger");
NodeStack ns = stack.push(v, -1, null, null);
if (qItem.getOption().size() > 0) {
List<IntegerType> list = new ArrayList<IntegerType>();
for (QuestionnaireItemOptionComponent components : qItem.getOption()) {
try {
list.add(components.getValueIntegerType());
} catch (FHIRException e) {
// If it's the wrong type, just keep going
}
}
if (list.isEmpty() && !openChoice) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type integer");
} else {
boolean found = false;
for (IntegerType item : list) {
if (item.getValue() == Integer.parseInt(v.primitiveValue())) {
found = true;
break;
}
}
if (!found) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The integer "+v.primitiveValue()+" is not a valid option");
}
}
} else
hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate integer answer option because no option list is provided");
}
private void checkDateOption( List<ValidationMessage> errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) {
Element v = answer.getNamedChild("valueDate");
NodeStack ns = stack.push(v, -1, null, null);
if (qItem.getOption().size() > 0) {
List<DateType> list = new ArrayList<DateType>();
for (QuestionnaireItemOptionComponent components : qItem.getOption()) {
try {
list.add(components.getValueDateType());
} catch (FHIRException e) {
// If it's the wrong type, just keep going
}
}
if (list.isEmpty() && !openChoice) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type date");
} else {
boolean found = false;
for (DateType item : list) {
if (item.getValue().equals(v.primitiveValue())) {
found = true;
break;
}
}
if (!found) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The date "+v.primitiveValue()+" is not a valid option");
}
}
} else
hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate date answer option because no option list is provided");
}
private void checkTimeOption( List<ValidationMessage> errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) {
Element v = answer.getNamedChild("valueTime");
NodeStack ns = stack.push(v, -1, null, null);
if (qItem.getOption().size() > 0) {
List<TimeType> list = new ArrayList<TimeType>();
for (QuestionnaireItemOptionComponent components : qItem.getOption()) {
try {
list.add(components.getValueTimeType());
} catch (FHIRException e) {
// If it's the wrong type, just keep going
}
}
if (list.isEmpty() && !openChoice) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type time");
} else {
boolean found = false;
for (TimeType item : list) {
if (item.getValue().equals(v.primitiveValue())) {
found = true;
break;
}
}
if (!found) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The time "+v.primitiveValue()+" is not a valid option");
}
}
} else
hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate time answer option because no option list is provided");
}
private void checkStringOption( List<ValidationMessage> errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) {
Element v = answer.getNamedChild("valueString");
NodeStack ns = stack.push(v, -1, null, null);
if (qItem.getOption().size() > 0) {
List<StringType> list = new ArrayList<StringType>();
for (QuestionnaireItemOptionComponent components : qItem.getOption()) {
try {
if (components.getValue() != null) {
list.add(components.getValueStringType());
}
} catch (FHIRException e) {
// If it's the wrong type, just keep going
}
}
if (list.isEmpty() && !openChoice) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type string");
} else {
boolean found = false;
for (StringType item : list) {
if (item.getValue().equals((v.primitiveValue()))) {
found = true;
break;
}
}
if (!found) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The string "+v.primitiveValue()+" is not a valid option");
}
}
} else {
hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate string answer option because no option list is provided");
}
}
private void checkCodingOption( List<ValidationMessage> errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) {
Element v = answer.getNamedChild("valueCoding");
String system = v.getNamedChildValue("system");
String code = v.getNamedChildValue("code");
NodeStack ns = stack.push(v, -1, null, null);
if (qItem.getOption().size() > 0) {
List<Coding> list = new ArrayList<Coding>();
for (QuestionnaireItemOptionComponent components : qItem.getOption()) {
try {
if (components.getValue() != null) {
list.add(components.getValueCoding());
}
} catch (FHIRException e) {
// If it's the wrong type, just keep going
}
}
if (list.isEmpty() && !openChoice) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type coding");
} else {
boolean found = false;
for (Coding item : list) {
if (ObjectUtil.equals(item.getSystem(), system) && ObjectUtil.equals(item.getCode(), code)) {
found = true;
break;
}
}
if (!found) {
rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The code "+system+"::"+code+" is not a valid option");
}
}
} else
hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate Coding option because no option list is provided");
}
private String tail(String path) {
return path.substring(path.lastIndexOf(".") + 1);
}
private String tryParse(String ref) {
String[] parts = ref.split("\\/");
switch (parts.length) {
case 1:
return null;
case 2:
return checkResourceType(parts[0]);
default:
if (parts[parts.length - 2].equals("_history"))
return checkResourceType(parts[parts.length - 4]);
else
return checkResourceType(parts[parts.length - 2]);
}
}
private boolean typesAreAllReference(List<TypeRefComponent> theType) {
for (TypeRefComponent typeRefComponent : theType) {
if (typeRefComponent.getCode().equals("Reference") == false) {
return false;
}
}
return true;
}
private void validateBundle(List<ValidationMessage> errors, Element bundle, NodeStack stack) {
List<Element> entries = new ArrayList<Element>();
bundle.getNamedChildren("entry", entries);
String type = bundle.getNamedChildValue("type");
if (entries.size() == 0) {
rule(errors, IssueType.INVALID, stack.getLiteralPath(), !(type.equals("document") || type.equals("message")), "Documents or Messages must contain at least one entry");
} else {
Element firstEntry = entries.get(0);
NodeStack firstStack = stack.push(firstEntry, 0, null, null);
String fullUrl = firstEntry.getNamedChildValue("fullUrl");
if (type.equals("document")) {
Element resource = firstEntry.getNamedChild("resource");
NodeStack localStack = firstStack.push(resource, -1, null, null);
String id = resource.getNamedChildValue("id");
if (rule(errors, IssueType.INVALID, firstEntry.line(), firstEntry.col(), stack.addToLiteralPath("entry", ":0"), resource != null, "No resource on first entry")) {
validateDocument(errors, entries, resource, localStack.push(resource, -1, null, null), fullUrl, id);
}
}
if (type.equals("message"))
validateMessage(errors, bundle);
}
}
private void validateBundleReference(List<ValidationMessage> errors, List<Element> entries, Element ref, String name, NodeStack stack, String fullUrl, String type, String id) {
if (ref != null && !Utilities.noString(ref.getNamedChildValue("reference"))) {
Element target = resolveInBundle(entries, ref.getNamedChildValue("reference"), fullUrl, type, id);
rule(errors, IssueType.INVALID, target.line(), target.col(), stack.addToLiteralPath("reference"), target != null, "Unable to resolve the target of the reference in the bundle (" + name + ")");
}
}
private void validateContains(List<ValidationMessage> errors, String path, ElementDefinition child, ElementDefinition context, Element resource, Element element, NodeStack stack, IdStatus idstatus) throws FHIRException, FHIRException {
String resourceName = element.getType();
long t = System.nanoTime();
StructureDefinition profile = this.context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + resourceName);
sdTime = sdTime + (System.nanoTime() - t);
// special case: resource wrapper is reset if we're crossing a bundle boundary, but not otherwise
if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY)
resource = element;
if (rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), profile != null, "No profile found for contained resource of type '" + resourceName + "'"))
validateResource(errors, resource, element, profile, idstatus, stack);
}
private void validateDocument(List<ValidationMessage> errors, List<Element> entries, Element composition, NodeStack stack, String fullUrl, String id) {
// first entry must be a composition
if (rule(errors, IssueType.INVALID, composition.line(), composition.col(), stack.getLiteralPath(), composition.getType().equals("Composition"),
"The first entry in a document must be a composition")) {
// the composition subject and section references must resolve in the bundle
Element elem = composition.getNamedChild("subject");
if (rule(errors, IssueType.INVALID, composition.line(), composition.col(), stack.getLiteralPath(), elem != null, "A document composition must have a subject"))
validateBundleReference(errors, entries, elem, "Composition Subject", stack.push(elem, -1, null, null), fullUrl, "Composition", id);
validateSections(errors, entries, composition, stack, fullUrl, id);
}
}
// rule(errors, IssueType.INVALID, bundle.line(), bundle.col(), "Bundle", !"urn:guid:".equals(base), "The base 'urn:guid:' is not valid (use urn:uuid:)");
// rule(errors, IssueType.INVALID, entry.line(), entry.col(), localStack.getLiteralPath(), !"urn:guid:".equals(ebase), "The base 'urn:guid:' is not valid");
// rule(errors, IssueType.INVALID, entry.line(), entry.col(), localStack.getLiteralPath(), !Utilities.noString(base) || !Utilities.noString(ebase), "entry
// does not have a base");
// String firstBase = null;
// firstBase = ebase == null ? base : ebase;
long time = 0;
private void validateElement(List<ValidationMessage> errors, StructureDefinition profile, ElementDefinition definition, StructureDefinition cprofile, ElementDefinition context,
Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept) throws FHIRException, FHIRException {
// element.markValidation(profile, definition);
// System.out.println(" "+stack.getLiteralPath()+" "+Long.toString((System.nanoTime() - time) / 1000000));
// time = System.nanoTime();
checkInvariants(errors, stack.getLiteralPath(), profile, definition, null, null, resource, element);
// get the list of direct defined children, including slices
List<ElementDefinition> childDefinitions = ProfileUtilities.getChildMap(profile, definition.getName(), definition.getPath(), definition.getContentReference());
// 1. List the children, and remember their exact path (convenience)
List<ElementInfo> children = new ArrayList<InstanceValidator.ElementInfo>();
ChildIterator iter = new ChildIterator(stack.getLiteralPath(), element);
while (iter.next())
children.add(new ElementInfo(iter.name(), iter.element(), iter.path(), iter.count()));
// 2. assign children to a definition
// for each definition, for each child, check whether it belongs in the slice
ElementDefinition slice = null;
for (int i = 0; i < childDefinitions.size(); i++) {
ElementDefinition ed = childDefinitions.get(i);
boolean process = true;
// where are we with slicing
if (ed.hasSlicing()) {
if (slice != null && slice.getPath().equals(ed.getPath()))
throw new DefinitionException("Slice encountered midway through path on " + slice.getPath());
slice = ed;
process = false;
} else if (slice != null && !slice.getPath().equals(ed.getPath()))
slice = null;
if (process) {
for (ElementInfo ei : children) {
boolean match = false;
if (slice == null) {
match = nameMatches(ei.name, tail(ed.getPath()));
} else {
if (nameMatches(ei.name, tail(ed.getPath())))
match = sliceMatches(ei.element, ei.path, slice, ed, profile);
}
if (match) {
if (rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, ei.definition == null, "Element matches more than one slice")) {
ei.definition = ed;
ei.index = i;
}
}
}
}
}
int last = -1;
for (ElementInfo ei : children) {
if (ei.path.endsWith(".extension"))
rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, ei.definition != null, "Element is unknown or does not match any slice (url=\"" + ei.element.getNamedChildValue("url") + "\")");
else
rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, (ei.definition != null), "Element is unknown or does not match any slice");
rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, (ei.definition == null) || (ei.index >= last), "Element is out of order");
last = ei.index;
}
// 3. report any definitions that have a cardinality problem
for (ElementDefinition ed : childDefinitions) {
if (ed.getRepresentation().isEmpty()) { // ignore xml attributes
int count = 0;
for (ElementInfo ei : children)
if (ei.definition == ed)
count++;
if (ed.getMin() > 0) {
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(),
"Element '" + stack.getLiteralPath() + "." + tail(ed.getPath()) + "': minimum required = " + Integer.toString(ed.getMin()) + ", but only found " + Integer.toString(count));
}
if (ed.hasMax() && !ed.getMax().equals("*")) {
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), count <= Integer.parseInt(ed.getMax()),
"Element " + tail(ed.getPath()) + " @ " + stack.getLiteralPath() + ": max allowed = " + ed.getMax() + ", but found " + Integer.toString(count));
}
}
}
// 4. check order if any slices are orderd. (todo)
// 5. inspect each child for validity
for (ElementInfo ei : children) {
if (ei.definition != null) {
String type = null;
ElementDefinition typeDefn = null;
if (ei.definition.getType().size() == 1 && !ei.definition.getType().get(0).getCode().equals("*") && !ei.definition.getType().get(0).getCode().equals("Element")
&& !ei.definition.getType().get(0).getCode().equals("BackboneElement"))
type = ei.definition.getType().get(0).getCode();
else if (ei.definition.getType().size() == 1 && ei.definition.getType().get(0).getCode().equals("*")) {
String prefix = tail(ei.definition.getPath());
assert prefix.endsWith("[x]");
type = ei.name.substring(prefix.length() - 3);
if (isPrimitiveType(type))
type = Utilities.uncapitalize(type);
} else if (ei.definition.getType().size() > 1) {
String prefix = tail(ei.definition.getPath());
assert typesAreAllReference(ei.definition.getType()) || prefix.endsWith("[x]") : prefix;
prefix = prefix.substring(0, prefix.length() - 3);
for (TypeRefComponent t : ei.definition.getType())
if ((prefix + Utilities.capitalize(t.getCode())).equals(ei.name))
type = t.getCode();
if (type == null) {
TypeRefComponent trc = ei.definition.getType().get(0);
if (trc.getCode().equals("Reference"))
type = "Reference";
else
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false,
"The element " + ei.name + " is illegal. Valid types at this point are " + describeTypes(ei.definition.getType()));
}
} else if (ei.definition.getContentReference() != null) {
typeDefn = resolveNameReference(profile.getSnapshot(), ei.definition.getContentReference());
}
if (type != null) {
if (type.startsWith("@")) {
ei.definition = findElement(profile, type.substring(1));
type = null;
}
}
NodeStack localStack = stack.push(ei.element, ei.count, ei.definition, type == null ? typeDefn : resolveType(type));
String localStackLiterapPath = localStack.getLiteralPath();
String eiPath = ei.path;
assert(eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.path + " - localStack.getLiteralPath: " + localStackLiterapPath;
boolean thisIsCodeableConcept = false;
if (type != null) {
if (isPrimitiveType(type))
checkPrimitive(errors, ei.path, type, ei.definition, ei.element, profile);
else {
if (type.equals("Identifier"))
checkIdentifier(errors, ei.path, ei.element, ei.definition);
else if (type.equals("Coding"))
checkCoding(errors, ei.path, ei.element, profile, ei.definition, inCodeableConcept);
else if (type.equals("CodeableConcept")) {
checkCodeableConcept(errors, ei.path, ei.element, profile, ei.definition);
thisIsCodeableConcept = true;
} else if (type.equals("Reference"))
checkReference(errors, ei.path, ei.element, profile, ei.definition, actualType, localStack);
if (type.equals("Extension"))
checkExtension(errors, ei.path, ei.element, ei.definition, profile, localStack);
else if (type.equals("Resource"))
validateContains(errors, ei.path, ei.definition, definition, resource, ei.element, localStack, idStatusForEntry(element, ei)); // if
// (str.matches(".*([.,/])work\\1$"))
else {
StructureDefinition p = getProfileForType(type);
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.path, p != null, "Unknown type " + type)) {
validateElement(errors, p, p.getSnapshot().getElement().get(0), profile, ei.definition, resource, ei.element, type, localStack, thisIsCodeableConcept);
}
}
}
} else {
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), ei.definition != null, "Unrecognised Content " + ei.name))
validateElement(errors, profile, ei.definition, null, null, resource, ei.element, type, localStack, false);
}
}
}
}
private IdStatus idStatusForEntry(Element ep, ElementInfo ei) {
if (isBundleEntry(ei.path)) {
Element req = ep.getNamedChild("request");
Element resp = ep.getNamedChild("response");
Element fullUrl = ep.getNamedChild("fullUrl");
Element method = null;
Element url = null;
if (req != null) {
method = req.getNamedChild("method");
url = req.getNamedChild("url");
}
if (resp != null) {
return IdStatus.OPTIONAL;
} if (method == null) {
if (fullUrl == null)
return IdStatus.REQUIRED;
else if (fullUrl.primitiveValue().startsWith("urn:uuid:"))
return IdStatus.OPTIONAL;
else
return IdStatus.REQUIRED;
} else {
String s = method.primitiveValue();
if (s.equals("PUT")) {
if (url == null)
return IdStatus.REQUIRED;
else
return IdStatus.OPTIONAL; // or maybe prohibited? not clear
} else if (s.equals("POST"))
return IdStatus.OPTIONAL; // this should be prohibited, but see task 9102
else // actually, we should never get to here; a bundle entry with method get/delete should not have a resource
return IdStatus.OPTIONAL;
}
} else if (isParametersEntry(ei.path))
return IdStatus.OPTIONAL;
else
return IdStatus.REQUIRED;
}
private void checkInvariants(List<ValidationMessage> errors, String path, StructureDefinition profile, ElementDefinition ed, String typename, String typeProfile, Element resource, Element element) throws FHIRException, FHIRException {
for (ElementDefinitionConstraintComponent inv : ed.getConstraint()) {
if (inv.hasExpression()) {
ExpressionNode n = (ExpressionNode) inv.getUserData("validator.expression.cache");
if (n == null) {
long t = System.nanoTime();
n = fpe.parse(inv.getExpression());
fpeTime = fpeTime + (System.nanoTime() - t);
inv.setUserData("validator.expression.cache", n);
}
String msg;
boolean ok;
try {
long t = System.nanoTime();
ok = fpe.evaluateToBoolean(resource, element, n);
fpeTime = fpeTime + (System.nanoTime() - t);
msg = fpe.forLog();
} catch (Exception ex) {
ok = false;
msg = ex.getMessage();
}
if (!ok) {
if (inv.getSeverity() == ConstraintSeverity.ERROR)
rule(errors, IssueType.INVARIANT, element.line(), element.col(), path, ok, inv.getHuman()+" ("+msg+") ["+inv.getExpression()+"]");
else if (inv.getSeverity() == ConstraintSeverity.WARNING)
warning(errors, IssueType.INVARIANT, element.line(), element.line(), path, ok, inv.getHuman()+" ("+msg+") ["+inv.getExpression()+"]");
}
}
}
}
private void validateMessage(List<ValidationMessage> errors, Element bundle) {
// TODO Auto-generated method stub
}
private void validateObservation(List<ValidationMessage> errors, Element element, NodeStack stack) {
// all observations should have a subject, a performer, and a time
bpCheck(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), element.getNamedChild("subject") != null, "All observations should have a subject");
bpCheck(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), element.getNamedChild("performer") != null, "All observations should have a performer");
bpCheck(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), element.getNamedChild("effectiveDateTime") != null || element.getNamedChild("effectivePeriod") != null,
"All observations should have an effectiveDateTime or an effectivePeriod");
}
/*
* The actual base entry point
*/
private void validateResource(List<ValidationMessage> errors, Element resource, Element element, StructureDefinition profile, IdStatus idstatus, NodeStack stack) throws FHIRException, FHIRException {
assert stack != null;
assert resource != null;
// getting going - either we got a profile, or not.
boolean ok = true;
if (ok) {
String resourceName = element.getType();
if (profile == null) {
long t = System.nanoTime();
profile = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + resourceName);
sdTime = sdTime + (System.nanoTime() - t);
ok = rule(errors, IssueType.INVALID, element.line(), element.col(), stack.addToLiteralPath(resourceName), profile != null, "No profile found for resource type '" + resourceName + "'");
} else {
String type = profile.getKind() == StructureDefinitionKind.LOGICAL ? profile.getId() : profile.hasBaseType() && profile.getDerivation() == TypeDerivationRule.CONSTRAINT ? profile.getBaseType() : profile.getName();
// special case: we have a bundle, and the profile is not for a bundle. We'll try the first entry instead
if (!type.equals(resourceName) && resourceName.equals("Bundle")) {
Element first = getFirstEntry(element);
if (first != null && first.getType().equals(type)) {
element = first;
resourceName = element.getType();
idstatus = IdStatus.OPTIONAL; // why?
}
}
ok = rule(errors, IssueType.INVALID, -1, -1, stack.getLiteralPath(), type.equals(resourceName),
"Specified profile type was '" + type + "', but found type '" + resourceName + "'");
}
}
if (ok) {
if (idstatus == IdStatus.REQUIRED && (element.getNamedChild("id") == null))
rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), false, "Resource requires an id, but none is present");
else if (idstatus == IdStatus.PROHIBITED && (element.getNamedChild("id") != null))
rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), false, "Resource has an id, but none is allowed");
start(errors, resource, element, profile, stack); // root is both definition and type
}
}
private Element getFirstEntry(Element bundle) {
List<Element> list = new ArrayList<Element>();
bundle.getNamedChildren("entry", list);
if (list.isEmpty())
return null;
Element resource = list.get(0).getNamedChild("resource");
if (resource == null)
return null;
else
return resource;
}
private void validateSections(List<ValidationMessage> errors, List<Element> entries, Element focus, NodeStack stack, String fullUrl, String id) {
List<Element> sections = new ArrayList<Element>();
focus.getNamedChildren("entry", sections);
int i = 0;
for (Element section : sections) {
NodeStack localStack = stack.push(section, 1, null, null);
validateBundleReference(errors, entries, section.getNamedChild("content"), "Section Content", localStack, fullUrl, "Composition", id);
validateSections(errors, entries, section, localStack, fullUrl, id);
i++;
}
}
private boolean valueMatchesCriteria(Element value, ElementDefinition criteria) {
// throw new Error("validation of slices not done yet");
return false;
}
private boolean yearIsValid(String v) {
if (v == null) {
return false;
}
try {
int i = Integer.parseInt(v.substring(0, Math.min(4, v.length())));
return i >= 1800 && i <= 2100;
} catch (NumberFormatException e) {
return false;
}
}
public class ChildIterator {
private String basePath;
private Element parent;
private int cursor;
private int lastCount;
public ChildIterator(String path, Element element) {
parent = element;
basePath = path;
cursor = -1;
}
public int count() {
String nb = cursor == 0 ? "--" : parent.getChildren().get(cursor-1).getName();
String na = cursor >= parent.getChildren().size() - 1 ? "--" : parent.getChildren().get(cursor+1).getName();
if (name().equals(nb) || name().equals(na) ) {
return lastCount + 1;
} else
return -1;
}
public Element element() {
return parent.getChildren().get(cursor);
}
public String name() {
return element().getName();
}
public boolean next() {
if (cursor == -1) {
cursor++;
lastCount = 0;
} else {
String lastName = name();
cursor++;
if (cursor < parent.getChildren().size() && name().equals(lastName))
lastCount++;
else
lastCount = 0;
}
return cursor < parent.getChildren().size();
}
public String path() {
int i = count();
String sfx = "";
if (i > -1) {
sfx = "[" + Integer.toString(lastCount + 1) + "]";
}
return basePath + "." + name() + sfx;
}
}
private class NodeStack {
private ElementDefinition definition;
private Element element;
private ElementDefinition extension;
private String literalPath; // xpath format
private List<String> logicalPaths; // dotted format, various entry points
private NodeStack parent;
private ElementDefinition type;
public NodeStack() {
}
public NodeStack(Element element) {
this.element = element;
literalPath = element.getName();
}
public String addToLiteralPath(String... path) {
StringBuilder b = new StringBuilder();
b.append(getLiteralPath());
for (String p : path) {
if (p.startsWith(":")) {
b.append("[");
b.append(p.substring(1));
b.append("]");
} else {
b.append(".");
b.append(p);
}
}
return b.toString();
}
private ElementDefinition getDefinition() {
return definition;
}
private Element getElement() {
return element;
}
private String getLiteralPath() {
return literalPath == null ? "" : literalPath;
}
private List<String> getLogicalPaths() {
return logicalPaths == null ? new ArrayList<String>() : logicalPaths;
}
private ElementDefinition getType() {
return type;
}
private NodeStack push(Element element, int count, ElementDefinition definition, ElementDefinition type) {
NodeStack res = new NodeStack();
res.parent = this;
res.element = element;
res.definition = definition;
res.literalPath = getLiteralPath() + "." + element.getName();
if (count > -1)
res.literalPath = res.literalPath + "[" + Integer.toString(count) + "]";
res.logicalPaths = new ArrayList<String>();
if (type != null) {
// type will be bull if we on a stitching point of a contained resource, or if....
res.type = type;
String t = tail(definition.getPath());
for (String lp : getLogicalPaths()) {
res.logicalPaths.add(lp + "." + t);
if (t.endsWith("[x]"))
res.logicalPaths.add(lp + "." + t.substring(0, t.length() - 3) + type.getPath());
}
res.logicalPaths.add(type.getPath());
} else if (definition != null) {
for (String lp : getLogicalPaths())
res.logicalPaths.add(lp + "." + element.getName());
} else
res.logicalPaths.addAll(getLogicalPaths());
// CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
// for (String lp : res.logicalPaths)
// b.append(lp);
// System.out.println(res.literalPath+" : "+b.toString());
return res;
}
private void setType(ElementDefinition type) {
this.type = type;
}
}
private void checkForProcessingInstruction(List<ValidationMessage> errors, Document document) {
Node node = document.getFirstChild();
while (node != null) {
rule(errors, IssueType.INVALID, -1, -1, "(document)", node.getNodeType() != Node.PROCESSING_INSTRUCTION_NODE, "No processing instructions allowed in resources");
node = node.getNextSibling();
}
}
public class ElementInfo {
public int index;
public int count;
public ElementDefinition definition;
private Element element;
private String name;
private String path;
public ElementInfo(String name, Element element, String path, int count) {
this.name = name;
this.element = element;
this.path = path;
this.count = count;
}
public int col() {
return element.col();
}
public int line() {
return element.line();
}
}
public String reportTimes() {
String s = String.format("Times: overall = %d, tx = %d, sd = %d, load = %d, fpe = %d", overall, txTime, sdTime, loadTime, fpeTime);
overall = 0;
txTime = 0;
sdTime = 0;
loadTime = 0;
fpeTime = 0;
return s;
}
}