[GF#21240]: support for pattern primitive Types and CodeableConcept
This commit is contained in:
Oliver Egger
parent
9a0c619d28
commit
e6f0b26e81
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@ -121,6 +121,7 @@ import org.hl7.fhir.r5.model.TypeDetails;
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import org.hl7.fhir.r5.model.UriType;
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import org.hl7.fhir.r5.model.ValueSet;
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import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
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import org.hl7.fhir.r5.test.utils.TestingUtilities;
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import org.hl7.fhir.r5.utils.FHIRLexer.FHIRLexerException;
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import org.hl7.fhir.r5.utils.FHIRPathEngine;
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import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
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@ -872,15 +873,55 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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return true;
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return false;
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}
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private void checkCodeableConcept(List<ValidationMessage> errors, String path, Element focus, CodeableConcept fixed) {
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private boolean hasErrors(List<ValidationMessage> errors) {
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if (errors!=null) {
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for (ValidationMessage vm : errors) {
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if (vm.getLevel() == IssueSeverity.FATAL || vm.getLevel() == IssueSeverity.ERROR) {
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return true;
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}
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}
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}
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return false;
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}
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private void checkCodeableConcept(List<ValidationMessage> errors, String path, Element focus, CodeableConcept fixed,
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boolean pattern) {
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checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), "text", focus);
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List<Element> codings = new ArrayList<Element>();
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focus.getNamedChildren("coding", codings);
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if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() == fixed.getCoding().size(),
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"Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size()) + " coding elements")) {
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for (int i = 0; i < codings.size(); i++)
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checkFixedValue(errors, path + ".coding", codings.get(i), fixed.getCoding().get(i), "coding", focus);
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if (pattern) {
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if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() >= fixed.getCoding().size(),
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"Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size())
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+ " coding elements")) {
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for (int i = 0; i < fixed.getCoding().size(); i++) {
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Coding fixedCoding = fixed.getCoding().get(i);
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boolean found = false;
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List<ValidationMessage> errorsFixed = null;
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for (int j = 0; j < codings.size() && !found; ++j) {
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errorsFixed = new ArrayList<ValidationMessage>();
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checkFixedValue(errorsFixed, path + ".coding", codings.get(j), fixedCoding, "coding", focus);
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if (!hasErrors(errorsFixed)) {
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found = true;
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}
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}
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if (!found) {
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rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false,
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"Expected patternCodeableConcept not found for"+
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" system: " + fixedCoding.getSystemElement().asStringValue() +
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" code: " + fixedCoding.getCodeElement().asStringValue() +
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" display: " + fixedCoding.getDisplayElement().asStringValue());
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}
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}
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}
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} else {
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if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() == fixed.getCoding().size(),
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"Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size())
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+ " coding elements")) {
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for (int i = 0; i < codings.size(); i++)
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checkFixedValue(errors, path + ".coding", codings.get(i), fixed.getCoding().get(i), "coding", focus);
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}
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}
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}
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@ -1292,8 +1333,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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// return b.toString();
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// }
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//
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private void checkFixedValue(List<ValidationMessage> errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String propName, Element parent) {
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checkFixedValue(errors, path, focus, fixed, propName, parent, false);
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}
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private void checkFixedValue(List<ValidationMessage> errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String propName, Element parent, boolean pattern) {
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if ((fixed == null || fixed.isEmpty()) && focus == null)
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; // this is all good
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else if (fixed == null && focus != null)
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@ -1356,7 +1401,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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else if (fixed instanceof HumanName)
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checkHumanName(errors, path, focus, (HumanName) fixed);
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else if (fixed instanceof CodeableConcept)
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checkCodeableConcept(errors, path, focus, (CodeableConcept) fixed);
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checkCodeableConcept(errors, path, focus, (CodeableConcept) fixed, pattern);
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else if (fixed instanceof Timing)
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checkTiming(errors, path, focus, (Timing) fixed);
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else if (fixed instanceof Period)
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@ -1622,8 +1667,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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}
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}
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if (context.hasFixed())
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checkFixedValue(errors,path,e, context.getFixed(), context.getSliceName(), null);
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if (context.hasFixed()) {
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checkFixedValue(errors,path,e, context.getFixed(), context.getSliceName(), null, false);
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}
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if (context.hasPattern()) {
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checkFixedValue(errors, path, e, context.getPattern(), context.getSliceName(), null, true);
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}
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// for nothing to check
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}
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@ -3819,6 +3868,9 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
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if (ei.definition.hasFixed()) {
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checkFixedValue(errors,ei.path, ei.element, ei.definition.getFixed(), ei.definition.getSliceName(), null);
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}
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if (ei.definition.hasPattern()) {
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checkFixedValue(errors,ei.path, ei.element, ei.definition.getPattern(), ei.definition.getSliceName(), null, true);
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}
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}
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if (type.equals("Identifier")) {
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checkIdentifier(errors, ei.path, ei.element, ei.definition);
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@ -484,11 +484,18 @@
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"errors": ["ERROR: Observation.code.coding.code: Value is '13457-7' but must be '35200-5'","ERROR: Observation.code.coding.display: Value is 'Cholesterol in LDL [Mass/volume] in Serum or Plasma by calculation' but must be 'Cholesterol [Moles/?volume] in Serum or Plasma'"]
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},
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"observation-triglyceride-good.xml" : {
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"errorCount": 0
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"warningCount": 1,
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"errorCount": 0,
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"warnings": ["WARNING: Observation.code.coding[1]: The display \"Triglyceride [Moles/volume] in Serum or Plasma\" is not a valid display for the code {http://loinc.org}35217-9 - should be one of [\"Triglyceride [Mass or Moles/volume] in Serum or Plasma\",\"Trigl SerPl-msCnc\""]
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},
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"observation-triglyceride-good2.xml" : {
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"warningCount": 1,
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"errorCount": 0,
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"warnings": ["WARNING: Observation.code.coding[2]: The display \"Triglyceride [Moles/volume] in Serum or Plasma\" is not a valid display for the code {http://loinc.org}35217-9 - should be one of [\"Triglyceride [Mass or Moles/volume] in Serum or Plasma\",\"Trigl SerPl-msCnc\""]
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},
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"observation-triglyceride-bad-wrongcode.xml" : {
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"errorCount": 1,
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"errors": ["ERROR: "]
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"errors": ["ERROR: Observation.code: Expected patternCodeableConcept not found for system: http://loinc.org code: 35217-9 display: Triglyceride [Moles/volume] in Serum or Plasma"]
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}
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}
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}
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@ -69,7 +69,7 @@
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<system value="http://loinc.org" />
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<code value="35217-9" />
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<display
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value="Triglyceride [Moles/​volume] in Serum or Plasma" />
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value="Triglyceride [Moles/​volume] in Serum or Plasma" />
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</coding>
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<coding>
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<system value="http://snomed.info/sct" />
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@ -0,0 +1,108 @@
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<Observation xmlns="http://hl7.org/fhir">
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<!-- extract from http://hl7.org/fhir/triglyceride-examples.html, changed
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id from triglyceride and added explicit profile reference to http://hl7.org/fhir/StructureDefinition/triglyceride
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and added snomed ct code for triglyceride -->
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<id value="observation-triglyceride-good2" />
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<meta>
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<profile
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value="http://hl7.org/fhir/StructureDefinition/triglyceride" />
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</meta>
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<text>
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<status value="generated" />
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<div xmlns="http://www.w3.org/1999/xhtml">
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<p>
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<b> Generated Narrative with Details</b>
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</p>
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<p>
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<b> id</b>
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: triglyceride
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</p>
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<p>
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<b> status</b>
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: final
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</p>
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<p>
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<b> code</b>
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: Triglyceride
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<span> (Details : {LOINC code '35217-9' = 'Triglyceride [Mass or
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Moles/volume] in Serum or Plasma',
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given as 'Triglyceride
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[Moles/​volume] in Serum or Plasma'})
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</span>
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</p>
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<p>
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<b> subject</b>
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:
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<a> Patient/pat2</a>
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</p>
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<p>
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<b> performer</b>
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:
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<a> Acme Laboratory, Inc</a>
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</p>
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<p>
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<b> value</b>
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: 1.3 mmol/L
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<span> (Details: UCUM code mmol/L = 'mmol/L')</span>
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</p>
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<h3> ReferenceRanges</h3>
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<table>
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<tr>
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<td> -</td>
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<td>
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<b> High</b>
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</td>
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</tr>
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<tr>
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<td> *</td>
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<td>
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2.0 mmol/L
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<span> (Details: UCUM code mmol/L = 'mmol/L')</span>
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</td>
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</tr>
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</table>
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</div>
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</text>
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<status value="final" />
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<code>
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<coding>
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<system value="http://snomed.info/sct" />
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<code value="85600001" />
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<display value="Triacylglycerol" />
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</coding>
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<coding>
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<system value="http://loinc.org" />
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<code value="35217-9" />
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<display
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value="Triglyceride [Moles/​volume] in Serum or Plasma" />
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</coding>
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<coding>
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<system value="http://snomed.info/sct" />
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<code value="85600001" />
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<display value="Triacylglycerol" />
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</coding>
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<text value="Triglyceride" />
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</code>
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<subject>
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<reference value="Patient/pat2" />
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</subject>
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<performer>
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<reference
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value="Organization/1832473e-2fe0-452d-abe9-3cdb9879522f" />
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<display value="Acme Laboratory, Inc" />
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</performer>
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<valueQuantity>
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<value value="1.3" />
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<unit value="mmol/L" />
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<system value="http://unitsofmeasure.org" />
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<code value="mmol/L" />
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</valueQuantity>
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<referenceRange>
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<high>
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<value value="2.0" />
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<unit value="mmol/L" />
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<system value="http://unitsofmeasure.org" />
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<code value="mmol/L" />
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</high>
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</referenceRange>
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</Observation>
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