[GF#21240]: support for pattern primitive Types and CodeableConcept

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidator.java

@@ -121,6 +121,7 @@ import org.hl7.fhir.r5.model.TypeDetails;
 import org.hl7.fhir.r5.model.UriType;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.FHIRLexer.FHIRLexerException;
 import org.hl7.fhir.r5.utils.FHIRPathEngine;
 import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
@@ -872,15 +873,55 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         return true;
     return false;
   }
-
+  
-  private void checkCodeableConcept(List<ValidationMessage> errors, String path, Element focus, CodeableConcept fixed) {
+  
+  private boolean hasErrors(List<ValidationMessage> errors) {
+    if (errors!=null) {
+      for (ValidationMessage vm : errors) {
+        if (vm.getLevel() == IssueSeverity.FATAL || vm.getLevel() == IssueSeverity.ERROR) {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+  
+  private void checkCodeableConcept(List<ValidationMessage> errors, String path, Element focus, CodeableConcept fixed,
+      boolean pattern) {
     checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), "text", focus);
     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(),
+    if (pattern) {
-        "Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size()) + " coding elements")) {
+      if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() >= fixed.getCoding().size(),
-      for (int i = 0; i < codings.size(); i++)
+          "Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size())
-        checkFixedValue(errors, path + ".coding", codings.get(i), fixed.getCoding().get(i), "coding", focus);
+              + " coding elements")) {
+        for (int i = 0; i < fixed.getCoding().size(); i++) {
+          Coding fixedCoding = fixed.getCoding().get(i);
+          boolean found = false;
+          List<ValidationMessage> errorsFixed = null;
+          for (int j = 0; j < codings.size() && !found; ++j) {
+            errorsFixed = new ArrayList<ValidationMessage>();
+            checkFixedValue(errorsFixed, path + ".coding", codings.get(j), fixedCoding, "coding", focus);
+            if (!hasErrors(errorsFixed)) {
+              found = true;
+            }
+          }
+          if (!found) {
+            rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false,
+                "Expected patternCodeableConcept not found for"+
+                    " system: " + fixedCoding.getSystemElement().asStringValue() +
+                    " code: " + fixedCoding.getCodeElement().asStringValue() +
+                    " display: " + fixedCoding.getDisplayElement().asStringValue());
+          }
+        }
+      }
+    } else {
+      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", focus);
+      }
     }
   }
 
@@ -1292,8 +1333,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   // return b.toString();
   // }
   //
-
+  
   private void checkFixedValue(List<ValidationMessage> errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String propName, Element parent) {
+	  checkFixedValue(errors, path, focus, fixed, propName, parent, false);
+  }
+
+  private void checkFixedValue(List<ValidationMessage> errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String propName, Element parent, boolean pattern) {
     if ((fixed == null || fixed.isEmpty()) && focus == null)
       ; // this is all good
     else if (fixed == null && focus != null)
@@ -1356,7 +1401,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       else if (fixed instanceof HumanName)
         checkHumanName(errors, path, focus, (HumanName) fixed);
       else if (fixed instanceof CodeableConcept)
-        checkCodeableConcept(errors, path, focus, (CodeableConcept) fixed);
+        checkCodeableConcept(errors, path, focus, (CodeableConcept) fixed, pattern);
       else if (fixed instanceof Timing)
         checkTiming(errors, path, focus, (Timing) fixed);
       else if (fixed instanceof Period)
@@ -1622,8 +1667,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       }
     }
 
-    if (context.hasFixed())
+    if (context.hasFixed()) {
-      checkFixedValue(errors,path,e, context.getFixed(), context.getSliceName(), null);
+      checkFixedValue(errors,path,e, context.getFixed(), context.getSliceName(), null, false);
+    } 
+    if (context.hasPattern()) {
+      checkFixedValue(errors, path, e, context.getPattern(), context.getSliceName(), null, true);
+    }
 
     // for nothing to check
   }
@@ -3819,6 +3868,9 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
             if (ei.definition.hasFixed()) {
               checkFixedValue(errors,ei.path, ei.element, ei.definition.getFixed(), ei.definition.getSliceName(), null);
             }
+            if (ei.definition.hasPattern()) {
+                checkFixedValue(errors,ei.path, ei.element, ei.definition.getPattern(), ei.definition.getSliceName(), null, true);
+            }
           }
           if (type.equals("Identifier")) {
             checkIdentifier(errors, ei.path, ei.element, ei.definition);

org.hl7.fhir.validation/src/test/resources/validation-examples/manifest.json

@@ -484,11 +484,18 @@
         "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'"]
       },
       "observation-triglyceride-good.xml" : {
-        "errorCount": 0
+        "warningCount": 1,
+        "errorCount": 0,
+        "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\""]
       }, 
+      "observation-triglyceride-good2.xml" : {
+        "warningCount": 1,
+        "errorCount": 0,
+        "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\""]
+      },       
       "observation-triglyceride-bad-wrongcode.xml" : {
         "errorCount": 1,
-        "errors": ["ERROR: "]
+        "errors": ["ERROR: Observation.code: Expected patternCodeableConcept not found for system: http://loinc.org code: 35217-9 display: Triglyceride [Moles/​volume] in Serum or Plasma"]
       }
 		}
 	}

org.hl7.fhir.validation/src/test/resources/validation-examples/observation-triglyceride-good.xml

@@ -69,7 +69,7 @@
 			<system value="http://loinc.org" />
 			<code value="35217-9" />
 			<display
-				value="Triglyceride [Moles/​volume] in Serum or Plasma" />
+				value="Triglyceride [Moles/&#x200B;volume] in Serum or Plasma" />
 		</coding>
 		<coding>
 			<system value="http://snomed.info/sct" />

org.hl7.fhir.validation/src/test/resources/validation-examples/observation-triglyceride-good2.xml

@@ -0,0 +1,108 @@
+<Observation xmlns="http://hl7.org/fhir">
+	<!-- extract from http://hl7.org/fhir/triglyceride-examples.html, changed 
+		id from triglyceride and added explicit profile reference to http://hl7.org/fhir/StructureDefinition/triglyceride 
+		and added snomed ct code for triglyceride -->
+	<id value="observation-triglyceride-good2" />
+	<meta>
+		<profile
+			value="http://hl7.org/fhir/StructureDefinition/triglyceride" />
+	</meta>
+	<text>
+		<status value="generated" />
+		<div xmlns="http://www.w3.org/1999/xhtml">
+			<p>
+				<b> Generated Narrative with Details</b>
+			</p>
+			<p>
+				<b> id</b>
+				: triglyceride
+			</p>
+			<p>
+				<b> status</b>
+				: final
+			</p>
+			<p>
+				<b> code</b>
+				: Triglyceride
+				<span> (Details : {LOINC code '35217-9' = 'Triglyceride [Mass or
+					Moles/volume] in Serum or Plasma',
+					given as 'Triglyceride
+					[Moles/​volume] in Serum or Plasma'})
+				</span>
+			</p>
+			<p>
+				<b> subject</b>
+				:
+				<a> Patient/pat2</a>
+			</p>
+			<p>
+				<b> performer</b>
+				:
+				<a> Acme Laboratory, Inc</a>
+			</p>
+			<p>
+				<b> value</b>
+				: 1.3 mmol/L
+				<span> (Details: UCUM code mmol/L = 'mmol/L')</span>
+			</p>
+			<h3> ReferenceRanges</h3>
+			<table>
+				<tr>
+					<td> -</td>
+					<td>
+						<b> High</b>
+					</td>
+				</tr>
+				<tr>
+					<td> *</td>
+					<td>
+						2.0 mmol/L
+						<span> (Details: UCUM code mmol/L = 'mmol/L')</span>
+					</td>
+				</tr>
+			</table>
+		</div>
+	</text>
+	<status value="final" />
+	<code>
+    <coding>
+      <system value="http://snomed.info/sct" />
+      <code value="85600001" />
+      <display value="Triacylglycerol" />
+    </coding>
+		<coding>
+			<system value="http://loinc.org" />
+			<code value="35217-9" />
+			<display
+				value="Triglyceride [Moles/&#x200B;volume] in Serum or Plasma" />
+		</coding>
+    <coding>
+      <system value="http://snomed.info/sct" />
+      <code value="85600001" />
+      <display value="Triacylglycerol" />
+    </coding>
+		<text value="Triglyceride" />
+	</code>
+	<subject>
+		<reference value="Patient/pat2" />
+	</subject>
+	<performer>
+		<reference
+			value="Organization/1832473e-2fe0-452d-abe9-3cdb9879522f" />
+		<display value="Acme Laboratory, Inc" />
+	</performer>
+	<valueQuantity>
+		<value value="1.3" />
+		<unit value="mmol/L" />
+		<system value="http://unitsofmeasure.org" />
+		<code value="mmol/L" />
+	</valueQuantity>
+	<referenceRange>
+		<high>
+			<value value="2.0" />
+			<unit value="mmol/L" />
+			<system value="http://unitsofmeasure.org" />
+			<code value="mmol/L" />
+		</high>
+	</referenceRange>
+</Observation>