Issue #1107 - add support for Identifier pattern value constraints (#…

…1115)

Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>

docs/src/pages/guides/FHIRValidationGuide.md

@@ -32,7 +32,7 @@ Given a FHIR profile (structure definition) as input, the IBM FHIR Server Profil
 
 - Cardinality constraints (required and prohibited elements)
 - Fixed value constraints (Code and Uri data types)
-- Pattern value constraints (CodeableConcept daa type)
+- Pattern value constraints (CodeableConcept and Identifier data types)
 - Reference type constraints (FHIRPath resolve/is/conformsTo functions)
 - Extension constraints (FHIRPath `conformsTo` function)
 - Vocabulary constraints (FHIRPath `memberOf` function)

fhir-examples/src/main/resources/profiles-fhir-ig-carin-bb-json.txt

@@ -1,6 +1,6 @@
 OK         json/profiles/fhir-ig-carin-bb/Coverage-Coverage1.json
 OK         json/profiles/fhir-ig-carin-bb/ExplanationOfBenefit-EOB1.json
 OK         json/profiles/fhir-ig-carin-bb/Organization-Org1.json
-VALIDATION json/profiles/fhir-ig-carin-bb/Organization-Org45.json
+OK         json/profiles/fhir-ig-carin-bb/Organization-Org45.json
 OK         json/profiles/fhir-ig-carin-bb/Patient-Patient1.json
 OK         json/profiles/fhir-ig-carin-bb/PractitionerRole-PractitionerRole1.json

fhir-examples/src/main/resources/profiles-fhir-ig-carin-bb-xml.txt

@@ -1,6 +1,6 @@
 OK         xml/profiles/fhir-ig-carin-bb/Coverage-Coverage1.xml
 OK         xml/profiles/fhir-ig-carin-bb/ExplanationOfBenefit-EOB1.xml
 OK         xml/profiles/fhir-ig-carin-bb/Organization-Org1.xml
-VALIDATION xml/profiles/fhir-ig-carin-bb/Organization-Org45.xml
+OK         xml/profiles/fhir-ig-carin-bb/Organization-Org45.xml
 OK         xml/profiles/fhir-ig-carin-bb/Patient-Patient1.xml
 OK         xml/profiles/fhir-ig-carin-bb/PractitionerRole-PractitionerRole1.xml

fhir-ig-carin-bb/pom.xml

@@ -20,6 +20,11 @@
             <artifactId>fhir-registry</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-ig-us-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.testng</groupId>
             <artifactId>testng</artifactId>
@@ -31,6 +36,13 @@
             <version>${project.version}</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-validation</artifactId>
+            <version>${project.version}</version>
+            <scope>test</scope>
+            <type>test-jar</type>
+        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>fhir-examples</artifactId>

fhir-ig-carin-bb/src/test/java/com/ibm/fhir/ig/carin/bb/test/BBValidationTest.java

@@ -29,7 +29,7 @@ public void testBBValidation1() throws Exception {
             List<Issue> issues = FHIRValidator.validator().validate(explanationOfBenefit);
             issues.forEach(System.out::println);
             Assert.assertEquals(countErrors(issues), 1);
-            Assert.assertEquals(countWarnings(issues), 8);
+            Assert.assertEquals(countWarnings(issues), 7);
         }
     }
 
@@ -51,7 +51,7 @@ public void testBBValidation3() throws Exception {
             List<Issue> issues = FHIRValidator.validator().validate(explanationOfBenefit);
             issues.forEach(System.out::println);
             Assert.assertEquals(countErrors(issues), 1);
-            Assert.assertEquals(countWarnings(issues), 8);
+            Assert.assertEquals(countWarnings(issues), 7);
         }
     }
 

fhir-ig-carin-bb/src/test/java/com/ibm/fhir/ig/carin/bb/test/ExamplesValidationTest.java

@@ -6,64 +6,29 @@
 
 package com.ibm.fhir.ig.carin.bb.test;
 
-import static com.ibm.fhir.validation.util.FHIRValidationUtil.countErrors;
-import static org.testng.Assert.assertEquals;
-
-import java.io.BufferedReader;
-import java.io.Reader;
-import java.util.List;
-
 import org.testng.annotations.Test;
 
-import com.ibm.fhir.examples.ExamplesUtil;
 import com.ibm.fhir.examples.Index;
-import com.ibm.fhir.model.format.Format;
-import com.ibm.fhir.model.parser.FHIRParser;
-import com.ibm.fhir.model.resource.OperationOutcome.Issue;
-import com.ibm.fhir.model.resource.Resource;
-import com.ibm.fhir.model.spec.test.Expectation;
-import com.ibm.fhir.validation.FHIRValidator;
+import com.ibm.fhir.model.spec.test.R4ExamplesDriver;
+import com.ibm.fhir.model.spec.test.SerializationProcessor;
+import com.ibm.fhir.validation.test.ValidationProcessor;
 
 public class ExamplesValidationTest {
     @Test
     public void testBBValidationJson() throws Exception {
-        try (Reader reader = ExamplesUtil.indexReader(Index.PROFILES_CARRIN_BB_JSON); BufferedReader br = new BufferedReader(reader);) {
-            String line = br.readLine();
-            while (line != null) {
-                String[] tokens = line.split("\\s+");
-                Expectation exp = Expectation.valueOf(tokens[0]);
-                try (Reader in = ExamplesUtil.resourceReader(tokens[1])) {
-                    Resource resource = FHIRParser.parser(Format.JSON).parse(in);
-                    List<Issue> issues = FHIRValidator.validator().validate(resource);
-                    // Left for debug issues.forEach(System.out::println);
-
-                    if(!exp.equals(Expectation.VALIDATION) && !exp.equals(Expectation.PROCESS)) {
-                        assertEquals(countErrors(issues), 0);
-                    }
-                }
-                line = br.readLine();
-            }
-        }
+        R4ExamplesDriver driver = new R4ExamplesDriver();
+        SerializationProcessor processor = new SerializationProcessor();
+        driver.setProcessor(processor);
+        driver.setValidator(new ValidationProcessor());
+        driver.processIndex(Index.PROFILES_CARRIN_BB_JSON);
     }
 
     @Test
     public void testBBValidationXML() throws Exception {
-        try (Reader reader = ExamplesUtil.indexReader(Index.PROFILES_CARRIN_BB_XML); BufferedReader br = new BufferedReader(reader);) {
-            String line = br.readLine();
-            while (line != null) {
-                String[] tokens = line.split("\\s+");
-                Expectation exp = Expectation.valueOf(tokens[0]);
-                try (Reader in = ExamplesUtil.resourceReader(tokens[1])) {
-                    Resource resource = FHIRParser.parser(Format.XML).parse(in);
-                    List<Issue> issues = FHIRValidator.validator().validate(resource);
-                    // Left for debug issues.forEach(System.out::println);
-
-                    if(!exp.equals(Expectation.VALIDATION) && !exp.equals(Expectation.PROCESS)) {
-                        assertEquals(countErrors(issues), 0);
-                    }
-                }
-                line = br.readLine();
-            }
-        }
+        R4ExamplesDriver driver = new R4ExamplesDriver();
+        SerializationProcessor processor = new SerializationProcessor();
+        driver.setProcessor(processor);
+        driver.setValidator(new ValidationProcessor());
+        driver.processIndex(Index.PROFILES_CARRIN_BB_XML);
     }
 }

fhir-path/src/main/java/com/ibm/fhir/path/function/MemberOfFunction.java

@@ -31,7 +31,6 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
-import com.ibm.fhir.model.resource.CodeSystem;
 import com.ibm.fhir.model.resource.ValueSet;
 import com.ibm.fhir.model.resource.ValueSet.Expansion;
 import com.ibm.fhir.model.resource.ValueSet.Expansion.Contains;
@@ -103,9 +102,8 @@ public Collection<FHIRPathNode> apply(EvaluationContext evaluationContext, Colle
             if (!codeSetMap.isEmpty()) {
                 if (element.is(Code.class)) {
                     String system = getSystem(evaluationContext.getTree().getParent(elementNode));
-                    String version = FHIRRegistry.getInstance().getLatestVersion(system, CodeSystem.class);
                     String code = element.as(Code.class).getValue();
-                    if (contains(codeSetMap, system, version, code)) {
+                    if (contains(codeSetMap, system, null, code)) {
                         return SINGLETON_TRUE;
                     }
                 } else if (element.is(Coding.class)) {
@@ -150,7 +148,7 @@ private Collection<FHIRPathNode> membershipCheckFailed(EvaluationContext evaluat
 
     private boolean contains(Map<String, Set<String>> codeSetMap, Coding coding) {
         String system = (coding.getSystem() != null) ? coding.getSystem().getValue() : null;
-        String version = (coding.getVersion() != null) ? coding.getVersion().getValue() : FHIRRegistry.getInstance().getLatestVersion(system, CodeSystem.class);
+        String version = (coding.getVersion() != null) ? coding.getVersion().getValue() : null;
         String code = (coding.getCode() != null) ? coding.getCode().getValue() : null;
         return contains(codeSetMap, system, version, code);
     }

fhir-profile/src/main/java/com/ibm/fhir/profile/ConstraintGenerator.java

@@ -34,6 +34,7 @@
 import com.ibm.fhir.model.type.ElementDefinition;
 import com.ibm.fhir.model.type.ElementDefinition.Binding;
 import com.ibm.fhir.model.type.ElementDefinition.Type;
+import com.ibm.fhir.model.type.Identifier;
 import com.ibm.fhir.model.type.Uri;
 import com.ibm.fhir.model.type.code.BindingStrength;
 import com.ibm.fhir.model.util.ModelSupport;
@@ -161,7 +162,7 @@ private String generate(Node node) {
         ElementDefinition elementDefinition = node.elementDefinition;
 
         if (hasValueConstraint(elementDefinition)) {
-            return generateValueConstraint(elementDefinition);
+            return generateValueConstraint(node);
         }
 
         if (hasReferenceTypeConstraint(elementDefinition)) {
@@ -170,7 +171,7 @@ private String generate(Node node) {
 
         if (hasVocabularyConstraint(elementDefinition)) {
             String expr = generateVocabularyConstraint(elementDefinition);
-            if (node.children.stream().noneMatch(child -> hasConstraint(child))) {
+            if (node.children.isEmpty()) {
                 // no constraints exist on the children of this node, the expression is complete
                 return expr;
             }
@@ -219,18 +220,8 @@ private String generate(Node node) {
                 sb.append(".where(");
             }
 
-            StringJoiner joiner = new StringJoiner(" and ");
-            for (Node child : node.children) {
-                if (isExtensionUrl(child.elementDefinition)) {
-                    continue;
-                }
-                if (isOptional(child.elementDefinition)) {
-                    joiner.add("(" + generate(child) + ")");
-                } else {
-                    joiner.add(generate(child));
-                }
-            }
-            sb.append(joiner.toString());
+            sb.append(generate(node.children));
+
             sb.append(")");
 
             if (!isRepeating(elementDefinition) || isSlice(elementDefinition)) {
@@ -250,16 +241,32 @@ private String generate(Node node) {
         return sb.toString();
     }
 
+    private String generate(List<Node> nodes) {
+        StringJoiner joiner = new StringJoiner(" and ");
+        for (Node node : nodes) {
+            if (isExtensionUrl(node.elementDefinition)) {
+                continue;
+            }
+            if (isOptional(node.elementDefinition)) {
+                joiner.add("(" + generate(node) + ")");
+            } else {
+                joiner.add(generate(node));
+            }
+        }
+        return joiner.toString();
+    }
+
     private String generateExtensionConstraint(ElementDefinition elementDefinition) {
         StringBuilder sb = new StringBuilder();
 
         Type type = getTypes(elementDefinition).get(0);
         String profile = getProfiles(type).get(0);
 
+        sb.append("extension('").append(profile).append("').count()");
+
         Integer min = elementDefinition.getMin().getValue();
         String max = elementDefinition.getMax().getValue();
 
-        sb.append("extension('").append(profile).append("').count()");
         if ("*".equals(max)) {
             sb.append(" >= ").append(min);
         } else if ("1".equals(max)) {
@@ -293,9 +300,11 @@ private String generateFixedValueConstraint(ElementDefinition elementDefinition)
         return sb.toString();
     }
 
-    private String generatePatternValueConstraint(ElementDefinition elementDefinition) {
+    private String generatePatternValueConstraint(Node node) {
         StringBuilder sb = new StringBuilder();
 
+        ElementDefinition elementDefinition = node.elementDefinition;
+
         String identifier = getIdentifier(elementDefinition);
         sb.append(identifier);
 
@@ -304,13 +313,38 @@ private String generatePatternValueConstraint(ElementDefinition elementDefinitio
             CodeableConcept codeableConcept = pattern.as(CodeableConcept.class);
             Coding coding = codeableConcept.getCoding().get(0);
             String system = (coding.getSystem() != null) ? coding.getSystem().getValue() : null;
+
             sb.append(".where(coding.where(");
+
             if (system != null) {
                 sb.append("system = '").append(system).append("' and ");
             }
-            sb.append("code = '")
-                .append(coding.getCode().getValue())
-                .append("').exists()).exists()");
+
+            sb.append("code = '").append(coding.getCode().getValue()).append("').exists()).exists()");
+        } else if (pattern.is(Identifier.class)) {
+            Identifier _identifier = pattern.as(Identifier.class);
+            String system = _identifier.getSystem().getValue();
+
+            sb.append(".where(system = '").append(system).append("').count()");
+
+            Integer min = elementDefinition.getMin().getValue();
+            String max = elementDefinition.getMax().getValue();
+
+            if ("*".equals(max)) {
+                sb.append(" >= ").append(min);
+            } else if ("1".equals(max)) {
+                if (min == 0) {
+                    sb.append(" <= 1");
+                } else {
+                    sb.append(" = 1");
+                }
+            } else {
+                sb.append(" >= ").append(min).append(" and ").append(identifier).append(".where(system = '").append(system).append("').count() <= ").append(max);
+            }
+
+            if (!node.children.isEmpty()) {
+                sb.append(" and (").append(identifier).append(".where(system = '").append(system).append("').exists()").append(" implies (").append(identifier).append(".where(system = '").append(system).append("' and ").append(generate(node.children)).append(")))");
+            }
         }
 
         return sb.toString();
@@ -358,8 +392,8 @@ private String generateReferenceTypeConstraint(ElementDefinition elementDefiniti
         return sb.toString();
     }
 
-    private String generateValueConstraint(ElementDefinition elementDefinition) {
-        return hasFixedValueConstraint(elementDefinition) ? generateFixedValueConstraint(elementDefinition) : generatePatternValueConstraint(elementDefinition);
+    private String generateValueConstraint(Node node) {
+        return hasFixedValueConstraint(node.elementDefinition) ? generateFixedValueConstraint(node.elementDefinition) : generatePatternValueConstraint(node);
     }
 
     private String generateVocabularyConstraint(ElementDefinition elementDefinition) {
@@ -494,9 +528,13 @@ private boolean hasFixedValueConstraint(ElementDefinition elementDefinition) {
     }
 
     private boolean hasPatternValueConstraint(ElementDefinition elementDefinition) {
-        return (elementDefinition.getPattern() instanceof CodeableConcept) &&
-                (elementDefinition.getPattern().as(CodeableConcept.class).getCoding().stream()
-                        .allMatch(coding -> (coding.getCode() != null && coding.getCode().getValue() != null)));
+        Element pattern = elementDefinition.getPattern();
+        return ((pattern instanceof CodeableConcept) &&
+                (pattern.as(CodeableConcept.class).getCoding().stream()
+                        .allMatch(coding -> (coding.getCode() != null && coding.getCode().getValue() != null)))) ||
+               ((pattern instanceof Identifier) &&
+                (pattern.as(Identifier.class).getSystem() != null) &&
+                (pattern.as(Identifier.class).getSystem().getValue() != null));
     }
 
     private boolean hasReferenceTypeConstraint(ElementDefinition elementDefinition) {