Issue #2162 - introduce a new closure method signature

Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
LinuxForHealth · Apr 6, 2021 · f7ed8ac · f7ed8ac
1 parent 81c6aa5
commit f7ed8ac
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Showing 11 changed files with 213 additions and 14 deletions.
diff --git a/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/provider/GraphTermServiceProvider.java b/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/provider/GraphTermServiceProvider.java
@@ -20,6 +20,7 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
@@ -115,6 +116,16 @@ public Set<Concept> closure(CodeSystem codeSystem, Code code) {
         return concepts;
     }
 
+    @Override
+    public Map<Code, Set<Concept>> closure(CodeSystem codeSystem, Set<Code> codes) {
+        Map<Code, Set<Concept>> result = new LinkedHashMap<>();
+        for (Code code : codes) {
+            Set<Concept> closure = closure(codeSystem, code);
+            result.put(code, closure);
+        }
+        return result;
+    }
+
     @Override
     public Concept getConcept(CodeSystem codeSystem, Code code) {
         checkArguments(codeSystem, code);

diff --git a/...-graph/src/test/java/com/ibm/fhir/term/graph/test/SnomedRegistryResourceProviderTest.java b/...-graph/src/test/java/com/ibm/fhir/term/graph/test/SnomedRegistryResourceProviderTest.java
@@ -8,6 +8,7 @@
 
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import org.testng.Assert;
@@ -33,6 +34,11 @@ public Set<Concept> closure(CodeSystem codeSystem, Code code) {
                 return Collections.emptySet();
             }
 
+            @Override
+            public Map<Code, Set<Concept>> closure(CodeSystem codeSystem, Set<Code> codes) {
+                return Collections.emptyMap();
+            }
+
             @Override
             public Concept getConcept(CodeSystem codeSystem, Code code) {
                 return Concept.builder()

diff --git a/fhir-term/src/main/java/com/ibm/fhir/term/service/FHIRTermService.java b/fhir-term/src/main/java/com/ibm/fhir/term/service/FHIRTermService.java
@@ -13,7 +13,10 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Objects;
 import java.util.ServiceLoader;
 import java.util.Set;
@@ -59,6 +62,11 @@ public Set<Concept> closure(CodeSystem codeSystem, Code code) {
             return Collections.emptySet();
         }
 
+        @Override
+        public Map<Code, Set<Concept>> closure(CodeSystem codeSystem, Set<Code> codes) {
+            return Collections.emptyMap();
+        }
+
         @Override
         public Concept getConcept(CodeSystem codeSystem, Code code) {
             return null;
@@ -126,7 +134,9 @@ public Set<Concept> closure(Coding coding) {
         if (system != null && code != null) {
             java.lang.String url = (version != null) ? system.getValue() + "|" + version : system.getValue();
             CodeSystem codeSystem = CodeSystemSupport.getCodeSystem(url);
-            if (codeSystem != null && CodeSystemHierarchyMeaning.IS_A.equals(codeSystem.getHierarchyMeaning())) {
+            if (codeSystem != null &&
+                    (CodeSystemHierarchyMeaning.IS_A.equals(codeSystem.getHierarchyMeaning()) ||
+                            codeSystem.getHierarchyMeaning() == null)) {
                 FHIRTermServiceProvider provider = findProvider(codeSystem);
                 if (provider.hasConcept(codeSystem, code)) {
                     return provider.closure(codeSystem, code);
@@ -137,6 +147,80 @@ public Set<Concept> closure(Coding coding) {
         return Collections.emptySet();
     }
 
+    /**
+     * Generate a map containing the transitive closures for the code system concepts represented by the giving codings
+     *
+     * @param codings
+     *     the codings
+     * @return
+     *     a map of sets containing the transitive closures for the code system concepts represented by the given codings
+     */
+    public Map<Coding, Set<Concept>> closure(Set<Coding> codings) {
+        Map<Coding, Set<Concept>> result = new LinkedHashMap<>();
+
+        Map<CodeSystem, Set<Code>> codeSetMap = new LinkedHashMap<>();
+        Map<CodeSystem, Map<Code, Coding>> codingMapMap = new LinkedHashMap<>();
+
+        for (Coding coding : codings) {
+            Uri system = coding.getSystem();
+            java.lang.String version = (coding.getVersion() != null) ? coding.getVersion().getValue() : null;
+            Code code = coding.getCode();
+
+            if (system == null || code == null) {
+                return Collections.emptyMap();
+            }
+
+            java.lang.String url = (version != null) ? system.getValue() + "|" + version : system.getValue();
+
+            CodeSystem codeSystem = CodeSystemSupport.getCodeSystem(url);
+
+            if (codeSystem == null ||
+                    (!CodeSystemHierarchyMeaning.IS_A.equals(codeSystem.getHierarchyMeaning()) &&
+                            codeSystem.getHierarchyMeaning() != null)) {
+                return Collections.emptyMap();
+            }
+
+            codeSetMap.computeIfAbsent(codeSystem, k -> new LinkedHashSet<>()).add(code);
+            codingMapMap.computeIfAbsent(codeSystem, k -> new LinkedHashMap<>()).put(code, coding);
+        }
+
+        for (CodeSystem codeSystem : codeSetMap.keySet()) {
+            Set<Code> codes = codeSetMap.get(codeSystem);
+
+            FHIRTermServiceProvider provider = findProvider(codeSystem);
+            for (Code code : codes) {
+                if (!provider.hasConcept(codeSystem, code)) {
+                    return Collections.emptyMap();
+                }
+            }
+
+            Map<Code, Set<Concept>> closureMap = provider.closure(codeSystem, codes);
+
+            for (Code code : closureMap.keySet()) {
+                Coding coding = codingMapMap.get(codeSystem).get(code);
+                Set<Concept> closure = closureMap.get(code);
+                result.put(coding, closure);
+            }
+        }
+
+        return result;
+    }
+
+    /**
+     * Get a map of sets containing {@link CodeSystem.Concept} instances where all structural
+     * hierarchies have been flattened
+     *
+     * @param codeSystem
+     *     the code system
+     * @param codes
+     *     the set of roots of hierarchies containing the Concept instances to be flattened
+     * @return
+     *     a map containing flattened sets of Concept instances for the given trees
+     */
+    public Map<Code, Set<Concept>> closure(CodeSystem codeSystem, Set<Code> codes) {
+        return findProvider(codeSystem).closure(codeSystem, codes);
+    }
+
     /**
      * Expand the given value set
      *

diff --git a/fhir-term/src/main/java/com/ibm/fhir/term/service/provider/RegistryTermServiceProvider.java b/fhir-term/src/main/java/com/ibm/fhir/term/service/provider/RegistryTermServiceProvider.java
@@ -7,8 +7,10 @@
 package com.ibm.fhir.term.service.provider;
 
 import java.util.Collections;
+import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 
@@ -32,6 +34,16 @@ public Set<Concept> closure(CodeSystem codeSystem, Code code) {
         return CodeSystemSupport.getConcepts(concept);
     }
 
+    @Override
+    public Map<Code, Set<Concept>> closure(CodeSystem codeSystem, Set<Code> codes) {
+        Map<Code, Set<Concept>> result = new LinkedHashMap<>();
+        for (Code code : codes) {
+            Set<Concept> closure = closure(codeSystem, code);
+            result.put(code, closure);
+        }
+        return result;
+    }
+
     @Override
     public Concept getConcept(CodeSystem codeSystem, Code code) {
         Concept concept = CodeSystemSupport.findConcept(codeSystem, code);

diff --git a/fhir-term/src/main/java/com/ibm/fhir/term/spi/FHIRTermServiceProvider.java b/fhir-term/src/main/java/com/ibm/fhir/term/spi/FHIRTermServiceProvider.java
@@ -7,6 +7,7 @@
 package com.ibm.fhir.term.spi;
 
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import com.ibm.fhir.model.resource.CodeSystem;
@@ -28,6 +29,19 @@ public interface FHIRTermServiceProvider {
      */
     Set<Concept> closure(CodeSystem codeSystem, Code code);
 
+    /**
+     * Get a map of sets containing {@link CodeSystem.Concept} instances where all structural
+     * hierarchies have been flattened
+     *
+     * @param codeSystem
+     *     the code system
+     * @param codes
+     *     the set of roots of hierarchies containing the Concept instances to be flattened
+     * @return
+     *     a map containing flattened sets of Concept instances for the given trees
+     */
+    Map<Code, Set<Concept>> closure(CodeSystem codeSystem, Set<Code> codes);
+
     /**
      * Get the concept in the provided code system with the specified code.
      * Consumers should not expect the returned Concept to contain child concepts, even where

diff --git a/...rm/src/test/java/com/ibm/fhir/term/service/provider/test/FHIRTermServiceProviderTest.java b/...rm/src/test/java/com/ibm/fhir/term/service/provider/test/FHIRTermServiceProviderTest.java
@@ -13,6 +13,7 @@
 import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 
@@ -716,4 +717,40 @@ public void testHasConcept() {
         Assert.assertTrue(provider.hasConcept(codeSystem, Code.of("a")));
         Assert.assertFalse(provider.hasConcept(codeSystem, Code.of("zzz")));
     }
+
+    @Test
+    public void testClosure1() {
+        Set<Concept> concepts = provider.closure(codeSystem, Code.of("d"));
+
+        List<String> actual = concepts.stream()
+                .map(concept -> concept.getCode().getValue())
+                .collect(Collectors.toList());
+
+        List<String> expected = Arrays.asList("d", "q", "r", "s");
+
+        Assert.assertEquals(actual, expected);
+    }
+
+    @Test
+    public void testClosure2() {
+        Code code1 = Code.of("c");
+        Code code2 = Code.of("d");
+
+        Map<Code, Set<Concept>> closureMap = provider.closure(codeSystem, new HashSet<>(Arrays.asList(code1, code2)));
+
+        List<String> actual1 = closureMap.get(code1).stream()
+                .map(concept -> concept.getCode().getValue())
+                .collect(Collectors.toList());
+
+        List<String> expected1 = Arrays.asList("c", "o", "p");
+
+        List<String> actual2 = closureMap.get(code2).stream()
+                .map(concept -> concept.getCode().getValue())
+                .collect(Collectors.toList());
+
+        List<String> expected2 = Arrays.asList("d", "q", "r", "s");
+
+        Assert.assertEquals(actual1, expected1);
+        Assert.assertEquals(actual2, expected2);
+    }
 }
diff --git a/fhir-term/src/test/java/com/ibm/fhir/term/service/test/FHIRTermServiceTest.java b/fhir-term/src/test/java/com/ibm/fhir/term/service/test/FHIRTermServiceTest.java
@@ -18,7 +18,9 @@
 
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 
@@ -188,7 +190,7 @@ public void testSubsumes4() throws Exception {
     }
 
     @Test
-    public void testClosure() throws Exception {
+    public void testClosure1() throws Exception {
         Coding coding = Coding.builder()
                 .system(Uri.of("http://ibm.com/fhir/CodeSystem/cs5"))
                 .version(string("1.0.0"))
@@ -204,6 +206,34 @@ public void testClosure() throws Exception {
         assertEquals(actual, Arrays.asList("m", "p", "q", "r"));
     }
 
+    @Test
+    public void testClosure2() throws Exception {
+        Coding coding1 = Coding.builder()
+                .system(Uri.of("http://ibm.com/fhir/CodeSystem/cs5"))
+                .version(string("1.0.0"))
+                .code(Code.of("m"))
+                .build();
+
+        Coding coding2 = Coding.builder()
+                .system(Uri.of("http://ibm.com/fhir/CodeSystem/cs5"))
+                .version(string("1.0.0"))
+                .code(Code.of("n"))
+                .build();
+
+        Map<Coding, Set<Concept>> closure = FHIRTermService.getInstance().closure(new HashSet<>(Arrays.asList(coding1, coding2)));
+
+        Set<String> actual1 = closure.get(coding1).stream()
+                .map(contains -> contains.getCode().getValue())
+                .collect(Collectors.toSet());
+
+        Set<String> actual2 = closure.get(coding2).stream()
+                .map(contains -> contains.getCode().getValue())
+                .collect(Collectors.toSet());
+
+        assertEquals(actual1, new HashSet<>(Arrays.asList("m", "p", "q", "r")));
+        assertEquals(actual2, new HashSet<>(Arrays.asList("n", "s")));
+    }
+
     @Test
     public void testValidateCode1() throws Exception {
         Coding coding = Coding.builder()

diff --git a/...ation/fhir-operation-term/src/main/java/com/ibm/fhir/operation/term/ClosureOperation.java b/...ation/fhir-operation-term/src/main/java/com/ibm/fhir/operation/term/ClosureOperation.java
@@ -11,7 +11,6 @@
 import static com.ibm.fhir.server.util.FHIROperationUtil.getOutputParameters;
 
 import java.time.ZoneOffset;
-import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.Map;
 import java.util.Map.Entry;
@@ -33,6 +32,7 @@
 import com.ibm.fhir.model.type.DateTime;
 import com.ibm.fhir.model.type.Uri;
 import com.ibm.fhir.model.type.code.ConceptMapEquivalence;
+import com.ibm.fhir.model.type.code.IssueType;
 import com.ibm.fhir.model.type.code.PublicationStatus;
 import com.ibm.fhir.registry.FHIRRegistry;
 import com.ibm.fhir.server.operation.spi.FHIROperationContext;
@@ -60,15 +60,17 @@ protected Parameters doInvoke(
             String name = getName(parameters);
             Set<Coding> codingSet = getCodingSet(parameters);
             if (codingSet.stream().anyMatch(coding -> coding.getSystem() == null || coding.getCode() == null)) {
-                throw new FHIROperationException("Parameter(s) named 'concept' must have both a system and a code present");
+                throw buildExceptionWithIssue("Parameter(s) named 'concept' must have both a system and a code present", IssueType.INVALID);
             }
-            Map<Coding, Set<Concept>> result = new LinkedHashMap<>();
-            for (Coding coding : codingSet) {
-                Set<Concept> concepts = service.closure(coding);
+            Map<Coding, Set<Concept>> result = service.closure(codingSet);
+            if (result.isEmpty()) {
+                throw buildExceptionWithIssue("Closure cannot be computed for the provided input parameters", IssueType.NOT_SUPPORTED);
+            }
+            for (Coding coding : result.keySet()) {
+                Set<Concept> concepts = result.get(coding);
                 if (concepts.isEmpty()) {
-                    throw new FHIROperationException(String.format("Closure cannot be computed for concept '%s' from system '%s'", coding.getCode().getValue(), coding.getSystem().getValue()));
+                    throw buildExceptionWithIssue(String.format("Closure cannot be computed for concept '%s' from system '%s'", coding.getCode().getValue(), coding.getSystem().getValue()), IssueType.NOT_SUPPORTED);
                 }
-                result.put(coding, concepts);
             }
             ConceptMap conceptMap = buildConceptMap(name, result);
             return getOutputParameters(conceptMap);

diff --git a/...ation-term/src/main/java/com/ibm/fhir/operation/term/CodeSystemValidateCodeOperation.java b/...ation-term/src/main/java/com/ibm/fhir/operation/term/CodeSystemValidateCodeOperation.java
@@ -14,6 +14,7 @@
 import com.ibm.fhir.model.type.CodeableConcept;
 import com.ibm.fhir.model.type.Coding;
 import com.ibm.fhir.model.type.Element;
+import com.ibm.fhir.model.type.code.IssueType;
 import com.ibm.fhir.registry.FHIRRegistry;
 import com.ibm.fhir.server.operation.spi.FHIROperationContext;
 import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
@@ -67,15 +68,15 @@ private void validate(CodeSystem codeSystem, Element codedElement) throws FHIROp
                     return;
                 }
             }
-            throw new FHIROperationException("CodeableConcept does not contain a coding element that matches the specified CodeSystem url and/or version");
+            throw buildExceptionWithIssue("CodeableConcept does not contain a coding element that matches the specified CodeSystem url and/or version", IssueType.INVALID);
         }
         // codedElement.is(Coding.class)
         Coding coding = codedElement.as(Coding.class);
         if (coding.getSystem() != null && codeSystem.getUrl() != null && !coding.getSystem().equals(codeSystem.getUrl())) {
-            throw new FHIROperationException("Coding system does not match the specified CodeSystem url");
+            throw buildExceptionWithIssue("Coding system does not match the specified CodeSystem url", IssueType.INVALID);
         }
         if (coding.getVersion() != null && codeSystem.getVersion() != null && !coding.getVersion().equals(codeSystem.getVersion())) {
-            throw new FHIROperationException("Coding version does not match the specified CodeSystem version");
+            throw buildExceptionWithIssue("Coding version does not match the specified CodeSystem version", IssueType.INVALID);
         }
     }
 }