Issue #2162 - miscellaneous updates

Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
LinuxForHealth · Apr 7, 2021 · 28680ec · 28680ec
1 parent 83d6560
commit 28680ec
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Showing 27 changed files with 339 additions and 157 deletions.
diff --git a/fhir-path/src/main/java/com/ibm/fhir/path/function/ExpandFunction.java b/fhir-path/src/main/java/com/ibm/fhir/path/function/ExpandFunction.java
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -33,7 +33,7 @@
 import com.ibm.fhir.path.FHIRPathNode;
 import com.ibm.fhir.path.FHIRPathResourceNode;
 import com.ibm.fhir.path.evaluator.FHIRPathEvaluator.EvaluationContext;
-import com.ibm.fhir.term.spi.ExpansionParameters;
+import com.ibm.fhir.term.service.ExpansionParameters;
 
 public class ExpandFunction extends FHIRPathAbstractTermFunction {
     @Override

diff --git a/fhir-path/src/main/java/com/ibm/fhir/path/function/LookupFunction.java b/fhir-path/src/main/java/com/ibm/fhir/path/function/LookupFunction.java
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -29,8 +29,8 @@
 import com.ibm.fhir.path.FHIRPathNode;
 import com.ibm.fhir.path.FHIRPathResourceNode;
 import com.ibm.fhir.path.evaluator.FHIRPathEvaluator.EvaluationContext;
-import com.ibm.fhir.term.spi.LookupOutcome;
-import com.ibm.fhir.term.spi.LookupParameters;
+import com.ibm.fhir.term.service.LookupOutcome;
+import com.ibm.fhir.term.service.LookupParameters;
 
 public class LookupFunction extends FHIRPathAbstractTermFunction {
     @Override

diff --git a/fhir-path/src/main/java/com/ibm/fhir/path/function/MemberOfFunction.java b/fhir-path/src/main/java/com/ibm/fhir/path/function/MemberOfFunction.java
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2019, 2020
+ * (C) Copyright IBM Corp. 2019, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -40,7 +40,7 @@
 import com.ibm.fhir.path.FHIRPathType;
 import com.ibm.fhir.path.evaluator.FHIRPathEvaluator.EvaluationContext;
 import com.ibm.fhir.term.service.FHIRTermService;
-import com.ibm.fhir.term.spi.ValidationOutcome;
+import com.ibm.fhir.term.service.ValidationOutcome;
 
 /**
  * Implementation of the 'memberOf' FHIRPath function per: <a href="http://hl7.org/fhir/fhirpath.html#functions">http://hl7.org/fhir/fhirpath.html#functions</a>

diff --git a/fhir-path/src/main/java/com/ibm/fhir/path/function/TranslateFunction.java b/fhir-path/src/main/java/com/ibm/fhir/path/function/TranslateFunction.java
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -31,8 +31,8 @@
 import com.ibm.fhir.path.FHIRPathNode;
 import com.ibm.fhir.path.FHIRPathResourceNode;
 import com.ibm.fhir.path.evaluator.FHIRPathEvaluator.EvaluationContext;
-import com.ibm.fhir.term.spi.TranslationOutcome;
-import com.ibm.fhir.term.spi.TranslationParameters;
+import com.ibm.fhir.term.service.TranslationOutcome;
+import com.ibm.fhir.term.service.TranslationParameters;
 
 public class TranslateFunction extends FHIRPathAbstractTermFunction {
     @Override

diff --git a/fhir-path/src/main/java/com/ibm/fhir/path/function/ValidateCSFunction.java b/fhir-path/src/main/java/com/ibm/fhir/path/function/ValidateCSFunction.java
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -33,8 +33,8 @@
 import com.ibm.fhir.path.FHIRPathNode;
 import com.ibm.fhir.path.FHIRPathResourceNode;
 import com.ibm.fhir.path.evaluator.FHIRPathEvaluator.EvaluationContext;
-import com.ibm.fhir.term.spi.ValidationOutcome;
-import com.ibm.fhir.term.spi.ValidationParameters;
+import com.ibm.fhir.term.service.ValidationOutcome;
+import com.ibm.fhir.term.service.ValidationParameters;
 
 public class ValidateCSFunction extends FHIRPathAbstractTermFunction {
     @Override

diff --git a/fhir-path/src/main/java/com/ibm/fhir/path/function/ValidateVSFunction.java b/fhir-path/src/main/java/com/ibm/fhir/path/function/ValidateVSFunction.java
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -33,8 +33,8 @@
 import com.ibm.fhir.path.FHIRPathNode;
 import com.ibm.fhir.path.FHIRPathResourceNode;
 import com.ibm.fhir.path.evaluator.FHIRPathEvaluator.EvaluationContext;
-import com.ibm.fhir.term.spi.ValidationOutcome;
-import com.ibm.fhir.term.spi.ValidationParameters;
+import com.ibm.fhir.term.service.ValidationOutcome;
+import com.ibm.fhir.term.service.ValidationParameters;
 
 public class ValidateVSFunction extends FHIRPathAbstractTermFunction {
     @Override

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
@@ -20,12 +20,12 @@
 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;
 import java.util.Optional;
 import java.util.Set;
+import java.util.function.Function;
 import java.util.stream.Collectors;
 
 import org.apache.commons.configuration.Configuration;
@@ -116,16 +116,6 @@ 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);
@@ -134,16 +124,21 @@ public Concept getConcept(CodeSystem codeSystem, Code code) {
 
     @Override
     public Set<Concept> getConcepts(CodeSystem codeSystem) {
+        return getConcepts(codeSystem, Function.identity());
+    }
+
+    @Override
+    public <R> Set<R> getConcepts(CodeSystem codeSystem, Function<Concept, ? extends R> mapper) {
         checkArgument(codeSystem);
 
-        Set<Concept> concepts = new LinkedHashSet<>(getCount(codeSystem));
+        Set<R> concepts = new LinkedHashSet<>(getCount(codeSystem));
 
         GraphTraversal<Vertex, Vertex> g = hasVersion(hasUrl(vertices(), codeSystem.getUrl()), codeSystem.getVersion())
             .out("concept")
             .timeLimit(timeLimit);
         TimeLimitStep<?> timeLimitStep = getTimeLimitStep(g);
 
-        g.elementMap().toStream().forEach(elementMap -> concepts.add(createConcept(elementMap)));
+        g.elementMap().toStream().forEach(elementMap -> concepts.add(mapper.apply(createConcept(elementMap))));
 
         checkTimeLimit(timeLimitStep);
 
@@ -152,9 +147,14 @@ public Set<Concept> getConcepts(CodeSystem codeSystem) {
 
     @Override
     public Set<Concept> getConcepts(CodeSystem codeSystem, List<Filter> filters) {
+        return getConcepts(codeSystem, filters, Function.identity());
+    }
+
+    @Override
+    public <R> Set<R> getConcepts(CodeSystem codeSystem, List<Filter> filters, Function<Concept, ? extends R> mapper) {
         checkArguments(codeSystem, filters);
 
-        Set<Concept> concepts = new LinkedHashSet<>();
+        Set<R> concepts = new LinkedHashSet<>();
 
         GraphTraversal<Vertex, Vertex> g = vertices();
 
@@ -203,7 +203,7 @@ public Set<Concept> getConcepts(CodeSystem codeSystem, List<Filter> filters) {
         g = g.timeLimit(timeLimit);
         TimeLimitStep<?> timeLimitStep = getTimeLimitStep(g);
 
-        g.elementMap().toStream().forEach(elementMap -> concepts.add(createConcept(elementMap)));
+        g.elementMap().toStream().forEach(elementMap -> concepts.add(mapper.apply(createConcept(elementMap))));
 
         checkTimeLimit(timeLimitStep);
 

diff --git a/...-graph/src/main/java/com/ibm/fhir/term/graph/registry/SnomedRegistryResourceProvider.java b/...-graph/src/main/java/com/ibm/fhir/term/graph/registry/SnomedRegistryResourceProvider.java
@@ -35,7 +35,7 @@
 import com.ibm.fhir.registry.resource.FHIRRegistryResource;
 import com.ibm.fhir.term.registry.ImplicitValueSetRegistryResourceProvider;
 import com.ibm.fhir.term.service.FHIRTermService;
-import com.ibm.fhir.term.spi.ValidationOutcome;
+import com.ibm.fhir.term.service.ValidationOutcome;
 
 public class SnomedRegistryResourceProvider extends ImplicitValueSetRegistryResourceProvider {
     private static final Logger log = Logger.getLogger(SnomedRegistryResourceProvider.class.getName());

diff --git a/...bm/fhir/term/spi/ExpansionParameters.java → ...hir/term/service/ExpansionParameters.java b/...bm/fhir/term/spi/ExpansionParameters.java → ...hir/term/service/ExpansionParameters.java
@@ -1,10 +1,10 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
 
-package com.ibm.fhir.term.spi;
+package com.ibm.fhir.term.service;
 
 import static com.ibm.fhir.term.service.util.FHIRTermServiceUtil.getParameter;
 import static com.ibm.fhir.term.service.util.FHIRTermServiceUtil.getParameters;

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
@@ -21,6 +21,7 @@
 import java.util.ServiceLoader;
 import java.util.Set;
 import java.util.concurrent.CopyOnWriteArrayList;
+import java.util.function.Function;
 import java.util.stream.Collectors;
 
 import com.ibm.fhir.model.resource.CodeSystem;
@@ -39,18 +40,11 @@
 import com.ibm.fhir.model.type.Uri;
 import com.ibm.fhir.model.type.code.CodeSystemHierarchyMeaning;
 import com.ibm.fhir.model.type.code.ConceptSubsumptionOutcome;
+import com.ibm.fhir.term.service.LookupOutcome.Designation;
+import com.ibm.fhir.term.service.LookupOutcome.Property;
+import com.ibm.fhir.term.service.TranslationOutcome.Match;
 import com.ibm.fhir.term.service.provider.RegistryTermServiceProvider;
-import com.ibm.fhir.term.spi.ExpansionParameters;
 import com.ibm.fhir.term.spi.FHIRTermServiceProvider;
-import com.ibm.fhir.term.spi.LookupOutcome;
-import com.ibm.fhir.term.spi.LookupOutcome.Designation;
-import com.ibm.fhir.term.spi.LookupOutcome.Property;
-import com.ibm.fhir.term.spi.LookupParameters;
-import com.ibm.fhir.term.spi.TranslationOutcome;
-import com.ibm.fhir.term.spi.TranslationOutcome.Match;
-import com.ibm.fhir.term.spi.TranslationParameters;
-import com.ibm.fhir.term.spi.ValidationOutcome;
-import com.ibm.fhir.term.spi.ValidationParameters;
 import com.ibm.fhir.term.util.CodeSystemSupport;
 import com.ibm.fhir.term.util.ValueSetSupport;
 
@@ -267,14 +261,31 @@ public Concept getConcept(CodeSystem codeSystem, Code code) {
      * hierarchies have been flattened.
      *
      * @param codeSystem
-     *     the code system
+     *     the code system containing the set of Concept instances to be flattened
      * @return
-     *     flattened list of Concept instances for the given code system
+     *     flattened set of Concept instances for the given code system
      */
     public Set<Concept> getConcepts(CodeSystem codeSystem) {
         return findProvider(codeSystem).getConcepts(codeSystem);
     }
 
+    /**
+     * Get a set containing {@link R} instances mapped from concepts where all structural
+     * hierarchies have been flattened.
+     *
+     * @param <R>
+     *     the element type of the result set
+     * @param codeSystem
+     *     the code system containing the set of Concept instances to be flattened
+     * @param mapper
+     *     the function to be applied
+     * @return
+     *     flattened set of {@link R} instances mapped from concepts for the given code system
+     */
+    public <R> Set<R> getConcepts(CodeSystem codeSystem, Function<Concept, ? extends R> mapper) {
+        return findProvider(codeSystem).getConcepts(codeSystem, mapper);
+    }
+
     /**
      * Get a set containing {@link CodeSystem.Concept} instances where all structural
      * hierarchies have been flattened and filtered by the given set of value set include filters.
@@ -290,6 +301,25 @@ public Set<Concept> getConcepts(CodeSystem codeSystem, List<Filter> filters) {
         return findProvider(codeSystem).getConcepts(codeSystem, filters);
     }
 
+    /**
+     * Get a set containing {@link R} instances mapped from concepts where all structural
+     * hierarchies have been flattened and filtered by the given set of value set include filters.
+     *
+     * @param <R>
+     *     the element type of the result set
+     * @param codeSystem
+     *     the code system containing the set of Concept instances to be flattened / filtered
+     * @param filters
+     *     the value set include filters
+     * @param mapper
+     *     the function to be applied
+     * @return
+     *     flattened / filtered set of {@link R} instances mapped from concepts for the given code system
+     */
+    public <R> Set<R> getConcepts(CodeSystem codeSystem, List<Filter> filters, Function<Concept, ? extends R> mapper) {
+        return findProvider(codeSystem).getConcepts(codeSystem, filters, mapper);
+    }
+
     /**
      * Indicates whether the given code system contains a concept with the specified code.
      *

diff --git a/.../com/ibm/fhir/term/spi/LookupOutcome.java → .../ibm/fhir/term/service/LookupOutcome.java b/.../com/ibm/fhir/term/spi/LookupOutcome.java → .../ibm/fhir/term/service/LookupOutcome.java
@@ -4,7 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-package com.ibm.fhir.term.spi;
+package com.ibm.fhir.term.service;
 
 import static com.ibm.fhir.model.type.String.string;
 

diff --git a/...m/ibm/fhir/term/spi/LookupParameters.java → ...m/fhir/term/service/LookupParameters.java b/...m/ibm/fhir/term/spi/LookupParameters.java → ...m/fhir/term/service/LookupParameters.java
@@ -1,10 +1,10 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
 
-package com.ibm.fhir.term.spi;
+package com.ibm.fhir.term.service;
 
 import static com.ibm.fhir.term.service.util.FHIRTermServiceUtil.getParameter;
 import static com.ibm.fhir.term.service.util.FHIRTermServiceUtil.getParameters;

diff --git a/...ibm/fhir/term/spi/TranslationOutcome.java → ...fhir/term/service/TranslationOutcome.java b/...ibm/fhir/term/spi/TranslationOutcome.java → ...fhir/term/service/TranslationOutcome.java
@@ -1,10 +1,10 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
 
-package com.ibm.fhir.term.spi;
+package com.ibm.fhir.term.service;
 
 import static com.ibm.fhir.model.type.String.string;
 
@@ -21,7 +21,7 @@
 import com.ibm.fhir.model.type.String;
 import com.ibm.fhir.model.type.Uri;
 import com.ibm.fhir.model.type.code.ConceptMapEquivalence;
-import com.ibm.fhir.term.spi.TranslationOutcome.Match.Product;
+import com.ibm.fhir.term.service.TranslationOutcome.Match.Product;
 
 /**
  * This class is used to represent the outcome of the translate operation:

diff --git a/.../fhir/term/spi/TranslationParameters.java → ...r/term/service/TranslationParameters.java b/.../fhir/term/spi/TranslationParameters.java → ...r/term/service/TranslationParameters.java
@@ -1,10 +1,10 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
 
-package com.ibm.fhir.term.spi;
+package com.ibm.fhir.term.service;
 
 import static com.ibm.fhir.term.service.util.FHIRTermServiceUtil.getParameter;
 import static com.ibm.fhir.term.service.util.FHIRTermServiceUtil.getParameters;

diff --git a/.../ibm/fhir/term/spi/ValidationOutcome.java → .../fhir/term/service/ValidationOutcome.java b/.../ibm/fhir/term/spi/ValidationOutcome.java → .../fhir/term/service/ValidationOutcome.java
@@ -1,10 +1,10 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
 
-package com.ibm.fhir.term.spi;
+package com.ibm.fhir.term.service;
 
 import static com.ibm.fhir.model.type.String.string;
 

diff --git a/...m/fhir/term/spi/ValidationParameters.java → ...ir/term/service/ValidationParameters.java b/...m/fhir/term/spi/ValidationParameters.java → ...ir/term/service/ValidationParameters.java
@@ -1,10 +1,10 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
 
-package com.ibm.fhir.term.spi;
+package com.ibm.fhir.term.service;
 
 import static com.ibm.fhir.term.service.util.FHIRTermServiceUtil.getParameter;