Terminology: Reimplementing 'subsumes()' and 'subsumedBy()' with colu…

…mnar approach.

fhir-server/src/test/java/au/csiro/pathling/fhirpath/parser/ParserTest.java

@@ -316,6 +316,28 @@ void testCount() {
         .hasRows(expectedCountResult.changeValue(PATIENT_ID_bbd33563, 0L));
   }
 
+
+
+  @Test
+  void testSimpleSubsumesAndSubsumedBy() {
+
+    setupSubsumes(terminologyService);
+    // Viral sinusitis (disorder) = http://snomed.info/sct|444814009 not in (PATIENT_ID_2b36c1e2,
+    // PATIENT_ID_bbd33563, PATIENT_ID_7001ad9c)
+    // Chronic sinusitis (disorder) = http://snomed.info/sct|40055000 in (PATIENT_ID_7001ad9c)
+
+    assertThatResultOf(ResourceType.CONDITION,
+        "code.subsumedBy(http://snomed.info/sct|40055000)")
+        .isElementPath(BooleanCollection.class)
+        .selectOrderedResult()
+        .hasRows(spark, "responses/ParserTest/testSimpleSubsumes-one.tsv");
+
+    assertThatResultOf(ResourceType.CONDITION,
+        "code.subsumedBy($this)")
+        .isElementPath(BooleanCollection.class)
+        .selectOrderedResult()
+        .hasRows(spark, "responses/ParserTest/testSimpleSubsumes-self.tsv");
+  }
   @Test
   void testSubsumesAndSubsumedBy() {
 

fhir-server/src/test/resources/responses/ParserTest/testSimpleSubsumes-one.tsv

@@ -0,0 +1,71 @@
+01fac610-c309-46f8-9a0f-6b0f55c9915a	false
+031f1c86-16ec-42e1-a155-81456e778fed	false
+0447de38-1f2a-411c-9fd2-a9c62ab1f221	false
+061521f0-7f7e-41a5-ad35-b30fe958dea7	false
+06e446da-6d66-4d97-a457-4abf2a0d2e24	false
+08b4f1b6-f99b-400d-90f1-ec5cc6ed1556	false
+1146cf52-573f-4667-97c3-abf235f9a83b	false
+1452c50c-b0b9-472c-afb7-2f9e5a3c4717	false
+171ad058-c082-46ab-b9cc-d7bba6e4e3cd	true
+1cea8432-f8a0-4746-ab5c-8f195fc07c55	false
+1dcedab1-cf3c-46dc-859b-cc3fb63e8375	false
+21372b39-2be0-4d0d-85c4-5d7e250d8f78	false
+248e951c-e0ce-4e4b-afae-6273fd109c9d	false
+251ddff9-1588-4790-8f40-cd6ab1d9b7fc	false
+258191b8-2b42-4473-9ba2-be0ba3561767	false
+29386b12-9af9-4c21-9f82-858998b388bb	false
+31393667-dd7f-4c94-90c3-6cde75c67d3e	false
+31925a68-7a48-412c-b4f8-aef92498dda1	false
+38171e22-b35d-4161-be15-80243be37b99	false
+39170d67-8205-4636-84d7-d8575115d14c	false
+4025ceb3-04a6-41fb-8569-16a8dcce7ccc	false
+46d69851-eca3-42e2-b142-88c5578f6cff	false
+475461a2-3bd2-43fd-a5aa-7ce424203ae8	false
+4dd7824b-4b41-4402-bc42-de016e1bfcd9	false
+5300158c-92cb-40fe-bc14-a449d7b3c1c5	false
+5378726d-7f2b-4c83-9762-eaf385915fa7	false
+549d3ef5-a05e-4b8e-acba-3d70f26a82f6	false
+55cde383-2eb1-42d9-b5c6-698d6eade389	false
+5a406b78-ae23-4b4f-a3c8-9d9ed2f9d325	false
+5ef84858-0480-4a34-8f43-fc962fe627b2	false
+6464e20b-55ec-4685-be3e-55bc3b9602d4	false
+66b38727-96ea-43ad-bff7-5f4df5d779a9	false
+6794fbaf-e715-4e22-bafa-b7e594550ff7	false
+77fc5f45-e51d-41e2-8356-daa27ebd8268	false
+7d18555a-54c9-4c0a-bf3b-6305d0392a2a	false
+7ed34fb1-0bbf-4c41-a101-1316ec483aa7	false
+80787532-559e-4999-ac25-75c462ce4ef1	false
+8922ff1b-4bc5-41b4-8512-5aad1517e2eb	false
+8ddb74fc-46d5-4e94-a0ee-6761b292ae95	false
+8dfd419b-0b83-4ba7-8fe6-324e2f382bd6	false
+8f3ad6ad-a457-484e-a455-f0711e77b2ba	false
+9e598086-27bb-4e50-8988-9a40eb3c178f	false
+9ed0f743-5a93-46ba-bf3f-e00c6f8c5bbc	false
+a16f311d-d6dc-486e-8eb0-7cd53a5333ee	false
+aa5a32b3-3993-4eb5-afce-489d0e7413cf	false
+abecd476-3911-4a6b-a1c6-b8ecea2fe63e	false
+ad679e19-3e17-4c67-8b0d-dd4f7d862207	false
+b77b04ef-5eda-418c-a6fb-528a2d0a171a	false
+b8eccdce-7261-4402-9aa0-7360ae6bf53b	false
+b972a4a8-4f7e-4e9b-8e2c-71140bf0c6cc	false
+badbd940-9839-4472-aa66-3382d8823c80	false
+bb9c4fc1-795a-4492-b065-1f497fe18bb2	false
+be4b757d-70f1-464c-bb29-6f9a0f6cb05e	false
+c39927f7-d23a-475c-b325-c1de4b51e280	false
+c879c300-7fdf-4b53-aa6a-a2b4a266b30c	false
+c892bf2f-a7bc-407e-9508-c778a9b8761c	false
+d12274a5-9e03-4c78-ae3e-6cc27e91d737	false
+d554ba19-e081-4979-9c0c-a72cd6e5e8ea	false
+da8db730-f051-42d0-a2db-a3577d96e9bd	false
+db8c0b3e-48f0-43ac-aa03-9ae9a251cb82	false
+df98a2ea-8129-4d1a-9a9f-13a0292f6d1d	false
+e2f8e85b-ed68-42a1-bae2-b5d7c2a69a76	false
+e35f5823-4533-49e5-9652-79d733be6bef	false
+e620d7ee-6cfe-4f04-ba06-1d0b39f7624d	false
+e87fbe4b-74ef-44e4-8e36-70b2abb48895	false
+eaee8845-e4ed-42e1-9098-99b3f7e14dc3	false
+eaf99c09-419d-4162-8417-5a9d7e042cd4	false
+eb373264-da60-4e98-af7c-e3021fdd8d4b	false
+f1dd0d5f-c410-484b-984c-2ba38cee79ba	false
+f1fd855c-802c-417a-ab7c-14a3c9daafc6	false
+f41b6458-2358-43e7-ae34-d2a0fbe083d8	false

fhir-server/src/test/resources/responses/ParserTest/testSimpleSubsumes-self.tsv

@@ -0,0 +1,71 @@
+01fac610-c309-46f8-9a0f-6b0f55c9915a	true
+031f1c86-16ec-42e1-a155-81456e778fed	true
+0447de38-1f2a-411c-9fd2-a9c62ab1f221	true
+061521f0-7f7e-41a5-ad35-b30fe958dea7	true
+06e446da-6d66-4d97-a457-4abf2a0d2e24	true
+08b4f1b6-f99b-400d-90f1-ec5cc6ed1556	true
+1146cf52-573f-4667-97c3-abf235f9a83b	true
+1452c50c-b0b9-472c-afb7-2f9e5a3c4717	true
+171ad058-c082-46ab-b9cc-d7bba6e4e3cd	true
+1cea8432-f8a0-4746-ab5c-8f195fc07c55	true
+1dcedab1-cf3c-46dc-859b-cc3fb63e8375	true
+21372b39-2be0-4d0d-85c4-5d7e250d8f78	true
+248e951c-e0ce-4e4b-afae-6273fd109c9d	true
+251ddff9-1588-4790-8f40-cd6ab1d9b7fc	true
+258191b8-2b42-4473-9ba2-be0ba3561767	true
+29386b12-9af9-4c21-9f82-858998b388bb	true
+31393667-dd7f-4c94-90c3-6cde75c67d3e	true
+31925a68-7a48-412c-b4f8-aef92498dda1	true
+38171e22-b35d-4161-be15-80243be37b99	true
+39170d67-8205-4636-84d7-d8575115d14c	true
+4025ceb3-04a6-41fb-8569-16a8dcce7ccc	true
+46d69851-eca3-42e2-b142-88c5578f6cff	true
+475461a2-3bd2-43fd-a5aa-7ce424203ae8	true
+4dd7824b-4b41-4402-bc42-de016e1bfcd9	true
+5300158c-92cb-40fe-bc14-a449d7b3c1c5	true
+5378726d-7f2b-4c83-9762-eaf385915fa7	true
+549d3ef5-a05e-4b8e-acba-3d70f26a82f6	true
+55cde383-2eb1-42d9-b5c6-698d6eade389	true
+5a406b78-ae23-4b4f-a3c8-9d9ed2f9d325	true
+5ef84858-0480-4a34-8f43-fc962fe627b2	true
+6464e20b-55ec-4685-be3e-55bc3b9602d4	true
+66b38727-96ea-43ad-bff7-5f4df5d779a9	true
+6794fbaf-e715-4e22-bafa-b7e594550ff7	true
+77fc5f45-e51d-41e2-8356-daa27ebd8268	true
+7d18555a-54c9-4c0a-bf3b-6305d0392a2a	true
+7ed34fb1-0bbf-4c41-a101-1316ec483aa7	true
+80787532-559e-4999-ac25-75c462ce4ef1	true
+8922ff1b-4bc5-41b4-8512-5aad1517e2eb	true
+8ddb74fc-46d5-4e94-a0ee-6761b292ae95	true
+8dfd419b-0b83-4ba7-8fe6-324e2f382bd6	true
+8f3ad6ad-a457-484e-a455-f0711e77b2ba	true
+9e598086-27bb-4e50-8988-9a40eb3c178f	true
+9ed0f743-5a93-46ba-bf3f-e00c6f8c5bbc	true
+a16f311d-d6dc-486e-8eb0-7cd53a5333ee	true
+aa5a32b3-3993-4eb5-afce-489d0e7413cf	true
+abecd476-3911-4a6b-a1c6-b8ecea2fe63e	true
+ad679e19-3e17-4c67-8b0d-dd4f7d862207	true
+b77b04ef-5eda-418c-a6fb-528a2d0a171a	true
+b8eccdce-7261-4402-9aa0-7360ae6bf53b	true
+b972a4a8-4f7e-4e9b-8e2c-71140bf0c6cc	true
+badbd940-9839-4472-aa66-3382d8823c80	true
+bb9c4fc1-795a-4492-b065-1f497fe18bb2	true
+be4b757d-70f1-464c-bb29-6f9a0f6cb05e	true
+c39927f7-d23a-475c-b325-c1de4b51e280	true
+c879c300-7fdf-4b53-aa6a-a2b4a266b30c	true
+c892bf2f-a7bc-407e-9508-c778a9b8761c	true
+d12274a5-9e03-4c78-ae3e-6cc27e91d737	true
+d554ba19-e081-4979-9c0c-a72cd6e5e8ea	true
+da8db730-f051-42d0-a2db-a3577d96e9bd	true
+db8c0b3e-48f0-43ac-aa03-9ae9a251cb82	true
+df98a2ea-8129-4d1a-9a9f-13a0292f6d1d	true
+e2f8e85b-ed68-42a1-bae2-b5d7c2a69a76	true
+e35f5823-4533-49e5-9652-79d733be6bef	true
+e620d7ee-6cfe-4f04-ba06-1d0b39f7624d	true
+e87fbe4b-74ef-44e4-8e36-70b2abb48895	true
+eaee8845-e4ed-42e1-9098-99b3f7e14dc3	true
+eaf99c09-419d-4162-8417-5a9d7e042cd4	true
+eb373264-da60-4e98-af7c-e3021fdd8d4b	true
+f1dd0d5f-c410-484b-984c-2ba38cee79ba	true
+f1fd855c-802c-417a-ab7c-14a3c9daafc6	true
+f41b6458-2358-43e7-ae34-d2a0fbe083d8	true

fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/TerminologyFunctions.java

@@ -23,6 +23,7 @@
 import au.csiro.pathling.fhirpath.collection.StringCollection;
 import au.csiro.pathling.fhirpath.column.ColumnCtx;
 import au.csiro.pathling.fhirpath.validation.FhirpathFunction;
+import au.csiro.pathling.sql.Terminology;
 import java.util.Optional;
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
@@ -93,9 +94,9 @@ public static StringCollection designation(@Nonnull final CodingCollection input
   }
 
   /**
-   * A function that takes a set of Codings or CodeableConcepts as inputs and returns a set of boolean
-   * values, based upon whether each item is present within the ValueSet identified by the supplied
-   * URL.
+   * A function that takes a set of Codings or CodeableConcepts as inputs and returns a set of
+   * boolean values, based upon whether each item is present within the ValueSet identified by the
+   * supplied URL.
    *
    * @author John Grimes
    * @see <a href="https://pathling.csiro.au/docs/fhirpath/functions.html#memberof">memberOf</a>
@@ -107,4 +108,35 @@ public static BooleanCollection memberOf(@Nonnull final CodingCollection input,
         input.getCtx().callUDF("member_of", valueSetURL.getCtx().singular())
     );
   }
+
+
+  /**
+   * A function that takes a set of Codings or CodeableConcepts as inputs and returns a set of
+   * boolean values whether based upon whether each item subsumes one or more Codings or
+   * CodeableConcepts in the argument set.
+   *
+   * @author John Grimes
+   * @author Piotr Szul
+   * @see <a href="https://hl7.org/fhir/R4/fhirpath.html#functions">Additional functions</a>
+   */
+  @FhirpathFunction
+  public static BooleanCollection subsumes(@Nonnull final CodingCollection input,
+      @Nonnull final CodingCollection codes) {
+    return BooleanCollection.build(Terminology.subsumes(input.getColumn(), codes.getColumn()));
+  }
+
+  /**
+   * A function that takes a set of Codings or CodeableConcepts as inputs and returns a set of
+   * boolean values whether based upon whether each item  is subsumedBy one or more Codings or
+   * CodeableConcepts in the argument set.
+   *
+   * @author John Grimes
+   * @author Piotr Szul
+   * @see <a href="https://hl7.org/fhir/R4/fhirpath.html#functions">Additional functions</a>
+   */
+  @FhirpathFunction
+  public static BooleanCollection subsumedBy(@Nonnull final CodingCollection input,
+      @Nonnull final CodingCollection codes) {
+    return BooleanCollection.build(Terminology.subsumed_by(input.getColumn(), codes.getColumn()));
+  }
 }

fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/WrappedFunction.java

@@ -81,7 +81,7 @@ public Object resolveArgument(@Nonnull final Parameter parameter,
         //         "Parameter " + parameter + " is not nullable and no argument was provided"));
       } else if (Collection.class.isAssignableFrom(parameter.getType())) {
         // evaluate collection types 
-        return argument.eval(input, evaluationContext).getPureValue();
+        return resolveCollection(argument.eval(input, evaluationContext).getPureValue(), parameter);
       } else if (CollectionExpression.class.isAssignableFrom(parameter.getType())) {
         // bind with context
         return (CollectionExpression) (c -> argument.eval(c, evaluationContext).getPureValue());
@@ -97,19 +97,19 @@ public Object resolveArgument(@Nonnull final Parameter parameter,
     }
   }
 
-  public static Object resolveInput(@Nonnull final Collection input,
-      @Nonnull final Parameter inputParameter) {
-    if (CodingCollection.class.isAssignableFrom(inputParameter.getType())) {
+  public static Object resolveCollection(@Nonnull final Collection collection,
+      @Nonnull final Parameter parameter) {
+    if (CodingCollection.class.isAssignableFrom(parameter.getType())) {
       // evaluate collection types 
-      return input.asCoding().orElseThrow();
-    } else if (Collection.class.isAssignableFrom(inputParameter.getType())) {
+      return collection.asCoding().orElseThrow();
+    } else if (Collection.class.isAssignableFrom(parameter.getType())) {
       // evaluate collection types 
-      return input;
+      return collection;
     } else {
-      throw new RuntimeException("Cannot resolve input:" + inputParameter);
+      throw new RuntimeException("Cannot resolve input:" + parameter);
     }
   }
-  
+
   @Override
   @Nonnull
   public One<Collection> eval(@Nonnull final FunctionInput functionInput) {
@@ -130,7 +130,7 @@ public One<Collection> eval(@Nonnull final FunctionInput functionInput) {
 
     // we also may need to map the input here ....
 
-    final Object input = resolveInput(functionInput.getInput(), method.getParameters()[0]);
+    final Object input = resolveCollection(functionInput.getInput(), method.getParameters()[0]);
 
     final Object[] invocationArgs = Stream.concat(Stream.of(input),
         resolvedArguments).toArray(Object[]::new);

fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/registry/StaticFunctionRegistry.java

@@ -8,7 +8,6 @@
 import au.csiro.pathling.fhirpath.function.TerminologyFunctions;
 import au.csiro.pathling.fhirpath.function.UntilFunction;
 import au.csiro.pathling.fhirpath.function.WrappedFunction;
-import au.csiro.pathling.fhirpath.function.terminology.SubsumesFunction;
 import au.csiro.pathling.fhirpath.function.terminology.TranslateFunction;
 import com.google.common.collect.ImmutableMap.Builder;
 
@@ -26,8 +25,6 @@ public class StaticFunctionRegistry extends InMemoryFunctionRegistry<NamedFuncti
   public StaticFunctionRegistry() {
     super(new Builder<String, NamedFunction>()
         .put("resolve", new ResolveFunction())
-        .put("subsumes", new SubsumesFunction())
-        .put("subsumedBy", new SubsumesFunction(true))
         .put("iif", new IifFunction())
         .put("translate", new TranslateFunction())
         .put("until", new UntilFunction())