Add support for additional data during CQL evaluation (google#2420)

* Add support for additional data during CQL evaluation * Add unit test * Fix failing tests ✅ * Spotless Apply - Ignore white spaces on XML diff assertion * Refactor + Clean up build 💚 * Add default values for nullable params * Spotless clean * Collapse all overloaded FhirOperator evaluateLibrary functions to one * Fix build 💚 * Update test data ✅ * Fix failing benchmark test ✅ --------- Co-authored-by: Jing Tang <[email protected]>
opensrp · Mar 22, 2024 · a4f5f0f · a4f5f0f
1 parent bb19c19
commit a4f5f0f
Show file tree

Hide file tree

Showing 7 changed files with 77 additions and 106 deletions.
diff --git a/workflow-testing/src/main/resources/immunity-check/ImmunityCheck.json b/workflow-testing/src/main/resources/immunity-check/ImmunityCheck.json
diff --git a/workflow-testing/src/main/resources/immunity-check/ImmunizationHistory.json b/workflow-testing/src/main/resources/immunity-check/ImmunizationHistory.json
@@ -38,7 +38,10 @@
             "doseNumberPositiveInt": 2,
             "seriesDosesPositiveInt": 2
           }
-        ]
+        ],
+        "location": {
+          "reference": "Location/nairobi-047"
+        }
       }
     }
   ]

diff --git a/.../androidTest/java/com/google/android/fhir/workflow/benchmark/D_FhirJsonParserBenchmark.kt b/.../androidTest/java/com/google/android/fhir/workflow/benchmark/D_FhirJsonParserBenchmark.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright 2022-2023 Google LLC
+ * Copyright 2022-2024 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -71,7 +71,7 @@ class D_FhirJsonParserBenchmark {
       val fhirHelpersLibrary = jsonParser.parseResource(fhirHelpersJson) as Library
 
       assertThat(immunityCheckLibrary.id).isEqualTo("Library/ImmunityCheck-1.0.0")
-      assertThat(immunityCheckLibrary.content[0].data.size).isEqualTo(575)
+      assertThat(immunityCheckLibrary.content[0].data.size).isEqualTo(810)
       assertThat(fhirHelpersLibrary.id).isEqualTo("Library/FHIRHelpers-4.0.1")
       assertThat(fhirHelpersLibrary.content[0].data.size).isEqualTo(17845)
     }

diff --git a/...rc/androidTest/java/com/google/android/fhir/workflow/benchmark/F_CqlEvaluatorBenchmark.kt b/...rc/androidTest/java/com/google/android/fhir/workflow/benchmark/F_CqlEvaluatorBenchmark.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright 2022-2023 Google LLC
+ * Copyright 2022-2024 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -84,9 +84,9 @@ class F_CqlEvaluatorBenchmark {
 
       val results =
         fhirOperator.evaluateLibrary(
-          "http://localhost/Library/ImmunityCheck|1.0.0",
-          "d4d35004-24f8-40e4-8084-1ad75924514f",
-          setOf("CompletedImmunization"),
+          libraryUrl = "http://localhost/Library/ImmunityCheck|1.0.0",
+          patientId = "d4d35004-24f8-40e4-8084-1ad75924514f",
+          expressions = setOf("CompletedImmunization"),
         ) as Parameters
 
       assertThat(results.getParameterBool("CompletedImmunization")).isTrue()

diff --git a/.../src/androidTest/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateTest.kt b/.../src/androidTest/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateTest.kt
@@ -32,6 +32,7 @@ import kotlinx.coroutines.runBlocking
 import org.hl7.fhir.instance.model.api.IBaseResource
 import org.hl7.fhir.r4.model.Bundle
 import org.hl7.fhir.r4.model.Library
+import org.hl7.fhir.r4.model.Location
 import org.hl7.fhir.r4.model.Parameters
 import org.junit.Before
 import org.junit.Rule
@@ -122,15 +123,58 @@ class FhirOperatorLibraryEvaluateTest {
     // Load Library that checks if Patient has taken a vaccine
     knowledgeManager.install(copy("/immunity-check/ImmunityCheck.json"))
 
+    // Evaluates a specific Patient
+    val results =
+      fhirOperator.evaluateLibrary(
+        libraryUrl = "http://localhost/Library/ImmunityCheck|1.0.0",
+        patientId = "d4d35004-24f8-40e4-8084-1ad75924514f",
+        expressions = setOf("CompletedImmunization"),
+      ) as Parameters
+
+    assertThat(results.getParameterBool("CompletedImmunization")).isTrue()
+  }
+
+  @Test
+  fun evaluateImmunityCheckWithAdditionalData() = runBlocking {
+    val patientImmunizationHistory = load("/immunity-check/ImmunizationHistory.json") as Bundle
+    for (entry in patientImmunizationHistory.entry) {
+      fhirEngine.create(entry.resource)
+    }
+
+    // Load Library that checks if Patient has taken a vaccine
+    knowledgeManager.install(copy("/immunity-check/ImmunityCheck.json"))
+    knowledgeManager.install(copy("/immunity-check/FhirHelpers.json"))
+
+    val location =
+      """
+          {
+              "resourceType": "Location",
+              "id": "nairobi-047",
+              "name": "Nairobi mobile clinic"
+          }
+        """
+        .trimIndent()
+
+    val additionalDataBundle =
+      Bundle().apply {
+        addEntry(
+          Bundle.BundleEntryComponent().apply {
+            resource = jsonParser.parseResource(location) as Location
+          },
+        )
+      }
+
     // Evaluates a specific Patient
     val results =
       fhirOperator.evaluateLibrary(
         "http://localhost/Library/ImmunityCheck|1.0.0",
         "d4d35004-24f8-40e4-8084-1ad75924514f",
-        setOf("CompletedImmunization"),
+        null,
+        additionalDataBundle,
+        null,
       ) as Parameters
 
-    assertThat(results.getParameterBool("CompletedImmunization")).isTrue()
+    assertThat(results.hasParameter("GetFinalDoseWithLocationData")).isTrue()
   }
 
   @Test

diff --git a/workflow/src/main/java/com/google/android/fhir/workflow/FhirOperator.kt b/workflow/src/main/java/com/google/android/fhir/workflow/FhirOperator.kt
@@ -71,70 +71,6 @@ internal constructor(
   private val measureProcessor = R4MeasureProcessor(repository, measureEvaluationOptions)
   private val planDefinitionProcessor = PlanDefinitionProcessor(repository, evaluationSettings)
 
-  /**
-   * The function evaluates a FHIR library against the database.
-   *
-   * NOTE: The API may internally result in a blocking IO operation. The user should call the API
-   * from a worker thread or it may throw [BlockingMainThreadException] exception.
-   *
-   * @param libraryUrl the url of the Library to evaluate
-   * @param expressions names of expressions in the Library to evaluate. If null the result contains
-   *   all evaluations or variables in library.
-   * @return a Parameters resource that contains an evaluation result for each expression requested.
-   *   Or if expressions param is null then result contains all evaluations or variables in given
-   *   library.
-   */
-  @WorkerThread
-  fun evaluateLibrary(libraryUrl: String, expressions: Set<String>?): IBaseParameters {
-    return evaluateLibrary(libraryUrl, null, null, expressions)
-  }
-
-  /**
-   * The function evaluates a FHIR library against a patient's records.
-   *
-   * NOTE: The API may internally result in a blocking IO operation. The user should call the API
-   * from a worker thread or it may throw [BlockingMainThreadException] exception.
-   *
-   * @param libraryUrl the url of the Library to evaluate
-   * @param patientId the Id of the patient to be evaluated
-   * @param expressions names of expressions in the Library to evaluate. If null the result contains
-   *   all evaluations or variables in library.
-   * @return a Parameters resource that contains an evaluation result for each expression requested.
-   *   Or if expressions param is null then result contains all evaluations or variables in given
-   *   library.
-   */
-  @WorkerThread
-  fun evaluateLibrary(
-    libraryUrl: String,
-    patientId: String,
-    expressions: Set<String>?,
-  ): IBaseParameters {
-    return evaluateLibrary(libraryUrl, patientId, null, expressions)
-  }
-
-  /**
-   * The function evaluates a FHIR library against the database.
-   *
-   * NOTE: The API may internally result in a blocking IO operation. The user should call the API
-   * from a worker thread or it may throw [BlockingMainThreadException] exception.
-   *
-   * @param libraryUrl the url of the Library to evaluate
-   * @param parameters list of parameters to be passed to the CQL library
-   * @param expressions names of expressions in the Library to evaluate. If null the result contains
-   *   all evaluations or variables in library.
-   * @return a Parameters resource that contains an evaluation result for each expression requested.
-   *   Or if expressions param is null then result contains all evaluations or variables in given
-   *   library.
-   */
-  @WorkerThread
-  fun evaluateLibrary(
-    libraryUrl: String,
-    parameters: Parameters,
-    expressions: Set<String>?,
-  ): IBaseParameters {
-    return evaluateLibrary(libraryUrl, null, parameters, expressions)
-  }
-
   /**
    * The function evaluates a FHIR library against the database.
    *
@@ -144,6 +80,8 @@ internal constructor(
    * @param libraryUrl the url of the Library to evaluate
    * @param patientId the Id of the patient to be evaluated, if applicable
    * @param parameters list of parameters to be passed to the CQL library, if applicable
+   * @param additionalData Bundle of additional resources to be passed to the CQL library, if
+   *   applicable
    * @param expressions names of expressions in the Library to evaluate. If null the result contains
    *   all evaluations or variables in library.
    * @return a Parameters resource that contains an evaluation result for each expression requested.
@@ -153,15 +91,16 @@ internal constructor(
   @WorkerThread
   fun evaluateLibrary(
     libraryUrl: String,
-    patientId: String?,
-    parameters: Parameters?,
-    expressions: Set<String>?,
+    patientId: String? = null,
+    parameters: Parameters? = null,
+    additionalData: IBaseBundle? = null,
+    expressions: Set<String>? = null,
   ): IBaseParameters {
     return libraryProcessor.evaluate(
       /* url = */ libraryUrl,
       /* patientId = */ patientId,
       /* parameters = */ parameters,
-      /* additionalData = */ null,
+      /* additionalData = */ additionalData,
       /* expressions = */ expressions,
     )
   }

diff --git a/...low/src/test/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateJavaTest.kt b/...low/src/test/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateJavaTest.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright 2022-2023 Google LLC
+ * Copyright 2022-2024 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -116,9 +116,9 @@ class FhirOperatorLibraryEvaluateJavaTest {
     // Evaluates a specific Patient
     val results =
       fhirOperator.evaluateLibrary(
-        "http://localhost/Library/ImmunityCheck|1.0.0",
-        "d4d35004-24f8-40e4-8084-1ad75924514f",
-        setOf("CompletedImmunization"),
+        libraryUrl = "http://localhost/Library/ImmunityCheck|1.0.0",
+        patientId = "d4d35004-24f8-40e4-8084-1ad75924514f",
+        expressions = setOf("CompletedImmunization"),
       ) as Parameters
 
     assertThat(results.getParameterBool("CompletedImmunization")).isTrue()
@@ -140,7 +140,9 @@ class FhirOperatorLibraryEvaluateJavaTest {
     knowledgeManager.install(writeToFile(library))
 
     // Evaluates expression without any extra data
-    val results = fhirOperator.evaluateLibrary(library.url, setOf("GetName")) as Parameters
+    val results =
+      fhirOperator.evaluateLibrary(libraryUrl = library.url, expressions = setOf("GetName"))
+        as Parameters
 
     assertThat((results.parameterFirstRep.value as StringType).value).isEqualTo("MyName")
   }
@@ -171,7 +173,12 @@ class FhirOperatorLibraryEvaluateJavaTest {
       }
 
     // Evaluates the library with a parameter
-    val results = fhirOperator.evaluateLibrary(library.url, params, setOf("SumOne")) as Parameters
+    val results =
+      fhirOperator.evaluateLibrary(
+        libraryUrl = library.url,
+        parameters = params,
+        expressions = setOf("SumOne"),
+      ) as Parameters
 
     assertThat((results.parameterFirstRep.value as DecimalType).value).isEqualTo(BigDecimal(2))
   }