Merge pull request #48 from medizininformatik-initiative/support-refe…

…rence-resolve Add Support for Reference Resolve
medizininformatik-initiative · Nov 21, 2024 · 19cce29 · 19cce29
2 parents 370cabe + 06a56a7
commit 19cce29
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diff --git a/.github/integration-test/evaluate-reference-resolve.sh b/.github/integration-test/evaluate-reference-resolve.sh
@@ -0,0 +1,32 @@
+#!/bin/bash -e
+
+DOCKER_COMPOSE_FILE=.github/integration-test/$1/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/reference-resolve-measure.json
+export FDE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-reference-resolve-test
+export FDE_CONVERT_TO_CSV=false
+
+mkdir "$FDE_OUTPUT_DIR"
+docker compose -f "$DOCKER_COMPOSE_FILE" run -e TZ="$(cat /etc/timezone)" fhir-data-evaluator
+
+today=$(date +"%Y-%m-%d")
+OUTPUT_DIR=$(find "$FDE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
+REPORT=$(cat "$OUTPUT_DIR"/measure-report.json)
+
+EXPECTED_POPULATION_COUNT=1
+EXPECTED_STRATIFIER_COUNT=1
+
+POPULATION_COUNT=$(echo "$REPORT" | jq '.group[0].population[0].count')
+if [ "$POPULATION_COUNT" = "$EXPECTED_POPULATION_COUNT" ]; then
+  echo "OK 👍: population count ($POPULATION_COUNT) equals the expected count"
+else
+  echo "Fail 😞: population count ($POPULATION_COUNT) != $EXPECTED_POPULATION_COUNT"
+  exit 1
+fi
+
+STRATIFIER_COUNT=$(echo "$REPORT" | jq -r '.group[0].stratifier[0].stratum[0].population[0].count')
+if [ "$STRATIFIER_COUNT" = "$EXPECTED_STRATIFIER_COUNT" ]; then
+  echo "OK 👍: stratifier count ($STRATIFIER_COUNT) equals the expected count"
+else
+  echo "Fail 😞: stratifier ($STRATIFIER_COUNT) != $EXPECTED_STRATIFIER_COUNT"
+  exit 1
+fi
diff --git a/.github/integration-test/measures/reference-resolve-measure.json b/.github/integration-test/measures/reference-resolve-measure.json
@@ -0,0 +1,56 @@
+{
+  "resourceType": "Measure",
+  "meta": {
+    "profile": [
+      "http://fhir-data-evaluator/StructureDefinition/FhirDataEvaluatorBasicMeasure"
+    ]
+  },
+  "version": "1.0",
+  "url": "https://medizininformatik-initiative.de/fhir/fdpg/Measure/ExampleReferenceResolve",
+  "status": "active",
+  "experimental": false,
+  "publisher": "FDPG-Plus",
+  "name": "ExampleReferenceResolve",
+  "title": "Example Reference Resolve",
+  "description": "Example Measure to resolve references.",
+  "date": "2024-05-10",
+  "group": [
+    {
+      "description": "Simple Stratifier concept",
+      "population": [
+        {
+          "code": {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/measure-population",
+                "code": "initial-population"
+              }
+            ]
+          },
+          "criteria": {
+            "language": "text/x-fhir-query",
+            "expression": "MedicationAdministration?_include=MedicationAdministration:medication"
+          },
+          "id": "initial-population-identifier"
+        }
+      ],
+      "stratifier": [
+        {
+          "criteria": {
+            "language": "text/fhirpath",
+            "expression": "MedicationAdministration.medication.resolve().ofType(Medication).code.coding"
+          },
+          "code": {
+            "coding": [
+              {
+                "system": "http://fhir-evaluator/strat/system",
+                "code": "medication-coding"
+              }
+            ]
+          },
+          "id": "strat-1"
+        }
+      ]
+    }
+  ]
+}
diff --git a/.github/integration-test/test-data/Bundle.json b/.github/integration-test/test-data/Bundle.json
@@ -122,6 +122,53 @@
         "method": "POST",
         "url": "Observation/18c097fd-4263-8f4e-4307-f21ed5b01bcd"
       }
+    },
+    {
+      "resource": {
+        "resourceType": "MedicationAdministration",
+        "id": "med-adm-1",
+        "meta": {
+          "versionId": "974",
+          "lastUpdated": "2024-04-16T15:02:56.856Z"
+        },
+        "status": "completed",
+        "medicationReference": {
+          "reference": "Medication/med-1"
+        },
+        "effectiveDateTime": "2016-06-13T10:04:58Z"
+      },
+      "request": {
+        "method": "PUT",
+        "url": "MedicationAdministration/med-adm-1"
+      }
+    },
+    {
+      "resource": {
+        "resourceType": "Medication",
+        "id": "med-1",
+        "meta": {
+          "versionId": "974",
+          "lastUpdated": "2024-04-16T15:02:56.856Z",
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication"
+          ]
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
+              "code": "1000126",
+              "display": "1 ML medroxyprogesterone acetate 150 MG/ML Injection"
+            }
+          ],
+          "text": "1 ML medroxyprogesterone acetate 150 MG/ML Injection"
+        },
+        "status": "active"
+      },
+      "request": {
+        "method": "PUT",
+        "url": "Medication/med-1"
+      }
     }
   ]
 }
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -149,6 +149,9 @@ jobs:
       - name: Run Integration Test for Unique Count with Components and with CSV
         run: .github/integration-test/evaluate-unique-count-with-components-to-csv.sh ${{ matrix.test }}
 
+      - name: Run Integration Test for Reference Resolve
+        run: .github/integration-test/evaluate-reference-resolve.sh ${{ matrix.test }}
+
       - name: Run Integration Test to check if it correctly exits when there are insufficient writing permissions
         run: .github/integration-test/missing-permissions-test.sh
 

diff --git a/Documentation/example-measures/example-measure-11.json b/Documentation/example-measures/example-measure-11.json
@@ -0,0 +1,56 @@
+{
+  "resourceType": "Measure",
+  "meta": {
+    "profile": [
+      "http://fhir-data-evaluator/StructureDefinition/FhirDataEvaluatorBasicMeasure"
+    ]
+  },
+  "version": "1.0",
+  "url": "https://medizininformatik-initiative.de/fhir/fdpg/Measure/ExampleReferenceResolve",
+  "status": "active",
+  "experimental": false,
+  "publisher": "FDPG-Plus",
+  "name": "ExampleReferenceResolve",
+  "title": "Example Reference Resolve",
+  "description": "Example Measure to resolve references.",
+  "date": "2024-05-10",
+  "group": [
+    {
+      "description": "Simple Stratifier concept",
+      "population": [
+        {
+          "code": {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/measure-population",
+                "code": "initial-population"
+              }
+            ]
+          },
+          "criteria": {
+            "language": "text/x-fhir-query",
+            "expression": "MedicationAdministration?_include=MedicationAdministration:medication"
+          },
+          "id": "initial-population-identifier"
+        }
+      ],
+      "stratifier": [
+        {
+          "criteria": {
+            "language": "text/fhirpath",
+            "expression": "MedicationAdministration.medication.resolve().ofType(Medication).code.coding.where(system='http://fhir.de/CodeSystem/bfarm/atc')"
+          },
+          "code": {
+            "coding": [
+              {
+                "system": "http://fhir-evaluator/strat/system",
+                "code": "medication-coding"
+              }
+            ]
+          },
+          "id": "strat-1"
+        }
+      ]
+    }
+  ]
+}