Release v1.0.0

.github/integration-test/evaluate-multiple-stratifiers.sh

@@ -0,0 +1,93 @@
+#!/bin/bash -e
+
+INPUT_MEASURE=$1
+BASE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-multiple-stratifiers
+mkdir "$BASE_OUTPUT_DIR"
+
+docker run -v "$INPUT_MEASURE":/app/measure.json -v "$BASE_OUTPUT_DIR":/app/output/ -e FHIR_SERVER=http://fhir-server:8080/fhir \
+      -e TZ="$(cat /etc/timezone)" --network integration-test_testing-network fhir-data-evaluator
+
+today=$(date +"%Y-%m-%d")
+OUTPUT_DIR=$(find "$BASE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
+REPORT="$OUTPUT_DIR/measure-report.json"
+
+find_stratum() {
+  local STRATIFIER_INDEX="$1"
+  local EXPECTED_VALUE="$2"
+  local STRATUM=$(jq -c --arg EXPECTED_VALUE "$EXPECTED_VALUE" --argjson STRATIFIER_INDEX "$STRATIFIER_INDEX" '
+              .group[0].stratifier[$STRATIFIER_INDEX].stratum[] | select(.value.coding[0].code == $EXPECTED_VALUE)' "$REPORT" )
+  echo "$STRATUM"
+}
+
+validate_stratum() {
+  local STRATUM="$1"
+  local STRATUM_VALUE="$2"
+  local EXPECTED_INITIAL_POP_COUNT="$3"
+  local EXPECTED_MEASURE_POP_COUNT="$4"
+  local EXPECTED_OBSERVATION_POP_COUNT="$5"
+  local EXPECTED_MEASURE_SCORE="$6"
+
+  local INITIAL_POP_COUNT=$(jq '.population[] | select(.code.coding[0].code == "initial-population").count' <<< "$STRATUM")
+  local MEASURE_POP_COUNT=$(jq '.population[] | select(.code.coding[0].code == "measure-population").count' <<< "$STRATUM")
+  local OBSERVATION_POP_COUNT=$(jq '.population[] | select(.code.coding[0].code == "measure-observation").count' <<< "$STRATUM")
+  local MEASURE_SCORE=$(jq '.measureScore.value' <<< "$STRATUM")
+
+
+
+  if [ "$INITIAL_POP_COUNT" = "$EXPECTED_INITIAL_POP_COUNT" ]; then
+    echo "OK 👍: initial population count ($INITIAL_POP_COUNT) equals the expected count for (value=$STRATUM_VALUE)"
+  else
+    echo "Fail 😞: stratum count ($INITIAL_POP_COUNT) != $EXPECTED_INITIAL_POP_COUNT for initial population (value=$STRATUM_VALUE)"
+    exit 1
+  fi
+
+  if [ "$MEASURE_POP_COUNT" = "$EXPECTED_MEASURE_POP_COUNT" ]; then
+      echo "OK 👍: measure population count ($MEASURE_POP_COUNT) equals the expected count for (value=$STRATUM_VALUE)"
+    else
+      echo "Fail 😞: stratum count ($MEASURE_POP_COUNT) != $EXPECTED_MEASURE_POP_COUNT for measure population (value=$STRATUM_VALUE)"
+      exit 1
+  fi
+
+if [ "$OBSERVATION_POP_COUNT" = "$EXPECTED_OBSERVATION_POP_COUNT" ]; then
+    echo "OK 👍: observation population count ($OBSERVATION_POP_COUNT) equals the expected count for (value=$STRATUM_VALUE)"
+  else
+    echo "Fail 😞: stratum count ($OBSERVATION_POP_COUNT) != $EXPECTED_OBSERVATION_POP_COUNT for measure observation (value=$STRATUM_VALUE)"
+    exit 1
+  fi
+
+  if [ "$MEASURE_SCORE" = "$EXPECTED_MEASURE_SCORE" ]; then
+      echo "OK 👍: measure score ($MEASURE_SCORE) equals the expected count for (value=$STRATUM_VALUE)"
+    else
+      echo "Fail 😞: stratum count ($MEASURE_SCORE) != $EXPECTED_MEASURE_SCORE for measure score (value=$STRATUM_VALUE)"
+      exit 1
+  fi
+}
+
+get_stratum() {
+  local STRATIFIER_INDEX="$1"
+  local STRATUM_INDEX="$2"
+  echo $(jq --argjson STRATIFIER_INDEX "$STRATIFIER_INDEX" --argjson STRATUM_INDEX "STRATUM_INDEX" '.population[]
+          | select(.code.coding[0].code == "initial-population").count' "$STRATUM")
+}
+
+
+EXPECTED_STRATUM_VALUE_1="I48.0"
+EXPECTED_STRATUM_INITIAL_POP_1=108
+EXPECTED_STRATUM_MEASURE_POP_1=108
+EXPECTED_STRATUM_OBESERVATION_POP_1=108
+EXPECTED_STRATUM_MEASURE_SCORE_1=108
+
+EXPECTED_STRATUM_VALUE_2="fail-no-value-found"
+EXPECTED_STRATUM_INITIAL_POP_2=12072
+EXPECTED_STRATUM_MEASURE_POP_2=12072
+EXPECTED_STRATUM_OBESERVATION_POP_2=12072
+EXPECTED_STRATUM_MEASURE_SCORE_2=12040
+
+
+STRATUM=$(find_stratum 0 $EXPECTED_STRATUM_VALUE_1)
+validate_stratum "$STRATUM" $EXPECTED_STRATUM_VALUE_1 $EXPECTED_STRATUM_INITIAL_POP_1 $EXPECTED_STRATUM_MEASURE_POP_1 \
+                 $EXPECTED_STRATUM_OBESERVATION_POP_1 $EXPECTED_STRATUM_MEASURE_SCORE_1
+
+STRATUM=$(find_stratum 1 $EXPECTED_STRATUM_VALUE_2)
+validate_stratum "$STRATUM" $EXPECTED_STRATUM_VALUE_2 $EXPECTED_STRATUM_INITIAL_POP_2 $EXPECTED_STRATUM_MEASURE_POP_2 \
+                 $EXPECTED_STRATUM_OBESERVATION_POP_2 $EXPECTED_STRATUM_MEASURE_SCORE_2

.github/integration-test/measures/multiple-stratifiers.json

@@ -0,0 +1,109 @@
+{
+  "resourceType": "Measure",
+  "meta": {
+    "profile": [
+      "http://fhir-data-evaluator/StructureDefinition/FhirDataEvaluatorContinuousVariableMeasure"
+    ]
+  },
+  "version": "1.0",
+  "url": "https://medizininformatik-initiative.de/fhir/fdpg/Measure/ExampleCdsCriteria",
+  "status": "active",
+  "experimental": false,
+  "publisher": "FDPG-Plus",
+  "name": "ExampleCdsCriteria",
+  "title": "Example Measure To Count CDS Criteria",
+  "description": "Example measure to count CDS criteria",
+  "group": [
+    {
+      "population": [
+        {
+          "code": {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/measure-population",
+                "code": "initial-population"
+              }
+            ]
+          },
+          "criteria": {
+            "language": "text/x-fhir-query",
+            "expression": "Condition?_profile=https://www.medizininformatik-initiative.de/fhir/core/modul-diagnose/StructureDefinition/Diagnose"
+          },
+          "id": "initial-population-identifier-1"
+        },
+        {
+          "code": {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/measure-population",
+                "code": "measure-population"
+              }
+            ]
+          },
+          "criteria": {
+            "language": "text/fhirpath",
+            "expression": "Condition"
+          },
+          "id": "measure-population-identifier-1"
+        },
+        {
+          "code": {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/measure-population",
+                "code": "measure-observation"
+              }
+            ]
+          },
+          "criteria": {
+            "language": "text/fhirpath",
+            "expression": "Condition.subject.reference"
+          },
+          "extension": [
+            {
+              "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-aggregateMethod",
+              "valueCode": "unique-count"
+            },
+            {
+              "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-criteriaReference",
+              "valueString": "measure-population-identifier-1"
+            }
+          ],
+          "id": "measure-observation-identifier-1"
+        }
+      ],
+      "stratifier": [
+        {
+          "criteria": {
+            "language": "text/fhirpath",
+            "expression": "Condition.code.coding.where(system='http://fhir.de/CodeSystem/bfarm/icd-10-gm')"
+          },
+          "code": {
+            "coding": [
+              {
+                "system": "http://fhir-evaluator/strat/system",
+                "code": "condition-icd10-code"
+              }
+            ]
+          },
+          "id": "strat-1"
+        },
+        {
+          "criteria": {
+            "language": "text/fhirpath",
+            "expression": "Condition.code.coding.where(system='http://snomed.info/sct')"
+          },
+          "code": {
+            "coding": [
+              {
+                "system": "http://fhir-evaluator/strat/system",
+                "code": "condition-sct-code"
+              }
+            ]
+          },
+          "id": "strat-2"
+        }
+      ]
+    }
+  ]
+}

.github/integration-test/missing-permissions-test.sh

@@ -0,0 +1,19 @@
+#!/bin/bash -e
+
+BASE_OUTPUT_DIR=$PWD/.github/integration-test/missing-permissions-test
+mkdir "$BASE_OUTPUT_DIR"
+
+# Allow docker to exit with an error
+set +e
+OUTPUT=$(docker run -v "$PWD"/.github/integration-test/measures/code-measure.json:/app/measure.json \
+      -v "$BASE_OUTPUT_DIR":/app/output:ro --network integration-test_testing-network -e FHIR_SERVER=http://fhir-server:8080/fhir \
+      fhir-data-evaluator 2>&1)
+EXIT_CODE=$?
+set -e
+
+if [ "$OUTPUT" = "Missing writing permissions on output directory" ] && [ $EXIT_CODE = 1 ]; then
+  echo "OK 👍: docker container exited with code 1 and with the correct error message"
+else
+  echo "Fail 😞: docker container did not exit with code 1 or with a different error message"
+  exit 1
+fi

.github/integration-test/test-data/get-mii-testdata.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+MII_TESTDATA_DOWNLOAD_URL="https://health-atlas.de/data_files/594/download?version=1"
+
+wget -O testdata.zip "$MII_TESTDATA_DOWNLOAD_URL"
+unzip testdata.zip -d testdata-temp
+cd testdata-temp/Vorhofflimmern || exit
+
+for file in *.json.zip
+do
+    unzip -o "$file" -d ../../.github/integration-test/Vorhofflimmern
+done
+
+cd ../../
+rm testdata.zip
+rm -rf testdata-temp

.github/workflows/build.yml

@@ -142,6 +142,27 @@ 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 /${PWD}/.github/integration-test/measures/unique-count-with-components-measure.json
 
+      - name: Run Integration Test to check if it correctly exits when there are insufficient writing permissions
+        run: .github/integration-test/missing-permissions-test.sh
+
+      - name: Remove Blaze volumes
+        run: docker compose -f .github/integration-test/docker-compose.yml down -v
+
+      - name: Run Blaze with fresh volumes
+        run: docker compose -f .github/integration-test/docker-compose.yml up -d
+
+      - name: Wait for Blaze
+        run: .github/scripts/wait-for-url.sh http://localhost:8082/health
+
+      - name: Download New Data
+        run: .github/integration-test/test-data/get-mii-testdata.sh
+
+      - name: Upload New Data
+        run: blazectl --no-progress --server http://localhost:8082/fhir upload .github/integration-test/Vorhofflimmern
+
+      - name: Run Integration Test multiple stratifiers
+        run: .github/integration-test/evaluate-multiple-stratifiers.sh /${PWD}/.github/integration-test/measures/multiple-stratifiers.json
+
 
   push-image:
     needs:

.gitignore

@@ -32,3 +32,6 @@ build/
 
 ### VS Code ###
 .vscode/
+output
+
+docker/.env

CHANGELOG.md

@@ -13,6 +13,21 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Fixed
 ### Security
 
+## [1.0.0] - 2024-09-25
+
+### Added
+- Add Retry to DataStore
+- Add Writing Permission Check to Docker Entrypoint
+- Add Docker Compose File
+- Add Immutable Individuals of Populations to Prevent Further Bugs
+
+### Changed
+- Update KDS Measure
+- Improve Readme
+
+### Fixed
+- Fix Wrong Unique Count
+
 ## [0.1.0] - 2024-08-08
 
 ### Added