Merge pull request #45 from medizininformatik-initiative/release-v1.1.0

Release v1.1.0

.github/integration-test/basic-auth/docker-compose.yml

@@ -0,0 +1,29 @@
+services:
+  fhir-server:
+    image: "samply/blaze:0.30"
+    environment:
+      BASE_URL: "http://fhir-server:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx1g"
+      LOG_LEVEL: "debug"
+      ENFORCE_REFERENTIAL_INTEGRITY: false
+    ports:
+      - "8082:8080"
+    volumes:
+      - "data-store-data:/app/data"
+  proxy:
+    image: "nginx:1.27.0"
+    volumes:
+      - "./nginx.conf:/etc/nginx/nginx.conf"
+      - "./proxy.htpasswd:/etc/auth/.htpasswd"
+  fhir-data-evaluator:
+    image: fhir-data-evaluator
+    environment:
+      CONVERT_TO_CSV: ${FDE_CONVERT_TO_CSV:-true}
+      FHIR_SERVER: "http://proxy:8080/fhir"
+      FHIR_USER: "test"
+      FHIR_PASSWORD: "bar"
+    volumes:
+      - "${FDE_INPUT_MEASURE:-../Documentation/example-measures/example-measure-kds.json}:/app/measure.json"
+      - "${FDE_OUTPUT_DIR:-../output}:/app/output"
+volumes:
+  data-store-data:

.github/integration-test/basic-auth/load-data.sh

@@ -0,0 +1,5 @@
+#!/bin/bash -e
+
+DIR="$1"
+
+blazectl --no-progress --server http://localhost:8082/fhir upload "$DIR"

.github/integration-test/basic-auth/nginx.conf

@@ -0,0 +1,37 @@
+user  nginx;
+worker_processes  1;
+
+error_log  /var/log/nginx/error.log debug;
+pid        /var/run/nginx.pid;
+
+events {
+    worker_connections  1024;
+}
+
+http {
+    include     /etc/nginx/mime.types;
+    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
+                      '$status $body_bytes_sent "$http_referer" '
+                      '"$http_user_agent" "$http_x_forwarded_for"';
+    access_log  /var/log/nginx/access.log  main;
+    sendfile        on;
+    keepalive_timeout  65;
+
+    server {
+        listen 8080;
+        listen [::]:8080;
+
+        location / {
+            root /usr/share/nginx/html;
+            index index.html;
+        }
+
+        location /fhir {
+            auth_basic "Test Area";
+            auth_basic_user_file /etc/auth/.htpasswd;
+
+            proxy_pass http://fhir-server:8080;
+            proxy_read_timeout 43200s;
+        }
+    }
+}

.github/integration-test/basic-auth/proxy.htpasswd

@@ -0,0 +1 @@
+test:$apr1$ZHbwVw0h$6uvjvv1NqGY47sVmYEvwE0

.github/integration-test/evaluate-and-post-different-doc-ref.sh

@@ -0,0 +1,28 @@
+#!/bin/bash -e
+
+PROJECT_IDENTIFIER_VALUE="$1"
+
+DOCKER_COMPOSE_FILE=.github/integration-test/no-auth/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/icd10-measure.json
+export FDE_CONVERT_TO_CSV=false
+export FDE_FHIR_REPORT_DESTINATION_SERVER=http://fhir-server:8080/fhir
+export FDE_AUTHOR_IDENTIFIER_SYSTEM=http://dsf.dev/sid/organization-identifier
+export FDE_AUTHOR_IDENTIFIER_VALUE=Test_DIC1
+export FDE_PROJECT_IDENTIFIER_SYSTEM=http://medizininformatik-initiative.de/sid/project-identifier
+export FDE_PROJECT_IDENTIFIER_VALUE="$PROJECT_IDENTIFIER_VALUE"
+export FDE_SEND_REPORT_TO_SERVER=true
+
+docker compose -f "$DOCKER_COMPOSE_FILE" run -e TZ="$(cat /etc/timezone)" fhir-data-evaluator
+
+reference_response=$(curl -s "http://localhost:8082/fhir/DocumentReference" \
+    -H "Content-Type: application/fhir+json")
+
+reference_count=$(echo "$reference_response" | jq -r '.entry | length')
+
+EXPECTED_REFERENCE_COUNT=2
+if [ "$reference_count" = "$EXPECTED_REFERENCE_COUNT" ]; then
+  echo "OK 👍: reference count ($reference_count) equals the expected count"
+else
+  echo "Fail 😞: reference count ($reference_count) != ($EXPECTED_REFERENCE_COUNT)"
+  exit 1
+fi

.github/integration-test/evaluate-and-post-report.sh

@@ -0,0 +1,50 @@
+#!/bin/bash -e
+
+PROJECT_IDENTIFIER_VALUE="$1"
+DOCKER_COMPOSE_FILE=.github/integration-test/no-auth/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/icd10-measure.json
+export FDE_CONVERT_TO_CSV=false
+export FDE_FHIR_REPORT_DESTINATION_SERVER=http://fhir-server:8080/fhir
+export FDE_AUTHOR_IDENTIFIER_SYSTEM=http://dsf.dev/sid/organization-identifier
+export FDE_AUTHOR_IDENTIFIER_VALUE=Test_DIC1
+export FDE_PROJECT_IDENTIFIER_SYSTEM=http://medizininformatik-initiative.de/sid/project-identifier
+export FDE_PROJECT_IDENTIFIER_VALUE="$PROJECT_IDENTIFIER_VALUE"
+export FDE_SEND_REPORT_TO_SERVER=true
+
+docker compose -f "$DOCKER_COMPOSE_FILE" run -e TZ="$(cat /etc/timezone)" fhir-data-evaluator
+
+report_response=$(curl -s "http://localhost:8082/fhir/MeasureReport" \
+     -H "Content-Type: application/fhir+json")
+
+reference_response=$(curl -s "http://localhost:8082/fhir/DocumentReference" \
+    -H "Content-Type: application/fhir+json")
+
+report_url=MeasureReport/$(echo "$report_response" | jq -r  '.entry[0].resource.id')
+reference_url=$(echo "$reference_response" | jq -r '.entry[0].resource.content[0].attachment.url')
+
+if [ "$report_url" = "$reference_url" ]; then
+  echo "OK 👍: Id of MeasureReport is the same as the referenced attachment in the DocumentReference"
+else
+  echo "Fail 😞: Id of MeasureReport ($report_url) is not the same as the referenced attachment in the DocumentReference ($reference_url)"
+  exit 1
+fi
+
+REPORT=$(echo "$report_response" | jq '.entry[0].resource')
+EXPECTED_POPULATION_COUNT=2
+EXPECTED_STRATIFIER_COUNT=2
+
+POPULATION_COUNT=$(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

.github/integration-test/evaluate-and-post-update.sh

@@ -0,0 +1,51 @@
+#!/bin/bash -e
+
+PROJECT_IDENTIFIER_VALUE="$1"
+
+DOCKER_COMPOSE_FILE=.github/integration-test/no-auth/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/icd10-measure.json
+export FDE_CONVERT_TO_CSV=false
+export FDE_FHIR_REPORT_DESTINATION_SERVER=http://fhir-server:8080/fhir
+export FDE_AUTHOR_IDENTIFIER_SYSTEM=http://dsf.dev/sid/organization-identifier
+export FDE_AUTHOR_IDENTIFIER_VALUE=Test_DIC1
+export FDE_PROJECT_IDENTIFIER_SYSTEM=http://medizininformatik-initiative.de/sid/project-identifier
+export FDE_PROJECT_IDENTIFIER_VALUE="$PROJECT_IDENTIFIER_VALUE"
+export FDE_SEND_REPORT_TO_SERVER=true
+
+reference_response=$(curl -s "http://localhost:8082/fhir/DocumentReference" \
+    -H "Content-Type: application/fhir+json")
+reference_url_before=$(echo "$reference_response" | jq -r '.entry[0].resource.content[0].attachment.url')
+
+docker compose -f "$DOCKER_COMPOSE_FILE" run -e TZ="$(cat /etc/timezone)" fhir-data-evaluator
+
+report_response=$(curl -s "http://localhost:8082/fhir/MeasureReport" \
+     -H "Content-Type: application/fhir+json")
+reference_response=$(curl -s "http://localhost:8082/fhir/DocumentReference" \
+    -H "Content-Type: application/fhir+json")
+
+report_count=$(echo "$report_response" | jq -r  '.entry | length')
+reference_count=$(echo "$reference_response" | jq -r '.entry | length')
+reference_url_after=$(echo "$reference_response" | jq -r '.entry[0].resource.content[0].attachment.url')
+
+EXPECTED_REPORT_COUNT=2
+if [ "$report_count" = "$EXPECTED_REPORT_COUNT" ]; then
+  echo "OK 👍: report count ($report_count) equals the expected count"
+else
+  echo "Fail 😞: report count ($report_count) != ($EXPECTED_REPORT_COUNT)"
+  exit 1
+fi
+
+EXPECTED_REFERENCE_COUNT=1
+if [ "$reference_count" = "$EXPECTED_REFERENCE_COUNT" ]; then
+  echo "OK 👍: reference count ($reference_count) equals the expected count"
+else
+  echo "Fail 😞: reference count ($reference_count) != ($EXPECTED_REFERENCE_COUNT)"
+  exit 1
+fi
+
+if [ "$reference_url_before" != "$reference_url_after" ]; then
+  echo "OK 👍: referenced measure report url changed"
+else
+  echo "Fail 😞: referenced measure report url did not change"
+  exit 1
+fi

.github/integration-test/evaluate-code.sh

@@ -1,14 +1,15 @@
 #!/bin/bash -e
 
-INPUT_MEASURE=$1
-BASE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-code-test
-mkdir "$BASE_OUTPUT_DIR"
+DOCKER_COMPOSE_FILE=.github/integration-test/$1/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/code-measure.json
+export FDE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-code-test
+export FDE_CONVERT_TO_CSV=false
 
-docker run -v "$INPUT_MEASURE":/app/measure.json -v "$BASE_OUTPUT_DIR":/app/output/ -e FHIR_SERVER=http://fhir-server:8080/fhir \
-      -e TZ="$(cat /etc/timezone)" --network integration-test_testing-network fhir-data-evaluator
+mkdir "$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 "$BASE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
+OUTPUT_DIR=$(find "$FDE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
 REPORT="$OUTPUT_DIR/measure-report.json"
 
 EXPECTED_POPULATION_COUNT=2

.github/integration-test/evaluate-exists.sh

@@ -1,14 +1,15 @@
 #!/bin/bash -e
 
-INPUT_MEASURE=$1
-BASE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-exists-test
-mkdir "$BASE_OUTPUT_DIR"
+DOCKER_COMPOSE_FILE=.github/integration-test/$1/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/exists-measure.json
+export FDE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-exists-test
+export FDE_CONVERT_TO_CSV=false
 
-docker run -v "$INPUT_MEASURE":/app/measure.json -v "$BASE_OUTPUT_DIR":/app/output/ -e FHIR_SERVER=http://fhir-server:8080/fhir \
-      -e TZ="$(cat /etc/timezone)" --network integration-test_testing-network fhir-data-evaluator
+mkdir "$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 "$BASE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
+OUTPUT_DIR=$(find "$FDE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
 REPORT="$OUTPUT_DIR/measure-report.json"
 
 EXPECTED_POPULATION_COUNT=2

.github/integration-test/evaluate-icd10-to-csv.sh

@@ -1,14 +1,15 @@
 #!/bin/bash -e
 
-INPUT_MEASURE=$1
-BASE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-icd10-test-to-csv-test
-mkdir "$BASE_OUTPUT_DIR"
+DOCKER_COMPOSE_FILE=.github/integration-test/$1/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/icd10-measure.json
+export FDE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-icd10-to-csv-test
+export FDE_CONVERT_TO_CSV=true
 
-docker run -v "$INPUT_MEASURE":/app/measure.json -v "$BASE_OUTPUT_DIR":/app/output/ -e FHIR_SERVER=http://fhir-server:8080/fhir \
-       -e CONVERT_TO_CSV=true -e TZ="$(cat /etc/timezone)" --network integration-test_testing-network fhir-data-evaluator
+mkdir "$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 "$BASE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
+OUTPUT_DIR=$(find "$FDE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
 
 #wait for csv file creation
 sleep 1

.github/integration-test/evaluate-icd10.sh

@@ -1,14 +1,15 @@
 #!/bin/bash -e
 
-INPUT_MEASURE=$1
-BASE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-icd10-test
-mkdir "$BASE_OUTPUT_DIR"
+DOCKER_COMPOSE_FILE=.github/integration-test/$1/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/icd10-measure.json
+export FDE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-icd10-test
+export FDE_CONVERT_TO_CSV=false
 
-docker run -v "$INPUT_MEASURE":/app/measure.json -v "$BASE_OUTPUT_DIR":/app/output/ -e FHIR_SERVER=http://fhir-server:8080/fhir \
-      -e TZ="$(cat /etc/timezone)" --network integration-test_testing-network fhir-data-evaluator
+mkdir "$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 "$BASE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
+OUTPUT_DIR=$(find "$FDE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
 REPORT=$(cat "$OUTPUT_DIR"/measure-report.json)
 
 EXPECTED_POPULATION_COUNT=2

.github/integration-test/evaluate-icd10WithStatus-to-csv.sh

@@ -1,14 +1,15 @@
 #!/bin/bash -e
 
-INPUT_MEASURE=$1
-BASE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-icd10WithStatus-to-csv-test
-mkdir "$BASE_OUTPUT_DIR"
+DOCKER_COMPOSE_FILE=.github/integration-test/$1/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/icd10withStatus-measure.json
+export FDE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-icd10withStatus-to-csv-test
+export FDE_CONVERT_TO_CSV=true
 
-docker run -v "$INPUT_MEASURE":/app/measure.json -v "$BASE_OUTPUT_DIR":/app/output/ -e FHIR_SERVER=http://fhir-server:8080/fhir \
-       -e CONVERT_TO_CSV=true -e TZ="$(cat /etc/timezone)" --network integration-test_testing-network fhir-data-evaluator
+mkdir "$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 "$BASE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
+OUTPUT_DIR=$(find "$FDE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
 
 #wait for csv file creation
 sleep 1

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

@@ -1,14 +1,15 @@
 #!/bin/bash -e
 
-INPUT_MEASURE=$1
-BASE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-multiple-stratifiers
-mkdir "$BASE_OUTPUT_DIR"
+DOCKER_COMPOSE_FILE=.github/integration-test/$1/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/multiple-stratifiers-measure.json
+export FDE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-multiple-stratifiers-test
+export FDE_CONVERT_TO_CSV=false
 
-docker run -v "$INPUT_MEASURE":/app/measure.json -v "$BASE_OUTPUT_DIR":/app/output/ -e FHIR_SERVER=http://fhir-server:8080/fhir \
-      -e TZ="$(cat /etc/timezone)" --network integration-test_testing-network fhir-data-evaluator
+mkdir "$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 "$BASE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
+OUTPUT_DIR=$(find "$FDE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
 REPORT="$OUTPUT_DIR/measure-report.json"
 
 find_stratum() {

.github/integration-test/evaluate-unique-count-to-csv.sh

@@ -1,14 +1,15 @@
 #!/bin/bash -e
 
-INPUT_MEASURE=$1
-BASE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-unique-count-with-components-test
-mkdir "$BASE_OUTPUT_DIR"
+DOCKER_COMPOSE_FILE=.github/integration-test/$1/docker-compose.yml
+export FDE_INPUT_MEASURE=/${PWD}/.github/integration-test/measures/unique-count-measure.json
+export FDE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-unique-count-to-csv-test
+export FDE_CONVERT_TO_CSV=true
 
-docker run -v "$INPUT_MEASURE":/app/measure.json -v "$BASE_OUTPUT_DIR":/app/output/ -e FHIR_SERVER=http://fhir-server:8080/fhir \
-      -e TZ="$(cat /etc/timezone)" --network integration-test_testing-network -e CONVERT_TO_CSV=true fhir-data-evaluator
+mkdir "$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 "$BASE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
+OUTPUT_DIR=$(find "$FDE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1)
 
 #wait for csv file creation
 sleep 1