Release v6.0.0 alpha.5

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

@@ -8,6 +8,7 @@ services:
     depends_on:
       - dataportal-postgres
     environment:
+      JAVA_OPTS: ""
       QUERYRESULT_PUBLIC_KEY: "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"
       # ----- app
       QUERY_VALIDATION_ENABLED: "true"
@@ -16,7 +17,6 @@ services:
       API_BASE_URL: "http://localhost:8091/api/"
       ALLOWED_ORIGINS: "https://localhost"
       QUERYRESULT_EXPIRY_MINUTES: 5
-      ELASTIC_SEARCH_ENABLED: "false"
       # ---- db config
       DATABASE_HOST: "dataportal-postgres"
       DATABASE_PORT: 5432
@@ -60,6 +60,10 @@ services:
       PRIVACY_QUOTA_READ_DETAILED_OBFUSCATED_INTERVALSECONDS: 7200
       PRIVACY_THRESHOLD_RESULTS: 0
       PRIVACY_THRESHOLD_SITES: 0
+      # ---- Elastic Search
+      ELASTIC_SEARCH_ENABLED: true
+      ELASTIC_SEARCH_HOST: dataportal-elastic:9200
+      ELASTIC_SEARCH_FILTER: context,terminology,kds_module
       # ---- logging
       LOG_LEVEL_SQL: "warn"
       LOG_LEVEL: "warn"
@@ -82,8 +86,26 @@ services:
       POSTGRES_PASSWORD: "dataportalpw"
       POSTGRES_DB: "dataportal"
 
+  dataportal-elastic:
+    image: docker.elastic.co/elasticsearch/elasticsearch:8.16.0
+    container_name: dataportal-elastic
+    ports:
+      - '9200:9200'
+      - '9300:9300'
+    healthcheck:
+      test: [ "CMD-SHELL", "curl --silent --fail localhost:9200/_cluster/health || exit 1" ]
+      interval: 30s
+      timeout: 30s
+      retries: 3
+    environment:
+      discovery.type: single-node
+      ES_JAVA_OPTS: -Xmx512m -Xms512m
+      node.name: es01
+      cluster.name: elasticsearch
+      xpack.security.enabled: false
+
   blaze:
-    image: "samply/blaze:0.29"
+    image: "samply/blaze:0.30"
     environment:
       BASE_URL: "http://blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx1g"
@@ -94,7 +116,7 @@ services:
       - "blaze-data:/app/data"
 
   flare:
-    image: ghcr.io/medizininformatik-initiative/flare:2.2.0
+    image: ghcr.io/medizininformatik-initiative/flare:2.3.0
     ports:
       - "8092:8080"
     environment:
@@ -138,4 +160,4 @@ services:
 
 volumes:
   dataportal-auth-db:
-  blaze-data:
+  blaze-data:

.github/scripts/check-if-running-as-user-10001.sh

@@ -0,0 +1,10 @@
+#!/bin/bash -e
+
+if docker exec -u0 dataportal-backend pgrep -u 10001 java > /dev/null
+then
+    echo "Java process is running as user 10001"
+    exit 0
+else
+    echo "Java process is not running as user 10001"
+    exit 1
+fi

.github/scripts/download-and-unpack-ontology.sh

@@ -1,7 +1,7 @@
 #!/bin/bash -e
 
 mkdir --parents .github/integration-test/ontology/ui_profiles .github/integration-test/ontology/migration
-curl -L https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/v3.0.0-test.1/example/fdpg-ontology/backend.zip -o .github/integration-test/ontology/backend.zip
+curl -L https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/${ONTOLOGY_GIT_TAG}/example/fdpg-ontology/backend.zip -o .github/integration-test/ontology/backend.zip
 unzip -jod .github/integration-test/ontology/ui_profiles/ .github/integration-test/ontology/backend.zip
 mv .github/integration-test/ontology/ui_profiles/R__Load_latest_ui_profile.sql .github/integration-test/ontology/migration/
 rm .github/integration-test/ontology/backend.zip

elastic-init.sh → .github/scripts/init-elasticsearch.sh

@@ -1,49 +1,41 @@
-#!/bin/sh
+#!/bin/bash -e
 
-# Wait for Elasticsearch to start up before doing anything
-until curl -X GET "$ELASTIC_HOST/_cluster/health" | grep -q '"status":"green"\|"status":"yellow"'; do
-    echo "Waiting for Elasticsearch..."
-    sleep 5
-done
-
-ABSOLUTE_FILEPATH="${ELASTIC_FILEPATH//TAGPLACEHOLDER/$ELASTIC_GIT_TAG}$ELASTIC_FILENAME"
+ABSOLUTE_FILEPATH="${ELASTIC_FILEPATH//TAGPLACEHOLDER/$ONTOLOGY_GIT_TAG}$ELASTIC_FILENAME"
 echo "Downloading $ABSOLUTE_FILEPATH"
 response_onto_dl=$(curl --write-out "%{http_code}" -sLO "$ABSOLUTE_FILEPATH")
 
 if [ "$response_onto_dl" -ne 200 ]; then
-  echo "Could not download ontology file. Maybe the tag $ELASTIC_GIT_TAG does not exist? Error code was $response_onto_dl"
+  echo "Could not download ontology file. Maybe the tag $ONTOLOGY_GIT_TAG does not exist? Error code was $response_onto_dl"
   exit 1
 fi
 
 unzip -o "$ELASTIC_FILENAME"
 
-if [ "$OVERRIDE_EXISTING" = "true" ]; then
-  echo "(Trying to) delete existing indices"
-  curl -s -DELETE "$ELASTIC_HOST/ontology"
-  curl -s -DELETE "$ELASTIC_HOST/codeable_concept"
-fi
+echo "(Trying to) delete existing indices"
+curl --request DELETE "$ELASTIC_HOST/ontology"
+curl --request DELETE "$ELASTIC_HOST/codeable_concept"
 
 echo "Creating ontology index..."
 response_onto=$(curl --write-out "%{http_code}" -s --output /dev/null -XPUT -H 'Content-Type: application/json' "$ELASTIC_HOST/ontology" -d @elastic/ontology_index.json)
 echo "Creating codeable concept index..."
 response_cc=$(curl --write-out "%{http_code}" -s --output /dev/null -XPUT -H 'Content-Type: application/json' "$ELASTIC_HOST/codeable_concept" -d @elastic/codeable_concept_index.json)
-echo "Done"
+echo "Done."
 
 for FILE in elastic/*; do
   if [ -f "$FILE" ]; then
     BASENAME=$(basename "$FILE")
     if [[ $BASENAME == onto_es__ontology* && $BASENAME == *.json ]]; then
       if [[ "$response_onto" -eq 200 || "$OVERRIDE_EXISTING" = "true" ]]; then
         echo "Uploading $BASENAME"
-        curl -s --output /dev/null -XPOST -H 'Content-Type: application/json' --data-binary @"$FILE" "$ELASTIC_HOST/ontology/_bulk?pretty"
+        curl -s --output /dev/null -XPOST -H 'Content-Type: application/json' --data-binary @"$FILE" "$ELASTIC_HOST/ontology/_bulk"
       else
         echo "Skipping $BASENAME because index was already existing. Set OVERRIDE_EXISTING to true to force creating a new index"
       fi
     fi
     if [[ $BASENAME == onto_es__codeable_concept* && $BASENAME == *.json ]]; then
       if [[ "$response_cc" -eq 200 || "$OVERRIDE_EXISTING" = "true" ]]; then
         echo "Uploading $BASENAME"
-        curl -s --output /dev/null -XPOST -H 'Content-Type: application/json' --data-binary @"$FILE" "$ELASTIC_HOST/codeable_concept/_bulk?pretty"
+        curl -s --output /dev/null -XPOST -H 'Content-Type: application/json' --data-binary @"$FILE" "$ELASTIC_HOST/codeable_concept/_bulk"
       else
         echo "Skipping $BASENAME because index was already existing. Set OVERRIDE_EXISTING to true to force creating a new index"
       fi

.github/scripts/post-elastic-test-queries.sh

@@ -0,0 +1,96 @@
+#!/bin/bash -e
+
+curl "$ELASTIC_HOST/_cat/indices"
+
+response=$(curl -s -w "%{http_code}" -o response_body "$ELASTIC_HOST/ontology/_doc/9c2328b0-ac4e-3d69-8f2f-d8b905875348")
+http_code="${response: -3}"
+json_body=$(cat response_body)
+
+if [ "$http_code" -eq 200 ]; then
+    if echo "$json_body" | jq '.found == true' | grep -q true; then
+        echo "Ontology Document found in elastic search"
+    else
+        echo "Empty or nonexistent response from elastic search"
+        exit 1
+    fi
+else
+    echo "Response code $http_code"
+    exit 1
+fi
+
+
+response=$(curl -s -w "%{http_code}" -o response_body "$ELASTIC_HOST/codeable_concept/_doc/d676be36-7f34-3ea6-9838-c0c9e1ca3dcc")
+http_code="${response: -3}"
+json_body=$(cat response_body)
+
+if [ "$http_code" -eq 200 ]; then
+    if echo "$json_body" | jq '.found == true' | grep -q true; then
+        echo "Codeable Concept Document found in elastic search"
+    else
+        echo "Empty or nonexistent response from elastic search"
+        exit 1
+    fi
+else
+    echo "Response code $http_code"
+    exit 1
+fi
+
+access_token="$(curl -s --request POST \
+  --url http://localhost:8083/auth/realms/dataportal/protocol/openid-connect/token \
+  --header 'Content-Type: application/x-www-form-urlencoded' \
+  --data grant_type=password \
+  --data client_id=dataportal-webapp \
+  --data username=testuser \
+  --data password=testpassword \
+  --data scope=openid | jq '.access_token' | tr -d '"')"
+
+response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/terminology/entry/search?searchterm=Blutdruck")
+http_code="${response: -3}"
+json_body=$(cat response_body)
+
+if [ "$http_code" -eq 200 ]; then
+    if echo "$json_body" | jq '.totalHits > 0' | grep -q true; then
+        echo "OK response with non-empty array"
+    else
+        echo "Empty or nonexistent response"
+        exit 1
+    fi
+else
+    echo "Response code $http_code"
+    exit 1
+fi
+
+response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/codeable-concept/entry/search?searchterm=Vectorcardiogram")
+http_code="${response: -3}"
+json_body=$(cat response_body)
+
+if [ "$http_code" -eq 200 ]; then
+    if echo "$json_body" | jq '.totalHits > 0' | grep -q true; then
+        echo "OK response with non-empty array"
+    else
+        echo "Empty or nonexistent response"
+        exit 1
+    fi
+else
+    echo "Response code $http_code"
+    exit 1
+fi
+
+response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/codeable-concept/entry/d676be36-7f34-3ea6-9838-c0c9e1ca3dcc")
+http_code="${response: -3}"
+json_body=$(cat response_body)
+
+if [ "$http_code" -eq 200 ]; then
+    if echo "$json_body" | jq -e '.code and .code != ""' | grep -q true; then
+        echo "OK response with non-empty array"
+    else
+        echo "Empty or nonexistent response"
+        exit 1
+    fi
+else
+    echo "Response code $http_code"
+    exit 1
+fi
+
+echo "All elastic search tests completed"
+exit 0