feat: changes for the pipeline run

.github/comp_override/compose.override.yaml

@@ -4,6 +4,7 @@ services:
     environment:
       PARSING_MAP_PATH: "/opt/fhir-module/util/default_csv_map.json"
       MATERIAL_TYPE_MAP_PATH: "/opt/fhir-module/util/default_csv_material_type_map.json"
+      MIABIS_MATERIAL_TYPE_MAP_PATH: "/opt/fhir-module/util/default_csv_miabis_material_type_map.json"
       RECORDS_FILE_TYPE: "csv"
       COLLECTION_MAPPING_ATTRIBUTE : "diagnosis"
     volumes:

.github/scripts/check-patient-exists.sh

@@ -1,8 +1,18 @@
 #!/bin/bash -e
 
-NUM_OF_PATIENTS=$(curl -X GET http://localhost:8080/fhir/Patient?_summary=count | jq .total)
-NUM_OF_CONDITIONS=$(curl -X GET http://localhost:8080/fhir/Condition?_summary=count | jq .total)
-NUM_OF_SPECIMENS=$(curl -X GET http://localhost:8080/fhir/Specimen?_summary=count | jq .total)
+# Check if a URL was provided as an argument
+if [ -z "$1" ]; then
+    echo "Usage: $0 <base-url>"
+    echo "Example: $0 http://localhost:8080/fhir"
+    exit 1
+fi
+
+# Get the base URL from the first argument
+BASE_URL="$1"
+
+NUM_OF_PATIENTS=$(curl -X GET ${BASE_URL}/Patient?_summary=count | jq .total)
+NUM_OF_CONDITIONS=$(curl -X GET ${BASE_URL}/fhir/Condition?_summary=count | jq .total)
+NUM_OF_SPECIMENS=$(curl -X GET ${BASE_URL}/fhir/Specimen?_summary=count | jq .total)
 if [ "$NUM_OF_PATIENTS" = 0 ] || [ "$NUM_OF_CONDITIONS" = 0 ] || [ "$NUM_OF_SPECIMENS" = 0 ]; then
 	echo "The upload of resources failed." && exit 1
 fi

.github/workflows/build.yml

@@ -137,15 +137,20 @@ jobs:
       - name: Wait for Blaze
         run: .github/scripts/wait-for-url.sh  http://localhost:8080/health
 
+      - name: Wait for MIABIS Blaze
+        run: .github/scripts/wait-for-url.sh  http://localhost:5432/health
+
       - name: Docker Logs
         run: docker logs blaze
 
       - name: Docker Logs
         run: sleep 20 && docker logs fhir-module
 
-      - name: Verify upload succeeded
-        run: .github/scripts/check-patient-exists.sh
+      - name: Verify upload succeeded for blaze
+        run: .github/scripts/check-patient-exists.sh http://localhost:8080/fhir
 
+      - name: Verify upload succeeded for MIABIS blaze
+        run: .github/scripts/check-patient-exists.sh http://localhost:5432/fhir
 
   system-test-csv:
     name: System test csv files
@@ -177,15 +182,20 @@ jobs:
       - name: Wait for Blaze
         run: .github/scripts/wait-for-url.sh  http://localhost:8080/health
 
+      - name: Wait for MIABIS Blaze
+        run: .github/scripts/wait-for-url.sh  http://localhost:5432/health
+
       - name: Docker Logs
         run: docker logs blaze
 
       - name: Docker Logs
         run: sleep 20 && docker logs fhir-module
 
       - name: Verify upload succeeded
-        run: .github/scripts/check-patient-exists.sh
+        run: .github/scripts/check-patient-exists.sh http://localhost:8080/fhir
 
+      - name: Verify upload succeeded for MIABIS blaze
+        run: .github/scripts/check-patient-exists.sh http://localhost:5432/fhir
 
 
   build-push-image:

compose.yaml

@@ -1,8 +1,6 @@
-version: "3.9"
-
 services:
   fhir-module:
-    image: ghcr.io/bbmri-cz/fhir-module:latest
+    image: local_fhir_module
     container_name: fhir-module
     profiles:
       - dev
@@ -11,7 +9,8 @@ services:
       - fhir-integration
     restart: no
     environment:
-      BLAZE_URL: "http://blaze:8080/fhir"
+      BLAZE_URL: "http://test-blaze:8080/fhir"
+      MIABIS_BLAZE_URL: "http://miabis-blaze:8080/fhir"
       DIR_PATH: "/opt/records"
       PYTHONWARNINGS: "ignore:Unverified HTTPS request"
     volumes:
@@ -20,19 +19,43 @@ services:
         target: "/opt/records"
 
 
-  blaze:
-    container_name: blaze
-    image: "samply/blaze:0.22"
+
+  miabis-blaze:
+    container_name: miabis-blaze
+    image: "samply/blaze:latest"
+    networks:
+      - fhir-integration
+    profiles:
+      - dev
+      - prod
+    environment:
+      JAVA_TOOL_OPTIONS: "-Xmx2g"
+      DB_SEARCH_PARAM_BUNDLE: "/app/searchParamBundle.json"
+      LOG_LEVEL: "debug"
+    ports:
+      - "5432:8080"
+    volumes:
+      - type: bind
+        source: "util/searchParamBundle.json"
+        target: "/app/searchParamBundle.json"
+
+  test-blaze:
+    container_name: test-blaze
+    image: "samply/blaze:latest"
     networks:
       - fhir-integration
     profiles:
       - dev
     environment:
-      BASE_URL: "http://localhost:8080"
       JAVA_TOOL_OPTIONS: "-Xmx2g"
+      DB_SEARCH_PARAM_BUNDLE: "/app/searchParamBundle.json"
       LOG_LEVEL: "debug"
     ports:
       - "8080:8080"
+    volumes:
+      - type: bind
+        source: "util/searchParamBundle.json"
+        target: "/app/searchParamBundle.json"
 
 networks:
-  fhir-integration:
+  fhir-integration:

test/xml_data/MMCI_1.xml

@@ -50,7 +50,7 @@
         </tissue>
     </LTS>
     <STS>
-        <diagnosisMaterial number="136043" sampleId="&amp;:2032:136043" year="2032">
+        <diagnosisMaterial number="136043" sampleId="BBM:2032:136043" year="2032">
             <materialType>S</materialType>
             <diagnosis>C509</diagnosis>
             <takingDate>2032-10-4T10:02:00</takingDate>