comments_alex

CHANGELOG.md

@@ -7,31 +7,43 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ## [UNRELEASED] - yyyy-mm-dd
 
 ### Added
+
 ### Changed
+
 ### Deprecated
+
 ### Removed
+
 ### Fixed
+
 ### Security
 
 ## [v1.0.0-alpha.1] - 2024-10-21
 
 ### Added
-- **Open Id Connect Authenticatoon**
+
+- **Open Id Connect Authentication**
 - **Filter Resources by Consent selected in CCDL**
 - **Expand concept code filter**
 - **CQL cohort execution**
 - **Ontology integration**
 
-
 ## [v1.0.0-alpha] - 2024-09-19
 
 ### Added
-- **FHIR Server and Flare Server Integration**: Implemented interaction with a local FHIR server and Flare Server to extract patient resources using CRTDL and CDS profiles.
-- **CRTDL Support**: Added support for parsing the Clinical Resource Transfer Definition Language (CRTDL) in JSON format, allowing specification of attributes and filters.
-- **$Extract-Data Endpoint**: Introduced the `$extract-data` operation, allowing bulk data extraction via FHIR Parameters resources.
-- **Async Bulk Pattern**: Implemented the async bulk pattern with a kick-off request and polling location for data extraction results.
-- **Batch Processing**: Implemented NDJSON format for batched transformation results, including links to the generated data bundles.
-- **Multi FHIR Profile Handling**: Added the ability to handle multiple FHIR profiles per resource, selecting the first known profile greedily.
+
+- **FHIR Server and Flare Server Integration**: Implemented interaction with a local FHIR server and Flare Server to
+  extract patient resources using CRTDL and CDS profiles.
+- **CRTDL Support**: Added support for parsing the Clinical Resource Transfer Definition Language (CRTDL) in JSON
+  format, allowing specification of attributes and filters.
+- **$Extract-Data Endpoint**: Introduced the `$extract-data` operation, allowing bulk data extraction via FHIR
+  Parameters resources.
+- **Async Bulk Pattern**: Implemented the async bulk pattern with a kick-off request and polling location for data
+  extraction results.
+- **Batch Processing**: Implemented NDJSON format for batched transformation results, including links to the generated
+  data bundles.
+- **Multi FHIR Profile Handling**: Added the ability to handle multiple FHIR profiles per resource, selecting the first
+  known profile greedily.
 - **Resource Redaction and Copying**: Introduced basic functionality for redacting and copying patient resources.
 
 

docker-compose.yml

@@ -2,9 +2,9 @@ services:
   torch-data-store:
     image: "samply/blaze:0.30"
     environment:
-      BASE_URL: "http://torch-data-store:8080"
+      BASE_URL: ${TORCH_BASE_URL:-http://torch-data-store:8080}
       JAVA_TOOL_OPTIONS: "-Xmx2g"
-      LOG_LEVEL: "info"
+      LOG_LEVEL: ${TORCH_LOG_LEVEL:-info}
     ports:
       - "8082:8080"
     volumes:
@@ -30,13 +30,13 @@ services:
     restart: unless-stopped
     image: nginxinc/nginx-unprivileged:1.25.5-alpine
     ports:
-      - ${PORT_TORCH_NGINX:-127.0.0.1:80}:8080
+      - ${PORT_TORCH_NGINX:-127.0.0.1:8085}:8080
     volumes:
       - ./nginx.conf.template:/etc/nginx/nginx.conf.template
       - ./start-nginx.sh:/start-nginx.sh
       - torch-data-store:/app/output  # Shared with torch service
       - ./output:/app/output
-    entrypoint: ["/bin/sh", "/start-nginx.sh"]
+    entrypoint: [ "/bin/sh", "/start-nginx.sh" ]
   torch:
     restart: unless-stopped
     build:
@@ -52,10 +52,10 @@ services:
       TORCH_FHIR_URL: http://torch-data-store:8080/fhir
       TORCH_FLARE_URL: http://torch-flare:8080
       TORCH_RESULTS_DIR: /app/output
-      TORCH_RESULTS_PERSISTENCE: PT12H30M5S
+      TORCH_RESULTS_PERSISTENCE: PT2160H
       LOG_LEVEL: debug
       NGINX_SERVERNAME: localhost
-      NGINX_FILELOCATION: http://localhost:80
+      NGINX_FILELOCATION: http://localhost:8085
       TORCH_BATCHSIZE: 100
       TORCH_MAXCONCURRENCY: 4
       TORCH_MAPPINGSFILE: /app/ontology/mapping_cql.json