feat(cli, export): re-write using CLI and add export command

.gitignore

@@ -1,8 +1,9 @@
 # IDE
+.DS_Store
 .idea
 
 # Build
 dist
 
 # Versioning
-node_modules
+node_modules

Dockerfile

@@ -12,4 +12,6 @@ COPY fhirsnake /app
 
 EXPOSE 8000
 
-CMD ["poetry", "run", "uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000"]
+ENTRYPOINT ["poetry", "run", "python3", "cli.py"]
+
+CMD ["server"]

Dockerfile.resources

@@ -1,4 +1,4 @@
 FROM bedasoftware/fhirsnake:latest
 
 COPY resources /app/resources
-# The destination should be exactly the same!
+# The destination should be exactly the same!

README.md

@@ -36,13 +36,17 @@ resources/
 2. Adjust source destination in `Dockerfile.resources` if required
 3. Option A: Run a container
     ```bash
-    docker run -p 8002:8000 -v ./resources:/app/resources  bedasoftware/fhirsnake
+    docker run -p 8002:8000 -v ./resources:/app/resources bedasoftware/fhirsnake
     ```
 3. Option B: Build an image using the base image
     ```bash
     docker build -t fhirsnake-resources:latest -f Dockerfile.resources .
     docker run -p 8000:8000 fhirsnake-resources 
     ```
+4. Option C: Export resources as .ndjson or ndjson.gz
+    ```bash
+    docker run -v ./resources:/app/resources -v ./output:/output bedasoftware/fhirsnake export --output /output/seeds.ndjson.gz
+    ```
 
 ## Contribution and feedback
 Please, use [Issues](https://github.com/beda-software/fhirsnake/issues)

fhirsnake/cli.py

@@ -0,0 +1,72 @@
+import argparse
+import gzip
+import logging
+
+import ndjson
+import uvicorn
+
+from initial_resources import initial_resources
+
+logging.basicConfig(level=logging.INFO)
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description="CLI for fhirsnake")
+
+    subparsers = parser.add_subparsers(dest="command", required=True, help="Sub-command to run")
+
+    export_parser = subparsers.add_parser("export", help="Export resources as .ndjson or .ndjson.gz")
+    export_parser.add_argument(
+        "--output",
+        required=True,
+        help="Specify the output filename",
+    )
+
+    server_parser = subparsers.add_parser("server", help="Run fhirsnake FHIR server")
+    server_parser.add_argument(
+        "--host",
+        default="0.0.0.0",
+        help="Host",
+    )
+
+    server_parser.add_argument(
+        "--port",
+        type=int,
+        default=8000,
+        help="Port",
+    )
+
+    args = parser.parse_args()
+
+    if args.command == "export":
+        export_resources(args.output)
+
+    if args.command == "server":
+        server(args.host, args.port)
+
+
+def server(host: str, port: int) -> None:
+    config = uvicorn.Config("server:app", host=host, port=port)
+    server = uvicorn.Server(config)
+    server.run()
+
+
+def export_resources(output: str) -> None:
+    gzipped = output.endswith(".gz")
+    resources_list = flatten_resources(initial_resources)
+    dumped_resources = ndjson.dumps(resources_list)
+
+    if gzipped:
+        with gzip.open(output, "w+") as f:
+            f.write(dumped_resources.encode())
+    else:
+        with open(output, "w+") as f:
+            f.write(dumped_resources)
+
+
+def flatten_resources(resources: dict[str, dict[str, dict]]) -> list[dict]:
+    return [resource for by_resource_type in resources.values() for resource in by_resource_type.values()]
+
+
+if __name__ == "__main__":
+    main()

fhirsnake/initial_resources.py

@@ -0,0 +1,20 @@
+import logging
+import os
+import sys
+
+from files import load_resources
+
+REPOSITORY_URL = "https://github.com/beda-software/fhirsnake/"
+RESOURCE_DIR = "resources"
+
+root_dir = os.path.dirname(os.path.abspath(__name__))
+resources_abs_path = os.path.join(root_dir, RESOURCE_DIR)
+
+if not os.path.isdir(resources_abs_path):
+    logging.error(
+        f"Required directory '{resources_abs_path}' does not exist. \
+        Check {REPOSITORY_URL} for details. Stopping application."
+    )
+    sys.exit(1)
+
+initial_resources = load_resources(resources_abs_path)

fhirsnake/main.py → fhirsnake/server.py

@@ -1,33 +1,18 @@
 import logging
-import os
-import sys
 import uuid
 
 from fastapi import FastAPI, HTTPException
-from files import load_resources
+from initial_resources import initial_resources
 
 logging.basicConfig(level=logging.INFO)
 
-REPOSITORY_URL = "https://github.com/beda-software/fhirsnake/"
 
 app = FastAPI()
 
 
 @app.on_event("startup")
 async def load_app_data():
-    root_dir = os.path.dirname(os.path.abspath(__name__))
-    logging.warning(root_dir)
-    resource_dir = "resources"
-    resources_abs_path = os.path.join(root_dir, resource_dir)
-
-    if not os.path.isdir(resources_abs_path):
-        logging.error(
-            f"Required directory '{resources_abs_path}' does not exist. \
-            Check {REPOSITORY_URL} for details. Stopping application."
-        )
-        sys.exit(1)
-
-    app.state.resources = load_resources(resources_abs_path)
+    app.state.resources = initial_resources
 
 
 @app.get("/")

pyproject.toml

@@ -11,6 +11,7 @@ python = "^3.11"
 fastapi = "^0.112.1"
 uvicorn = "^0.30.6"
 pyyaml = "^6.0.2"
+ndjson = "^0.3.1"
 
 [tool.poetry.dev-dependencies]
 ruff = "^0.6.2"