feat: add support for input dirs (multiple for watch and export)

Author: ruscoder

README.md

@@ -8,8 +8,8 @@
 **fhirsnake** is a minimalistic FHIR server that serve yaml and json files as FHIR resources
 
 ## How it works?
-The server reads all `yaml` and `json` files from `resources` directory.
-Resources directory should have subdirectories with names equal resource types:
+The server reads all `yaml` and `json` files from an input directory (`resources` by default).
+The input directory should have subdirectories with names equal to resource types:
 ```markdown
 resources/
 ├── Patient/
@@ -19,10 +19,12 @@ resources/
 ├── Questionnaire/
 │   ├── questionnaire1.yaml
 │   ├── questionnaire2.yaml
-│   └── sudbir/
+│   └── subdir/
 │       └── questionnaire3.yaml
 ```
 
+Use the `--input` flag to specify a custom input directory. For `export` and `watch` commands, `--input` can be passed multiple times to load resources from several directories.
+
 ## Environment variable substitution
 
 To use environment variables in resources, you can use the syntax `${VAR_NAME}`.
@@ -44,32 +46,92 @@ NOTE: The syntax `$VAR` without braces is not supported because it might be used
 1. Organize resources in a directory
 
 ### Server
-1. Option A: Run a container
-    ```bash
-    docker run -p 8002:8000 -v ./resources:/app/resources bedasoftware/fhirsnake
-    ```
-2. Option B: Adjust source destination in `Dockerfile.resources` if required
-2.1. Build an image using the base image
-    ```bash
-    docker build -t fhirsnake-resources:latest -f Dockerfile.resources .
-    docker run -p 8000:8000 fhirsnake-resources 
-    ```
+
+```bash
+docker run \
+  -p 8002:8000 \
+  -v ./resources:/resources \
+  bedasoftware/fhirsnake server --input /resources
+```
+
+Or build a custom image with `Dockerfile.resources`:
+```bash
+docker build -t bedasoftware/fhirsnake -f Dockerfile.resources .
+docker run -p 8000:8000 fhirsnake-resources
+```
 
 ### Export
-1. Export resources as .json (Bundle) or .ndjson or ndjson.gz
-    ```bash
-    docker run -v ./resources:/app/resources -v ./output:/output bedasoftware/fhirsnake export --external-questionnaire-fce-fhir-converter-url=http://host.docker.internal:3000/to-fhir --output /output/seeds.ndjson.gz
-    ```
+
+Export resources as `.json` (Bundle), `.ndjson`, or `.ndjson.gz`:
+
+```bash
+docker run \
+  -v ./resources:/resources \
+  -v ./output:/output \
+  bedasoftware/fhirsnake export \
+    --input /resources \
+    --output /output/seeds.ndjson.gz
+```
+
+Multiple input directories:
+```bash
+docker run \
+  -v ./resources1:/resources1 \
+  -v ./resources2:/resources2 \
+  -v ./output:/output \
+  bedasoftware/fhirsnake export \
+    --input /resources1 \
+    --input /resources2 \
+    --output /output/seeds.ndjson.gz
+```
+
+With external FCE->FHIR converter:
+```bash
+docker run \
+  -v ./resources:/resources \
+  -v ./output:/output \
+  bedasoftware/fhirsnake export \
+    --input /resources \
+    --output /output/seeds.ndjson.gz \
+    --external-questionnaire-fce-fhir-converter-url http://host.docker.internal:3000/to-fhir
+```
 
 ### Watch
-1. Watch resources for changes and send as PUT requests to external fhir server
-    ```bash
-    docker run -v ./resources:/app/resources -v ./output:/output bedasoftware/fhirsnake watch --external-fhir-server-url http://host.docker.internal:8080 --external-fhir-server-header "Authorization: Token token" --external-questionnaire-fce-fhir-converter-url=http://host.docker.internal:3000/to-fhir
-    ```    
 
-### Using external questionnaire FCE->FHIR converter
+Watch resources for changes and send as PUT requests to an external FHIR server:
+
+```bash
+docker run \
+  -v ./resources:/resources \
+  bedasoftware/fhirsnake watch \
+    --input /resources \
+    --external-fhir-server-url http://host.docker.internal:8080
+```
+
+With auth headers:
+```bash
+docker run \
+  -v ./resources:/resources \
+  bedasoftware/fhirsnake watch \
+    --input /resources \
+    --external-fhir-server-url http://host.docker.internal:8080 \
+    --external-fhir-server-header "Authorization: Token token"
+```
+
+Multiple input directories:
+```bash
+docker run \
+  -v ./resources1:/resources1 \
+  -v ./resources2:/resources2 \
+  bedasoftware/fhirsnake watch \
+    --input /resources1 \
+    --input /resources2 \
+    --external-fhir-server-url http://host.docker.internal:8080
+```
+
+### External questionnaire FCE->FHIR converter
 
-There's an image `bedasoftware/questionnaire-fce-fhir-converter:latest` available that provides `/to-fhir` endpoint that can be used along with `--external-questionnaire-fce-fhir-converter-url` args for watch and export commands.
+The image `bedasoftware/questionnaire-fce-fhir-converter:latest` provides a `/to-fhir` endpoint that can be used with the `--external-questionnaire-fce-fhir-converter-url` flag in `export` and `watch` commands.
 
 
 ## Contribution and feedback

entrypoint.sh

@@ -1,2 +1,2 @@
 #!/bin/sh
-poetry run python3 cli.py "$@"
+exec poetry run python3 cli.py "$@"

fhirsnake/cli.py

@@ -1,12 +1,18 @@
 import argparse
 import logging
+import os
 
 import uvicorn
 from export import export_resources
 from watch import start_watcher
 
 logging.basicConfig(level=logging.INFO)
 
+DEFAULT_INPUT_DIR = "resources"
+
+root_dir = os.path.dirname(os.path.abspath(__file__))
+default_input_dir_abs_path = os.path.join(root_dir, DEFAULT_INPUT_DIR)
+
 
 def main() -> None:
     parser = argparse.ArgumentParser(description="CLI for fhirsnake")
@@ -15,13 +21,15 @@ def main() -> None:
 
     # TODO: add "serve" as alias
     server_parser = subparsers.add_parser("server", help="Run fhirsnake FHIR server")
-
+    server_parser.add_argument(
+        "--input",
+        help=f"Directory of FHIR JSON resources to load (default: {default_input_dir_abs_path})",
+    )
     server_parser.add_argument(
         "--host",
         default="0.0.0.0",
         help="Host",
     )
-
     server_parser.add_argument(
         "--port",
         type=int,
@@ -30,6 +38,11 @@ def main() -> None:
     )
 
     export_parser = subparsers.add_parser("export", help="Export resources as .json (Bundle) or .ndjson or .ndjson.gz")
+    export_parser.add_argument(
+        "--input",
+        action="append",
+        help=f"Input directories to load resources from (default: {default_input_dir_abs_path})",
+    )
     export_parser.add_argument(
         "--external-questionnaire-fce-fhir-converter-url",
         required=False,
@@ -43,20 +56,23 @@ def main() -> None:
     )
 
     watch_parser = subparsers.add_parser("watch", help="Watch resources changes and send them to FHIR server")
+    watch_parser.add_argument(
+        "--input",
+        action="append",
+        help=f"Input directories to load resources from (default: {default_input_dir_abs_path})",
+    )
     watch_parser.add_argument(
         "--external-questionnaire-fce-fhir-converter-url",
         required=False,
         type=str,
         help="External Questionnaire FCE FHIR Converter URL",
     )
-
     watch_parser.add_argument(
         "--external-fhir-server-url",
         required=True,
         type=str,
         help="External FHIR Server URL",
     )
-
     watch_parser.add_argument(
         "--external-fhir-server-header",
         required=False,
@@ -67,32 +83,55 @@ def main() -> None:
     args = parser.parse_args()
 
     if args.command == "server":
-        server(args.host, args.port)
+        server(args.input or default_input_dir_abs_path, args.host, args.port)
 
     if args.command == "export":
-        export(args.output, args.external_questionnaire_fce_fhir_converter_url)
+        export(
+            args.input or [default_input_dir_abs_path], args.output, args.external_questionnaire_fce_fhir_converter_url
+        )
 
     if args.command == "watch":
         watch(
+            args.input or [default_input_dir_abs_path],
             args.external_fhir_server_url,
             args.external_fhir_server_header,
             args.external_questionnaire_fce_fhir_converter_url,
         )
 
 
-def server(host: str, port: int) -> None:
-    config = uvicorn.Config("server:app", host=host, port=port)
-    server = uvicorn.Server(config)
-    server.run()
+def validate_input_dirs(input_dirs: list[str]) -> None:
+    for input_dir in input_dirs:
+        if not os.path.isdir(input_dir):
+            raise RuntimeError(f"Required directory '{input_dir}' does not exist. Stopping application.")
+
 
+def server(input_dir: str, host: str, port: int) -> None:
+    from server import create_app
 
-def export(output: str, external_questionnaire_fce_fhir_converter_url: str | None):
-    export_resources(output, external_questionnaire_fce_fhir_converter_url)
+    validate_input_dirs([input_dir])
+    config = uvicorn.Config(create_app(input_dir), host=host, port=port)
+    server = uvicorn.Server(config)
+    server.run()
 
 
-def watch(url: str, headers_list: list[str] | None, external_questionnaire_fce_fhir_converter_url: str | None):
-    headers = {v.split(":", 1)[0]: v.split(":", 1)[1] for v in (headers_list or [])}
-    start_watcher(url, headers, external_questionnaire_fce_fhir_converter_url)
+def export(
+    input_dirs: list[str],
+    output: str,
+    external_questionnaire_fce_fhir_converter_url: str | None,
+):
+    validate_input_dirs(input_dirs)
+    export_resources(input_dirs, output, external_questionnaire_fce_fhir_converter_url)
+
+
+def watch(
+    input_dirs: list[str],
+    url: str,
+    headers_list: list[str] | None,
+    external_questionnaire_fce_fhir_converter_url: str | None,
+):
+    validate_input_dirs(input_dirs)
+    headers = {v.split(":", 1)[0].strip(): v.split(":", 1)[1].strip() for v in (headers_list or [])}
+    start_watcher(input_dirs, url, headers, external_questionnaire_fce_fhir_converter_url)
 
 
 if __name__ == "__main__":

fhirsnake/export.py

@@ -3,15 +3,20 @@
 
 import ndjson
 from converter import convert_resources
-from initial_resources import get_initial_resources
+from files import load_resources
 from utils import substitute_env_vars
 
 
-def export_resources(output: str, external_questionnaire_fce_fhir_converter_url: str | None) -> None:
+def export_resources(
+    input_dirs: list[str],
+    output: str,
+    external_questionnaire_fce_fhir_converter_url: str | None,
+) -> None:
     is_ndjson = "ndjson" in output
     gzipped = output.endswith(".gz")
-    resources_list = flatten_resources(get_initial_resources())
-
+    resources_list = []
+    for input_dir in input_dirs:
+        resources_list.extend(flatten_resources(load_resources(input_dir)))
     if external_questionnaire_fce_fhir_converter_url:
         resources_list = convert_resources(resources_list, external_questionnaire_fce_fhir_converter_url)
 
@@ -25,7 +30,10 @@ def export_resources(output: str, external_questionnaire_fce_fhir_converter_url:
                 "entry": [
                     {
                         "fullUrl": f"urn:uuid:{resource['resourceType']}:{resource['id']}",
-                        "request": {"method": "PUT", "url": f"/{resource['resourceType']}/{resource['id']}"},
+                        "request": {
+                            "method": "PUT",
+                            "url": f"/{resource['resourceType']}/{resource['id']}",
+                        },
                         "resource": resource,
                     }
                     for resource in resources_list