[ENH] Made base_api_url an environment variable (#37)

* Made base_api_url an environment variable * Made changes to the test file * Update app/api/url_generator.py Co-authored-by: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com> * Update README.md Co-authored-by: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com> * Update tests/test_url_generator.py Co-authored-by: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com> * Required changes made * Changes made to the test * Raised runtime error for missing env var * Minor change --------- Co-authored-by: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com>
neurobagel · Aug 14, 2024 · c119ea4 · c119ea4
1 parent c81129f
commit c119ea4
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Showing 4 changed files with 50 additions and 17 deletions.
diff --git a/README.md b/README.md
@@ -18,8 +18,10 @@ The aim of query-tool-ai would be to make this search process more user-friendly
   ### Set the environment variables - 
    | Environment Variable   | Type    | Required                                 | Default Value if Not Set | Example                                                   |
    | ---------------------- | ------- | ---------------------------------------- | ------------------------ | --------------------------------------------------------- |
+   | `NB_API_QUERY_URL`                 | string  | Yes                                       | -                | `https://api.neurobagel.org/query/?`                                               |
    | `HOST`                 | string  | No                                       | `0.0.0.0`                | `127.0.0.1`                                               |
    | `PORT`                 | integer | No                                       | `8000`                   | `8080`                                                    |
+
 
   ### Option 1 : Docker :
   - #### First, [install Docker](https://docs.docker.com/get-docker/).

diff --git a/app/api/url_generator.py b/app/api/url_generator.py
@@ -1,4 +1,6 @@
 import json
+import os
+from dotenv import load_dotenv
 from app.llm_processing.extractions import extract_information
 from app.api.validators import (
     validate_age_order,
@@ -11,6 +13,8 @@
     get_image_modality_termURL,
 )
 
+load_dotenv()
+
 
 def get_api_url(user_query: str) -> str:
     """
@@ -22,7 +26,13 @@ def get_api_url(user_query: str) -> str:
     Returns:
         str: The constructed API URL.
     """
-    base_api_url = "https://api.neurobagel.org/query/?"
+    base_api_url = os.getenv("NB_API_QUERY_URL")
+    if not base_api_url:
+        raise RuntimeError(
+            "The application was launched but could not find the NB_API_QUERY_URL environment variable."
+        )
+
+
     llm_response = extract_information(user_query)
 
     try:

diff --git a/entrypoint.sh b/entrypoint.sh
@@ -2,6 +2,7 @@
 
 # Start the Ollama services first
 ollama serve &
+ollama pull mistral &
 ollama run mistral &
 
 # Start the FastAPI application

diff --git a/tests/test_url_generator.py b/tests/test_url_generator.py
@@ -3,16 +3,30 @@
 from app.api.url_generator import get_api_url
 
 
+def test_get_api_url_without_env_var(monkeypatch):
+    # Unset the environment variable
+    monkeypatch.delenv("NB_API_QUERY_URL", raising=False)
+
+    user_query = "Some query"
+
+    with pytest.raises(RuntimeError, match="The application was launched but could not find the NB_API_QUERY_URL environment variable."):
+        get_api_url(user_query)
+
+
 def test_json_decode_error():
-    with patch(
-        "app.api.url_generator.extract_information",
-        return_value="{invalid_json: true",
+    with patch.dict(
+        "os.environ",
+        {"NB_API_QUERY_URL": "https://api.neurobagel.org/query/?"},
     ):
-        result = get_api_url("some user query")
-        assert (
-            result
-            == "I'm sorry, but I couldn't find the information you're looking for. Could you provide more details or clarify your question?"
-        )
+        with patch(
+            "app.api.url_generator.extract_information",
+            return_value="{invalid_json: true",
+        ):
+            result = get_api_url("some user query")
+            assert (
+                result
+                == "I'm sorry, but I couldn't find the information you're looking for. Could you provide more details or clarify your question?"
+            )
 
 
 # Define the mock responses for diagnosis and assessment term URLs
@@ -105,13 +119,19 @@ def test_get_api_url(
     mock_input_side_effect,
     expected_output,
 ):
-    with patch(
-        "app.api.url_generator.extract_information",
-        return_value=mock_llm_response,
+    with patch.dict(
+        "os.environ",
+        {"NB_API_QUERY_URL": "https://api.neurobagel.org/query/?"},
     ):
-        if mock_input_side_effect is not None:
-            with patch("builtins.input", side_effect=mock_input_side_effect):
+        with patch(
+            "app.api.url_generator.extract_information",
+            return_value=mock_llm_response,
+        ):
+            if mock_input_side_effect is not None:
+                with patch(
+                    "builtins.input", side_effect=mock_input_side_effect
+                ):
+                    result = get_api_url(user_query)
+            else:
                 result = get_api_url(user_query)
-        else:
-            result = get_api_url(user_query)
-        assert result == expected_output
+            assert result == expected_output