[ENH] Removed local_node_query profile (#72)

* Removed `local_node_query` profile * Update README.md Co-authored-by: Alyssa Dai <[email protected]> * Updated README.md * Updated `template.env` * Updated `neurobagel_environment_variables.tsv` * Updated README.md * Update README.md Co-authored-by: Alyssa Dai <[email protected]> --------- Co-authored-by: Alyssa Dai <[email protected]>
neurobagel · Aug 8, 2024 · 4923feb · 4923feb
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diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 Configuration files for a Neurobagel deployment.
 
 ## How to use
-For detailed instructions on the deployment options for Neurobagel, see the official Neurobagel documentation on [setting up a local knowledge graph (node)](https://neurobagel.org/infrastructure/) and [local query federation](https://neurobagel.org/federate/).
+For detailed instructions on deploying Neurobagel for your use case, see the official Neurobagel documentation on [setting up a local knowledge graph (node)](https://neurobagel.org/getting_started/) and [configuration options](https://neurobagel.org/config/).
 
 ### Using the full-stack Docker Compose file
 
@@ -21,12 +21,12 @@ For detailed instructions on the deployment options for Neurobagel, see the offi
 
     Ensure to edit the configuration file(s) according to your deployment.
 
-    :warning: **Note**: You **must** change the value of the `NB_API_QUERY_URL` variable in the `.env` file before you can launch any service stack that includes a query tool (i.e., `local_node_query`, `full_stack`, `local_federation`). 
+    :warning: **Note**: You **must** change the value of the `NB_API_QUERY_URL` variable in the `.env` file before you can launch any service stack that includes a query tool (i.e., `full_stack`, `local_federation`). 
 See comments in the `.env` file for more information.
 
 3. In the repository root, start the Docker Compose stack and specify your desired deployment profile
 
-    **To set up only a local node:**
+    **To set up only a local node (without a graphical query tool):**
     ```bash
     docker compose up -d
     ```
@@ -35,12 +35,7 @@ See comments in the `.env` file for more information.
     docker compose --profile local_node up -d
     ```
 
-    **To set up a local node with a graphical query tool:**
-    ```bash
-    docker compose --profile local_node_query up -d
-    ```
-
-    **To set up a local node and local federation (including a graphical query tool) all at once:**
+    **To set up a local node along with a graphical query tool and optional federation:**
     ```bash
     docker compose --profile full_stack up -d
     ```

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -4,7 +4,6 @@ services:
     image: "neurobagel/api:${NB_NAPI_TAG:-latest}"
     profiles:
       - "local_node"
-      - "local_node_query"
       - "full_stack"
     ports:
       - "${NB_NAPI_PORT_HOST:-8000}:${NB_NAPI_PORT:-8000}"
@@ -29,7 +28,6 @@ services:
     image: "${NB_GRAPH_IMG:-ontotext/graphdb:10.3.1}"
     profiles:
       - "local_node"
-      - "local_node_query"
       - "full_stack"
     volumes:
       - "graphdb_home:/opt/graphdb/home"
@@ -75,20 +73,6 @@ services:
       - "${NB_QUERY_PORT_HOST:-3000}:5173"
     environment:
       NB_API_QUERY_URL: ${NB_API_QUERY_URL}
-      NB_IS_FEDERATION_API: "true"
-      NB_QUERY_URL_PATH: ${NB_QUERY_URL_PATH:-/}
-      NB_ENABLE_AUTH: ${NB_ENABLE_AUTH:-false}
-      NB_QUERY_CLIENT_ID: ${NB_QUERY_CLIENT_ID}
-
-  query_local:
-    image: "neurobagel/query_tool:${NB_QUERY_TAG:-latest}"
-    profiles:
-      - "local_node_query"
-    ports:
-      - "${NB_QUERY_PORT_HOST:-3000}:5173"
-    environment:
-      NB_API_QUERY_URL: ${NB_API_QUERY_URL}
-      NB_IS_FEDERATION_API: "false"
       NB_QUERY_URL_PATH: ${NB_QUERY_URL_PATH:-/}
       NB_ENABLE_AUTH: ${NB_ENABLE_AUTH:-false}
       NB_QUERY_CLIENT_ID: ${NB_QUERY_CLIENT_ID}

diff --git a/docs/neurobagel_environment_variables.tsv b/docs/neurobagel_environment_variables.tsv
@@ -19,7 +19,7 @@ Environment variable	Set manually in .env?	Description	Default value if not set
 `NB_GRAPH_PORT`	No	Port number used by the _graph server container_	`7200` *	Docker, Python
 `NB_QUERY_TAG`	No	Docker image tag for the query tool	`latest`	Docker
 `NB_QUERY_PORT_HOST`	No	Port number used by the `query_tool` on the host machine	`3000`	Docker
-`NB_FEDERATE_REMOTE_PUBLIC_NODES`	Yes 	If "True", include public nodes in federation	`true`	Docker, Python
+`NB_FEDERATE_REMOTE_PUBLIC_NODES`	Yes 	If "True", include public nodes in federation. If "False", only locally specified nodes in `local_nb_nodes.json` are queried.	`true`	Docker, Python
 `NB_QUERY_URL_PATH`	No	The URL path for the query tool, determines the specific URL at which the app should be rendered for users to access it	`/`	Docker
 `NB_ENABLE_AUTH`	Yes	**(Experimental, for dev deployments only)** Whether to enable authentication for cohort queries. One of [true, false]	`false`	Docker, Python
 `NB_QUERY_CLIENT_ID`	Yes	**(Experimental, for dev deployments only)** OAuth client ID for the query tool. Required if NB_ENABLE_AUTH is set to true.	-	Docker, Python
diff --git a/template.env b/template.env
@@ -60,14 +60,14 @@ NB_RETURN_AGG=true
 # ---------------------------------
 
 # ---- CONFIGURATION FOR QUERY TOOL ----
-# You MUST replace http://XX.XX.XX.XX with the URL (and port, if needed) of the Neurobagel API the query tool should send requests to.
-# The query tool sends requests from a user's machine, so ensure you provide the URL of the API *as a user would access it from their own (external) machine*, 
-# even if the query tool and the Neurobagel API are hosted on the same physical machine.
+# You MUST replace http://XX.XX.XX.XX with the URL (and port, if needed) of the Neurobagel f-API the query tool should send requests to.
+# The query tool sends requests from a user's machine, so ensure you provide the URL of the f-API *as a user would access it from their own (external) machine*, 
+# even if the query tool and the Neurobagel f-API are hosted on the same physical machine.
 # e.g., https://neurobagel.myInstitute.edu/federation
 #
 # Exception: If you are testing your setup locally and will only access the query tool from the SAME machine 
-# that your API is hosted on, you can use localhost as the URL.
-# e.g., http://localhost:8000 (if NB_API_PORT_HOST=8000):
+# that your f-API is hosted on, you can use localhost as the URL.
+# e.g., http://localhost:8080 (if NB_FAPI_PORT_HOST=8080):
 NB_API_QUERY_URL=http://XX.XX.XX.XX
 
 # Additional configurable parameters - uncomment to change the defaults