remove container-internal ports and unneeded graph config vars (#80)

neurobagel · Aug 16, 2024 · 2a27db2 · 2a27db2
1 parent cef6f2c
commit 2a27db2
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Showing 3 changed files with 10 additions and 20 deletions.
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -6,14 +6,14 @@ services:
       - "local_node"
       - "full_stack"
     ports:
-      - "${NB_NAPI_PORT_HOST:-8000}:${NB_NAPI_PORT:-8000}"
+      - "${NB_NAPI_PORT_HOST:-8000}:8000"
     environment:
       NB_GRAPH_USERNAME: ${NB_GRAPH_USERNAME}
-      NB_GRAPH_ADDRESS: ${NB_GRAPH_ADDRESS:-graph}
-      NB_GRAPH_PORT: ${NB_GRAPH_PORT:-7200}
+      NB_GRAPH_ADDRESS: graph
+      NB_GRAPH_PORT: 7200
       NB_GRAPH_DB: ${NB_GRAPH_DB:-repositories/my_db}
       NB_RETURN_AGG: ${NB_RETURN_AGG:-true}
-      NB_API_PORT: ${NB_NAPI_PORT:-8000}
+      NB_API_PORT: 8000
       NB_API_ALLOWED_ORIGINS: ${NB_NAPI_ALLOWED_ORIGINS}
       NB_ENABLE_AUTH: ${NB_ENABLE_AUTH:-false}
       NB_QUERY_CLIENT_ID: ${NB_QUERY_CLIENT_ID}
@@ -25,7 +25,7 @@ services:
       - db_user_password
 
   graph:
-    image: "${NB_GRAPH_IMG:-ontotext/graphdb:10.3.1}"
+    image: "ontotext/graphdb:10.3.1"
     profiles:
       - "local_node"
       - "full_stack"
@@ -36,11 +36,11 @@ services:
       - "./vocab:/usr/src/neurobagel/vocab"
       - "${LOCAL_GRAPH_DATA:-./data}:/data"
     ports:
-      - "${NB_GRAPH_PORT_HOST:-7200}:${NB_GRAPH_PORT:-7200}"
+      - "${NB_GRAPH_PORT_HOST:-7200}:7200"
     environment:
       NB_GRAPH_USERNAME: ${NB_GRAPH_USERNAME}
-      NB_GRAPH_ADDRESS: ${NB_GRAPH_ADDRESS:-graph}
-      NB_GRAPH_PORT: ${NB_GRAPH_PORT:-7200}
+      NB_GRAPH_ADDRESS: graph
+      NB_GRAPH_PORT: 7200
       NB_GRAPH_DB: ${NB_GRAPH_DB:-repositories/my_db}
     entrypoint:
       - "/usr/src/neurobagel/scripts/setup.sh"
@@ -55,11 +55,11 @@ services:
       - "local_federation"
       - "full_stack"
     ports:
-      - "${NB_FAPI_PORT_HOST:-8080}:${NB_FAPI_PORT:-8000}"
+      - "${NB_FAPI_PORT_HOST:-8080}:8000"
     volumes:
       - "./local_nb_nodes.json:/usr/src/local_nb_nodes.json:ro"
     environment:
-      NB_API_PORT: ${NB_FAPI_PORT:-8000}
+      NB_API_PORT: 8000
       NB_FEDERATE_REMOTE_PUBLIC_NODES: ${NB_FEDERATE_REMOTE_PUBLIC_NODES:-True}
       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
@@ -9,14 +9,9 @@ Environment variable	Set manually in .env?	Description	Default value if not set
 `NB_RETURN_AGG`	Yes	Whether to return only aggregate, dataset-level query results (excluding subject/session-level attributes). One of [true, false]	`true`	Docker, Python
 `NB_NAPI_TAG`	No	Docker image tag for the Neurobagel node API	`latest`	Docker
 `NB_NAPI_PORT_HOST`	No	Port number on the _host machine_ to map the Neurobagel node API container port to	`8000`	Docker
-`NB_NAPI_PORT`	No	Port number on which to run the Neurobagel node API _in the API container_	`8000`	Docker
 `NB_FAPI_TAG`	No	Docker image tag for the Neurobagel federation API	`latest`	Docker
 `NB_FAPI_PORT_HOST`	No	Port number on the _host machine_ to map the Neurobagel federation API container port to	`8080`	Docker
-`NB_FAPI_PORT`	No	Port number on which to run the Neurobagel federation API _in the API container_	`8000`	Docker
-`NB_GRAPH_IMG`	No	Graph server Docker image	`ontotext/graphdb:10.3.1`	Docker
-`NB_GRAPH_ADDRESS`	No	IP address for the graph database (or container name, if graph is hosted locally)	`206.12.99.17 (graph)` **	Docker, Python
 `NB_GRAPH_PORT_HOST`	No	Port number on the _host machine_ to map the graph server container port to	`7200`	Docker
-`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. If "False", only locally specified nodes in `local_nb_nodes.json` are queried.	`true`	Docker, Python

diff --git a/template.env b/template.env
@@ -32,9 +32,6 @@ LOCAL_GRAPH_DATA=./data
 # Additional configurable parameters - uncomment to change the defaults
 # Change NB_GRAPH_PORT_HOST if port 7200 is already in use on the machine
 # NB_GRAPH_PORT_HOST=7200
-# NB_GRAPH_PORT=7200
-# NB_GRAPH_IMG=ontotext/graphdb:10.3.1
-# NB_GRAPH_ADDRESS=graph
 # ---------------------------------
 
 # ---- CONFIGURATION FOR n-API ----
@@ -46,15 +43,13 @@ NB_RETURN_AGG=true
 # Additional configurable parameters - uncomment to change the defaults
 # Change NB_NAPI_PORT_HOST if port 8000 is already in use on the machine
 # NB_NAPI_PORT_HOST=8000
-# NB_NAPI_PORT=8000
 # NB_NAPI_TAG=latest
 # ---------------------------------
 
 # ---- CONFIGURATION FOR f-API ----
 # Additional configurable parameters - uncomment to change the defaults
 # Change NB_FAPI_PORT_HOST if port 8080 is already in use on the machine
 # NB_FAPI_PORT_HOST=8080
-# NB_FAPI_PORT=8000
 # NB_FAPI_TAG=latest
 # NB_FEDERATE_REMOTE_PUBLIC_NODES=True
 # ---------------------------------