[FIX] Remove default NB_API_QUERY_URL value and fix ports used by f…

…ull-stack setup script (#42)

* use internal port in graph container for GraphDB operations

* replace usable default for NB_API_QUERY_URL with placeholder

* echo port used inside graph container

* switch to above-line comments only

dev/docker-compose.yml

@@ -58,4 +58,4 @@ services:
     ports:
       - "${NB_QUERY_PORT_HOST:-3000}:5173"
     environment:
-      NB_API_QUERY_URL: ${NB_API_QUERY_URL:-http://localhost:8000/}
+      NB_API_QUERY_URL: ${NB_API_QUERY_URL}

dev/graphdb_setup.sh

@@ -128,12 +128,12 @@ echo "Environment variables have been set from ${ENV_FILE_PATH}."
 
 # Extract just the database name
 DB_NAME="${NB_GRAPH_DB#repositories/}"
-NB_GRAPH_PORT_HOST=${NB_GRAPH_PORT_HOST:-7200}
+NB_GRAPH_PORT=${NB_GRAPH_PORT:-7200}
 
 # Get the directory of this script to be able to find the data-config_template.ttl file
 SCRIPT_DIR=$(dirname "$0")
 
-echo "The GraphDB server is being accessed at http://localhost:${NB_GRAPH_PORT_HOST}."
+echo "The GraphDB server is being accessed at http://localhost:${NB_GRAPH_PORT}."
 
 ##### First time GraphDB setup #####
 
@@ -143,14 +143,14 @@ if [ "${RUN_USER_SETUP}" = "on" ]; then
     # 1. Change database admin password
     echo "Changing the admin password (note: if you have previously set the admin password, this has no effect)..."
 	# TODO: To change a *previously set* admin password, we need to also provide the current password via -u
-    curl -X PATCH --header 'Content-Type: application/json' http://localhost:${NB_GRAPH_PORT_HOST}/rest/security/users/admin -d "{\"password\": \""${ADMIN_PASS}"\"}"
+    curl -X PATCH --header 'Content-Type: application/json' http://localhost:${NB_GRAPH_PORT}/rest/security/users/admin -d "{\"password\": \""${ADMIN_PASS}"\"}"
 
 	# 2. If security is not enabled, enable it (i.e. allow only authenticated users access)
-	is_security_enabled=$(curl -s -X GET http://localhost:${NB_GRAPH_PORT_HOST}/rest/security)
+	is_security_enabled=$(curl -s -X GET http://localhost:${NB_GRAPH_PORT}/rest/security)
 	if [ "${is_security_enabled}" = "false" ]; then
 		echo "Enabling password-based access control to all databases ..."
 		# NOTE: This command fails without credentials once security is enabled
-		curl -X POST --header 'Content-Type: application/json' -d true http://localhost:${NB_GRAPH_PORT_HOST}/rest/security
+		curl -X POST --header 'Content-Type: application/json' -d true http://localhost:${NB_GRAPH_PORT}/rest/security
 	else
 		echo "Password-based access control has already been enabled."
 	fi
@@ -159,7 +159,7 @@ if [ "${RUN_USER_SETUP}" = "on" ]; then
 	# TODO: Separate this out from the first-time setup? As this can technically be run at any time to create additional users.
 	# NOTE: If user already exists, response will be "An account with the given username already exists." OK for script.
 	echo "Creating a new database user ${NB_GRAPH_USERNAME}..."
-    curl -X POST --header 'Content-Type: application/json' -u "admin:${ADMIN_PASS}" -d @- http://localhost:${NB_GRAPH_PORT_HOST}/rest/security/users/${NB_GRAPH_USERNAME} <<EOF
+    curl -X POST --header 'Content-Type: application/json' -u "admin:${ADMIN_PASS}" -d @- http://localhost:${NB_GRAPH_PORT}/rest/security/users/${NB_GRAPH_USERNAME} <<EOF
     {
         "username": "${NB_GRAPH_USERNAME}",
         "password": "${NB_GRAPH_PASSWORD}"
@@ -178,7 +178,7 @@ sed 's/rep:repositoryID "my_db" ;/rep:repositoryID "'"${DB_NAME}"'" ;/' ${SCRIPT
 # 5. Create a new database
 # Assumes data-config.ttl is in the same directory as this script!
 echo "Creating the GraphDB database ${DB_NAME}..."
-curl -X PUT -u "admin:${ADMIN_PASS}" http://localhost:${NB_GRAPH_PORT_HOST}/${NB_GRAPH_DB} --data-binary "@data-config.ttl" -H "Content-Type: application/x-turtle"
+curl -X PUT -u "admin:${ADMIN_PASS}" http://localhost:${NB_GRAPH_PORT}/${NB_GRAPH_DB} --data-binary "@data-config.ttl" -H "Content-Type: application/x-turtle"
 
 # 6. Grant newly created user access permission to the database
 # Confirm user wants to proceed with changing user permissions
@@ -193,7 +193,7 @@ curl -X PUT -u "admin:${ADMIN_PASS}" http://localhost:${NB_GRAPH_PORT_HOST}/${NB
 
 echo "Granting user ${NB_GRAPH_USERNAME} read/write permissions to database ${DB_NAME}..."
 curl -X PUT --header 'Content-Type: application/json' -d "
-{\"grantedAuthorities\": [\"WRITE_REPO_${DB_NAME}\",\"READ_REPO_${DB_NAME}\"]}" http://localhost:${NB_GRAPH_PORT_HOST}/rest/security/users/${NB_GRAPH_USERNAME} -u "admin:${ADMIN_PASS}"
+{\"grantedAuthorities\": [\"WRITE_REPO_${DB_NAME}\",\"READ_REPO_${DB_NAME}\"]}" http://localhost:${NB_GRAPH_PORT}/rest/security/users/${NB_GRAPH_USERNAME} -u "admin:${ADMIN_PASS}"
 
 echo "Done."
 

dev/setup.sh

@@ -4,7 +4,7 @@
 GRAPHDB_PID=$!
 
 # Waiting for GraphDB to start
-while ! curl --silent "localhost:${NB_GRAPH_PORT_HOST}/rest/repositories" | grep '\[\]'; do
+while ! curl --silent "localhost:${NB_GRAPH_PORT}/rest/repositories" | grep '\[\]'; do
     :
 done
 
@@ -13,18 +13,19 @@ SCRIPT_DIR=$(dirname "$0")
 
 # Logic for main setup
 main() {
-    echo -e "Setting up a Neurobagel graph backend...\n"
+    echo "Setting up a Neurobagel graph backend..."
+    echo -e "(The GraphDB server is being accessed inside the GraphDB container at http://localhost:${NB_GRAPH_PORT}.)\n"
 
     echo "Setting up GraphDB server..."
     ./graphdb_setup.sh "${NB_GRAPH_ADMIN_PASSWORD}"
     echo "Finished server setup."
 
     echo "Adding datasets to the database..."
-    ./add_data_to_graph.sh ./data localhost:${NB_GRAPH_PORT_HOST} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
+    ./add_data_to_graph.sh ./data localhost:${NB_GRAPH_PORT} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
     echo "Finished adding datasets to databases."
 
     echo "Adding Neurobagel vocabulary to the database"
-    ./add_data_to_graph.sh ./vocab localhost:${NB_GRAPH_PORT_HOST} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
+    ./add_data_to_graph.sh ./vocab localhost:${NB_GRAPH_PORT} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
     echo "Finished adding the Neurobagel vocabulary to the database."
 
     echo "Finished setting up the Neurobagel graph backend."

dev/template.env

@@ -7,8 +7,13 @@ COMPOSE_PROFILES=local_node
 
 # ---- CONFIGURATION FOR graph ----
 NB_GRAPH_ADMIN_PASSWORD=ADMINPASSWORD
-NB_GRAPH_USERNAME=DBUSER  # REPLACE DBUSER WITH YOUR GRAPH DATABASE USERNAME
-NB_GRAPH_PASSWORD=DBPASSWORD  # REPLACE DBPASSWORD WITH YOUR GRAPH DATABASE PASSWORD
+
+# **REPLACE DBUSER** with your graph database username
+NB_GRAPH_USERNAME=DBUSER
+
+# **REPLACE DBPASSWORD** with your graph database password
+NB_GRAPH_PASSWORD=DBPASSWORD
+
 NB_GRAPH_DB=repositories/my_db
 NB_RETURN_AGG=true
 NB_NAPI_TAG=latest
@@ -17,7 +22,9 @@ LOCAL_GRAPH_DATA=./data  # REPLACE WITH PATH TO YOUR JSONLD FILES
 
 # ---- CONFIGURATION FOR n-API ----
 ## ADDITIONAL CONFIGURABLE PARAMETERS: Uncomment and modify values of the below variables as needed to use non-default values.
-NB_NAPI_ALLOWED_ORIGINS="*"  # Allow multiple origins of requests. e.g. For a query tool deployed locally using default ports, use: NB_API_ALLOWED_ORIGINS="http://localhost:3000 http://127.0.0.1:3000"
+# Allow multiple origins of requests. e.g. For a query tool deployed locally using default ports, use: NB_API_ALLOWED_ORIGINS="http://localhost:3000 http://127.0.0.1:3000"
+NB_NAPI_ALLOWED_ORIGINS="*"
+
 NB_NAPI_PORT_HOST=8000
 NB_NAPI_PORT=8000
 NB_GRAPH_ROOT_HOST=~/graphdb-home
@@ -37,9 +44,13 @@ NB_FAPI_PORT_HOST=8080
 NB_FAPI_TAG=latest
 
 # ---- CONFIGURATION FOR QUERY TOOL ----
-# URL of the f-API as it will appear to a user
-NB_API_QUERY_URL=http://localhost:8080
+# URL of the n-API/f-API the query to will talk to, as it appears to a user
+# **REPLACE http://XX.XX.XX.XX** with your API URL (and port, if applicable) as it appears on a user's machine, 
+# or localhost:<port> if query tool will only be accessed from its host machine
+NB_API_QUERY_URL=http://XX.XX.XX.XX
+
 # Docker image tag of the query tool (default latest)
 NB_QUERY_TAG=latest
+
 # Port that the query tool will be exposed on the host and likely the network (default 3000)
 NB_QUERY_PORT_HOST=3000