[REF] Consolidate deployment recipes and refactor template.env (#46)

* reorganize template.env

* remove deprecated deployment-specific recipes

* lift files + configs for full-stack recipe to root

* move setup.sh into scripts/

* make script executable

* update mount paths
- switch to relative paths to avoid creating duplicate directories

* update paths in scripts and create logs/ dir

* update README

* update compatibility tests

* More context in template.env and README

Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com>

* update environment variable table
- added new variables:
  - NB_GRAPH_ADMIN_PASSWORD
  - LOCAL_GRAPH_DATA
- split NB_API_PORT, NB_API_PORT_HOST, and NB_API_TAG into f-API and n-API

---------

Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com>

.github/workflows/compatibility-test copy.yaml

@@ -15,13 +15,13 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Rename files
-        working-directory: ./dev
+        working-directory: .
         run: |
           cp template.env .env
           cp local_nb_nodes.template.json local_nb_nodes.json
       
       - name: Run docker compose
-        working-directory: ./dev
+        working-directory: .
         run: |
           docker compose --profile full_stack up -d
 
@@ -34,9 +34,9 @@ jobs:
         run: npm install
 
       - name: wait for graph set up
-        working-directory: ./dev
+        working-directory: ./scripts
         run: |
-          while ! tail -n 0 -f ./DEPLOY.log | grep -q "Finished setting up the Neurobagel graph backend."; do
+          while ! tail -n 0 -f ./logs/DEPLOY.log | grep -q "Finished setting up the Neurobagel graph backend."; do
             :
           done
           echo "Finished setting up the Neurobagel graph backend."

.github/workflows/compatibility-test.yaml

@@ -12,14 +12,14 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Rename files
-        working-directory: ./dev
+        working-directory: .
         run: |
           cp template.env .env
           cp local_nb_nodes.template.json local_nb_nodes.json
           sed -i 's/latest/nightly/g' .env
       
       - name: Run docker compose
-        working-directory: ./dev
+        working-directory: .
         run: |
           docker compose --profile full_stack up -d
 
@@ -32,9 +32,9 @@ jobs:
         run: npm install
 
       - name: wait for graph set up
-        working-directory: ./dev
+        working-directory: ./scripts
         run: |
-          while ! tail -n 0 -f ./DEPLOY.log | grep -q "Finished setting up the Neurobagel graph backend."; do
+          while ! tail -n 0 -f ./logs/DEPLOY.log | grep -q "Finished setting up the Neurobagel graph backend."; do
             :
           done
           echo "Finished setting up the Neurobagel graph backend."

README.md

@@ -7,28 +7,24 @@ For detailed instructions on the deployment options for Neurobagel, see the offi
 ### Using the full-stack Docker Compose file
 
 1. Clone the repository
-```bash
-git clone https://github.com/neurobagel/recipes.git
-```
+    ```bash
+    git clone https://github.com/neurobagel/recipes.git
+    ```
+
+2. Copy and rename the required template configuration files
+    ```bash
+    cp template.env .env
 
-2. `cd` into the directory containing the Neurobagel deployment recipe
-<!---
-TODO: Change once we rename this directory for production!
--->
-```bash
-cd recipes/dev
-```
+    # if also setting up local federation
+    cp local_nb_nodes.template.json local_nb_nodes.json
+    ```
 
-3. Copy and rename template files in the directory
-```bash
-cp template.env .env
+    Ensure to edit the configuration file(s) according to your deployment.
 
-# if also setting up local federation
-cp local_nb_nodes.template.json local_nb_nodes.json
-```
-Ensure to edit the 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`). 
+See comments in the `.env` file for more information.
 
-4. Start the Docker Compose stack and specify your desired deployment profile
+3. In the repository root, start the Docker Compose stack and specify your desired deployment profile
 
     **To set up only a local node:**
     ```bash
@@ -48,30 +44,4 @@ Ensure to edit the file(s) according to your deployment.
     ```bash
     docker compose --profile full_stack up -d
     ```
-A log file `DEPLOY.log` will be automatically created in the current directory with a copy of the STDOUT from the automatic deployment process.
-
-### Using deployment type-specific Docker Compose files
-
-**Note: These instructions will soon be superceded by the full-stack Docker Compose file instructions.**
-
-1. Clone the repository
-```bash
-git clone https://github.com/neurobagel/recipes.git
-```
-
-2. `cd` into the directory containing the appropriate configuration files
-for your deployment scenario.
-
-3. Depending on your deployment scenario, 
-copy and/or rename the template files in the directory
-and edit them accordingly:
-
-    `local_federation/`
-    - `local_nb_nodes.json`
-    - `.env`
-
-    `local_node/`
-    - `.env`
-
-    `local_node_with_query_tool/`
-    - `.env`
+A log file `DEPLOY.log` will be automatically created under `scripts/logs/` with a copy of the STDOUT from the automatic deployment process.