[REF] Change the linked examples to recipe repo (#158)

* [REF] Change the linked examples to recipe repo * Apply suggestions from code review Co-authored-by: Alyssa Dai <[email protected]> --------- Co-authored-by: Alyssa Dai <[email protected]>
neurobagel · Feb 3, 2024 · a107d1a · a107d1a
1 parent 0c8a77b
commit a107d1a
Showing 1 changed file with 28 additions and 14 deletions.
diff --git a/docs/infrastructure.md b/docs/infrastructure.md
@@ -84,15 +84,24 @@ We have tested the following options:
 We recommend launching the Neurobagel API and your graph backend instance using `docker compose`.
 (To install the API from source, see [these instructions](https://github.com/neurobagel/api/blob/main/README.md#local-installation).)
 
-### Clone the API repo
+### Clone the configuration file templates
+
+The [`neurobagel/recipes`](https://github.com/neurobagel/recipes) repository contains templates of all files needed for configuring different types of Neurobagel deployments.
+
+Configuration files for setting up a single Neurobagel node are found in the [`local_node`](https://github.com/neurobagel/recipes/tree/main/local_node) subdirectory.
+**You can follow the below steps directly in this subdirectory, or in a new directory outside of the repository.**
 ```bash
-git clone https://github.com/neurobagel/api.git
+git clone https://github.com/neurobagel/recipes.git
+cd recipes/local_node
 ```
 
 ### Set the environment variables
-Create a `.env` file in the root of the repository to house the environment variables used by the Neurobagel API-graph network.
+Create a `.env` file to house the environment variables used by the Neurobagel API-graph network.
 
-The `neurobagel/api` repo contains a [`.template-env`](https://github.com/neurobagel/api/blob/main/.template-env) to get you started. Copy and rename this file to `.env` and then edit it as needed.
+The `neurobagel/recipes` repo contains a 
+[`template.env`](https://github.com/neurobagel/recipes/blob/main/local_node/template.env)
+in [the `local_node` recipe](https://github.com/neurobagel/recipes/tree/main/local_node) 
+to get you started. Copy and rename this file to `.env` and then edit it as needed.
 
 Below are all the possible Neurobagel environment variables that can be set in `.env`.
 
@@ -151,7 +160,7 @@ For a local deployment, we recommend to **explicitly set** at least the followin
 To spin up the Neurobagel API and graph backend containers using Docker Compose, 
 ensure that both [docker](https://docs.docker.com/get-docker/) and [docker compose](https://docs.docker.com/compose/install/) are installed.
 
-Run the following in the repository root (where the `docker-compose.yml` file is) to launch the containers:
+Run the following in the directory containing both the `docker-compose.yml` file from [the local_nodes recipe](https://github.com/neurobagel/recipes/tree/main/local_node) and the .env file you just created.
 
 !!! tip
     Double check that any environment variables you have customized in `.env` are resolved with your expected values using the command `docker compose config`.
@@ -418,7 +427,8 @@ with a name of `test_data`.
 
 ## Uploading data to the graph
 
-The `neurobagel/api` repo contains a helper script [`add_data_to_graph.sh`](https://github.com/neurobagel/api/blob/main/add_data_to_graph.sh) for automatically uploading all JSONLD and/or TTL files (i.e., graph-ready data) in a directory to a specific graph database, with the option to clear the existing data in the database first.
+The `neurobagel/recipes` repo contains a helper script [`add_data_to_graph.sh`](https://github.com/neurobagel/recipes/blob/main/scripts/add_data_to_graph.sh) in the `scripts` subdirectory for automatically uploading all JSONLD and/or TTL files (i.e., graph-ready data) in a directory to a specific graph database, 
+with the option to clear the existing data in the database first.
 In the context of Neurobagel, each `.jsonld` file is expected to correspond to a single **dataset**.
 
 To view all the command line arguments for add_data_to_graph.sh:
@@ -522,24 +532,24 @@ You can choose to omit the flag or explicitly specify `--no-clear-data` (default
 
 The participant variables modeled by Neurobagel are named using Neurobagel's own vocabulary (for more information, see this page on [controlled terms](./term_naming_standards.md)).
 This vocabulary, which defines internal relationships between vocabulary terms, 
-is serialized in the file [`nb_vocab.ttl`](https://github.com/neurobagel/api/blob/main/vocab/nb_vocab.ttl) available from the `neurobagel/api` repository.
-If you have cloned the api repository, you will already have downloaded the vocabulary file.
+is serialized in the file [`nb_vocab.ttl`](https://github.com/neurobagel/recipes/blob/main/vocab/nb_vocab.ttl) available from the `neurobagel/recipes` repository.
+If you have cloned this repository, you will already have downloaded the vocabulary file.
 
 **The `nb_vocab.ttl` file should be added to every created Neurobagel graph database.**
-This can be done using the same script we used to upload the dataset JSONLD files, [`add_data_to_graph.sh`](https://github.com/neurobagel/api/blob/main/add_data_to_graph.sh), which adds all `.ttl` and/or `.jsonld` files in a given directory to the specified graph.
+This can be done using the same script we used to upload the dataset JSONLD files, [`add_data_to_graph.sh`](https://github.com/neurobagel/recipes/blob/main/scripts/add_data_to_graph.sh), which adds all `.ttl` and/or `.jsonld` files in a given directory to the specified graph.
 
-Run the following code (assumes you are in the `api` directory):
+Run the following code (assumes you are in the `scripts` subdirectory inside the `recipes` repository):
 
 === "GraphDB"
     ``` bash
-    ./add_data_to_graph.sh vocab \
+    ./add_data_to_graph.sh ../vocab \
       localhost:7200 repositories/my_db DBUSER DBPASSWORD \
       --use-graphdb-syntax
     ```
 
 === "Stardog"
     ``` bash
-    ./add_data_to_graph.sh vocab \
+    ./add_data_to_graph.sh ../vocab \
       localhost:5820 test_data DBUSER DBPASSWORD
     ```
 
@@ -639,9 +649,13 @@ The `NB_API_ALLOWED_ORIGINS` variable defaults to an empty string (`""`) when un
 
 To make the Neurobagel API accessible by a frontend tool such as our [browser query tool](https://github.com/neurobagel/query-tool),
 you must explicitly specify the origin(s) for the frontend using `NB_API_ALLOWED_ORIGINS` in `.env`.
-For detailed instructions regarding the query tool see [Running cohort queries](query_tool.md).
+(Detailed instructions for using the query tool can be found in [Running cohort queries](query_tool.md).)
+
+For example, add the following line to your `.env` file to allow API requests from a query tool hosted at a specific port on `localhost` (see the [Docker Compose section](#docker-compose)).
 
-For example, the [`.template-env`](https://github.com/neurobagel/api/blob/main/.template-env) file in the Neurobagel API repo assumes you want to allow API requests from a query tool hosted at a specific port on `localhost` (see the [Docker Compose section](#docker-compose)).
+```bash
+NB_API_ALLOWED_ORIGINS="http://localhost:3000 http://127.0.0.1:3000"
+```
 
 !!! example "More examples of `NB_API_ALLOWED_ORIGINS`"