From dff55a5c8787f73e359f2856f91748cb80f2aeee Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Wed, 20 Nov 2024 17:40:41 -0500 Subject: [PATCH] [FIX] Update README links to user guide in docs (#95) * update README links * remove unneeded link to old docs page in setup script --- README.md | 4 ++-- scripts/graphdb_setup.sh | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index e2fe231..e6ce6e1 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ Configuration files for a Neurobagel deployment. ## How to use -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/). +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/user_guide/getting_started/) and [configuration options](https://neurobagel.org/user_guide/config/). ### Using the full-stack Docker Compose file @@ -26,7 +26,7 @@ For detailed instructions on deploying Neurobagel for your use case, see the off cp local_nb_nodes.template.json local_nb_nodes.json ``` - Ensure to edit the [configuration file(s)](https://neurobagel.org/config/) according to your deployment. + Ensure to edit the [configuration file(s)](https://neurobagel.org/user_guide/config/) according to your deployment. **We strongly recommend changing the default passwords for your GraphDB instance, which are set using `NB_GRAPH_ADMIN_PASSWORD.txt` and `NB_GRAPH_PASSWORD.txt` in the ./secrets subdirectory by default.** :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`). diff --git a/scripts/graphdb_setup.sh b/scripts/graphdb_setup.sh index 2a623b1..6b5f41b 100755 --- a/scripts/graphdb_setup.sh +++ b/scripts/graphdb_setup.sh @@ -3,7 +3,7 @@ # ARG_POSITIONAL_SINGLE([admin-pass],[Password for the "admin" superuser that GraphDB creates. If running the first-time user setup, this will be the password set for the admin. The admin user will only be used to create and modify permissions of other database users.]) # ARG_OPTIONAL_SINGLE([env-file-path],[],[Path to a .env file containing environment variables for Neurobagel node configuration.],[.env]) # ARG_OPTIONAL_BOOLEAN([run-user-setup],[],[Whether or not to run the first-time GraphDB setup steps, including changing the admin password and creating a new database user.],[on]) -# ARG_HELP([Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory. For more information, see https://neurobagel.org/infrastructure/.]) +# ARG_HELP([Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory.]) # ARGBASH_GO() # needed because of Argbash --> m4_ignore([ ### START OF CODE GENERATED BY Argbash v2.9.0 one line above ### @@ -37,7 +37,7 @@ _arg_run_user_setup="on" print_help() { - printf '%s\n' "Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory. For more information, see https://neurobagel.org/infrastructure/." + printf '%s\n' "Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory." printf 'Usage: %s [--env-file-path ] [--(no-)run-user-setup] [-h|--help] \n' "$0" printf '\t%s\n' ": Password for the \"admin\" superuser that GraphDB creates. If running the first-time user setup, this will be the password set for the admin. The admin user will only be used to create and modify permissions of other database users." printf '\t%s\n' "--env-file-path: Path to a .env file containing environment variables for Neurobagel node configuration. (default: '.env')"