Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[MNT] Use docker compose secrets for sensitive credentials #50

Merged
merged 2 commits into from
Apr 25, 2024
Merged

[MNT] Use docker compose secrets for sensitive credentials #50

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
78621bb
update graph and API entrypoints to fetch secrets
alyssadai Apr 25, 2024
447fc6c
mention local_federation profile in README
alyssadai Apr 25, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 17 additions & 5 deletions docker-compose.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,19 @@ services:
- "${NB_NAPI_PORT_HOST:-8000}:${NB_NAPI_PORT:-8000}"
environment:
NB_GRAPH_USERNAME: ${NB_GRAPH_USERNAME}
NB_GRAPH_PASSWORD: ${NB_GRAPH_PASSWORD}
NB_GRAPH_ADDRESS: ${NB_GRAPH_ADDRESS:-graph}
NB_GRAPH_PORT: ${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_ALLOWED_ORIGINS: ${NB_NAPI_ALLOWED_ORIGINS}

volumes:
- "./scripts/api_entrypoint.sh:/usr/src/api_entrypoint.sh"
entrypoint:
- "/usr/src/api_entrypoint.sh"
secrets:
- db_user_password

graph:
image: "${NB_GRAPH_IMG:-ontotext/graphdb:10.3.1}"
profiles:
Expand All @@ -36,15 +41,16 @@ services:
- "${NB_GRAPH_PORT_HOST:-7200}:${NB_GRAPH_PORT:-7200}"
environment:
NB_GRAPH_ROOT_CONT: ${NB_GRAPH_ROOT_CONT:-/opt/graphdb/home}
NB_GRAPH_ADMIN_PASSWORD: ${NB_GRAPH_ADMIN_PASSWORD}
NB_GRAPH_USERNAME: ${NB_GRAPH_USERNAME}
NB_GRAPH_PASSWORD: ${NB_GRAPH_PASSWORD}
NB_GRAPH_ADDRESS: ${NB_GRAPH_ADDRESS:-graph}
NB_GRAPH_PORT: ${NB_GRAPH_PORT:-7200}
NB_GRAPH_DB: ${NB_GRAPH_DB:-repositories/my_db}
entrypoint:
- "/usr/src/neurobagel/scripts/setup.sh"
working_dir: "/usr/src/neurobagel/scripts"
secrets:
- db_admin_password
- db_user_password

federation:
image: "neurobagel/federation_api:${NB_FAPI_TAG:-latest}"
Expand Down Expand Up @@ -77,4 +83,10 @@ services:
- "${NB_QUERY_PORT_HOST:-3000}:5173"
environment:
NB_API_QUERY_URL: ${NB_API_QUERY_URL}
NB_IS_FEDERATION_API: "false"
NB_IS_FEDERATION_API: "false"

secrets:
db_admin_password:
environment: "NB_GRAPH_ADMIN_PASSWORD"
db_user_password:
environment: "NB_GRAPH_PASSWORD"
5 changes: 5 additions & 0 deletions scripts/api_entrypoint.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
#!/bin/bash

export NB_GRAPH_PASSWORD=$(cat /run/secrets/db_user_password)

uvicorn app.main:app --proxy-headers --host 0.0.0.0 --port ${NB_API_PORT:-8000}
3 changes: 3 additions & 0 deletions scripts/setup.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@ done
SCRIPT_DIR=$(dirname "$0")
mkdir -p ${SCRIPT_DIR}/logs

export NB_GRAPH_ADMIN_PASSWORD=$(cat /run/secrets/db_admin_password)
export NB_GRAPH_PASSWORD=$(cat /run/secrets/db_user_password)

# Logic for main setup
main() {
echo "Setting up a Neurobagel graph backend..."
Expand Down