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Fix FATAL: role "postgres" does not exists for docker compose deployment #8240

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merged 3 commits into from
Dec 4, 2024

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@robert-oleynik robert-oleynik commented Nov 27, 2024

URL of deployed dev instance (used for testing):

  • None: Only affects instances deployed with docker compose.

Steps to test:

  • Start a new WebKnossos instance with docker compose up -d webknossos and attach to the logs of postgres docker compose logs -f webknossos-postgres-persistent-1. These log should not contains the above error message.
  • Note This error only effects the healthcheck and not postgres itself.

TODO

  • Healthcheck fails, but postgres is reported as healthy (pg_isready reports postgres as running, but does not check the user/db availability; The error is logged by postgres)

Issues:

  • fixes error message FATAL: role "postgres" does not exists

(Please delete unneeded items, merge only when none are left open)

@robert-oleynik robert-oleynik self-assigned this Nov 27, 2024
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coderabbitai bot commented Nov 27, 2024

📝 Walkthrough

Walkthrough

The pull request introduces multiple updates to the WEBKNOSSOS project, including new functionalities for dataset management and user interface improvements. Key changes involve the ability to ignore specific format prefixes in remote URIs, enhanced dataset tooltips, and the renaming of "resolution" to "magnification." Bug fixes address various issues in dataset handling, including performance and validation errors. Additionally, the docker-compose.yml file has been modified to improve the health check for the postgres service, ensuring it accurately reflects the database's readiness.

Changes

File Change Summary
CHANGELOG.unreleased.md Updated to document new features: ignoring format prefixes, dataset volume tooltips, renaming "resolution" to "magnification," asynchronous image reading, and various bug fixes.
docker-compose.yml Updated health check command for postgres service to include database name, with minor formatting adjustments.

Possibly related PRs

Suggested labels

bug, enhancement

Poem

🐰 In the garden where data grows,
New features bloom, and progress flows.
With magnification, we explore,
As bounding boxes open new doors.
Bugs are fixed, and health checks shine,
In WEBKNOSSOS, all is fine! 🌼


📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between c3729ea and 763003e.

📒 Files selected for processing (2)
  • CHANGELOG.unreleased.md (1 hunks)
  • docker-compose.yml (1 hunks)
🔇 Additional comments (3)
CHANGELOG.unreleased.md (1)

39-39: LGTM! Clear and well-placed changelog entry.

The changelog entry accurately describes the fix and is properly categorized under the "Fixed" section with the correct PR reference.

docker-compose.yml (2)

226-228: LGTM! Health check timing parameters are well-balanced.

The timing configuration provides a good balance between responsiveness and reliability:

  • 2s interval ensures quick health status updates
  • 5s timeout accommodates temporary slowdowns
  • 30 retries (60s total) allows sufficient time for database initialization

225-225: LGTM! Health check now correctly matches database configuration.

The updated health check command properly aligns with the PostgreSQL container configuration by:

  1. Using the correct database user (webknossos_user instead of postgres)
  2. Explicitly checking the webknossos database accessibility

Let's verify the configuration consistency:

✅ Verification successful

Health check configuration is consistent and well-configured

The verification confirms that:

  • Database user (webknossos_user) and database name (webknossos) in the health check command match the PostgreSQL environment variables
  • Health check timing parameters are reasonable:
    • 2s interval between checks
    • 5s timeout for each check
    • 30 retries before considering the service unhealthy
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify that health check parameters match the PostgreSQL configuration

# Check if the database name and user in health check match the environment variables
rg -A 3 'POSTGRES_(DB|USER)' docker-compose.yml

# Check if the health check timing parameters are reasonable
rg -A 3 'healthcheck:.*postgres' docker-compose.yml

Length of output: 799


Script:

#!/bin/bash
# Let's check the healthcheck configuration parameters for postgres service
rg -B 2 -A 5 'healthcheck:.*postgres|test:.*pg_isready' docker-compose.yml

Length of output: 306


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@robert-oleynik robert-oleynik marked this pull request as ready for review December 3, 2024 14:48
@fm3 fm3 requested a review from normanrz December 3, 2024 17:29
@robert-oleynik robert-oleynik merged commit 2781061 into master Dec 4, 2024
3 checks passed
@robert-oleynik robert-oleynik deleted the fix-postgres-healthcheck branch December 4, 2024 08:01
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2 participants