From 9d26f337b726bc6f48b708b5d8d62b36a511de29 Mon Sep 17 00:00:00 2001 From: IgorTatarnikov Date: Tue, 2 Jun 2026 21:09:37 +0100 Subject: [PATCH 1/2] WIP uploading atls to AWS instructions --- .../repositories/brainglobe-atlasapi/index.md | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/docs/source/community/developers/repositories/brainglobe-atlasapi/index.md b/docs/source/community/developers/repositories/brainglobe-atlasapi/index.md index 352359565..f604aaccc 100644 --- a/docs/source/community/developers/repositories/brainglobe-atlasapi/index.md +++ b/docs/source/community/developers/repositories/brainglobe-atlasapi/index.md @@ -34,3 +34,39 @@ include: In addition, we usually post about the atlas in any forum we think will find it useful, e.g. if we think there is a specific research community that may want to use the new atlas. + +## Uploading an atlas to AWS +::: {admonition} Set up instructions +:class: note +Ensure you have an AWS account with the correct permissions (write access to s3://brainglobe/atlas) + +Please install the [AWS CLI](https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html) and authenticate by running: + +```bash +aws login +``` +::: + + +1. Run the atlas script to generate the new atlas, and double-check it passes our validation. +2. Navigate to the `brainglobe-atlasapi` directory inside the packaging working directory: + * This directory should contain the `annotation-sets`, `atlases`, `coordinate-spaces`, `templates`, and `terminologies` subdirectories and nothing else +3. From this directory run to get a preview of the files that will be uploaded. +```bash +aws s3 sync --dry-run . s3://brainglobe/atlas +``` +4. If the output of the dry-run is correct, you can remove that argunent and run: +```bash +aws s3 sync . s3://brainglobe/atlas +``` +5. To update the `latest_versions.conf` file: + * Fetch the file by running: +```bash +aws s3 cp s3://brainglobe/atlas/atlases/last_versions.conf ./atlases/last_versions.conf +``` + * Add the new atlas name/version and run to sync back to the remote: +```bash +aws s3 cp ./atlases/last_versions.conf s3://brainglobe/atlas/atlases/last_versions.conf +``` + + From 57ca31a05fbb73a302bf06779e94bc7ee560df02 Mon Sep 17 00:00:00 2001 From: IgorTatarnikov Date: Tue, 2 Jun 2026 21:12:20 +0100 Subject: [PATCH 2/2] Update wording --- .../developers/repositories/brainglobe-atlasapi/index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/community/developers/repositories/brainglobe-atlasapi/index.md b/docs/source/community/developers/repositories/brainglobe-atlasapi/index.md index f604aaccc..36a994102 100644 --- a/docs/source/community/developers/repositories/brainglobe-atlasapi/index.md +++ b/docs/source/community/developers/repositories/brainglobe-atlasapi/index.md @@ -51,11 +51,11 @@ aws login 1. Run the atlas script to generate the new atlas, and double-check it passes our validation. 2. Navigate to the `brainglobe-atlasapi` directory inside the packaging working directory: * This directory should contain the `annotation-sets`, `atlases`, `coordinate-spaces`, `templates`, and `terminologies` subdirectories and nothing else -3. From this directory run to get a preview of the files that will be uploaded. +3. Get a preview of the files that will be synced with the remote by running: ```bash aws s3 sync --dry-run . s3://brainglobe/atlas ``` -4. If the output of the dry-run is correct, you can remove that argunent and run: +4. If the output of the dry-run is correct, upload the new atlas using: ```bash aws s3 sync . s3://brainglobe/atlas ```