Fileglancer Central

Central data service for Fileglancer deployments which makes it possible for Fileglancer to access Janelia services such as JIRA and the Janelia Confluence Wiki.

Development install

Clone the repo to your local environment and change directory to the new repo folder.

git clone git@github.com:JaneliaSciComp/fileglancer-central.git
cd fileglancer-central

Copy the config template and edit it to your liking:

cp config.yaml.template config.yaml

Install package in development mode:

pixi run dev-install

Then run the development server:

pixi run dev-launch

Production install

See fileglancer-hub for details on production releases.

Optional: configure file share path source

Note

Currently, the file share paths are only pulled from a Confluence Wiki. Future implementations may allow for other sources of file share paths.

To pull file share paths from Janelia's Confluence wiki, configure the atlassian_url in the config.yaml file. You also need a Confluence token. Under the "User" menu in the upper right corner of the Confluence UI, click "Profile" and then "Security" and then "Create and manage API tokens". Click "Create API token" and give it a name like "Fileglancer". Copy the token, then create a .env file in the repo root with the following content:

FGC_ATLASSIAN_USERNAME=your_email
FGC_ATLASSIAN_TOKEN=your_confluence_token

You should set the permissions on the .env file so that only the owner can read it:

chmod 600 .env

Optional: configure ticket system

Note

Currently, tickets are handled using JIRA. Future implementations may allow for other sources of ticket management systems.

Certain actions are handled using a ticket system so that they can be completed manually, such as complex file conversions. To configure JIRA, use the same actions as for the wiki. If necessary, you can customize the JIRA path used for ticket links by overriding jira_browse_url.

Architecture

The Fileglancer Central service is a backend service optionally used by Fileglancer to access various other services, including a shared metadata database. The diagram below shows how it fits into the larger Fileglancer deployment at Janelia.

Running unit tests

pixi run test

Building the Docker container

Run the Docker build, replacing <version> with your version number:

cd docker/
export VERSION=<version>
docker buildx build --platform linux/amd64,linux/arm64 --build-arg GIT_TAG=$VERSION -t ghcr.io/janeliascicomp/fileglancer-central:$VERSION -t ghcr.io/janeliascicomp/fileglancer-central:latest --push .

Release

First, increment the version in pyproject.toml and push it to GitHub. Create a Release there and then publish it to PyPI as follows.

To create a Python source package (.tar.gz) and the binary package (.whl) in the dist/ directory, do:

pixi run pypi-build

To upload the package to the PyPI, you'll need one of the project owners to add you as a collaborator. After setting up your access token, do:

pixi run pypi-upload

The new version should now be available on PyPI.