fuse-tool-template

Clone this repo to create a new FUSE-style tool.

FUSE stands for "FAIR", Usable, Sustainable, and Extensible.

FUSE tools can be run as a stand-alone tool (see up.sh below) or as a plugin to a FUSE deployment (e.g., fuse-immcellfie). FUSE tools are one of 3 flavors of appliances:

• provider: provides a common data access protocol to a digital object provider
• mapper: maps the data from a particular data provider type into a common data model with consistent syntax and semantics
• tool: analyzes data from a mapper, providing results and a specification that describes the data types and how to display them.

prerequisites:

• python 3.8 or higher
• Docker 20.10 or higher
• docker-compose v1.28 a
• perl 5.16.3 or higher (for testing the install)
• cpan
• jq

Tips for updating docker-compose on Centos:

sudo yum install jq
VERSION=$(curl --silent https://api.github.com/repos/docker/compose/releases/latest | jq .name -r)
sudo mv /usr/local/bin/docker-compose /usr/local/bin/docker-compose.old-version
DESTINATION=/usr/local/bin/docker-compose
sudo curl -L https://github.com/docker/compose/releases/download/${VERSION}/docker-compose-$(uname -s)-$(uname -m) -o $DESTINATION
sudo chmod 755 $DESTINATION

use this template:

Note, a tool must specify a pluginType, and for tools we use type 't' (for analysis'Tool')

• To add a new repository to the RENCI organization, click here and select this repo for the template, otherwise new repo will be added to your username.
• Get your new repo using the 'recursive' tag (see below)

git clone --recursive http://github.com/RENCI/<your-repo-name>

• Make sure the test passes (./up.sh; prove t/test.t - check t/test.t on how to install the test harness dependencies)
• Edit this README.md file and replace all occurrences of fuse-tool-template with your repo's name
• Update the source files appropriately:

• docker-compose.yml: replace fuse-tool-template with your repo's name and customize accordingly
• requirements.txt: add your version-locked library requirements to the list
• sample.env: add any required environmental variables, don't forget to also document them in this readme
• main.py:
  • Search for all occurrences of fuse-tool-template and replace
  • Define and add endpoints for your tool
  • Create objects and functions under ./fuse to support you endpoints, with unit tests, adding the unit tests to github actions (examples coming soon!)
• **write and run tests - look at t/test.t for examples
• contact the dockerhub/txscience organization administrator (email:[email protected]) to add a dockerhub repo for your container, if needed

• remove this section from the README.md
• checkin your mods:

git status # make sure everything looks OK
git commit -a -m 'Initial customization'
git push

configuration

1. Get this repository: `git clone --recursive http://github.com/RENCI/fuse-tool-template

2. Copy sample.env to .env and edit to suit your provider:

• API_PORT pick a unique port to avoid appliances colliding with each other

start

./up.sh

validate installation

Start container prior to validations:

./up.sh

Simple test from command line

curl -X 'GET' 'http://localhost:${API_PORT}/openapi.json' -H 'accept: application/json' |jq -r 2> /dev/null

Install test dependencies:

cpan App::cpanminus
# restart shell
cpanm --installdeps .

Run tests:

prove

More specific, detailed test results:

prove -v t/test.t :: --verbose

stop

./down.sh