packit

Web application for surfacing packet data and metadata. Packets are sets of files with related metadata conforming to the outpack format. Packets are produced as the result of running analysis scripts, typically using a package which supports outpack format, such as orderly or pyorderly, which also add their own custom metadata to the packets produced.

Packet metadata includes:

• timestamp
• parameter
• display name
• file metadata e.g. whether a file is input ("resource") or output ("artefact")

Packet data are the files included in the packet, which can be downloaded through the application.

The application can be used through the browser as a portal by researchers, to manage and track their packets, and by those who requested the analyses, to view packet outputs. Packets can also be created through the app by running an analysis.

Packit can also be used programmatically through its /outpack route, which forwards requests to outpack server.

Pre-requisites

Ensure you have logged into vault. If not, Run the following command to login with github PAT token:

export VAULT_ADDR=https://vault.dide.ic.ac.uk:8200
vault login -method=github

Quick start

To run the whole app (default is github auth):

./scripts/dev-start

The app will be available on port 3000. If you would like to create a super admin user then:

./scripts/dev-start --super-user

For more options:

./scripts/dev-start --help

The following commands achieve the same things but allow for finer control of each of the components:

1. ./scripts/run-dependencies to run the database and outpack_server
2. ./api/scripts/run to run the API i.If running basic auth mode, run ./scripts/basic-create-super-user. This will create a superadmin user that can be used. Ensure api has ran and created all DB tables first.
3. npm start --prefix=app to run the React app on port 3000.

There are 3 subdirectories in this repo, each corresponding to a different service. See individual READMEs for further details on developing each service. ./scripts/clear-docker is a useful command for reverting docker to a state without any of the containers, networks or volumes created by the services.

Database

See db/README.md

API

See api/README.md

App

See app/README.md

Authentication in Packit

See docs/auth.md