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WebProv

The goal of this project is the create a web platform (WebProv) to automatically visualize a provenance model. The data required to create these visualizations are stored in a graph database. The web platform also features an editor to allow users to manually create provenance models that can be stored within the database.

Link to Demo

Integrating Provenance Information into WebProv

(This section describes the usage of WebProv as used by Budde et al. (2021).)

Once all provenance information of a simulation study has been collected (or while doing so), this information can be included in WebProv. A user needs to do create a study, which needs a reference (last name of first author and year of publication) as well as the name of the signaling pathway the study is based on. If more than one signaling pathway is being considered, than all pathways should be in a set (e.g., {pathway1, pathway2}).

Next, one may add nodes and connect these nodes (right click to draw a connection). The nodes can be entities or activities. Each node requires meta-information as requested by our ontology. A label is automatically assigned to a node. They are consecutively numbered within one study.

Besides creating provenance graphs and entering provenance information one can also download or upload entire graphs as JSON. The export function only exports the visible graph and not everything that is stored in the Neo4J database.

More information is available when clickling on the "+" in the lower right corner and then on the "i" ("show help").

Environment Setup

1. Node

The first step to setting up your environment involves installing Node.js (if not already installed). The recommended way to do this is by using the Node Version Manager tool:

  1. Install Node Version Manager (NVM)
  2. Install Node.js and npm using nvm: nvm install node

2. Docker

Next, install Docker so that you can start the Neo4j development database. The installation instructions can be found here.

3. Environment File

In packages/backend, create a .env file if you don't already have one:

GRAPHENEDB_BOLT_URL=bolt://localhost:7687
GRAPHENEDB_BOLT_USER=neo4j
GRAPHENEDB_BOLT_PASSWORD=<PASSWORD>

Replace <PASSWORD> with the password that you want to use for development and save it for later.

4. NPM Dependencies

This repository uses lerna as it is a monorepo. All packages are located within the packages folder. The main benefit of lerna is that it can symlink repos together when one package depends on another within the same repository. Because there is symlinking involved, you must use lerna to install dependencies. Because we have a postinstall script defined in the package.json folder, the only command that you have to run is to install and symlink everything is:

npm install

Development

Before you can start developing, make sure that the database is running:

# Optionally add -d to run in the background
docker run -p7474:7474 -p7687:7687 -e NEO4J_AUTH=neo4j/<PASSWORD> neo4j:latest

Be sure to replace <PASSWORD> with your development password that you set above.

Next, to start the hot-reload development servers, create two terminals and run the dev command within the frontend and backend packages:

# make sure to cd into `packages/frontend` or `packages/backend`
make dev

Now you should be able to see the app running at http://localhost:8080.

Make sure that you have the backend server running before opening the app.

Structure

As mentioned above, the software uses lerna to manage the monorepo. All code is written in TypeScript and is located in three packages (frontend, backend and common).

Common

common contains the shared code between the frontend and backend packages. This includes utility functions and shared TypeScript type definitions. Whenever changes are made to common, the package needs to be rebuilt so that changes are picked up by the frontend and backend.

  • index.ts: Exports things from the other files.
  • backend.ts: Contains the TypeScript type definition for the backend API.
  • neon.ts: Contains TypeScript type helpers.
  • schemas.ts: Contains TypeScript schemas for Neo4j built using neon.ts. Although Neo4j is schemaless, I built a type system to try to validate my code during compilation.
  • utils.ts: Just utilities.

Backend

The backend is a fairly basic express app with CRUD endpoints for several node types and relationships. There is no authentication for this app which makes things a lot simpler!

  • index.ts: Contains the express app initialization and all of the route definitions.
  • data.ts: Contains the definitions for all of the nodes and relationships. These are created upon initialization if they haven't been created yet.
  • cypher.ts: Contains Cypher utility functions that play nicely with my express app.

Frontend

Finally, the frontend is a Vue application split across numerous files. Below, I will outline the most important files.

  • hooks.ts: A collection of Vue.js hooks using in Visualizer.vue.
  • d3.ts: A collection of types for D3.vue.
  • backend.ts: The interface to the backend. Based on axios.
  • components/D3.vue: A wrapper around d3 built for Vue. It manages all of the visualization & animation aspects of the application.
  • Visualizer.vue: The file where everything comes together. It's responsibilities include kicking off the initial requests to the backend, managing state and managing actions.

Deployment

The frontend and backend are automatically deployed when tags are pushed to the repo using GitHub Actions. The following sections describe how to push a new tag since the CI handles the rest! If you want to learn more about the deployment process, you can check out the CI files in .github/workflows/.

1. Set the new version

Use the npm-version command to bump the version in your package.json, make a commit with the new version number and a new tag (again with the same version number). Make sure to use the appropriate version type:

npm version patch

# or this command
npm version minor

# or this command
npm version major

2. Push your commits and tags

Then, push the commits and tags:

git push
git push --tags

That's it!

Contributing

See the branching instruction and rules here. Basically, when working on a feature or bug, create a branch off master. When you want to merge your changes, just create a PR.

If you want to install a package, avoid using npm as npm will remove symlinks during installation (if this happens, just bootstrap the project again). Instead, use the lerna add command. For example:

npx lerna add the-module-to-install --scope=the-package-to-add-the-module-to [--dev]

Dependencies/Acknowledgements

Frontend

Backend

Common