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TOFLIT 18

Repository holding the source code of the TOFLIT18's datascape.

Architecture

  • Neo4j database v >= 3
  • API coded for node.js using express wrapped in a dolman.
  • A web client coded in React and using Baobab as its state manager.
  • Scripts are run & built using kotatsu.

Folder structure

  • .output: folder created when installing and serving as a convenient place to output/store various files such as CSV exports etc.
  • api: folder holding the API's sources.
    • controllers: dolman controllers.
    • model: model files querying the Neo4j database.
    • queries: cypher queries used by the model.
    • app.js: file exporting the API express app.
    • connection.js: file exporting the Neo4j database connection.
    • middlewares.js: various express middlewares (authentication, mostly).
  • client: folder holding the web client's sources.
    • js
      • actions: files describing the actions the UI can apply on the tree.
      • cards: experimental devcards files.
      • components: React components describing the UI.
      • external: external library files such as sigma.js.
      • lib: generic code used throughout the UI.
      • client.js: the API client.
      • history.js: file exporting the routing history.
      • main.jsx: endpoint of the app.
      • monkeys.js: functions used as monkeys for the Baobab tree.
      • parrot.js: parrot of the app (will fecth some amount of data automagically).
      • state.js: the Baobab state of the app.
    • style: CSS/SASS files of the web client.
  • docs: miscellaneous markdown files describing some algorithms' processes.
  • lib: generic code used by both the API and the client.
  • scripts: scripts meant to be run through npm run in a shell.
  • test: unit tests.

Installation

Neo4j

It is recommended that you install Neo4j v3.

Also, you should probably set the following parameter to ensure that long queries won't clog the server:

dbms.transaction.timeout=20s

Node

It is recommended that you use the Node.js version 7.9.

Installing dependencies

This will install dependencies for both the server and client side and create the .output folder.

npm install

Editing config

Server-side

vi default.json

Client-side

cd client
vi default.json

Building files for production

Server-side

This will output a file in ./build/toflit18.js that you may run afterwards to start the API.

npm run build

Client-side

You'll then need to serve the client folder statically.

cd client
npm run build

Building the Neo4j database

You need to have access to the toflit18_data repository which is private for now.

This repository consists in a collection of CSV files.

You therefore have to run the import script taking those source files in order to produce two other CSV files fit for a Neo4j import (nodes.csv & edges.csv).

npm run import -- -- --path ../toflit18_data/

After this command has run succesfully (it can take some times, ~5 min), you should have the two needed csv files in the .output folder:

ls .output/
edges.csv  nodes.csv

Then we need to stop the running Neo4j instance, create the new database by importing our two files, swap the new with the old version and restart the database.

neo4j-import --into graph.db --nodes .output/nodes.csv  --relationships .output/edges.csv

Once this is done, you must create proper indices in the database using the following command:

npm run indices

Using Neo4J on a Docker container

You can use Neo4j on Docker by spawning a neo4j:3.5 container with the graph.db directory mounted as following:

docker run \
  --detach \
  --name toflit-neo4j \
  --publish 7474:7474 \
  --publish 7687:7687 \
  --env NEO4J_AUTH=none \
  --volume /local/path/to/graph.db:/data/databases/graph.db \
  neo4j:3.5

Serving

Development

Both the API and the client use some amount of HMR to hot-reload the code so you don't have to restart it each time.

Server-side

npm run dev

Client-side

cd client
npm run dev

Production

Server-side

# Using node
node build/toflit18.js
# Using pm2
pm2 start --name toflit18_api build/toflit18.js

Client-side

Use a reverse proxy for the API and serve the client folder statically with your favorite webserver.

The following is an example using nginx:

server {
  listen 80;
  server_name  "server.domain.tld";

  ### ROOT
  root /store/toflit18/toflit18/client;
  index index.html;

  ### API
  location /api/ {
    proxy_pass http://server.domain.tld:4000/;
  }

  ### LOGS
  access_log /var/log/nginx/toflit18.medialab.access.log main;
  error_log /var/log/nginx/toflit18.medialab.error.log error;
}

Commands

Miscellaneous

# Export some data from the Neo4j database into CSV files
npm run export

# Lint the whole source code
npm run lint

# Starting the API without building it
npm run start

# Running the unit tests
npm test

Rewiring

When one user want to modify one classification, it should :

  1. first export one classification through npm run export.
  2. Then modify the classification csv by hand.
  3. import the new version classification into the database (edit scripts/import.js)
  4. generate the rewire csv file Using Neo4j ids. 
    npm run rewire -- -- --classification 4 --patch 5 --rewire 6
npm run rewire -- -- --help
  5. edit this file, solve the ambigious cases and then you have a new version of the targeted classification (got to 3)