Gargantext with Haskell (Backend instance)

About the project
Installation
Initialization
Launch & develop GarganText
Uses cases
GraphQL
PostgreSQL

About the project

GarganText is a collaborative web-decentralized-based macro-service platform for the exploration of unstructured texts. It combines tools from natural language processing, text-data-mining bricks, complex networks analysis algorithms and interactive data visualization tools to pave the way toward new kinds of interactions with your textual and digital corpora.

This software is free (as "Libre" in French) software, developed by the CNRS Complex Systems Institute of Paris Île-de-France (ISC-PIF) and its partners.

GarganText Project: this repo builds the backend for the frontend server built by backend.

Installation

Disclaimer: since this project is still in development, this document remains in progress. Please report and improve this documentation if you encounter any issues.

Prerequisite

Clone the project.

git clone https://gitlab.iscpif.fr/gargantext/haskell-gargantext.git
cd haskell-gargantext

1. Install Stack

Install Stack (or Haskell Tool Stack):

curl -sSL https://get.haskellstack.org/ | sh

Verify the installation is complete with

stack --version
Version 2.9.1

2. Install Nix

Install Nix:

$ sh <(curl -L https://nixos.org/nix/install) --daemon

Verify the installation is complete with

$ nix-env --version
nix-env (Nix) 2.11.0

NOTE INFO (upgrade/downgrade if needed) Gargantext works with Nix 2.11.0 (older version than current 2.13.2). To downgrade your Nix version:

nix-channel --update; nix-env -iA nixpkgs.nixVersions.nix_2_11 nixpkgs.cacert; systemctl daemon-reload; systemctl restart nix-daemon

Upgrading Nix: https://nixos.org/manual/nix/unstable/installation/upgrading.html

Then, don't forget to exit Terminal and reload to take into account the version change

3. Build Core Code

NOTE: Default build (with optimizations) requires large amounts of RAM (16GB at least). To avoid heavy compilation times and swapping out your machine, it is recommended to stack build with the --fast flag, i.e.:

stack --nix build --fast

If the build is finishing without error, you are ready to launch GarganText! See next step.

Initialization

1. Docker-compose will configure your database and some NLP bricks (such as CoreNLP):

# If docker is not installed:
# curl -sSL https://gitlab.iscpif.fr/gargantext/haskell-gargantext/raw/dev/devops/docker/docker-install | sh
cd devops/docker
docker compose up

Initialization schema should be loaded automatically (from devops/postgres/schema.sql).

2. Then install:

stack --nix install

3. Copy the configuration file:

cp gargantext.ini_toModify gargantext.ini

Do not worry, .gitignore avoids adding this file to the repository by mistake, then you can change the passwords in gargantext.ini safely.

4. A user have to be created first as instance:

~/.local/bin/gargantext-init "gargantext.ini"

Now, user1 is created with password 1resu

5. Clone FRONTEND repository:

From the Backend root folder (haskell-gargantext):

git clone ssh://git@gitlab.iscpif.fr:20022/gargantext/purescript-gargantext.git

Launch & develop GarganText

From the Backend root folder (haskell-gargantext):

./start

The start script runs following commands: docker compose up to run the Docker for postgresql from devops/docker folder stack --nix exec gargantext-server -- --ini gargantext.ini --run Prod to run other services

For frontend development and compilation, see the Frontend Readme.md

Use Cases

Multi-User with Graphical User Interface (Server Mode)

~/.local/bin/stack --docker exec gargantext-server -- --ini "gargantext.ini" --run Prod

Then you can log in with user1 / 1resu

Command Line Mode tools

Simple cooccurrences computation and indexation from a list of Ngrams

stack --docker exec gargantext-cli -- CorpusFromGarg.csv ListFromGarg.csv Ouput.json

Analyzing the ngrams table repo

We store the repository in directory repos in the CBOR file format. To decode it to JSON and analyze, say, using jq, use the following command:

cat repos/repo.cbor.v5 | stack --nix exec gargantext-cbor2json | jq .

Documentation

To build documentation, run:

stack --nix build --haddock --no-haddock-deps --fast

(in .stack-work/dist/x86_64-linux-nix/Cabal-3.2.1.0/doc/html/gargantext).

GraphQL

Some introspection information.

Playground is located at http://localhost:8008/gql

List all GraphQL types in the Playground

{
  __schema {
    types {
      name
    }
  }
}

List details about a type in GraphQL

{
  __type(name:"User") {
  	fields {
    	name
      description
      type {
        name
      }
  	}
	}
}

PostgreSQL

Upgrading using Docker

https://www.cloudytuts.com/tutorials/docker/how-to-upgrade-postgresql-in-docker-and-kubernetes/

To upgrade PostgreSQL in Docker containers, for example from 11.x to 14.x, simply run:

docker exec -it <container-id> pg_dumpall -U gargantua > 11-db.dump

Then, shut down the container, replace image section in devops/docker/docker-compose.yaml with postgres:14. Also, it is a good practice to create a new volume, say garg-pgdata14 and bind the new container to it. If you want to keep the same volume, remember about removing it like so:

docker-compose rm postgres
docker volume rm docker_garg-pgdata

Now, start the container and execute:

# need to drop the empty DB first, since schema will be created when restoring the dump
docker exec -i <new-container-id> dropdb -U gargantua gargandbV5
# recreate the db, but empty with no schema
docker exec -i <new-container-id> createdb -U gargantua gargandbV5
# now we can restore the dump
docker exec -i <new-container-id> psql -U gargantua -d gargandbV5 < 11-db.dump

Upgrading using

There is a solution using pgupgrade_cluster but you need to manage the clusters version 14 and 13. Hence here is a simple solution to upgrade.

First save your data:

sudo su postgres
pg_dumpall > gargandb.dump

Upgrade postgresql:

sudo apt install postgresql-server-14 postgresql-client-14
sudo apt remove --purge postgresql-13

Restore your data:

sudo su postgres
psql < gargandb.dump

Maybe you need to restore the gargantua password

ALTER ROLE gargantua PASSWORD 'yourPasswordIn_gargantext.ini'

Maybe you need to change the port to 5433 for database connection in your gargantext.ini file.

naldoco / haskell-gargantext