Gargantext with Haskell (Backend instance)

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 tricks, complex networks analysis algorithms and interactive data visualization tools to pave the way toward new kinds of interactions with your digital corpora.

This software is free software, developed and offered 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: this project is still in development, this is work in progress. Please report and improve this documentation if you encounter issues.

Stack setup

You need to install stack first:

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

Verify the installation is complete with

stack --version

With Nix setup

First install nix:

curl -sSL https://nixos.org/nix/install | sh

Verify the installation is complete

$ nix-env
nix-env (Nix) 2.3.12

And just build:

stack --nix build --fast

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

or

stack --docker build --fast

Docker

curl -sSL https://gitlab.iscpif.fr/gargantext/haskell-gargantext/raw/dev/devops/docker/docker-install | sh

Debian

curl -sSL https://gitlab.iscpif.fr/gargantext/haskell-gargantext/raw/dev/devops/debian/install | sh

Ubuntu

curl -sSL https://gitlab.iscpif.fr/gargantext/haskell-gargantext/raw/dev/devops/ubuntu/install | sh

Add dependencies

1. CoreNLP is needed (EN and FR); This dependency will not be needed soon.

./devops/install-corenlp

Initialization

Docker

Run PostgreSQL first:

cd devops/docker
docker-compose up

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

Gargantext

Fix the passwords

Change the passwords in gargantext.ini_toModify then move it:

mv gargantext.ini_toModify gargantext.ini

(.gitignore avoids adding this file to the repository by mistake)

Run Gargantext

Users have to be created first (user1 is created as instance):

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

For Docker env, first create the appropriate image:

cd devops/docker
docker build -t cgenie/stack-build:lts-18.12-garg .

then run:

stack --docker exec gargantext-init -- gargantext.ini

Importing data

You can import some data with:

docker run --rm -it -p 9000:9000 cgenie/corenlp-garg
stack exec gargantext-import -- "corpusCsvHal" "user1" "IMT3" gargantext.ini 10000 ./1000.csv

Nix

It is also possible to build everything with Nix instead of Docker:

stack --nix build
stack --nix exec gargantext-import -- "corpusCsvHal" "user1" "IMT3" gargantext.ini 10000 ./1000.csv
stack --nix exec gargantext-server -- --ini gargantext.ini --run Prod

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 --docker 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.