Commit 3ea34423 authored by Przemyslaw Kaminski's avatar Przemyslaw Kaminski

Merge branch 'dev' into 234-dev-ngrams-score

parents 17b10bb7 41ecf1e2
Pipeline #1927 canceled with stage
use nix
# Gauge - metadata dir
.gauge
# Gauge - log files dir
logs
# Gauge - reports dir
reports
# Gauge - JavaScript node dependencies
node_modules
.DS_Store
/bower_components/
/node_modules/
/.cache/
......@@ -32,3 +45,4 @@ bundle.js
/.lesshst
/dist/js/**/*.map
/dist/styles/**/*.map
# Thanks to:
# https://vadosware.io/post/zero-to-continuous-integrated-testing-a-haskell-project-with-gitlab/
#
#
image: nixos/nix:latest
variables:
STACK_ROOT: "${CI_PROJECT_DIR}/.stack-root"
STACK_OPTS: "--system-ghc"
#before_script:
#- apt-get update
#- apt-get install make xz-utils
stages:
- test
test:
cache:
# cache per branch name
# key: ${CI_COMMIT_REF_SLUG}
# paths:
# - .stack-root/
# - .stack-work/
script:
# find 0.14.2 purescript version here:
# https://lazamar.co.uk/nix-versions/
- nix-env -i purescript-0.14.2 -f https://github.com/NixOS/nixpkgs/archive/bed08131cd29a85f19716d9351940bdc34834492.tar.gz
- nix-env -i git
- nix-env -i nodejs
- nix-env -i yarn
- yarn --skip-builds
- nix-shell shell.nix --run test-ps
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# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
# yarn lockfile v1
lastUpdateCheck 1611671086951
# Contributor Covenant Code of Conduct
## Our Pledge
In the interest of fostering an open and welcoming environment, we as
contributors and maintainers pledge to making participation in our project and
our community a harassment-free experience for everyone, regardless of age, body
size, disability, ethnicity, gender identity and expression, level of experience,
nationality, personal appearance, race, religion, or sexual identity and
orientation.
## Our Standards
Examples of behavior that contributes to creating a positive environment
include:
* Using welcoming and inclusive language
* Being respectful of differing viewpoints and experiences
* Gracefully accepting constructive criticism
* Focusing on what is best for the community
* Showing empathy towards other community members
Examples of unacceptable behavior by participants include:
* The use of sexualized language or imagery and unwelcome sexual attention or
advances
* Trolling, insulting/derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or electronic
address, without explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting
## Our Responsibilities
Project maintainers are responsible for clarifying the standards of acceptable
behavior and are expected to take appropriate and fair corrective action in
response to any instances of unacceptable behavior.
Project maintainers have the right and responsibility to remove, edit, or
reject comments, commits, code, wiki edits, issues, and other contributions
that are not aligned to this Code of Conduct, or to ban temporarily or
permanently any contributor for other behaviors that they deem inappropriate,
threatening, offensive, or harmful.
## Scope
This Code of Conduct applies both within project spaces and in public spaces
when an individual is representing the project or its community. Examples of
representing a project or community include using an official project e-mail
address, posting via an official social media account, or acting as an appointed
representative at an online or offline event. Representation of a project may be
further defined and clarified by project maintainers.
## Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported by contacting the project team at [sos AT gargantext DOT org]. All
complaints will be reviewed and investigated and will result in a response that
is deemed necessary and appropriate to the circumstances. The project team is
obligated to maintain confidentiality with regard to the reporter of an incident.
Further details of specific enforcement policies may be posted separately.
Project maintainers who do not follow or enforce the Code of Conduct in good
faith may face temporary or permanent repercussions as determined by other
members of the project's leadership.
## Attribution
This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
available at [http://contributor-covenant.org/version/1/4][version]
[homepage]: http://contributor-covenant.org
[version]: http://contributor-covenant.org/version/1/4/
......@@ -4,13 +4,12 @@
### Social contract
1. Use and promote welcoming behavior to respect the [Code of Conduct](https://gitlab.iscpif.fr/humanities/gargantext/blob/master/CODE_OF_CONDUCT.md)
1. Be nice, welcome and treat others with respect: [Code of Conduct](https://gitlab.iscpif.fr/humanities/gargantext/blob/master/CODE_OF_CONDUCT.md)
2. We are a team as whole: here to help each others
2. We are a team as whole: here to help each other
- knowing the unknown is a value but ignoring the unknown is a failure
- do not ask to ask: just ask
- there is no stupid question(s)
- there is no unique solution(s)
- there are no stupid questions
3. Watch deadlines individually and collectively
- at 0% of the time of the task, agree on the /estimate of time to fix the issue.
......@@ -82,30 +81,38 @@ Main branches are:
## Technicals
Please configure your editor accordingly (ask for tips if needed or put your tips here)
### Code main guidelines
### Code guidelines
#### Code Design
#### Basics
Please configure your editor accordingly (ask for tips if needed or put your tips here)
Line length:
* Good lines of code are no more than 80 characters long.
* Acceptable lines of code are no more than 100
* Bad lines of code are no more than 120.
Whitespace:
* 2 spaces per indentation stop, or more if needed by the compiler
* Do not use tab characters.
* Remove trailing whitespace from lines. Includes blank lines.
#### Layout
##### Line length
* all line length should be < 120 chars
##### Identation
* 2 spaces or more if needed by the compiler
* i.e. Tab character is avoided
* avoid trailing spaces, mostly spaces at the end of lines (remove it)
* HTML nodes:
```
div []
[ div []
[ a [] [...]
, a [] [...]
]
, div []
div {...}
[ div {...} [ a {} [...], a {...} [...] ]
, div {...}
, div
{ ...
, ...
}
[ ...
, ...
]
......
......@@ -9,6 +9,8 @@ RUN echo "deb https://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources
RUN apt-get update && apt-get install -y yarn
RUN curl -L https://github.com/coot/zephyr/releases/download/v0.3.2/Linux.tar.gz | tar zx -C /usr/bin --strip-components=1 zephyr/zephyr
RUN curl -L https://github.com/dhall-lang/dhall-haskell/releases/download/1.38.1/dhall-json-1.7.6-x86_64-linux.tar.bz2 | tar jx -C /usr/bin --strip-components=2 ./bin/dhall-to-json
WORKDIR /opt/app
EXPOSE 5000/tcp
CMD ["bash"]
\ No newline at end of file
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# Gargantext Purescript
# Gargantext with Purescript (FrontEnd instance)
## About this project
## About the project
Gargantext is a collaborative web platform for the exploration of sets
of unstructured documents. It combines tools from natural language
processing, text-mining, complex networks analysis and interactive data
visualization to pave the way toward new kinds of interactions with your
digital corpora.
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.
You will not find this software very useful without also running or being
granted access to a [backend](https://gitlab.iscpif.fr/gargantext/haskell-gargantext).
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
frontend for the backend server built by
[backend](https://gitlab.iscpif.fr/gargantext/haskell-gargantext).
This software is free software, developed by the CNRS Complex Systems
Institute of Paris Île-de-France (ISC-PIF) and its partners.
## Getting set up
There are two approaches to working with the build:
1. Use our docker setup
1. Use our Nix or Docker setup
2. Install our dependencies yourself
The javascript ecosystem kind of assumes if you're on linux, you're
running on debian or ubuntu. I haven't yet managed to get garg to
build on alpine linux, for example. If you're on an oddball system, I
*strongly* recommend you just use the docker setup.
### With Nix setup
First install [nix](https://nixos.org/guides/install-nix.html):
```shell
sh < (curl -L https://nixos.org/nix/install) --daemon
```
Verify the installation is complete
```shell
$ nix-env
nix-env (Nix) 2.3.12
```
To build the frontend just do:
```
nix-shell --run build
```
Just serve dist/index.html with any server and you are ready to be
connected to any backend.
### Docker setup
### With Docker setup
You will need docker and docker-compose installed.
......@@ -124,6 +144,7 @@ the docker container.
### Basic tasks
Now we must install our javascript and purescript dependencies:
*Note: if you're installing manually you might also need to manually install [psc-package](https://github.com/purescript/psc-package)*
```shell
darn install -D && darn install-ps # for docker setup
......@@ -190,7 +211,7 @@ yarn css # for manual setup
<!-- A `purs ide` connection will be available on port 9002 while the -->
<!-- development server is running. -->
A guide to getting set up with the IDE integration is coming soon, I hope.
A guide to getting set up with the IDE integration is coming soon.
### Testing
......@@ -213,7 +234,7 @@ runtime or `devDependencies` if it is not.
#### Add a purescript dependency?
Add it to `psc-package.json` without the `purescript-` prefix.
Add it to `spago.dhall` (or run `spago install ...`).
If is not in the package set, you will need to read the next section.
......@@ -223,20 +244,6 @@ You need to add an entry to the relevant map in
`packages.dhall`. There are comments in the file explaining how it
works. It's written in dhall, so you can use comments and such.
You will then need to rebuild the package set:
```shell
yarn rebuild-set # or darn rebuild-set
```
#### Upgrade the base package set local is based on to latest?
```shell
yarn rebase-set && yarn rebuild-set # or darn rebase-set && darn rebuild-set
```
This will occasionally result in swearing when you go on to build.
## Theory Introduction
Making sense of out text isn't actually that hard, but it does require
......@@ -244,21 +251,23 @@ a little background knowledge to understand.
### N-grams
N-grams are at the heart of how Gargantext makes sense out of text.
N-grams in contexts (of texts) are at the heart of how Gargantext makes
sense out of text.
There are two common meanings in the literature for n-gram:
- a sequence of `n` characters
- a sequence of `n` words
Gargantext is focused on words. Here are some example word n-grams;
Gargantext is focused on words. Here are some example word n-grams
usually extracted by our Natural Language Process toolkit;
- `coffee` (unigram or 1-gram)
- `need coffee` (bigram or 2-gram)
- `one coffee please` (trigram or 3-gram)
- `here is your coffee` (4-gram)
- `i need some more coffee` (5-gram)
- `black coffee` (bigram or 2-gram)
- `hot black coffee` (trigram or 3-gram)
- `arabica hot black coffee` (4-gram)
N-grams are matched case insensitively and across whole words. Examples:
N-grams are matched case insensitively and across whole words removing
the linked syntax if exists. Examples:
| Text | N-gram | Matches |
|--------------|--------------|----------------------|
......@@ -270,20 +279,23 @@ You may read more about n-grams [on wikipedia](https://en.wikipedia.org/wiki/N-g
<!-- TODO: Discuss punctuation -->
Gargantext allows you to define n-grams interactively in your browser
and explore the relationships they uncover across a corpus of text.
Gargantext allows you to define and refine n-grams interactively in your
browser and explore the relationships they uncover across a corpus of
text.
Various metrics can be applied to n-grams, the most common of which is
the number of times an n-gram appears in a document.
Various metrics can be applied to n-grams, the most common of which
is the number of times an n-gram appears in a document (occurrences).
GarganText uses extensively the cooccurrences: times 2 n-grams appear in
same context of text.
## Glossary
document
: One or more texts comprising a single logical document
field
: A portion of a document, e.g. `title`, `abstract`, `body`
: A portion of a document or metadata, e.g. `title`, `abstract`, `body`
corpus
: A collection of documents
: A collection of documents as set (with no repetition)
n-gram/ngram
: A word or words to be indexed, consisting of `n` words.
This technically includes skip-grams, but in the general case
......@@ -295,8 +307,10 @@ bigram/2-gram
trigram/3-gram
: A three-word n-gram, e.g. `coffee cup holder`
skip-gram
: An n-gram where the words are not all adjacent. Not yet supported.
: An n-gram where the words are not all adjacent. Group 2 different
n-grams to enable such feature.
k-skip-n-gram
: An n-gram where the words are at most distance k from each other.
: An n-gram where the words are at most distance k from each other. This
feature is used for advanced research in text (not yet supported in
GarganText)
#!/usr/bin/env bash
set -euo pipefail
yarn
test-ps
with (import <nixpkgs> {});
let
nodejs-with-packages = with nodePackages; [
bower
yarn
]; in
stdenv.mkDerivation rec {
name = "env";
env = buildEnv {
name = name;
paths = buildInputs;
};
buildInputs = [
nodejs-with-packages
yarn
yarn2nix
];
builder = builtins.toFile "builder.sh" ''
source $stdenv/setup
touch $out
'';
}
......@@ -11,7 +11,7 @@
<style> * {margin: 0; padding: 0; list-style: none;} </style>
</head>
<body>
<div id="app" class ="container-fluid"></div>
<div id="app"></div>
<div id="portal"></div>
<script src="bundle.js"></script>
</body>
......
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\ No newline at end of file
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\ No newline at end of file
......@@ -8,10 +8,12 @@
<link id="bootstrap-css" href="styles/bootstrap-default.css" rel="stylesheet" />
<link rel="stylesheet" type="text/css" href="styles/highlightjs-solarized-light.css" />
<link href="styles/sass.css" rel="stylesheet" type="text/css" />
<!-- <script type="text/javascript" src="/js/react-bootstrap.min.js"></script> -->
<script type="text/javascript" src="/js/react-bootstrap.js"></script>
<style> * {margin: 0; padding: 0; list-style: none;} </style>
</head>
<body>
<div id="app" class ="container-fluid"></div>
<div id="app"></div>
<div id="portal"></div>
<script src="bundle.js"></script>
</body>
......
{
"Language": "js",
"Plugins": [
"html-report"
]
}
\ No newline at end of file
{
"name": "js",
"description": "Gauge template for Javascript and Taiko",
"postInstallCmd": "npm install",
"postInstallMsg": "Run specifications with \"npm test\" in project root.",
"version": "1.0.5"
}
......@@ -5,8 +5,8 @@ import
pkgs.fetchFromGitHub {
owner = "justinwoo";
repo = "easy-purescript-nix";
rev = "c8c32741bc09e2ac0a94d5140cf51fa5de809e24";
sha256 = "1g1hlybld298kimd1varvwiflpb0k7sdqlmcqha3kswjvy5z4k6k";
rev = "d0f592b71b2be222f8dcfb4f4cefb52608bbc1ae";
sha256 = "0bq26y836bd1y8657f182wnsl4cdr1xxbykxdgz7xm9shpii48r5";
}
) {
inherit pkgs;
......
#!/usr/bin/env bash
set -e
## You should use the `shell.nix` file in our project, or install dhall-to-json yourself: https://github.com/dhall-lang/dhall-haskell/releases
dhall-to-json --file packages.dhall --output ./.psc-package/local/.set/packages.json
echo "generated packages.json"
#!/usr/bin/env nix-shell
#!nix-shell ./generate-packages-json.nix --run 'exit'
{ pkgs ? import ./pinned.nix { } }:
let
easy-dhall = import (
pkgs.fetchFromGitHub {
owner = "justinwoo";
repo = "easy-dhall-nix";
rev = "90957969850a44481c6e150350c56e8b53b29e1e";
sha256 = "1hsmp3cb0k554kh0jlfzpdzx2b8ndyh2gdykmw9hw41haaw16mmi";
}
) {
inherit pkgs;
};
in
pkgs.mkShell {
buildInputs = [ easy-dhall.dhall-simple easy-dhall.dhall-json-simple ];
shellHook = ''
dhall-to-json --file packages.dhall --output ./.psc-package/local/.set/packages.json
echo "generated packages.json"
'';
}
import (
builtins.fetchTarball {
url = "https://github.com/NixOS/nixpkgs/archive/20.03.tar.gz";
sha256 = "0182ys095dfx02vl2a20j1hz92dx3mfgz2a6fhn31bqlp1wa8hlq";
url = "https://github.com/NixOS/nixpkgs/archive/21.05.tar.gz";
sha256 = "1ckzhh24mgz6jd1xhfgx0i9mijk6xjqxwsshnvq789xsavrmsc36";
}
)
This diff is collapsed.
{
"name": "Gargantext",
"version": "0.0.2.7.1",
"version": "0.0.4.2",
"scripts": {
"rebase-set": "spago package-set-upgrade && spago psc-package-insdhall",
"rebuild-set": "spago psc-package-insdhall",
"install-ps": "psc-package install",
"compile": "pulp build",
"build": "pulp browserify -t dist/bundle.js",
"css": "sass src/sass/sass.sass:dist/styles/sass.css && sass src/sass/bootstrap/default.sass:dist/styles/bootstrap-default.css && cp node_modules/bootstrap-dark/src/bootstrap-dark.css dist/styles/bootstrap-dark.css && sass src/sass/bootstrap/greyson.scss:dist/styles/bootstrap-greyson.css && sass src/sass/bootstrap/monotony.scss:dist/styles/bootstrap-monotony.css && sass src/sass/bootstrap/darkster.scss:dist/styles/bootstrap-darkster.css && sass src/sass/bootstrap/herbie.scss:dist/styles/bootstrap-herbie.css",
"generate-purs-packages-nix": "./nix/generate-purs-packages.nix",
"generate-psc-packages-nix": "./nix/generate-packages-json.bash",
"css": "sass src/sass/sass.sass:dist/styles/sass.css && yarn css-themes",
"css-themes": "yarn css-default-theme && yarn css-dark-theme && yarn css-darkster-theme && yarn css-greyson-theme && yarn css-herbie-theme && yarn css-monotony-theme",
"css-default-theme": "sass src/sass/bootstrap/default.sass:dist/styles/bootstrap-default.css",
"css-dark-theme": "cp node_modules/bootstrap-dark/src/bootstrap-dark.css dist/styles/bootstrap-dark.css",
"css-darkster-theme": "sass src/sass/bootstrap/darkster.scss:dist/styles/bootstrap-darkster.css",
"css-greyson-theme": "sass src/sass/bootstrap/greyson.scss:dist/styles/bootstrap-greyson.css",
"css-herbie-theme": "sass src/sass/bootstrap/herbie.scss:dist/styles/bootstrap-herbie.css",
"css-monotony-theme": "sass src/sass/bootstrap/monotony.scss:dist/styles/bootstrap-monotony.css",
"docs": "pulp docs -- --format html",
"repl": "pulp repl",
"clean": "rm -Rf output node_modules",
"clean-js": "rm -Rf node_modules",
"clean-ps": "rm -Rf output",
"test": "pulp test",
"server": "serve dist",
"prod": "yarn prod:compile && yarn prod:dce && yarn prod:bundle && yarn prod:pack",
"prod:compile": "pulp build -- -g corefn",
"prod:dce": "zephyr -f Main.main",
"prod:bundle": "pulp browserify --skip-compile -o dce-output -t app.js",
"prod:pack": "parcel build index.html -d prod --public-url . --no-source-maps"
"prod:pack": "parcel build index.html -d prod --public-url . --no-source-maps",
"test-pulp": "pulp test",
"test": "gauge run specs/"
},
"dependencies": {
"@popperjs/core": "^2.9.2",
"aes-js": "^3.1.1",
"base-x": "^3.0.2",
"bootstrap": "4.4.1",
"bootstrap": "^4.6.0",
"bootstrap-dark": "^1.0.3",
"create-react-class": "^15.6.3",
"echarts": "^4.1.0",
"echarts-for-react": "^2.0.14",
"echarts": "^5.1.2",
"echarts-for-react": "^3.0.1",
"highlightjs": "^9.16.2",
"prop-types": "15.6.2",
"react": "^16.10",
"immer": "^9.0.5",
"prop-types": "^15.6.2",
"pullstate": "^1.20.6",
"react": "^17.0.2",
"react-awesome-popover": "^6.1.1",
"react-dom": "^16.10",
"react-bootstrap": "^1.5.2",
"react-dom": "^17.0.2",
"react-tooltip": "^4.2.8",
"secp256k1": "^3.3.0",
"secp256k1": "^4.0.2",
"sigma": "git://github.com/poorscript/sigma.js#garg"
},
"devDependencies": {
"@babel/core": "^7.12.9",
"@babel/core": "^7.15.0",
"@babel/preset-env": "^7.15.6",
"@babel/preset-react": "^7.12.7",
"parcel": "^1.12.4",
"psc-package": "^4.0.1",
"pulp": "^15.0.0",
"purescript": "^0.13.8",
"purescript-language-server": "^0.12.9",
"react-testing-library": "^6.1.2",
"sass": "^1.23.7",
"serve": "^11.3.1",
"spago": "^0.10.0",