p2m2 / ep2m2

Metabolomics target analyzes manager

EP2M2

ep2m2's Issues

Bouton "Tout suprrimer" enlever

trop dangereux dans le cadre de plsueiur sporjet

doc deploiement dans le readme

Manage only one file for initialize database

Manage only one file for initialize database

./db/init.js => just read ./db/init.sql

compose.yml -> docker-compose.yml

REUSE-compliante CI

REUSE-compliante CI

Add check merge request is REUSE-compliante with yaml (120 min)

• Execute before merge
• Run REUSE check
• Block merge if check is fail

Verify authentification in each page

When we go to page we have to user logged.

We use middleware contain login checking
We create a login page.

add eslint CI/CD

basic wireframe

Basic wireframe

Create wireframe for first part of web site.
Content:

• buttons to add files
• buttons to delete files
• list of file added
• button to extract

Extraction devrait etre seulement au format csv

• Un seul fichier en extraction.
• Si plusieurs fichiers , c est la fusion de tout les fichiers qui doit etre extrait (donc un unique csv)

miss comments

miss comments

Add legend

Add a legend to know the action of each button.

Rename repository / project

Rename repository / project

TaMAMa

→ Target Metabolic Analyse Manager

Tabs to navigate between project and series

Tabs to navigate between project and series.
We have two tabs

1. To go project page
2. To go series page

For that we use a layout.

• Write documentation
• Write test
• Create the layout

Note:
We have a layout in a layout (the navigate layout in default layout)

check database up

Check database up

When in server we have to call database, check database is up.
If it's down return a 503 error

Colonne "Team" dans l'affichae des projet

Nom des boutons "Télécharger"

"Telecharger" devrait etre "Importer" pour plus de clarter

Add table MACHINE

Add table MACHINE

This table is references of machine.

It contains:

• id → SERIAL PRIMARY KEY
• name → VARCHAR 255
• id_techno → SERIAL Foreign key of techno table
• description → Text

Add component to manage compound

Add component to manage compound.

The component provide:

• Visualization of all compound in database with search
• Add new compound
• Delete compound not used yet
• Archive compound

Create profile page

In this page user can change email and password.
The administrator can add/delete user.

For this page, I think change file structure to use route mechanism provide by Nuxt.
Add in database user's rules.

[feat] Upload file to extract

• Add Upload file
• Read File
• Extract information of file
• • Name
• • Size
• • Type
• Show summary in table

Add tab series (ligth)

Add tab series (ligth)

1. Get daughter solution file
2. Ask real area of each metabolite
3. Repeat 1 & 2 for all daughter solution files
4. Calculate ratio of each metabolite (A_real = A_machine * Ration)

• Add Series Table in database
• Add daughter table in database
• Add Ratio table in database
• Series tabs show series
• Series tabs provide function to add
• Documentation
• Tests

Ajouter la notion de projet

Un projet contient un ensemble de fichier "Run" à intégrer dans un unique CSV

use only one cookie

use only one cookie

we use token cookie to know your team and if you logged.

Add tutorial

Add tutorial

This tutorial explain quickly how create a project add export it.

It is:

• interactive
• open at first connection
• accessing in help menu

creation d une branche develop

• proteger la branche main

Affect series

Affect series

In project, we can select a series. And in result, we add a column Calculated_Area

• Change interface
• Select series in table
• Add Calculated_Area in result
• Documented
• Tested

Ajouter un lien vers l'ajout d'issue

Ajouter un lien vers l'ajout d'issue

Dès la page de login

[feat] skeleton of web site

Implemented skeleton defined in wireframe

Create help

Create Help menu

We have a link to open directly a help page.

This page contain :

• What's a project
• Quick start
• Manage project
• → New Project
• →Modify Project
• Basic Base compound Metabolic
• → Add basic compound
• → Add analyzer
• → Add fitting
• Index

Invisible add project button

Invisible add project button

Cause
In style of button we use a class with color variable but the variable's declaration removed.

Solution
Use only style define in vuetify.ts

[Feat] Reafactoring project to CI/CD and Test

Modify repository's structure to try respect format provide by metaboHub

remove deps nuxt-ui

Write Readme

Write Readme

Create default layout

Create default layout

This layout is a banner. Banner contain icon, language button, help button and logout button.

• Documented the layout
• Write tests of default layout
• create default layout
• Delete component BannerMain and ExtrasNav

Use Vuetify

Use Vuetify instead of Nuxt/UI

Nuxt/UI have issue with table
Vuetify sound like more mature.

Replace all component Nuxt/ui by vuetify

"EXTRAIRE" --> "EXPORT"

Internationalisation : i18n

Il faudrait une gestion des langues à prendre en compte des le debut du projet

Add login

create session user

Add, in database, compound table

Add, in database, compound table

We need 3 tables

• 1. COMPOUND → ref of compound

  • id SERIAL
  • name VARCHAR(255) UNIQUE
  • URL VARCHAR(255)
  • description TEXTAREA

Reset button in project box

Reset button in project box

Add button in project to cancel modification but stay in project.

Become REUSE-compliant

Become REUSE-compliant from reuse.software

• Create reuse branch (5 min)
• Install reuse (10 min)
• Add MIT licence with reuse (10 min)
• Add copyright and licensing information to each file (20 min)
• Confirm REUSE compliance (10 min)

connection to database don't close

connection to database don't close

Error message in container ep2m2-web:

[nuxt] [request error] [unhandled] [500] sorry, too many clients already

Reproduction:

1. Start web site
2. Use it several time
   => impossible to open web site

Readme

• ajouter une description courte
• badge couverture
• badge test

Tab serie 's structure

Tab serie 's structure

Create empty component to each tab .
Insert component in serie page (asynchronous loading component).

• Documentation
• Coding
• Testing