Mise en place schema

.gitignore

 /.project
 /.pydevproject
+*.pyc
+*/__pycache__*
+

README.md

+# API REST Django
+
+## Mise en place de l'environnement
+Ces étapes seront déjà réalisées dans la VM.<br>
+
+Installer virtualenv et éventuellement pip s'ils ne sont pas déjà installés :<br>
+`sudo apt-get install python3-venv`<br>
+`sudo apt-get install python3-pip`<br>
+
+Créer un environnement virtuel pour python :<br>
+`python3 -m venv django-vuejs`<br>
+
+Activer l'environnement virtuel :<br>
+`source django-vuejs/bin/activate`<br>
+
+Se déplacer dans le répertoire contenant le code source de l'api :<br>
+`cd /mon/repository/git/django-rest-api/`<br>
+
+Installer les dépendances :<br>
+`pip install -r requirements.txt`
+
+## Installer la base de données
+
+Pour l'atelier il sera peut être plus simple d'utiiser SQLite. Pour créer la base de données il suffit d'executer la commande suivante<br>
+`python manage.py migrate`
+

data_loader.py

+import json
+from django.db import transaction
+from protfamily.models import Family, Alignment, Stat, Tree
+
+DATA_REPO = '../django-vue.js/data/'
+
+ALIGNEMENTS_REPO = DATA_REPO+'/alignments/'
+STATS_REPO = DATA_REPO+'/stats/'
+TREES_REPO = DATA_REPO+'/trees/'
+
+FAMILIES = ['orthomcl10','orthomcl12','orthomcl17', 'orthomcl909']
+
+with transaction.atomic() :
+    for fam in FAMILIES :
+        family_object = Family.objects.create(name=fam)
+        
+        align_fh = open('{0}{1}.fasta'.format(ALIGNEMENTS_REPO, fam),'r')
+        align_object = None
+        sequence = ""
+        for line in align_fh.readlines() :
+            if line.startswith('>') :
+                if align_object != None:
+                    align_object.seq = sequence
+                    align_object.save()
+                    sequence = ""
+                align_object = Alignment()
+                align_object.seq_id = line[1:].strip()
+                align_object.family = family_object
+            else :
+                sequence = sequence+line.strip()
+        align_object.seq = sequence
+        align_object.save()
+        align_fh.close()
+        
+        stat_fh = open('{0}{1}.json'.format(STATS_REPO, fam),'r')
+        stats_data = json.load(stat_fh)
+        Stat.objects.create(family = family_object,
+                            proteins = stats_data['proteins'],
+                            species = stats_data['species'])
+        stat_fh.close()
+        
+        tree_fh = open('{0}{1}.newick'.format(TREES_REPO, fam),'r')
+        Tree.objects.create(family = family_object,
+                            tree = tree_fh.read().strip())
+        tree_fh.close()
+        
+        
+        
\ No newline at end of file

django_api/settings.py

+"""
+Django settings for django_api project.
+
+Generated by 'django-admin startproject' using Django 2.2.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/2.2/topics/settings/
+
+For the full list of settings and their values, see
+https://docs.djangoproject.com/en/2.2/ref/settings/
+"""
+
+import os
+
+# Build paths inside the project like this: os.path.join(BASE_DIR, ...)
+BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+
+
+# Quick-start development settings - unsuitable for production
+# See https://docs.djangoproject.com/en/2.2/howto/deployment/checklist/
+
+# SECURITY WARNING: keep the secret key used in production secret!
+SECRET_KEY = 'lt#3%qeyg%n&h(ozbu9z$!(dqttm+b(%)o2$^li81m-c3#d%-8'
+
+# SECURITY WARNING: don't run with debug turned on in production!
+DEBUG = True
+
+ALLOWED_HOSTS = []
+
+
+# Application definition
+
+INSTALLED_APPS = [
+    'django.contrib.admin',
+    'django.contrib.auth',
+    'django.contrib.contenttypes',
+    'django.contrib.sessions',
+    'django.contrib.messages',
+    'django.contrib.staticfiles',
+    'protfamily'
+]
+
+MIDDLEWARE = [
+    'django.middleware.security.SecurityMiddleware',
+    'django.contrib.sessions.middleware.SessionMiddleware',
+    'django.middleware.common.CommonMiddleware',
+    'django.middleware.csrf.CsrfViewMiddleware',
+    'django.contrib.auth.middleware.AuthenticationMiddleware',
+    'django.contrib.messages.middleware.MessageMiddleware',
+    'django.middleware.clickjacking.XFrameOptionsMiddleware',
+]
+
+ROOT_URLCONF = 'django_api.urls'
+
+TEMPLATES = [
+    {
+        'BACKEND': 'django.template.backends.django.DjangoTemplates',
+        'DIRS': [],
+        'APP_DIRS': True,
+        'OPTIONS': {
+            'context_processors': [
+                'django.template.context_processors.debug',
+                'django.template.context_processors.request',
+                'django.contrib.auth.context_processors.auth',
+                'django.contrib.messages.context_processors.messages',
+            ],
+        },
+    },
+]
+
+WSGI_APPLICATION = 'django_api.wsgi.application'
+
+
+# Database
+# https://docs.djangoproject.com/en/2.2/ref/settings/#databases
+
+DATABASES = {
+    'default': {
+        'ENGINE': 'django.db.backends.sqlite3',
+        'NAME': os.path.join(BASE_DIR, 'db.sqlite3'),
+    }
+}
+
+
+# Password validation
+# https://docs.djangoproject.com/en/2.2/ref/settings/#auth-password-validators
+
+AUTH_PASSWORD_VALIDATORS = [
+    {
+        'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator',
+    },
+    {
+        'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator',
+    },
+    {
+        'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator',
+    },
+    {
+        'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator',
+    },
+]
+
+
+# Internationalization
+# https://docs.djangoproject.com/en/2.2/topics/i18n/
+
+LANGUAGE_CODE = 'en-us'
+
+TIME_ZONE = 'UTC'
+
+USE_I18N = True
+
+USE_L10N = True
+
+USE_TZ = True
+
+
+# Static files (CSS, JavaScript, Images)
+# https://docs.djangoproject.com/en/2.2/howto/static-files/
+
+STATIC_URL = '/static/'

django_api/urls.py

+"""django_api URL Configuration
+
+The `urlpatterns` list routes URLs to views. For more information please see:
+    https://docs.djangoproject.com/en/2.2/topics/http/urls/
+Examples:
+Function views
+    1. Add an import:  from my_app import views
+    2. Add a URL to urlpatterns:  path('', views.home, name='home')
+Class-based views
+    1. Add an import:  from other_app.views import Home
+    2. Add a URL to urlpatterns:  path('', Home.as_view(), name='home')
+Including another URLconf
+    1. Import the include() function: from django.urls import include, path
+    2. Add a URL to urlpatterns:  path('blog/', include('blog.urls'))
+"""
+from django.contrib import admin
+from django.urls import path
+
+urlpatterns = [
+    path('admin/', admin.site.urls),
+]

django_api/wsgi.py

+"""
+WSGI config for django_api project.
+
+It exposes the WSGI callable as a module-level variable named ``application``.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/2.2/howto/deployment/wsgi/
+"""
+
+import os
+
+from django.core.wsgi import get_wsgi_application
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'django_api.settings')
+
+application = get_wsgi_application()

manage.py

+#!/usr/bin/env python
+"""Django's command-line utility for administrative tasks."""
+import os
+import sys
+
+
+def main():
+    os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'django_api.settings')
+    try:
+        from django.core.management import execute_from_command_line
+    except ImportError as exc:
+        raise ImportError(
+            "Couldn't import Django. Are you sure it's installed and "
+            "available on your PYTHONPATH environment variable? Did you "
+            "forget to activate a virtual environment?"
+        ) from exc
+    execute_from_command_line(sys.argv)
+
+
+if __name__ == '__main__':
+    main()

protfamily/admin.py

+from django.contrib import admin
+
+# Register your models here.

protfamily/apps.py

+from django.apps import AppConfig
+
+
+class ProtfamilyConfig(AppConfig):
+    name = 'protfamily'

protfamily/migrations/0001_initial.py

+# Generated by Django 2.2 on 2021-07-29 09:33
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Family',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=150, verbose_name='Family name')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Tree',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('tree', models.TextField(verbose_name='Tree')),
+                ('family', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='protfamily.Family')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Stat',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('proteins', models.TextField(verbose_name='Proteins')),
+                ('species', models.TextField(verbose_name='Species')),
+                ('family', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='protfamily.Family')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Alignment',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('seq_id', models.CharField(max_length=250, verbose_name='Id')),
+                ('seq', models.TextField(verbose_name='Sequence')),
+                ('family', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='protfamily.Family')),
+            ],
+        ),
+    ]

protfamily/models.py

+from django.db import models
+from django.db.models.deletion import CASCADE
+
+
+# Create your models here.
+class Family(models.Model):
+    name = models.CharField("Family name", max_length=150)
+    
+    def __str__(self):
+        return self.name
+
+class Alignment(models.Model):
+    seq_id = models.CharField("Id", max_length=250)
+    seq = models.TextField("Sequence")
+    family = models.ForeignKey('Family', on_delete=CASCADE)
+    def __str__(self):
+        return self.seq_id
+
+class Stat(models.Model):
+    proteins = models.TextField("Proteins")
+    species = models.TextField("Species")
+    family = models.ForeignKey('Family', on_delete=CASCADE)
+    
+    def __str__(self):
+        return self.family.name
+        
+class Tree(models.Model):
+    tree = models.TextField("Tree")
+    family = models.ForeignKey('Family', on_delete=CASCADE)
+    def __str__(self):
+        return self.family.name
+    
\ No newline at end of file

protfamily/tests.py

+from django.test import TestCase
+
+# Create your tests here.

protfamily/views.py

+from django.shortcuts import render
+
+# Create your views here.