New project initialization

.circleci/ci_django.yml

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+db:
+  name: circleci_db
+  user: circleci
+  password: ''
+  host: localhost
+  port: 5432

.circleci/config.yml

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+version: 2
+
+jobs:
+  tests:
+    docker:
+      # Primary docker container where the tests will be run
+      - image: circleci/python:3.6.8
+
+      # Secondary docker container for database service
+      - image: postgres:11.4
+        environment:
+          POSTGRES_USER: circleci
+
+    working_directory: ~/py3-adage-backend
+
+    steps:
+      - checkout
+      - run:
+          name: Set up Postgres
+          command: |
+            sudo apt-get update --quiet
+            sudo apt-get upgrade --yes --quiet
+            sudo apt-get install postgresql-client --yes
+            createdb --host=localhost --username=circleci circleci_db
+            cp .circleci/ci_django.yml adage/adage/config.yml
+      - run:
+          name: Set up venv
+          command: |
+            mkdir -p ~/.venv
+            python3 -m venv ~/.venv/adage
+      - run:
+          name: Backend tests
+          working_directory: ~/py3-adage-backend/adage
+          command: |
+            source ~/.venv/adage/bin/activate
+            pip install pip --upgrade
+            pip install -r requirements.txt
+            python3 manage.py makemigrations
+            python3 manage.py migrate
+            python3 manage.py test
+
+workflows:
+  version: 2
+  test:
+    jobs:
+      - tests

.gitignore

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+*~
+*.pyc
+*.sqlite3
+*.json_cache
+
+# Django config file
+adage/adage/config.yml
+
+# Adage-specific data files
+data/gene_history
+data/*.gene_info
+data/bootstrap_cache_*
+data/*_pickled_genesets

adage/adage/config_template.yml

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+# Database configuration (required)
+db:
+  name: database_name
+  user: db_user
+  password: not_secure
+  host: database_hostname
+  port: database_port_number
+
+# Django secret key (required for production server).
+# Optional for dev server, default: "django_secret_key"
+key: 'django_secret_key'
+
+# Debug flag (optional, default: True)
+debug: True
+
+# Allowed hosts (optional, default: blank list)
+allowed_hosts:
+  - localhost
+  - 127.0.0.1
+
+# Directory that hosts static files (optional, default: "<BASE_DIR>/static"
+static_root: '/home/ubuntu/www/static/'

adage/adage/settings.py

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+"""
+Django settings for adage project.
+
+Generated by 'django-admin startproject' using Django 2.2.5.
+
+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
+import yaml
+
+# Build paths inside the project like this: os.path.join(BASE_DIR, ...)
+BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+
+# Read secrets from YAML file
+path = os.path.join(BASE_DIR, 'adage', 'config.yml')
+with open(path) as read_file:
+    config = yaml.full_load(read_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 = config.get('secret_key', 'django_secret_key')
+
+# SECURITY WARNING: don't run with debug turned on in production!
+DEBUG = config.get('debug', True)
+
+ALLOWED_HOSTS = config.get('allowed_hosts', [])
+
+# Application definition
+
+INSTALLED_APPS = [
+    'django.contrib.admin',
+    'django.contrib.auth',
+    'django.contrib.contenttypes',
+    'django.contrib.sessions',
+    'django.contrib.messages',
+    'django.contrib.staticfiles',
+    'rest_framework',
+    'django_filters',
+    'corsheaders',
+    'organisms',
+    'genes',
+    'analyze',
+]
+
+REST_FRAMEWORK = {
+    'PAGE_SIZE': 25,
+    'DEFAULT_PAGINATION_CLASS': 'rest_framework.pagination.LimitOffsetPagination',
+    'DEFAULT_FILTER_BACKENDS': ('django_filters.rest_framework.DjangoFilterBackend',),
+}
+
+MIDDLEWARE = [
+    'django.middleware.security.SecurityMiddleware',
+    'django.contrib.sessions.middleware.SessionMiddleware',
+    'corsheaders.middleware.CorsMiddleware',
+    'django.middleware.common.CommonMiddleware',
+    'django.middleware.csrf.CsrfViewMiddleware',
+    'django.contrib.auth.middleware.AuthenticationMiddleware',
+    'django.contrib.messages.middleware.MessageMiddleware',
+    'django.middleware.clickjacking.XFrameOptionsMiddleware',
+]
+
+ROOT_URLCONF = 'adage.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 = 'adage.wsgi.application'
+
+
+# Database
+# https://docs.djangoproject.com/en/2.2/ref/settings/#databases
+
+DATABASES = {
+    'default': {
+        'ENGINE': 'django.db.backends.postgresql_psycopg2',
+        'NAME': config['db']['name'],
+        'USER': config['db']['user'],
+        'PASSWORD': config['db']['password'],
+        'HOST': config['db']['host'],
+        'PORT': config['db']['port'],
+    }
+}
+
+
+# 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 = 'America/New_York'
+
+USE_I18N = True
+
+USE_L10N = True
+
+USE_TZ = True
+
+
+# Static files (CSS, JavaScript, Images)
+# https://docs.djangoproject.com/en/2.2/howto/static-files/
+# Use "python manage.py collectstatic" command to populate static directory
+STATIC_ROOT = config.get('static_root', os.path.join(BASE_DIR, 'static'))
+STATIC_URL = '/static/'
+
+# CORS config
+# https://pypi.org/project/django-cors-headers/
+CORS_ORIGIN_ALLOW_ALL = True
+CORS_URLS_REGEX = r'^/api/v1/.*$'
+CORS_ALLOW_METHODS = ('GET', )

adage/adage/urls.py

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+"""adage URL Configuration"""
+
+from django.contrib import admin
+from django.urls import include, path
+from rest_framework import routers
+from analyze import views
+
+router = routers.DefaultRouter()
+router.register(r"mlmodels", views.MLModelViewSet)
+
+urlpatterns = [
+    path('admin/', admin.site.urls),
+    path('api/v1/', views.api_root),
+    path('api/v1/', include(router.urls)),
+]

adage/adage/wsgi.py

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+"""
+WSGI config for adage 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', 'adage.settings')
+
+application = get_wsgi_application()

adage/analyze/admin.py

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

adage/analyze/apps.py

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+from django.apps import AppConfig
+
+
+class AnalyzeConfig(AppConfig):
+    name = 'analyze'