Devel frontend citiation

.dockerignore

@@ -0,0 +1,52 @@
+engine/analyses/
+engine/results/
+engine/data/
+data/
+.snakemake
+engine/dist/
+engine/eggs/
+engine/lib/
+engine/build/
+engine/lib64/
+engine/__pycache__/
+
+media/*
+
+*.py[cod]
+*.egg-info/
+*.egg
+.DS_Store
+
+# dependencies
+lookupService/frontend/node_modules
+lookupService/frontend/.pnp
+.pnp.js
+
+# testing
+/coverage
+
+# production
+/build
+
+# misc
+.DS_Store
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+.env
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+.idea/
+db.sqlite3
+lookupService/static/frontend/**
+package-lock.json
+
+secret.txt
+Pipfile
+Pipfile.lock
+uwsgi.ini
+uwsgi_params

.gitignore

@@ -1,13 +1,51 @@
-analyses/
-results/
+engine/analyses/
+engine/results/
+engine/data/
 data/
 .snakemake
-dist/
-eggs/
-lib/
-build/
-lib64/
-__pycache__/
+engine/dist/
+engine/eggs/
+engine/lib/
+engine/build/
+engine/lib64/
+engine/__pycache__/
+
+media/*
+
 *.py[cod]
 *.egg-info/
 *.egg
+*.log
+.DS_Store
+
+# dependencies
+lookupService/frontend/node_modules
+lookupService/frontend/.pnp
+.pnp.js
+
+# testing
+/coverage
+
+# production
+/build
+
+# misc
+.DS_Store
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+.env
+.envdock
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+.idea/
+db.sqlite3
+lookupService/static/frontend/**
+package-lock.json
+static/**
+secret.txt
+

Dockerfile

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+# syntax=docker/dockerfile:1
+FROM continuumio/miniconda3:latest AS backend
+
+RUN apt update && \
+    apt install -y curl
+
+#RUN curl -fsSL https://deb.nodesource.com/setup_lts.x | bash
+#RUN apt install -y nodejs && \
+#    apt install -y npm
+
+RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.0/install.sh | bash
+ENV NODE_VERSION=16.13.0
+ENV NVM_DIR=/root/.nvm
+
+RUN . "$NVM_DIR/nvm.sh" && nvm install ${NODE_VERSION}
+RUN . "$NVM_DIR/nvm.sh" && nvm use v${NODE_VERSION}
+RUN . "$NVM_DIR/nvm.sh" && nvm alias default v${NODE_VERSION}
+ENV PATH="/root/.nvm/versions/node/v${NODE_VERSION}/bin/:${PATH}"
+
+WORKDIR /app
+
+COPY environment.yml ./
+
+RUN conda env create -f environment.yml -n mirmachine
+
+COPY . ./
+
+WORKDIR /app/lookupService/frontend
+
+RUN npm install
+
+RUN npm run build
+
+WORKDIR /app
+
+SHELL ["conda", "run", "-n", "mirmachine", "bin/bash", "-c"]
+
+RUN ["conda", "run", "--no-capture-output", "-n", "mirmachine", \
+     "python", "manage.py", "migrate"]
+
+EXPOSE 8000
+ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "mirmachine", \
+            "python", "manage.py", "runserver", "0.0.0.0:8000"]

LICENSE

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+MIT License
+
+Copyright (c) 2021 Håvard Trondsen & Sinan U. Umu
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MirMachineWebapp/asgi.py

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+"""
+ASGI config for MirMachineWebapp project.
+
+It exposes the ASGI callable as a module-level variable named ``application``.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/3.2/howto/deployment/asgi/
+"""
+
+from django.core.asgi import get_asgi_application
+import os
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'MirMachineWebapp.settings')
+django_asgi_application = get_asgi_application()
+
+from channels.routing import ProtocolTypeRouter, URLRouter
+from channels.auth import AuthMiddlewareStack
+import lookupService.urls
+import django
+
+django.setup()
+application = ProtocolTypeRouter({
+    'http': django_asgi_application,
+    'websocket': AuthMiddlewareStack(
+        URLRouter(
+            lookupService.urls.websocket_patterns
+        )
+    )
+})

MirMachineWebapp/settings.py

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+"""
+Django settings for MirMachineWebapp project.
+
+Generated by 'django-admin startproject' using Django 3.2.6.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/3.2/topics/settings/
+
+For the full list of settings and their values, see
+https://docs.djangoproject.com/en/3.2/ref/settings/
+"""
+import os
+from pathlib import Path
+from environ import Env
+
+env = Env()
+
+env.read_env(env_file='.env')
+
+# Build paths inside the project like this: BASE_DIR / 'subdir'.
+BASE_DIR = Path(__file__).resolve().parent.parent
+
+
+# Quick-start development settings - unsuitable for production
+# See https://docs.djangoproject.com/en/3.2/howto/deployment/checklist/
+
+# SECURITY WARNING: keep the secret key used in production secret!
+SECRET_KEY = env('DJANGO_SECRET_KEY')
+
+# SECURITY WARNING: don't run with debug turned on in production!
+DEBUG = True
+
+ALLOWED_HOSTS = ['mirmachine.org', 'localhost', '127.0.0.1']
+
+
+# Application definition
+
+INSTALLED_APPS = [
+    'django.contrib.admin',
+    'django.contrib.auth',
+    'django.contrib.contenttypes',
+    'django.contrib.sessions',
+    'django.contrib.messages',
+    'django.contrib.staticfiles',
+    'lookupService.apps.LookupserviceConfig',
+    'manifest_loader',
+    'rest_framework',
+    'channels',
+    'django_crontab',
+]
+
+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 = 'MirMachineWebapp.urls'
+
+TEMPLATES = [
+    {
+        'BACKEND': 'django.template.backends.django.DjangoTemplates',
+        'DIRS': [os.path.join(BASE_DIR, "lookupService", "templates")],
+        '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 = 'MirMachineWebapp.wsgi.application'
+ASGI_APPLICATION = 'MirMachineWebapp.asgi.application'
+
+# Database
+# https://docs.djangoproject.com/en/3.2/ref/settings/#databases
+
+DATABASES = {
+    'default': {
+        'ENGINE': 'django.db.backends.mysql',
+        'NAME': 'mirmachine_data',
+        'USER': env('DB_USER'),
+        'PASSWORD': env('DB_PASS'),
+        'HOST': 'localhost',
+        'PORT': '',
+    }
+}
+
+CHANNEL_LAYERS = {
+    "default": {
+        "BACKEND": "channels_redis.core.RedisChannelLayer",
+        "CONFIG": {
+            "hosts": [("127.0.0.1", 6379)]
+        },
+    },
+}
+
+
+# Password validation
+# https://docs.djangoproject.com/en/3.2/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/3.2/topics/i18n/
+
+LANGUAGE_CODE = 'en-us'
+
+TIME_ZONE = 'Europe/Oslo'
+
+USE_I18N = True
+
+USE_L10N = True
+
+USE_TZ = True
+
+
+# Static files (CSS, JavaScript, Images)
+# https://docs.djangoproject.com/en/3.2/howto/static-files/
+STATIC_ROOT = os.path.join(BASE_DIR, 'static')
+STATIC_URL = 'static/'
+STATICFILES_DIRS = (
+    os.path.join(BASE_DIR, 'lookupService', 'static', 'assets'),
+    os.path.join(BASE_DIR, 'lookupService', 'static', 'frontend'),
+)
+
+MEDIA_ROOT = os.path.join(BASE_DIR, 'media/')
+MEDIA_URL = 'media/'
+# Default primary key field type
+# https://docs.djangoproject.com/en/3.2/ref/settings/#default-auto-field
+
+DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField'
+
+EMAIL_BACKEND = 'django.core.mail.backends.smtp.EmailBackend'
+EMAIL_HOST = 'smtp.sendgrid.net'
+EMAIL_USER = env('MAIL_USER')
+EMAIL_HOST_USER = env('MAIL_HOST_USER')
+EMAIL_HOST_PASSWORD = env('MAIL_PASS')
+EMAIL_PORT = 587
+EMAIL_USE_TLS = True
+
+CRONJOBS = [
+    ('0 0 * * 2,4,6', 'lookupService.helpers.maintainer.delete_expired_jobs')
+]