Drugst.One django template

README.md

-# template-django
+# Drugst.One template-django
 
+This is a lightweight template for a django server running a python application that produces a list of genes and displays the result in a webpage. For the network visualization, the Drugst.One application is used. Feel free to adapt this project to your needs!
 
+## Get started
 
-## Getting started
+### 1. Installation
 
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+Create a python environment callend '.env':
 
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+`python -m venv .env`
 
-## Add your files
 
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
+Enter the environment on Mac/Linux:
 
-```
-cd existing_repo
-git remote add origin https://gitlab.rrz.uni-hamburg.de/cosy-bio/drugst.one/template-django.git
-git branch -M main
-git push -uf origin main
-```
+`source .env/bin/activate`
 
-## Integrate with your tools
+Enter the environment on Windows:
 
-- [ ] [Set up project integrations](https://gitlab.rrz.uni-hamburg.de/cosy-bio/drugst.one/template-django/-/settings/integrations)
+`.env/Scripts/activate`
 
-## Collaborate with your team
+Install all required python packages:
 
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
+`pip install -r requirements.txt`
 
-## Test and Deploy
 
-Use the built-in continuous integration in GitLab.
+### 2. Start the development server
 
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
+Change port according to your needs
 
-***
+`python manage.py runserver 0.0.0.0:8000`
 
-# Editing this README
+### 3. Finish development
 
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
+Read up more in the official django documentation on how to go from the development to the production server: https://docs.djangoproject.com/en/4.1/
\ No newline at end of file
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.

drugstone_template/drugstone_template/asgi.py

+"""
+ASGI config for drugstone_template 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/4.1/howto/deployment/asgi/
+"""
+
+import os
+
+from django.core.asgi import get_asgi_application
+
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "drugstone_template.settings")
+
+application = get_asgi_application()

drugstone_template/drugstone_template/settings.py

+"""
+Django settings for drugstone_template project.
+
+Generated by 'django-admin startproject' using Django 4.1.2.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/4.1/topics/settings/
+
+For the full list of settings and their values, see
+https://docs.djangoproject.com/en/4.1/ref/settings/
+"""
+
+from pathlib import Path
+
+# 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/4.1/howto/deployment/checklist/
+
+# SECURITY WARNING: keep the secret key used in production secret!
+SECRET_KEY = "django-insecure-j70yjbx*3$5)3l27f*2az5*r*s8iz-6yq=m)m+$7e=rele1v1u"
+
+# 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",
+    'my_app',
+]
+
+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 = "drugstone_template.urls"
+
+TEMPLATES = [
+    {
+        "BACKEND": "django.template.backends.django.DjangoTemplates",
+        "DIRS": [
+            '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 = "drugstone_template.wsgi.application"
+
+
+# Database
+# https://docs.djangoproject.com/en/4.1/ref/settings/#databases
+
+DATABASES = {
+    "default": {
+        "ENGINE": "django.db.backends.sqlite3",
+        "NAME": BASE_DIR / "db.sqlite3",
+    }
+}
+
+
+# Password validation
+# https://docs.djangoproject.com/en/4.1/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/4.1/topics/i18n/
+
+LANGUAGE_CODE = "en-us"
+
+TIME_ZONE = "UTC"
+
+USE_I18N = True
+
+USE_TZ = True
+
+
+# Static files (CSS, JavaScript, Images)
+# https://docs.djangoproject.com/en/4.1/howto/static-files/
+
+STATIC_URL = "static/"
+
+# Default primary key field type
+# https://docs.djangoproject.com/en/4.1/ref/settings/#default-auto-field
+
+DEFAULT_AUTO_FIELD = "django.db.models.BigAutoField"

drugstone_template/drugstone_template/urls.py

+"""drugstone_template URL Configuration
+
+The `urlpatterns` list routes URLs to views. For more information please see:
+    https://docs.djangoproject.com/en/4.1/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, include
+from django.shortcuts import redirect
+
+def redirect_root(request):
+    return redirect('/my_app/home')
+    
+urlpatterns = [
+    path('my_app/', include('my_app.urls')),
+    path('admin/', admin.site.urls),
+    path('', redirect_root),
+]

drugstone_template/drugstone_template/wsgi.py

+"""
+WSGI config for drugstone_template 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/4.1/howto/deployment/wsgi/
+"""
+
+import os
+
+from django.core.wsgi import get_wsgi_application
+
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "drugstone_template.settings")
+
+application = get_wsgi_application()

drugstone_template/manage.py

+#!/usr/bin/env python
+"""Django's command-line utility for administrative tasks."""
+import os
+import sys
+
+
+def main():
+    """Run administrative tasks."""
+    os.environ.setdefault("DJANGO_SETTINGS_MODULE", "drugstone_template.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()

drugstone_template/my_app/admin.py

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