ClusterCAD 1.0

.gitattributes

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+static/* linguist-vendored
+notebooks/* linguist-documentation
+pipeline/data/* linguist-documentation

.gitignore

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+.DS_Store
+pipeline/data/aa_sequence_analysis/plotcache.p
+*.pyc
+*~
+*.swp
+.ipynb_checkpoints
+notebooks/mibig/*
+screenlog.*
+clusterCAD/settings.py
+notebooks/*

LICENSE.txt

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+clusterCAD Copyright (C) 2016-2017, The Regents of the University of California, through
+Lawrence Berkeley National Laboratory (subject to receipt of any required
+approvals from the U.S. Dept. of Energy).  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+(1) Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence Berkeley National
+Laboratory, U.S. Dept. of Energy nor the names of its contributors may be used
+to endorse or promote products derived from this software without specific
+prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes, patches, or
+upgrades to the features, functionality or performance of the source code
+("Enhancements") to anyone; however, if you choose to make your Enhancements
+available either publicly, or directly to Lawrence Berkeley National Laboratory,
+without imposing a separate written license agreement for such Enhancements,
+then you hereby grant the following license: a  non-exclusive, royalty-free
+perpetual license to install, use, modify, prepare derivative works, incorporate
+into other computer software, distribute, and sublicense such enhancements or
+derivative works thereof, in binary and source code form.

README

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+ClusterCAD: a computational platform for type I modular polyketide synthase design
+
+Copyright (c) 2017, The Regents of the University of California, through
+Lawrence Berkeley National Laboratory (subject to receipt of any required
+approvals from the U.S. Dept. of Energy).  All rights reserved.
+
+Starting service (connect to HTTP on port 8000 with username and password 'pkscluster'):
+docker-compose up -d
+
+Loading PKS data into database:
+docker-compose exec web /bin/bash -c 'cd pipeline && make clean && make all'
+
+Shutting down (restart possible with up -d):
+docker-compose stop
+
+Shut down and delete all containers:
+docker-compose down 
+
+Building images:
+docker-compose build
+
+Running commands inside running web container:
+docker-compose exec web /bin/bash
+
+Creating a superuser for /admin:
+docker-compose exec web python3 manage.py createsuperuser
+
+Obtaining a Django shell:
+docker-compose exec web python3 manage.py shell
+
+Running jupyter notebook for development:
+docker-compose exec web jupyter notebook --no-browser --ip=* --allow-root

admin_notes.txt

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+# create a new app
+python3 manage.py startapp pks
+
+# create database tables for new app
+python3 manage.py migrate
+
+# update app migrations
+python3 manage.py makemigrations pks
+python3 manage.py migrate
+
+
+# example to create and save a cluster object
+from pks.models import Cluster
+a = Cluster(description="ok")
+a.save()
+
+Cluster.objects.all()
+
+# flush redis cache
+docker-compose exec redis redis-cli flushall

awsLaunch.sh

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+#!/bin/bash
+
+# this script launches this service on an aws container, after manually adding the servers ssh key to bitbucket
+# make sure to enable port 80 in Security groups for this container as well
+# also make sure you are using DEBUG = False, and settings ALLOWED_HOSTS to the correct server name
+# for production
+
+sudo yum update -y
+sudo yum install -y docker git
+sudo pip install docker-compose
+sudo service docker start
+
+# create ssh key and add to bitbucket before running this
+git clone https://github.com/JBEI/clusterCAD
+cd clusterCAD
+sudo /usr/local/bin/docker-compose build
+sudo /usr/local/bin/docker-compose up -d
+
+# example to forward ports back for devel
+ssh -L 80:localhost:80 8888:localhost:8888 ec2-user@<remote hostname>

clusterCAD/example_settings.py

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+"""
+Django settings for clusterCAD project.
+
+Generated by 'django-admin startproject' using Django 1.10.4.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/1.10/topics/settings/
+
+For the full list of settings and their values, see
+https://docs.djangoproject.com/en/1.10/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/1.10/howto/deployment/checklist/
+
+# SECURITY WARNING: keep the secret key used in production secret!
+SECRET_KEY = '28$$942hz#kd1c7c-!jkxu*#e+2stjy69v7$p)4mo2kh&q-97r'
+
+# 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',
+    'bootstrap3',
+    'pks',
+    'compounddb',
+    'structureSearch',
+    'sequenceSearch',
+]
+
+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 = 'clusterCAD.urls'
+
+TEMPLATES = [
+    {
+        'BACKEND': 'django.template.backends.django.DjangoTemplates',
+        'DIRS': [os.path.join(BASE_DIR, '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 = 'clusterCAD.wsgi.application'
+
+
+# Database
+# https://docs.djangoproject.com/en/1.10/ref/settings/#databases
+
+DATABASES = {
+    'default': {
+        'ENGINE': 'django.db.backends.postgresql',
+        'NAME': 'clustercad',
+        'USER': 'clustercad',
+        'PASSWORD': 'clustercad',
+        'HOST': 'db',
+        'PORT': 5432,
+    }
+}
+
+
+# Password validation
+# https://docs.djangoproject.com/en/1.10/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/1.10/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/1.10/howto/static-files/
+
+STATIC_URL = '/static/'
+STATIC_ROOT = "/www/static/"
+
+MEDIA_ROOT = '/www/static/media/'
+MEDIA_URL = '/static/media/'
+
+STATICFILES_DIRS = [
+    os.path.join(BASE_DIR, "static"),
+]
+
+# Default settings
+BOOTSTRAP3 = {
+    # The URL to the jQuery JavaScript file
+    'jquery_url': '/static/js/jquery.min.js',
+
+    # The Bootstrap base URL
+    'base_url': '/static/',
+}
+
+CACHES = {
+    "default": {
+        "BACKEND": "django_redis.cache.RedisCache",
+        "LOCATION": "redis://redis:6379/1",
+        "OPTIONS": {
+            "CLIENT_CLASS": "django_redis.client.DefaultClient",
+        }
+    }
+}

clusterCAD/urls.py

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+"""clusterCAD URL Configuration
+
+The `urlpatterns` list routes URLs to views. For more information please see:
+    https://docs.djangoproject.com/en/1.10/topics/http/urls/
+Examples:
+Function views
+    1. Add an import:  from my_app import views
+    2. Add a URL to urlpatterns:  url(r'^$', views.home, name='home')
+Class-based views
+    1. Add an import:  from other_app.views import Home
+    2. Add a URL to urlpatterns:  url(r'^$', Home.as_view(), name='home')
+Including another URLconf
+    1. Import the include() function: from django.conf.urls import url, include
+    2. Add a URL to urlpatterns:  url(r'^blog/', include('blog.urls'))
+"""
+from django.conf.urls import url, include
+from django.contrib import admin
+from django.views.generic import TemplateView
+
+urlpatterns = [
+    url(r'^admin/', admin.site.urls),
+    url(r'^pks/', include('pks.urls')),
+    url(r'^compounddb/', include('compounddb.urls')),
+    url(r'^structureSearch/', include('structureSearch.urls')),
+    url(r'^sequenceSearch/', include('sequenceSearch.urls')),
+    url(r'^$', TemplateView.as_view(template_name='home.html')),
+    url(r'^about/$', TemplateView.as_view(template_name='about.html')),
+]

clusterCAD/wsgi.py

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+"""
+WSGI config for clusterCAD 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/1.10/howto/deployment/wsgi/
+"""
+
+import os
+
+from django.core.wsgi import get_wsgi_application
+
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "clusterCAD.settings")
+
+application = get_wsgi_application()

compounddb/admin.py

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

compounddb/apps.py

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+from django.apps import AppConfig
+
+
+class CompounddbConfig(AppConfig):
+    name = 'compounddb'

compounddb/migrations/0001_initial.py

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+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-03-23 22:43
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Compound',
+            fields=[
+                ('inchiKey', models.CharField(max_length=27, primary_key=True, serialize=False)),
+                ('name', models.CharField(max_length=256)),
+                ('smiles', models.TextField()),
+            ],
+        ),
+    ]