first project commit

ippisite/ippidb/admin.py

+from django.contrib import admin
+
+from .models import Bibliography
+
+admin.site.register(Bibliography)

ippisite/ippidb/apps.py

+from django.apps import AppConfig
+
+
+class IppidbConfig(AppConfig):
+    name = 'ippidb'

ippisite/ippidb/migrations/0001_initial.py

+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-02-14 11:12
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Bibliography',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('source', models.CharField(choices=[('PM', 'PubMed article'), ('PT', 'Patent')], max_length=2, verbose_name='Bibliographic type')),
+                ('id_source', models.CharField(max_length=25, verbose_name='Bibliographic ID')),
+                ('title', models.CharField(max_length=300, verbose_name='Title')),
+                ('journal_name', models.CharField(max_length=50, verbose_name='Journal name')),
+                ('authors_list', models.CharField(max_length=500, verbose_name='Authors list')),
+                ('biblio_year', models.PositiveSmallIntegerField(verbose_name='Year')),
+                ('cytotox', models.BooleanField(verbose_name='Cytotoxicity data')),
+                ('in_silico', models.BooleanField(verbose_name='in silico study performed')),
+                ('in_vitro', models.BooleanField(verbose_name='in vitro study performed')),
+                ('in_vivo', models.BooleanField(verbose_name='in vivo study performed')),
+                ('in_cellulo', models.BooleanField(verbose_name='in cellulo study performed')),
+                ('pharmacokinetic', models.BooleanField(verbose_name='pharmacokinetic study performed')),
+                ('xray', models.BooleanField(verbose_name='contains xray data')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='BindingSite',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Complex',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('copy_nb', models.IntegerField(verbose_name='Number of copies')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Domain',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('pfam_acc', models.CharField(max_length=10, unique=True, verbose_name='Pfam Accession')),
+                ('pfam_id', models.CharField(max_length=20, verbose_name='Pfam Family Identifier')),
+                ('pfam_description', models.CharField(max_length=100, verbose_name='Pfam Description')),
+                ('domainfamily', models.CharField(max_length=25, verbose_name='')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='MolecularFunction',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('go_id', models.CharField(max_length=10, unique=True, verbose_name='Gene Ontology ID')),
+                ('description', models.CharField(max_length=500, verbose_name='description')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Ppi',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('binding_site_id_1', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='binding_site_id_1', to='ippidb.BindingSite')),
+                ('binding_site_id_2', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='binding_site_id_2', to='ippidb.BindingSite')),
+                ('complex_id_1', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='cplx_id_1', to='ippidb.Complex')),
+                ('complex_id_2', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='cplx_id_2', to='ippidb.Complex')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='PpiArchitecture',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('pdb_id', models.CharField(max_length=4, verbose_name='PDB ID')),
+                ('ppi_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Protein',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('uniprot_id', models.CharField(max_length=10, unique=True, verbose_name='Uniprot ID')),
+                ('recommended_name_long', models.CharField(max_length=75, verbose_name='Uniprot Recommended Name (long)')),
+                ('short_name', models.CharField(max_length=50, verbose_name='Short name')),
+                ('gene_name', models.CharField(max_length=30, unique=True, verbose_name='Gene name')),
+                ('entry_name', models.CharField(max_length=30, verbose_name='Entry name')),
+                ('molecular_functions', models.ManyToManyField(to='ippidb.MolecularFunction')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Taxonomy',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('taxonomy_id', models.DecimalField(decimal_places=0, max_digits=4, unique=True, verbose_name='NCBI TaxID')),
+                ('name', models.CharField(max_length=200, verbose_name='Organism name')),
+            ],
+        ),
+        migrations.AddField(
+            model_name='protein',
+            name='organism',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Taxonomy'),
+        ),
+        migrations.AddField(
+            model_name='complex',
+            name='protein_id',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Protein'),
+        ),
+        migrations.AddField(
+            model_name='bindingsite',
+            name='domain_id',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Domain'),
+        ),
+        migrations.AddField(
+            model_name='bindingsite',
+            name='protein_id',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Protein'),
+        ),
+    ]

ippisite/ippidb/templates/base.html

+{% load bootstrap3 %}
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <link rel="stylesheet" href="{% bootstrap_css_url %}" />
+    <title>IPPI-DB Maintenance {% block title %}{% endblock %}</title>
+</head>
+
+<body>
+    <nav class="navbar navbar-default">
+      <div class="container-fluid">
+        <!-- Brand and toggle get grouped for better mobile display -->
+        <div class="navbar-header">
+          <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1" aria-expanded="false">
+            <span class="sr-only">Toggle navigation</span>
+            <span class="icon-bar"></span>
+            <span class="icon-bar"></span>
+            <span class="icon-bar"></span>
+          </button>
+          <a class="navbar-brand" href="#">IPPI-DB</a>
+        </div>
+
+        <!-- Collect the nav links, forms, and other content for toggling -->
+        <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
+          <ul class="nav navbar-nav">
+            <li class="active"><a href="/ippidb/biblio/">Bibliographic references list<span class="sr-only">(current)</span></a></li>
+            <li><a href="/ippidb/biblio/add/">Add a new bibliographic reference<span class="sr-only">(current)</span></a></li>
+          </ul>
+        </div><!-- /.navbar-collapse -->
+      </div><!-- /.container-fluid -->
+    </nav>
+    <div id="content">
+        {% block content %}{% endblock %}
+    </div>
+</body>
+</html>

ippisite/ippidb/templates/ippidb/bibliography_detail.html

+{% extends "base.html" %}
+
+{% block title %}- biblio detail for {{object.title}} by {{object.authors_list}}{% endblock %}
+
+{% block content %}
+        <p>{{ object.get_source_display }}</p>
+        <p>{{ object.id_source}}</p>
+        <p>{{ object.title }}</p>
+        <p>{{ object.journal_name }}</p>
+        <p>{{ object.authors_list }}</p>
+        <p>{{ object.biblio_year }}</p>
+        <p>{{ object.cytotox }}</p>
+        <p>{{ object.in_silico }}</p>
+        <p>{{ object.in_vitro }}</p>
+        <p>{{ object.in_vivo }}</p>
+        <p>{{ object.in_cellulo }}</p>
+        <p>{{ object.pharmacokinetic }}</p>
+        <p>{{ object.xray }}</p>
+{% endblock %}

ippisite/ippidb/templates/ippidb/bibliography_form.html

+{% extends "base.html" %}
+{% load bootstrap3 %}
+
+{% block title %}- biblio edition{% endblock %}
+
+{% block content %}
+            {% csrf_token %}
+            {% bootstrap_form form %}
+            <input type="submit" name="submit" value="Save" />
+{% endblock %}

ippisite/ippidb/templates/ippidb/bibliography_list.html

+{% extends "base.html" %}
+
+{% block title %}- biblios list{% endblock %}
+
+{% block content %}
+        {% for biblio in object_list %}
+            <li><a href="{{biblio.get_absolute_url}}">{{ biblio.get_source_display }} {{ biblio.id_source}} - {{ biblio.title }}</a></li>
+        {% empty %}
+            <li>No articles yet.</li>
+        {% endfor %}
+{% endblock %}

ippisite/ippidb/tests.py

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

ippisite/ippidb/urls.py

+from django.conf.urls import url
+
+from .views import BibliographyCreate, BibliographyUpdate, BibliographyDelete, BibliographyDetail, BibliographyList
+
+urlpatterns = [
+    url(r'biblio/$', BibliographyList.as_view(), name='list'),
+    url(r'biblio/add/$', BibliographyCreate.as_view(), name='biblio-add'),
+    url(r'biblio/(?P<pk>[0-9]+)/$', BibliographyDetail.as_view(), name='biblio-detail'),
+    url(r'biblio/(?P<pk>[0-9]+)/edit/$', BibliographyUpdate.as_view(), name='biblio-update'),
+    url(r'biblio/(?P<pk>[0-9]+)/delete/$', BibliographyDelete.as_view(), name='biblio-delete'),
+]

ippisite/ippidb/views.py

+from django.http import HttpResponse
+from django.views.generic.edit import CreateView, UpdateView, DeleteView
+from django.views.generic.detail import DetailView
+from django.views.generic import ListView
+from django.urls import reverse_lazy
+from .models import Bibliography
+
+class BibliographyCreate(CreateView):
+    model = Bibliography
+    fields = '__all__'
+
+class BibliographyUpdate(UpdateView):
+    model = Bibliography
+    fields = '__all__'
+
+class BibliographyDelete(DeleteView):
+    model = Bibliography
+    success_url = reverse_lazy('biblio-list')
+
+class BibliographyDetail(DetailView):
+    model = Bibliography
+    fields = '__all__'
+
+class BibliographyList(ListView):
+    model = Bibliography
+

ippisite/ippidb/ws.py

+from bioservices.eutils import EUtils
+
+def get_pubmed_info(pmid):
+    eu = EUtils()
+    r = eu.EFetch('pubmed', pmid, retmode='dict', rettype='abstract')
+    article = r['PubmedArticleSet']['PubmedArticle']['MedlineCitation']['Article']
+    title = article['ArticleTitle']
+    authors_list = [a['LastName']+ ' ' + a['Initials'] for a in article['AuthorList']['Author']]
+    authors = ', '.join(authors_list)
+    journal_name = article['Journal']['Title']
+    biblio_year = article['Journal']['JournalIssue']['PubDate']['Year']
+    return {'title':title,
+            'journal_name':journal_name,
+            'biblio_year':biblio_year,
+            'authors_list': authors}

ippisite/ippisite/settings.py

+"""
+Django settings for ippisite project.
+
+Generated by 'django-admin startproject' using Django 1.10.5.
+
+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 = '&qc$2x5p&!qwvu2r=)sjp*jgg8a7ss97g8lwpennmu(q9ty4o$'
+
+# 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',
+    'ippidb'
+]
+
+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 = 'ippisite.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 = 'ippisite.wsgi.application'
+
+
+# Database
+# https://docs.djangoproject.com/en/1.10/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/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/'

ippisite/ippisite/urls.py

+"""ippisite 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 include, url
+from django.contrib import admin
+
+urlpatterns = [
+    url(r'^', include('ippidb.urls')),
+    url(r'^admin/', admin.site.urls),
+]

ippisite/ippisite/wsgi.py

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

ippisite/manage.py

+#!/usr/bin/env python
+import os
+import sys
+
+if __name__ == "__main__":
+    os.environ.setdefault("DJANGO_SETTINGS_MODULE", "ippisite.settings")
+    try:
+        from django.core.management import execute_from_command_line
+    except ImportError:
+        # The above import may fail for some other reason. Ensure that the
+        # issue is really that Django is missing to avoid masking other
+        # exceptions on Python 2.
+        try:
+            import django
+        except ImportError:
+            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?"
+            )
+        raise
+    execute_from_command_line(sys.argv)