Merge pull request #2 from C3BI-pasteur-fr/dev

Dev

NGPhylogeny_fr/settings.py

@@ -11,12 +11,11 @@
 """
 
 import os
-from galaxyconf import *
 
 # Build paths inside the project like this: os.path.join(BASE_DIR, ...)
 BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 
-LOGIN_URL = '/account/login'
+LOGIN_URL = '/galaxy/login'
 LOGIN_REDIRECT_URL = '/'
 # Quick-start development settings - unsuitable for production
 # See https://docs.djangoproject.com/en/1.9/howto/deployment/checklist/
@@ -27,7 +26,7 @@
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = True
 
-ALLOWED_HOSTS = []
+ALLOWED_HOSTS = ["127.0.0.1",]
 
 CRISPY_TEMPLATE_PACK = "bootstrap4"
 
@@ -44,6 +43,7 @@
     'formtools',
     'crispy_forms',
     'account',
+    'galaxy',
     'data',
     'tools',
     'workflows',
@@ -141,4 +141,21 @@
     # Don't forget to use absolute paths, not relative paths.
     os.path.join(BASE_DIR, 'static'),
 
-)
+)
+
+
+LOGGING = {
+    'version': 1,
+    'disable_existing_loggers': False,
+    'handlers': {
+        'console': {
+            'class': 'logging.StreamHandler',
+        },
+    },
+    'loggers': {
+        'django': {
+            'handlers': ['console'],
+            'level': os.getenv('DJANGO_LOG_LEVEL', 'INFO'),
+        },
+    },
+}

NGPhylogeny_fr/urls.py

@@ -20,14 +20,16 @@
 
 from account import urls as account_urls
 from data import urls as data_urls
+from galaxy import urls as galaxy_urls
 from tools import urls as tool_urls
 from workflows import urls as workflows_urls
 from workspace import urls as workspace_urls
 
 urlpatterns = [
-    url(r'^admin/', admin.site.urls),
+    url(r'^admin/', admin.site.urls, name='admin'),
     url(r'^documentation$', TemplateView.as_view(template_name="documentation.html"), name="documentation"),
     url(r'^analysis$', TemplateView.as_view(template_name="phylogeny_analysis_choices.html"), name="analysis_list"),
+    url(r'^galaxy/', include(galaxy_urls)),
     url(r'^account/', include(account_urls)),
     url(r'^tools/', include(tool_urls)),
     url(r'^data/', include(data_urls)),

account/models.py

@@ -1,85 +0,0 @@
-from __future__ import unicode_literals
-
-from django.db import models
-from django.contrib.auth.models import User
-
-from django.core.exceptions import ValidationError
-from galaxylib import GalaxyInstance
-
-
-class GalaxyServer(models.Model):
-    """
-    Galaxy Server Informations
-    """
-    name = models.CharField(max_length=80)
-    url = models.URLField(max_length=254, unique=True, null=False)
-    synopsis = models.CharField(max_length=254)
-    description = models.TextField(max_length=500)
-    contact = models.CharField(max_length=254)
-    version = models.CharField(max_length=9)
-
-    def __str__(self):
-
-        return "%s %s" %(self.name, self.url)
-
-
-class GalaxyConf(models.Model):
-    """
-    Model to setup Galaxy Configuration and manage activation of Galaxyserver
-    :galaxy_server: in GalaxyConf is used to Galaxy requests when status active is true.
-    """
-    name = models.CharField(max_length=80,)
-    galaxy_server = models.ForeignKey(GalaxyServer, on_delete=models.CASCADE)
-    anonymous_user_api_access = models.BooleanField(default=False,
-                                                    verbose_name="Enable Anonymous api?",
-                                                    help_text="If True, Anonymous user must be set")
-    anonymous_user = models.OneToOneField('GalaxyUser', on_delete=models.CASCADE,
-                                          blank=True, null=True,
-                                          verbose_name="Global Anonymous User",
-                                          help_text="This User is used to make Galaxy requests for NGPhylogeny Anonymous Users")
-    active = models.BooleanField(default=False, verbose_name="Active Configuration?")
-
-    def clean(self,*args, **kwargs):
-        """make anonymous_user as required field them anonymous_user_api_access is true"""
-        if self.anonymous_user_api_access == True and (not self.anonymous_user):
-            raise ValidationError({'anonymous_user': 'This field is required.',
-                                   })
-        if self.anonymous_user:
-            if not (self.anonymous_user.galaxy_server == self.galaxy_server):
-                raise ValidationError({'anonymous_user': 'Anonymous user must have the same Galaxy Server',
-                                       })
-        super(GalaxyConf,self).clean(*args, **kwargs)
-
-    def save(self, *args, ** kwargs):
-        if self.active is True:
-            """One configuration can be actived"""
-            deactivated_config = GalaxyConf.objects.all()
-            deactivated_config.update(active=False)
-        super(GalaxyConf, self).save(*args, **kwargs)
-
-    def __unicode__(self):
-        return self.name
-
-
-class GalaxyUser(models.Model):
-    """
-    Model to save User APIkey from Galaxy
-    """
-    user = models.ForeignKey(User, on_delete=models.CASCADE )
-    galaxy_server = models.ForeignKey(GalaxyServer, on_delete=models.CASCADE)
-    api_key = models.CharField(max_length=100, blank=True)
-
-    def get_galaxy_instance(self):
-        """:return bioblend Galaxy instance object
-        """
-        if self.api_key:
-            return GalaxyInstance(url=self.galaxy_server.url, key=self.api_key)
-        else:
-            raise "API key must be set"
-
-    def __unicode__(self):
-        return self.user.username
-
-    class Meta:
-
-        unique_together = ['user','galaxy_server']

account/urls.py

@@ -1,16 +1,13 @@
-
 from django.conf.urls import url
-from django.contrib.auth.views import login, logout
 from django.contrib.auth.decorators import login_required
-from django.views.generic import TemplateView
-
+from django.contrib.auth.views import login, logout
 
-from views import *
+from galaxy.views import *
 
 urlpatterns = [
     url(r'^login$', login, {'template_name': "account/login.html" }, name='login'),
     url(r'logout$', logout, {'next_page': "/"}, name='logout'),
-    url(r'^$',login_required( GalaxyUserUpdateApiKey.as_view() ), name='account'),
+    url(r'^$', login_required(UpdateApiKey.as_view()), name='account'),
     #url(r'^create_account/$', create_account),
     #url(r'^success/$', TemplateView.as_view(template_name='success.html'))
 ]

data/urls.py

@@ -1,28 +1,13 @@
-"""NGPhylogeny_fr URL Configuration
-
-The `urlpatterns` list routes URLs to views. For more information please see:
-    https://docs.djangoproject.com/en/1.9/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
-from views import *
-
-from account.decorator import connection_galaxy
 
+from views import *
 
 urlpatterns = [
     url(r'^upload/$', UploadView.as_view(), name='upload'),
 
     url(r'^display/(?P<file_id>[\w-]+)$', display_file, name="display_file"),
+    url(r'^displaytree/(?P<file_id>[\w-]+)$', tree_visualization, name="display_tree"),
     url(r'^download/(?P<file_id>[\w-]+)$', download_file, name="download_file"),
+    url(r'^export_to_itol/(?P<file_id>[\w-]+)$', export_to_itol, name="export_to_itol"),
     url(r'^export/(?P<file_id>[\w-]+)$', export_file, name="export_file"),
 ]