Merge pull request #3 from C3BI-pasteur-fr/dev

NGPhylogeny_fr/settings.py

@@ -27,6 +27,7 @@
 DEBUG = True
 
 ALLOWED_HOSTS = ["127.0.0.1",]
+INTERNAL_IPS = ["127.0.0.1",]
 
 CRISPY_TEMPLATE_PACK = "bootstrap4"
 
@@ -46,6 +47,7 @@
     'galaxy',
     'data',
     'tools',
+    'surveys',
     'workflows',
     'workspace',
 ]
@@ -62,8 +64,8 @@
     'debug_toolbar.middleware.DebugToolbarMiddleware'
 ]
 
-SESSION_ENGINE = 'django.contrib.sessions.backends.cache'
-SESSION_EXPIRE_AT_BROWSER_CLOSE = True
+SESSION_ENGINE = 'django.contrib.sessions.backends.cached_db'
+SESSION_EXPIRE_AT_BROWSER_CLOSE = False
 
 ROOT_URLCONF = 'NGPhylogeny_fr.urls'
 
@@ -158,4 +160,10 @@
             'level': os.getenv('DJANGO_LOG_LEVEL', 'INFO'),
         },
     },
-}
+}
+
+CACHES = {
+    'default': {
+        'BACKEND': 'django.core.cache.backends.locmem.LocMemCache',
+    }
+}

NGPhylogeny_fr/urls.py

@@ -21,12 +21,15 @@
 from account import urls as account_urls
 from data import urls as data_urls
 from galaxy import urls as galaxy_urls
+from surveys import urls as surveys_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, name='admin'),
+    url(r'^admin/', admin.site.urls, name='admin'), # Django ADMIN URLS
+    url(r'^about$', TemplateView.as_view(template_name="about.html"), name="about"),
+    url(r'^about/', include(surveys_urls)),
     url(r'^documentation$', TemplateView.as_view(template_name="documentation.html"), name="documentation"),
     url(r'^analysis$', TemplateView.as_view(template_name="phylogeny_analysis_choices.html"), name="analysis_list"),
     url(r'^galaxy/', include(galaxy_urls)),
@@ -37,3 +40,11 @@
     url(r'^workspace/', include(workspace_urls)),
     url(r'^$', TemplateView.as_view(template_name="home.html"), name="home"),
 ]
+
+from django.conf import settings
+
+if settings.DEBUG:
+    import debug_toolbar
+    urlpatterns = [
+        url(r'^__debug__/', include(debug_toolbar.urls)),
+    ] + urlpatterns

README.md

@@ -1,3 +1,4 @@
-# NG-Phylogeny.fr
+# NGPhylogeny.fr
+
 
 A Django web application to make Phylogeny analysis.

account/urls.py

@@ -2,7 +2,7 @@
 from django.contrib.auth.decorators import login_required
 from django.contrib.auth.views import login, logout
 
-from galaxy.views import *
+from galaxy.views import UpdateApiKey
 
 urlpatterns = [
     url(r'^login$', login, {'template_name': "account/login.html" }, name='login'),

data/forms.py

@@ -1,13 +1,44 @@
 # -*- coding: utf-8 -*-
 from crispy_forms.bootstrap import FormActions
+from crispy_forms.bootstrap import StrictButton
 from crispy_forms.helper import FormHelper
 from crispy_forms.layout import Submit, Layout
 from django import forms
 
 
 class UploadForm(forms.Form):
-    file = forms.FileField(widget=forms.FileInput(attrs={'multiple': 'true'}))
+    input_file = forms.FileField(widget=forms.FileInput())
+
+    def __init__(self, *args, **kwargs):
+        super(UploadForm, self).__init__(*args, **kwargs)
+        self.helper = FormHelper(self)
+        self.helper.form_method = 'POST'
+        self.helper.layout = Layout('input_file',
+                                    FormActions(
+                                        Submit('submit', 'Submit')))
+
+    class Media:
+
+        js = ("js/jquery.filer.min.js",)
+        css= {
+                'all':("css/jquery.filer.css",)
+              }
+
+
+class PastedContentForm(forms.Form):
+    pasted_text = forms.CharField(widget=forms.Textarea)
+    textarea_id = "id_pasted_text"
     helper = FormHelper()
     helper.form_method = 'POST'
-    helper.layout = Layout('file',
-                           FormActions(Submit('submit', 'Submit')))
+    helper.layout = Layout('pasted_text',
+                           FormActions(
+                                Submit('submit', 'Submit'),
+                                StrictButton( "<span class='glyphicon glyphicon-question-sign'></span> Example",
+                                         css_class="btn btn-info",
+                                         onclick="populateExample('"+textarea_id+"', FASTA_AA);"),
+                                StrictButton("<span class='glyphicon glyphicon-trash'></span>",
+                                        css_class="btn btn-default",
+                                        onclick="document.getElementById('"+textarea_id+"').value='';" ),
+                                ))
+    class Media:
+        js = ('js/form_examples.js',)

data/urls.py

@@ -3,7 +3,7 @@
 from views import *
 
 urlpatterns = [
-    url(r'^upload/$', UploadView.as_view(), name='upload'),
+    url(r'^upload/$', ImportPastedContentView.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"),

data/views.py

@@ -7,42 +7,83 @@
 from django.shortcuts import render, redirect
 from django.urls import reverse_lazy
 from django.utils.decorators import method_decorator
-from django.views.generic import FormView
+from django.views.generic.edit import FormView
 
-from forms import UploadForm
+from forms import UploadForm, PastedContentForm
 from galaxy.decorator import connection_galaxy
 from workspace.views import get_or_create_history
 
 
+class UploadMixin(object):
+
+    def upload_content(self, content, history_id=None):
+        """
+            send content into galaxy history: return galaxy response
+        """
+        if history_id:
+            self.history_id = history_id
+        else:
+            self.history_id = get_or_create_history(self.request)
+
+        return self.request.galaxy.tools.paste_content(content=content, file_name="pasted_data",
+                                                       history_id=self.history_id)
+
+
+    def upload_file(self, file, history_id=None):
+        """
+            upload file into galaxy history: return galaxy response
+        """
+
+        tmpfile = tempfile.NamedTemporaryFile()
+        for chunk in file.chunks():
+            tmpfile.write(chunk)
+        tmpfile.flush()
+
+        if history_id:
+            self.history_id = history_id
+        else:
+            self.history_id = get_or_create_history(self.request)
+
+        return self.request.galaxy.tools.upload_file(path=tmpfile.name,file_name=file.name, history_id=self.history_id)
+
+
+
 @method_decorator(connection_galaxy, name="dispatch")
-class UploadView(FormView):
+class UploadView(UploadMixin, FormView):
     """
-        Upload file into Galaxy Server
+       Upload file into Galaxy Server
     """
 
     template_name = 'upload_form.html'
     form_class = UploadForm
     success_url = reverse_lazy("home")
 
-    def upload_file(self, form):
-        """upload file into current galaxy history: return galaxy response
-        """
+    def form_valid(self, form):
+
         myfile = form.cleaned_data['file']
-        tmpfile = tempfile.NamedTemporaryFile()
-        for chunk in myfile.chunks():
-            tmpfile.write(chunk)
-        tmpfile.flush()
+        outputs = self.upload_file(myfile)
+        self.success_url = reverse_lazy("history_detail", kwargs={'history_id': self.history_id}, )
 
-        self.history_id = get_or_create_history(self.request)
-        return self.request.galaxy.tools.upload_file(tmpfile.name, self.history_id, file_name=myfile.name)
+        return super(UploadView, self).form_valid()
 
 
+@method_decorator(connection_galaxy, name="dispatch")
+class ImportPastedContentView(UploadMixin, FormView):
+    """
+       Import user pasted content into Galaxy Server
+    """
+
+    form_class = PastedContentForm
+    success_url = reverse_lazy("home")
+
     def form_valid(self, form):
 
-        outputs = self.upload_file(form)
+        p_content = form.cleaned_data['pasted_text']
+        outputs = self.upload_content(p_content)
         self.success_url = reverse_lazy("history_detail", kwargs={'history_id': self.history_id}, )
 
-        return super(UploadView, self).form_valid(form)
+        return super(ImportPastedContentView, self).form_valid()
+
 
 
 @connection_galaxy

galaxy/admin.py

@@ -1,8 +1,10 @@
+import requests
 from django.contrib import admin
 from django.contrib import messages
+from django.core.validators import ValidationError
 
 from tools.models import Tool
-from .models import *
+from .models import Server, GalaxyUser
 
 
 class GalaxyServerAdmin(admin.ModelAdmin):
@@ -11,7 +13,18 @@ class GalaxyServerAdmin(admin.ModelAdmin):
     """
     list_display = ('name', 'url', 'current')
     list_display_links = ('name', 'url')
-    actions = ['activate_configuration','import_new_tools' ]
+    actions = ['activate_configuration', 'import_new_tools']
+
+    def save_model(self, request, obj, form, change):
+        # get automatically Galaxy version if it not set
+        if not obj.version:
+            try:
+                r = requests.get(obj.url + '/api/version')
+                obj.version = r.json().get('version_major')
+            except Exception as e:
+                raise ValidationError(message="Please set the version of Galaxy, or make sure that URL is working")
+
+        super(GalaxyServerAdmin, self).save_model(request, obj, form, change)
 
     def import_new_tools(self, request, queryset):
         """
@@ -32,14 +45,14 @@ def activate_configuration(self, request, queryset):
             galaxy_server = queryset[0]
             galaxy_server.current = True
             galaxy_server.save()
-
-            self.message_user(request, "%s configuration is now activated and usable by the application" %(galaxy_server.name),
-                              level=messages.SUCCESS )
+            # TODO reset history session
+            self.message_user(request,
+                              "%s configuration is now activated and usable by the application" % (galaxy_server.name),
+                              level=messages.SUCCESS)
 
 
 class GalaxyUserAdmin(admin.ModelAdmin):
     """
-
     """
     list_display = ('user', 'galaxy_server', 'anonymous')
     list_filter = ('user', 'galaxy_server', 'anonymous')

galaxy/decorator.py

@@ -6,6 +6,7 @@
 from django.shortcuts import redirect
 
 from galaxy.models import Server, GalaxyUser
+
 logger = logging.getLogger(__name__)
 
 
@@ -17,7 +18,12 @@ def wrapper(request, *args, **kwargs):
         try:
             if hasattr(request, 'galaxy_server'):
                 galaxy_server = request.galaxy_server
+
+            elif request.session.get('galaxy_server'):
+                galaxy_server = Server.objects.get(id=request.session.get('galaxy_server'))
+
             else:
+                #by default use the current Galaxy server
                 galaxy_server = Server.objects.get(current=True)
 
         except Server.DoesNotExist :
@@ -31,6 +37,7 @@ def wrapper(request, *args, **kwargs):
             raise HttpResponseGone()
 
         request.galaxy_server = galaxy_server
+        request.session['galaxy_server'] = galaxy_server.id
 
         if request.user.is_authenticated():
             """Try to use related Galaxy user information"""
@@ -41,7 +48,7 @@ def wrapper(request, *args, **kwargs):
 
                 """If the key api is not defined, prompts the user to define it"""
                 if gu.api_key:
-                    request.galaxy = gu.get_galaxy_instance()
+                    request.galaxy = gu.get_galaxy_instance
                 else:
                     return redirect('galaxy_account')
 
@@ -60,7 +67,7 @@ def wrapper(request, *args, **kwargs):
             """If user is not an authenticated, use the anonymous Galaxy user set"""
             try:
                 gu = GalaxyUser.objects.get(anonymous=True, galaxy_server=galaxy_server)
-                request.galaxy = gu.get_galaxy_instance()
+                request.galaxy = gu.get_galaxy_instance
 
             except GalaxyUser.DoesNotExist :
                 msg = "NGPhylogeny server is not properly configured, " \
@@ -69,8 +76,8 @@ def wrapper(request, *args, **kwargs):
                 logger.exception("Anonymous user not set")
                 raise Http404(msg)
 
-            except:
-                logger.exception("Galaxy account Error")
+            except Exception as e:
+                logger.exception("Galaxy anonymous account Error: "+e)
                 return HttpResponseGone()
 
         return view_function(request, *args, **kwargs)