Merge branch 'develop' of https://github.com/parklab/refinery-platform …

…into develop

refinery/core/api.py

@@ -25,7 +25,7 @@
 from core.models import Project, NodeSet, NodeRelationship, NodePair, \
     Workflow, WorkflowInputRelationships, Analysis, DataSet, \
     ExternalToolStatus, ResourceStatistics, GroupManagement, ExtendedGroup, \
-    UserAuthentication, Invitation, EmailInvite
+    UserAuthentication, Invitation, EmailInvite, UserProfile
 from core.tasks import check_tool_status
 from data_set_manager.api import StudyResource, AssayResource
 from data_set_manager.models import Node, Study
@@ -112,13 +112,13 @@ def list_to_queryset(self, res_list):
     # Apply filters.
     def do_filtering(self, res_list, get_req_dict):
         mod_list = res_list
-        
+
         for k in get_req_dict:
             # Skip if res does not have the attribute. Done to help avoid
             # whatever internal filtering can be performed on other things,
             # like limiting the return amount.
             mod_list = [x for x in mod_list
-                        if not hasattr(x, k) or 
+                        if not hasattr(x, k) or
                         str(getattr(x, k)) == get_req_dict[k]]
 
         return mod_list
@@ -139,7 +139,7 @@ def build_res_list(self, user, res_list, request, **kwargs):
 
         # Filter for query flags.
         res_list = self.do_filtering(res_list, request.GET)
- 
+
         return res_list
 
     def build_bundle_list(self, request, res_list, **kwargs):
@@ -295,8 +295,21 @@ def obj_get_list(self, bundle, **kwargs):
                                                          bundle,
                                                          **kwargs)
 
-    def get_object_list(self, request):
-        return SharableResourceAPIInterface.get_object_list(self, request)
+    # def get_object_list(self, request):
+    #     return SharableResourceAPIInterface.get_object_list(self, request)
+
+    def get_object_list(self, request, **kwargs):
+        if(request.user.is_authenticated()):
+            return get_objects_for_user(
+                request.user,
+                "core.read_project"
+            ).filter(is_catch_all=False)
+        else:
+            group = ExtendedGroup.objects.public_group()
+            return get_objects_for_group(
+                group,
+                'core.read_project'
+            ).filter(is_catch_all=False)
 
 
 class DataSetResource(ModelResource, SharableResourceAPIInterface):
@@ -316,7 +329,6 @@ class Meta:
         # authentication = SessionAuthentication()
         # authorization = GuardianAuthorization()
         filtering = {'uuid': ALL}
-        # fields = ['uuid']
 
     def prepend_urls(self):
         prepend_urls_list = SharableResourceAPIInterface.prepend_urls(self) + [
@@ -339,8 +351,28 @@ def obj_get_list(self, bundle, **kwargs):
                                                          bundle,
                                                          **kwargs)
 
-    def get_object_list(self, request):
-        return SharableResourceAPIInterface.get_object_list(self, request)
+    # def get_object_list(self, request):
+    #     return SharableResourceAPIInterface.get_object_list(self, request)
+
+    def get_object_list(self, request, **kwargs):
+        if(request.user.is_authenticated()):
+            data_sets = get_objects_for_user(
+                request.user,
+                'core.read_dataset'
+            )
+            for data_set in data_sets:
+                # Assuming that only owners can share an object.
+                # add_dataset is not unique to owners unfortunately
+                data_set.is_owner = request.user.has_perm(
+                    'core.share_dataset',
+                    data_set
+                )
+                data_set.public = data_set.is_public
+        else:
+            group = ExtendedGroup.objects.public_group()
+            data_sets = get_objects_for_group(group, 'core.read_dataset')
+
+        return data_sets
 
     def obj_create(self, bundle, **kwargs):
         return SharableResourceAPIInterface.obj_create(self, bundle, **kwargs)
@@ -448,8 +480,21 @@ def obj_get_list(self, bundle, **kwargs):
                                                          bundle,
                                                          **kwargs)
 
-    def get_object_list(self, request):
-        return SharableResourceAPIInterface.get_object_list(self, request)
+    # def get_object_list(self, request):
+    #     return SharableResourceAPIInterface.get_object_list(self, request)
+
+    def get_object_list(self, request, **kwargs):
+        if(request.user.is_authenticated()):
+            return get_objects_for_user(
+                request.user,
+                "core.read_workflow"
+            ).filter(is_active=True)
+        else:
+            group = ExtendedGroup.objects.public_group()
+            return get_objects_for_group(
+                group,
+                'core.read_workflow'
+            ).filter(is_active=True)
 
     def obj_create(self, bundle, **kwargs):
         return SharableResourceAPIInterface.obj_create(self, bundle, **kwargs)
@@ -523,6 +568,16 @@ class Meta:
         }
         ordering = ['name', 'creation_date']
 
+    def get_object_list(self, request, **kwargs):
+        if(request.user.is_authenticated()):
+            return UserProfile.objects.get(
+                user=User.objects.get(
+                    username=request.user
+                )
+            ).catch_all_project.analyses.all().order_by("-time_start")
+        else:
+            return Analysis.objects.none()
+
 
 class NodeResource(ModelResource):
     parents = fields.ToManyField('core.api.NodeResource', 'parents')
@@ -1193,7 +1248,7 @@ def user_authorized(self, user, group):
     def has_expired(self, token):
         if token.expires is None:
             return True
- 
+
         return (datetime.datetime.now() - token.expires).total_seconds() >= 0
 
     def prepend_urls(self):
@@ -1208,9 +1263,10 @@ def prepend_urls(self):
                 self.wrap_view('update_db'),
                 name='api_invitation_update_db'),
             url(r'^invitation/send/(?P<group_id>%s)/(?P<email>%s)/$'
-                    % (self.group_id_regex, self.email_regex),
+                % (self.group_id_regex, self.email_regex),
                 self.wrap_view('email_token'),
                 name='api_invitation_email_token'),
+
         ]
 
     def get_token(self, request, **kwargs):
@@ -1219,7 +1275,7 @@ def get_token(self, request, **kwargs):
         if request.method == 'GET':
             user = request.user
             group = self.get_group(int(kwargs['group_id']))
-            
+
             if not self.user_authorized(user, group):
                 return HttpUnauthorized()
 
@@ -1267,6 +1323,7 @@ def update_db(self, request, **kwargs):
 
         return HttpNoContent()
 
+
     def email_token(self, request, **kwargs):
         group = self.get_group(int(kwargs['group_id']))
 
@@ -1291,4 +1348,3 @@ def email_token(self, request, **kwargs):
         email = EmailMessage(subject, body, to=[address])
         email.send()
         return HttpAccepted()
-

refinery/data_set_manager/urls.py

@@ -8,8 +8,8 @@
 from django.contrib.auth.decorators import login_required
 from django.views.decorators.csrf import csrf_exempt
 from data_set_manager.views import (
-    ImportISATabView, ProcessISATabView, ProcessMetadataTableView,
-    CheckDataFilesView, FileUploadView, ChunkedFileUploadView,
+    DataSetImportView, ImportISATabView, ProcessISATabView,
+    ProcessMetadataTableView, CheckDataFilesView, ChunkedFileUploadView,
     ChunkedFileUploadCompleteView
 )
 
@@ -26,8 +26,9 @@
 
     url(r'^nodes/(?P<study_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/(?P<assay_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/(?P<type>[\w ]+)/annotate$', "node_annotate", name="data_set_manager_update_annotated_nodes" ),
 
+    url(r'^import/$', DataSetImportView.as_view(), name='import_data_set'),
     url(r'^import/isa-tab/$', csrf_exempt(ImportISATabView.as_view()),
-        name='import_isa_tab'),
+        name='import_isa_tab'),  # csrf_exempt required for POST requests from external sites
     url(r'^import/isa-tab-form/$', login_required(ProcessISATabView.as_view()),
         name='process_isa_tab'),
     url(r'^contents/(?P<study_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/(?P<assay_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/$', "contents", name="data_set_manager_contents" ),
@@ -36,8 +37,6 @@
         name='process_metadata_table'),
     url(r'^import/check_files/$', CheckDataFilesView.as_view(),
         name='check_files'),
-    url(r'^import/file-upload-form/$', login_required(FileUploadView.as_view()),
-        name='upload_files'),
     url(r'^import/chunked-upload/$',
         login_required(ChunkedFileUploadView.as_view()),
         name='api_chunked_upload'),

refinery/data_set_manager/views.py

@@ -99,54 +99,18 @@ def search_typeahead(request):
                             mimetype='application/json')
 
 
-# ===============================================================================
-# ISA-Tab import
-#===============================================================================
-class ImportISATabView(View):
-    '''Capture ISA archive URL from POST requests submitted from external sites
-
-    '''
-
-    def post(self, request, *args, **kwargs):
-        try:
-            isa_tab_url = request.POST['isa_tab_url']
-        except KeyError:
-            logger.error("ISA archive URL was not provided")
-            return HttpResponseBadRequest("Please provide an ISA archive URL")
-        else:
-            # set cookie and redirect to process_isa_tab view
-            response = HttpResponseRedirect(reverse('process_isa_tab'))
-            response.set_cookie('isa_tab_url', isa_tab_url)
-            return response
-
-
-class ImportISATabFileForm(forms.Form):
-    '''ISA-Tab file upload form
+# Data set import
 
-    '''
-    isa_tab_file = forms.FileField(label='ISA-Tab file', required=False)
-    isa_tab_url = forms.URLField(label='ISA-Tab URL', required=False,
-                                 widget=forms.TextInput(attrs={'size': '37'}))
+class DataSetImportView(View):
+    """Main view for data set importing
 
-    def clean(self):
-        cleaned_data = super(ImportISATabFileForm, self).clean()
-        f = cleaned_data.get("isa_tab_file")
-        url = cleaned_data.get("isa_tab_url")
-        # either a file or a URL must be provided
-        if f or url:
-            return cleaned_data
-        else:
-            raise forms.ValidationError("Please provide either a file or a URL")
-
-
-class ProcessISATabView(View):
-    '''Process ISA-Tab archive
-
-    '''
-    template_name = 'data_set_manager/isa-tab-import.html'
+    """
+    template_name = "data_set_manager/import.html"
     success_view_name = 'data_set'
     isa_tab_cookie_name = 'isa_tab_url'
 
+    # def get(self, request, *args, **kwargs):
+    #     return render(request, self.template_name)
     # a workaround for automatic ISA archive import after logging in
     def get(self, request, *args, **kwargs):
         try:
@@ -200,6 +164,52 @@ def get(self, request, *args, **kwargs):
             response.delete_cookie(self.isa_tab_cookie_name)
             return response
 
+
+class ImportISATabView(View):
+    '''Capture ISA archive URL from POST requests submitted from external sites
+
+    '''
+
+    def post(self, request, *args, **kwargs):
+        try:
+            isa_tab_url = request.POST['isa_tab_url']
+        except KeyError:
+            logger.error("ISA archive URL was not provided")
+            return HttpResponseBadRequest("Please provide an ISA archive URL")
+        else:
+            # set cookie and redirect to process_isa_tab view
+            response = HttpResponseRedirect(reverse('process_isa_tab'))
+            response.set_cookie('isa_tab_url', isa_tab_url)
+            return response
+
+
+class ImportISATabFileForm(forms.Form):
+    '''ISA-Tab file upload form
+
+    '''
+    isa_tab_file = forms.FileField(label='ISA-Tab file', required=False)
+    isa_tab_url = forms.URLField(label='ISA-Tab URL', required=False,
+                                 widget=forms.TextInput(attrs={'size': '37'}))
+
+    def clean(self):
+        cleaned_data = super(ImportISATabFileForm, self).clean()
+        f = cleaned_data.get("isa_tab_file")
+        url = cleaned_data.get("isa_tab_url")
+        # either a file or a URL must be provided
+        if f or url:
+            return cleaned_data
+        else:
+            raise forms.ValidationError("Please provide either a file or a URL")
+
+
+class ProcessISATabView(View):
+    '''Process ISA-Tab archive
+
+    '''
+    template_name = 'data_set_manager/isa-tab-import.html'
+    success_view_name = 'data_set'
+    isa_tab_cookie_name = 'isa_tab_url'
+
     def post(self, request, *args, **kwargs):
         form = ImportISATabFileForm(request.POST, request.FILES)
         if form.is_valid():
@@ -352,16 +362,6 @@ def post(self, request, *args, **kwargs):
                             content_type="application/json")
 
 
-class FileUploadView(TemplateView):
-    """Data file upload form view
-
-    """
-    template_name = 'data_set_manager/import.html'
-
-    def get(self, request, *args, **kwargs):
-        return render(request, self.template_name)
-
-
 class ChunkedFileUploadView(ChunkedUploadView):
 
     model = ChunkedUpload

refinery/settings.json.sample

@@ -1,4 +1,5 @@
 {
+  "DEBUG_TOOLBAR": false,
   "DEBUG": true,
   "STATICFILES": [
     "static/development",

refinery/settings.py

@@ -208,6 +208,14 @@ def get_setting(name, settings=local_settings):
     'chunked_upload',
 )
 
+# required for Django Debug Tool Bar
+if get_setting('DEBUG_TOOLBAR'):
+    INSTALLED_APPS += (
+        'debug_toolbar',
+    )
+    INTERNAL_IPS = ('192.168.50.1' )
+
+
 # NG: added for django-guardian
 AUTHENTICATION_BACKENDS = (
     'django.contrib.auth.backends.ModelBackend',  # default

refinery/templates/base.html

@@ -5,7 +5,8 @@
 
 <html lang="en">
 <head>
-	<meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta content="text/html">
+  	<meta name="viewport" content="width=device-width, initial-scale=1.0">
     <meta name="description" content="">
     <meta name="author" content="">
 

refinery/templates/core/home.html

@@ -49,7 +49,7 @@ <h3><i class="icon-file m-r-1-4"></i>Data Sets</h3>
 				{% if user.is_authenticated and not REFINERY_REPOSITORY_MODE %}
 					<span class="refinery-header-right">
 						<h4>
-              <a href={% url "process_isa_tab" %} class="no-underline-hover">
+              <a href={% url "import_data_set" %} class="no-underline-hover">
                 <i class="icon-plus-sign"></i>
               </a>
             </h4>