Merge branch '79-add-annotation-to-downloaded-files' into 'master'

Resolve "Add annotation to downloaded files + file upload regression fix"

Closes #79

See merge request !35

portal/urls.py

@@ -21,7 +21,8 @@ from .views.secure.datafile import (AdminDataFileAnnotateView,
                                     ajax_batch_datafile_annotations_JSON,
                                     DataFileBatchRemoveAnnotation,
                                     DataFileBatchAddAnnotation,
-                                    DataFileUploadServletView)
+                                    DataFileUploadServletView,
+                                    DataFileAnnotationDownloadView)
 from .views.secure.dataset import (AdminDataSetCreateView,
                                    AdminDataSetDeleteView,
                                    AdminDataSetJSONListView,
@@ -74,6 +75,7 @@ urlpatterns = [
     path('secure/datafiles/annotate', DataFileAnnotateView.as_view(), name='user.datafile-annotate'),
     path('secure/datafiles/upload', DataFileUploadView.as_view(), name='user.datafile-upload'),
     path('secure/datafiles/download/<int:pk>', DataFileDownloadView.as_view(), name='user.datafile-download'),
+    path('secure/datafiles/download/annotation/<int:pk>', DataFileAnnotationDownloadView.as_view(), name='user.datafile-annotation-download'),
     path('secure/datafiles/delete/<int:pk>', DataFileDeleteView.as_view(), name='user.datafile-delete'),
     path('secure/datafiles/update/<int:pk>', DataFileUpdateView.as_view(), name='user.datafile-update'),
     path('secure/datafiles/annotations', ajax_batch_datafile_annotations_JSON, name='user.ajax_batch_datafile_annotations_JSON'),

portal/views/secure/datafile.py

 import logging
 import json
+import os
 
 from django.contrib.auth.mixins import LoginRequiredMixin
 from django.contrib.auth.decorators import login_required
@@ -7,7 +8,7 @@ from django.contrib import messages
 from django.contrib.messages import get_messages
 from django.db.models import Q, F
 from django.http import JsonResponse
-from django.http.response import HttpResponseRedirect
+from django.http.response import HttpResponseRedirect, HttpResponse
 from django.template import defaultfilters as filters
 from django.template.loader import render_to_string
 from django.urls import reverse, reverse_lazy
@@ -268,20 +269,9 @@ class DataFileUploadView(LoginRequiredMixin, ActivePageViewMixin, CreateView):
             uploaded_by=self.request.user.profile,
             file=self.request.FILES['file'])
 
-        if form.cleaned_data.get('annotations'):
-            file.annotations = form.cleaned_data['annotations']
-
-        if form.cleaned_data.get('lab'):
-            file.lab = form.cleaned_data['lab']
-
         file.save()
         return JsonResponse({'fid': file.id})
 
-    def get_form(self, form_class=None):
-        if form_class is None:
-            form_class = self.get_form_class()
-        return form_class(self.request, **self.get_form_kwargs())
-
     def form_invalid(self, form):
         # TODO move this to some form of logging and handle error return
         logger.debug(form)
@@ -306,7 +296,7 @@ class DataFileUploadServletView(LoginRequiredMixin, ActivePageViewMixin, CreateV
 
         if form.cleaned_data.get('lab'):
             file.lab = form.cleaned_data['lab']
-      
+
         file.save()
 
         dataset = form.cleaned_data.get('dataset')
@@ -339,6 +329,16 @@ class DataFileDownloadView(LoginRequiredMixin, PrivateStorageDetailView):
         )
 
 
+class DataFileAnnotationDownloadView(DataFileDownloadView):
+    model = DataFile
+
+    def get(self, request, pk):
+        df = self.get_object()
+        resp = HttpResponse(json.dumps(df.annotations), content_type="application/json")
+        resp['Content-Disposition'] = 'attachment; filename={}.annotation.json'.format(str(df.name)).encode("utf-8")
+        return resp
+
+
 class DataFileUpdateView(LoginRequiredMixin, UpdateViewMixin, UpdateView):
     model = DataFile
     form_class = DataFileForm

portal/views/secure/dataset.py

@@ -2,6 +2,7 @@ import logging
 import os
 import zipfile
 from io import BytesIO
+import json
 
 from django.db.models import Q
 from django.http import HttpResponse, HttpResponseForbidden, HttpResponseRedirect
@@ -88,19 +89,22 @@ class DataSetDownload(LoginRequiredMixin, SuccessMessageMixin, DetailView):
 
         # only allow download if user has access to dataset
         if DataSet.objects.accessible_to_profile(self.request.user.profile).filter(id=dataset.id).exists():
-            fpaths = [f.file.path for f in dataset.files.all()]
+            datafiles = dataset.files.all()
 
-            total_size = sum([os.path.getsize(fpath) for fpath in fpaths])
+            total_size = sum([df.file.size for df in datafiles])
             if total_size > 104857600:  # 100MB
-               messages.error(self.request, _("Cannot zip dataset. The total size of files contained in this dataset is larger than 100MB."))
-               return HttpResponseRedirect(request.META.get('HTTP_REFERER', '/'))
+                messages.error(self.request, _("Cannot zip dataset. The total size of files contained in this dataset is larger than 100MB."))
+                return HttpResponseRedirect(request.META.get('HTTP_REFERER', '/'))
 
             s = BytesIO()
             zf = zipfile.ZipFile(s, "w")
 
-            for fpath in fpaths:
-                fdir, fname = os.path.split(fpath)
-                zf.write(fpath, fname)
+            for df in datafiles:
+                fdir, fname = os.path.split(df.file.path)
+                zf.write(df.file.path, fname)
+
+                if df.annotations:
+                    zf.writestr(fname + ".annotation.json", json.dumps(df.annotations))
             zf.close()
 
             resp = HttpResponse(s.getvalue(), content_type="application/x-zip-compressed")
@@ -267,11 +271,11 @@ class DataSetFileListView(DataSetDetailsView):
 
     def get(self, request, *args, **kwargs):
         self.object = self.get_object()
-        return HttpResponse(
-            '\n'.join(
-                ['http://{0}{1}'.format(request.get_host(), reverse('user.datafile-download', args=[file.id])) for file in self.object.files.all()]),
-            content_type="text/plain"
-        )
+        files = ['http://{0}{1}'.format(request.get_host(), reverse('user.datafile-download', args=[file.id]))
+                 for file in self.object.files.all()]
+        annotations = ['http://{0}{1}'.format(request.get_host(), reverse('user.datafile-annotation-download', args=[file.id]))
+                       for file in self.object.files.filter(annotations__isnull=False).exclude(annotations__exact='').all()]
+        return HttpResponse('\n'.join(files + annotations), content_type="text/plain")
 
 
 class AdminDataSetJSONListView(StaffViewMixin, DataSetJSONListView):