Mccalluc/import into own space (#2061)

* Checkpoint

* Add a new field to the flat api response

* Get the url right, and renamed api attr for clarity

* Expose csrf on controller, and add it as an explicit field. Not the best idiom. TODO: After the POST we are directed to provenance

* Add linebreaks to url list

* reorder for grouping

* Rename names; more than is strictly necessary, but consistency is good

* Hide fields

* data_set -> provenance

* data_set2 -> data_set

* And rename the template

* Popover

* Only show button to logged-in user

* Help karma tests

* Another test tweak

* Vagrant tests pass locally

refinery/core/api.py

@@ -500,6 +500,7 @@ def dehydrate(self, bundle):
 
         if isa_archive:
             bundle.data["isa_archive"] = isa_archive.uuid
+            bundle.data["isa_archive_url"] = isa_archive.get_datafile_url()
 
         if pre_isa_archive:
             bundle.data["pre_isa_archive"] = pre_isa_archive.uuid

refinery/core/urls.py

@@ -21,55 +21,67 @@
     url(r'^collaboration/$', 'collaboration', name='collaboration'),
     url(r'^group_invite/(?P<token>' + UUID_RE + r')/$',
         'group_invite', name='group_invite'),
+
     url(r'^users/(?P<query>[\@\.\-\+a-z0-9]+)/$', 'user'),
     # "name" is required for use with the url tag in templates
     url(r'^users/(?P<query>' + UUID_RE + r')/$',
         'user', name="user"),
     url(r'^users/(?P<uuid>' + UUID_RE + r')/edit/$',
         'user_edit', name="user_edit"),
+
     url(r'^groups/(?P<query>' + UUID_RE + r')/$',
         'group', name="group"),
+
     url(r'^projects/(?P<uuid>' + UUID_RE + r')/$',
         'project', name="project"),
     url(r'^projects/new/$', 'project_new', name="project_new"),
     url(r'^projects/(?P<slug>[a-zA-Z0-9\_]+)/$',
         'project_slug', name="project_slug"),
     url(r'^projects/(?P<uuid>' + UUID_RE + r')/edit/$',
         'project_edit', name="project_edit"),
+
     url(r'^analyses/$', 'analyses', name="analyses"),
     url(r'^analyses/(?P<analysis_uuid>' + UUID_RE + r')/$',
         'analysis', name="analysis"),
-    url(r'^provenance/(?P<data_set_uuid>' + UUID_RE + r')/$',
-        'data_set', name="data_set"),
+
     url(r'^data_sets/(?P<data_set_uuid>' + UUID_RE + r')/$',
-        'data_set2', name="data_set2"),
+        'data_set', name="data_set"),
     url(r'^data_sets/(?P<slug>[a-zA-Z0-9\_]+)/$',
-        'data_set2_slug', name="data_set2_slug"),
+        'data_set_slug', name="data_set_slug"),
+
+    url(r'^provenance/(?P<data_set_uuid>' + UUID_RE + r')/$',
+        'provenance', name="provenance"),
     url(r'^provenance/(?P<data_set_uuid>' + UUID_RE + r')/'
         r'analysis/(?P<analysis_uuid>' + UUID_RE + r')/$',
-        'data_set', name="data_set_analysis"),
+        'provenance', name="provenance_analysis"),
     url(r'^provenance/(?P<slug>[a-zA-Z0-9\_]+)/$',
-        'data_set_slug', name="data_set_slug"),
+        'provenance_slug', name="provenance_slug"),
+
     url(r'^workflows/(?P<uuid>' + UUID_RE + r')/$',
         'workflow', name="workflow"),
     url(r'^workflows/(?P<uuid>' + UUID_RE + r')/edit/$',
         'workflow_edit', name="workflow_edit"),
     url(r'^workflows/(?P<slug>[a-zA-Z0-9\_]+)/$',
         'workflow_slug', name="workflow_slug"),
+
     url(r'^workflow_engines/(?P<uuid>' + UUID_RE + r')/$',
         'workflow_engine', name="workflow_engine"),
     url(r'^fastqc_viewer/$', 'fastqc_viewer', name='fastqc_viewer'),
     url(r'^visualize/genome/$', 'visualize_genome', name='visualize_genome'),
+
     url(r'^solr/igv/$', 'solr_igv'),
     url(r'^solr/core/select/$', 'solr_core_search', name="solr_core_search"),
     url(r'^solr/(?P<core>.+)/select/$', 'solr_select', name="solr_select"),
+
     url(r'^doi/(?P<id>.+)/', 'doi', name="doi"),
+
     url(r'^pubmed/abstract/(?P<id>.+)/',
         'pubmed_abstract', name="pubmed_abstract"),
     url(r'^pubmed/search/(?P<term>.+)/',
         'pubmed_search', name="pubmed_search"),
     url(r'^pubmed/summary/(?P<id>.+)/',
         'pubmed_summary', name="pubmed_summary"),
+
     url(r'^neo4j/annotations/$',
         'neo4j_dataset_annotations', name="neo4j_dataset_annotations"),
     url(r'^auto_login/$', 'auto_login', name='auto_login')

refinery/core/views.py

@@ -294,12 +294,12 @@ def project_edit(request, uuid):
                               context_instance=RequestContext(request))
 
 
-def data_set_slug(request, slug):
+def provenance_slug(request, slug):
     d = get_object_or_404(DataSet, slug=slug)
-    return data_set(request, d.uuid)
+    return provenance(request, d.uuid)
 
 
-def data_set(request, data_set_uuid, analysis_uuid=None):
+def provenance(request, data_set_uuid, analysis_uuid=None):
     data_set = get_object_or_404(DataSet, uuid=data_set_uuid)
     public_group = ExtendedGroup.objects.public_group()
 
@@ -364,12 +364,12 @@ def data_set(request, data_set_uuid, analysis_uuid=None):
         context_instance=RequestContext(request))
 
 
-def data_set2_slug(request, slug):
+def data_set_slug(request, slug):
     d = get_object_or_404(DataSet, slug=slug)
-    return data_set2(request, d.uuid)
+    return data_set(request, d.uuid)
 
 
-def data_set2(request, data_set_uuid, analysis_uuid=None):
+def data_set(request, data_set_uuid, analysis_uuid=None):
     data_set = get_object_or_404(DataSet, uuid=data_set_uuid)
     public_group = ExtendedGroup.objects.public_group()
 
@@ -416,7 +416,7 @@ def data_set2(request, data_set_uuid, analysis_uuid=None):
     except FileStoreItem.DoesNotExist:
         pass
     return render_to_response(
-        'core/data_set2.html',
+        'core/data_set.html',
         {
             "data_set": data_set,
             "analysis_uuid": analysis_uuid,