Mccalluc/data sets to plain data sets

refinery/core/forms.py

@@ -10,7 +10,7 @@
 
 from registration.forms import RegistrationForm, RegistrationFormUniqueEmail
 
-from .models import DataSet, Project, UserProfile, Workflow
+from .models import Project, UserProfile, Workflow
 
 
 class ProjectForm(ModelForm):
@@ -78,9 +78,3 @@ class WorkflowForm(ModelForm):
     class Meta:
         model = Workflow
         fields = ["name", "slug", "summary", "description", "is_active"]
-
-
-class DataSetForm(ModelForm):
-    class Meta:
-        model = DataSet
-        fields = ["summary", "description", "slug"]

refinery/core/models.py

@@ -1518,7 +1518,7 @@ def send_email(self):
             # TODO: avoid hardcoding URL protocol
             context_dict['url'] = urljoin(
                 "http://" + site_domain,
-                "data_sets2/{}/#/files/?{}".format(
+                "data_sets/{}/#/files/?{}".format(
                     data_set_uuid,
                     self.data_sets_query()
                 )

refinery/core/urls.py

@@ -39,18 +39,16 @@
     url(r'^analyses/$', 'analyses', name="analyses"),
     url(r'^analyses/(?P<analysis_uuid>' + UUID_RE + r')/$',
         'analysis', name="analysis"),
-    url(r'^data_sets_old/(?P<data_set_uuid>' + UUID_RE + r')/$',
+    url(r'^provenance/(?P<data_set_uuid>' + UUID_RE + r')/$',
         'data_set', name="data_set"),
-    url(r'^data_sets2/(?P<data_set_uuid>' + UUID_RE + r')/$',
+    url(r'^data_sets/(?P<data_set_uuid>' + UUID_RE + r')/$',
         'data_set2', name="data_set2"),
-    url(r'^data_sets2/(?P<slug>[a-zA-Z0-9\_]+)/$',
+    url(r'^data_sets/(?P<slug>[a-zA-Z0-9\_]+)/$',
         'data_set2_slug', name="data_set2_slug"),
-    url(r'^data_sets_old/(?P<data_set_uuid>' + UUID_RE + r')/'
+    url(r'^provenance/(?P<data_set_uuid>' + UUID_RE + r')/'
         r'analysis/(?P<analysis_uuid>' + UUID_RE + r')/$',
         'data_set', name="data_set_analysis"),
-    url(r'^data_sets_old/(?P<uuid>' + UUID_RE + r')/edit/$',
-        'data_set_edit', name="data_set_edit"),
-    url(r'^data_sets_old/(?P<slug>[a-zA-Z0-9\_]+)/$',
+    url(r'^provenance/(?P<slug>[a-zA-Z0-9\_]+)/$',
         'data_set_slug', name="data_set_slug"),
     url(r'^workflows/(?P<uuid>' + UUID_RE + r')/$',
         'workflow', name="workflow"),

refinery/core/views.py

@@ -42,8 +42,7 @@
 from file_store.models import FileStoreItem
 from visualization_manager.views import igv_multi_species
 
-from .forms import (DataSetForm, ProjectForm, UserForm, UserProfileForm,
-                    WorkflowForm)
+from .forms import ProjectForm, UserForm, UserProfileForm, WorkflowForm
 from .models import (Analysis, CustomRegistrationProfile, DataSet,
                      ExtendedGroup, Invitation, Ontology, Project, UserProfile,
                      Workflow, WorkflowEngine)
@@ -435,69 +434,6 @@ def data_set2(request, data_set_uuid, analysis_uuid=None):
         context_instance=RequestContext(request))
 
 
-def data_set_edit(request, uuid):
-    data_set = get_object_or_404(DataSet, uuid=uuid)
-
-    if not request.user.has_perm('core.change_dataset', data_set):
-        if request.user.is_authenticated():
-            return HttpResponseForbidden(
-                custom_error_page(request, '403.html',
-                                  {user: request.user,
-                                   'msg': "edit this data set"})
-            )
-        else:
-            return HttpResponse(
-                custom_error_page(request, '401.html',
-                                  {'msg': "edit this data set"}),
-                status='401'
-            )
-    # get studies
-    investigation = data_set.get_investigation()
-    studies = investigation.study_set.all()
-    study_uuid = studies[0].uuid
-    assay_uuid = studies[0].assay_set.all()[0].uuid
-    # TODO: catch errors
-    isatab_archive = None
-    pre_isatab_archive = None
-
-    try:
-        if investigation.isarchive_file is not None:
-            isatab_archive = FileStoreItem.objects.get(
-                uuid=investigation.isarchive_file
-            )
-    except FileStoreItem.DoesNotExist:
-        pass
-    try:
-        if investigation.pre_isarchive_file is not None:
-            pre_isatab_archive = FileStoreItem.objects.get(
-                uuid=investigation.pre_isarchive_file)
-    except FileStoreItem.DoesNotExist:
-        pass
-
-    if request.method == "POST":  # If the form has been submitted
-        # A form bound to the POST data
-        form = DataSetForm(data=request.POST, instance=data_set)
-        if form.is_valid():  # All validation rules pass
-            form.save()
-            # Process the data in form.cleaned_data
-            # Redirect after POST
-            return HttpResponseRedirect(
-                reverse('core.views.data_set', args=(uuid,)))
-    else:
-        form = DataSetForm(instance=data_set)  # An unbound form
-    return render_to_response('core/data_set_edit.html',
-                              {
-                                  'data_set': data_set,
-                                  "studies": studies,
-                                  "study_uuid": study_uuid,
-                                  "assay_uuid": assay_uuid,
-                                  "isatab_archive": isatab_archive,
-                                  "pre_isatab_archive": pre_isatab_archive,
-                                  'form': form
-                              },
-                              context_instance=RequestContext(request))
-
-
 def workflow_slug(request, slug):
     w = get_object_or_404(Workflow, slug=slug)
     return workflow(request, w.uuid)

refinery/static/source/js/refinery/contents.js

@@ -45,7 +45,7 @@
     var showAnnotation = false;
 
     // To avoid generation when in the data set 2 browser
-    if (window.location.href.indexOf('data_sets2') === -1) {
+    if (window.location.href.indexOf('data_sets') === -1) {
       configurator.initialize(function () {
         query = new SolrQuery(configurator, queryCommands);
         query.initialize();

refinery/static/source/js/refinery/solr/solr_document_table.js

@@ -107,7 +107,7 @@ SolrDocumentTable.prototype.render = function(solrResponse) {
     .trigger('refinery/solrTable/destroy')
     .html("");
    // Required while data set 2 lives in parallel.
-  if (window.location.href.indexOf('data_sets2') === -1) {
+  if (window.location.href.indexOf('data_sets') === -1) {
     self._renderTable(solrResponse);
     //$( "#" + self._parentElementId ).html( code );
     // attach event listeners

refinery/tool_manager/models.py

@@ -728,7 +728,7 @@ def launch(self):
 
         return JsonResponse(
             {
-                Tool.TOOL_URL: "/data_sets2/{}/#/analyses/".format(
+                Tool.TOOL_URL: "/data_sets/{}/#/analyses/".format(
                     self.dataset.uuid
                 )
             }

refinery/tool_manager/tests.py

@@ -1552,7 +1552,7 @@ def test_workflow_tool_launch_valid_workflow_object(self):
         self.assertEqual(self.tool.get_tool_type(), ToolDefinition.WORKFLOW)
         self.assertEqual(
             json.loads(self.post_response.content)[Tool.TOOL_URL],
-            '/data_sets2/{}/#/analyses/'.format(self.tool.dataset.uuid)
+            '/data_sets/{}/#/analyses/'.format(self.tool.dataset.uuid)
         )
 
     def test_many_tools_can_be_launched_from_same_dataset(self):

refinery/ui/source/js/analysis-monitor/directives/analyses-list.js

@@ -19,7 +19,7 @@ function analysisMonitorAnalysesList ($location, $window) {
         galaxyExport: 'Downloading analysis results from Galaxy'
       };
 
-      if ($location.absUrl().indexOf('data_sets2') > -1) {
+      if ($location.absUrl().indexOf('data_sets') > -1) {
         scope.AMCtrl.updateAnalysesList();
       } else {
         scope.$on('refinery/analyze-tab-active', function () {

refinery/ui/source/js/analysis-monitor/partials/analyses-list.html

@@ -97,7 +97,7 @@
           <div class="col-md-5 analysis-name">
             <span ng-switch on="analysis.status">
               <span ng-switch-when="SUCCESS">
-                <a ng-href="/data_sets2/{{analysis.data_set__uuid}}/#/files/?{{analysis.data_sets_query}}">
+                <a ng-href="/data_sets/{{analysis.data_set__uuid}}/#/files/?{{analysis.data_sets_query}}">
                   {{ analysis.name }}
                 </a>
               </span>

refinery/ui/source/js/analysis-monitor/partials/global-list-status-popover.html

@@ -39,7 +39,7 @@
                  
             </div>
             <div class="analyses-global-text">
-              <a id="analyses-popover-links" ng-href="/data_sets2/{{analysis.data_set__uuid}}/#/analyses/">
+              <a id="analyses-popover-links" ng-href="/data_sets/{{analysis.data_set__uuid}}/#/analyses/">
                 {{ analysis.name }}
               </a>
             </div>
@@ -55,12 +55,12 @@
             </div>
             <div class="analyses-global-text">
               <span ng-if="analysis.status === 'SUCCESS'">
-                <a id="analyses-popover-links" ng-href="/data_sets2/{{analysis.data_set__uuid}}/#/files/?{{analysis.data_sets_query}}">
+                <a id="analyses-popover-links" ng-href="/data_sets/{{analysis.data_set__uuid}}/#/files/?{{analysis.data_sets_query}}">
                   {{ analysis.name }}
                 </a>
               </span>
               <span ng-if="analysis.status !== 'SUCCESS'">
-                <a id="analyses-popover-links" ng-href="/data_sets2/{{ analysis.data_set__uuid }}/#/analyses/">
+                <a id="analyses-popover-links" ng-href="/data_sets/{{ analysis.data_set__uuid }}/#/analyses/">
                   {{ analysis.name }}
                 </a>
               </span>

refinery/ui/source/js/commons/router/settings-location-test.spec.js

@@ -27,7 +27,7 @@ describe('Constant: LocationTest', function () {
 
     expect(
       locationTest('www.refinery.com/datasets/',
-        'http://192.168.50.50:8000/data_sets_old/' +
+        'http://192.168.50.50:8000/provenance/' +
         '88d03196-0d41-42c7-9f16-4cf03657db07/#/' +
         'files/browse', 'true')
     ).toBe(false);
@@ -43,14 +43,14 @@ describe('Constant: LocationTest', function () {
     ).toBe(false);
 
     expect(
-      locationTest('http://192.168.50.50:8000/data_sets_old/' +
+      locationTest('http://192.168.50.50:8000/provenance/' +
         '88d03196-0d41-42c7-9f16-4cf03657db07/#/' +
         'files/browse', 'www.refinery.com/dataset/', 'false')
     ).toBe(false);
 
     expect(
       locationTest('www.refinery.com/dataset/',
-        'http://192.168.50.50:8000/data_sets_old/' +
+        'http://192.168.50.50:8000/provenance/' +
         '88d03196-0d41-42c7-9f16-4cf03657db07/#/' +
         'files/browse', 'true')
     ).toBe(false);

refinery/ui/source/js/commons/router/state.js

@@ -44,7 +44,7 @@ function RefineryStateProvider ($window, $stateProvider, _, locationTest) {
  * this:
  * http://sub.domain.tld:port/users/#/edit
  * http://sub.domain.tld:port/groups/#/edit
- * http://sub.domain.tld:port/data_sets_old//#/edit
+ * http://sub.domain.tld:port/provenance//#/edit
  *
  * <pre>
  * var app = angular.module('app', ['refineryRouter']);
@@ -88,7 +88,7 @@ function RefineryStateProvider ($window, $stateProvider, _, locationTest) {
  *        templateUrl: '/static/partials/group/edit.html',
  *        controller: 'DataSetsCtrl as dataSets'
  *      },
- *      '^\/data_sets_old\/.*\/$', true);
+ *      '^\/provenance\/.*\/$', true);
  * });
  * </pre>
  *