rename ENA Exporter -> Metadata Exporter

maxplanck-ie · Jun 11, 2018 · e8fc105 · e8fc105
1 parent 297be98
commit e8fc105
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Showing 22 changed files with 56 additions and 65 deletions.
diff --git a/ena_exporter/apps.py b/ena_exporter/apps.py
diff --git a/ena_exporter/__init__.py → metadata_exporter/__init__.py b/ena_exporter/__init__.py → metadata_exporter/__init__.py
diff --git a/metadata_exporter/apps.py b/metadata_exporter/apps.py
@@ -0,0 +1,5 @@
+from django.apps import AppConfig
+
+
+class MetadataExporterConfig(AppConfig):
+    name = 'metadata_exporter'
diff --git a/ena_exporter/serializers.py → metadata_exporter/serializers.py b/ena_exporter/serializers.py → metadata_exporter/serializers.py
@@ -87,7 +87,7 @@ def get_insert_size(self, obj):
             return None
 
 
-class ENASerializer(ModelSerializer):
+class MetadataSerializer(ModelSerializer):
     libraries = SampleSerializer(many=True)
     samples = SampleSerializer(many=True)
 
@@ -102,7 +102,6 @@ def to_representation(self, instance):
         if not any(data['libraries']) and not any(data['samples']):
             return []
 
-        # TODO: test this
         flowcell = instance.flowcell.only('sequencer__name').first()
         sequencer_name = flowcell.sequencer.name if flowcell else None
 

diff --git a/ena_exporter/tests.py → metadata_exporter/tests.py b/ena_exporter/tests.py → metadata_exporter/tests.py
diff --git a/ena_exporter/views.py → metadata_exporter/views.py b/ena_exporter/views.py → metadata_exporter/views.py
@@ -16,15 +16,15 @@
 from bioblend.galaxy import GalaxyInstance
 
 from common.views import CsrfExemptSessionAuthentication
-from .serializers import ENASerializer
+from .serializers import MetadataSerializer
 
 
 Request = apps.get_model('request', 'Request')
 Library = apps.get_model('library', 'Library')
 Sample = apps.get_model('sample', 'Sample')
 
 
-class ENAExporterViewSet(viewsets.ViewSet):
+class MetadataExporterViewSet(viewsets.ViewSet):
     def list(self, request):
         queryset = Request.objects.all().order_by('-create_time')
         if not request.user.is_staff:
@@ -83,7 +83,7 @@ def retrieve(self, request, pk=None):
             queryset = queryset.filter(user=request.user)
 
         req = get_object_or_404(queryset, pk=pk)
-        serializer = ENASerializer(req)
+        serializer = MetadataSerializer(req)
         data = serializer.data.get('result')
 
         data = sorted(data, key=lambda x: x['barcode'][3:])

diff --git a/static/main-hub/app/Application.js b/static/main-hub/app/Application.js
@@ -63,10 +63,10 @@ Ext.define('MainHub.Application', {
     'usage.LibraryTypes',
     'statistics.RunStatistics',
     'statistics.Sequences',
-    'enaexporter.Samples',
-    'enaexporter.StudyTypes',
-    'enaexporter.LibrarySources',
-    'enaexporter.LibrarySelections'
+    'metadataexporter.Samples',
+    'metadataexporter.StudyTypes',
+    'metadataexporter.LibrarySources',
+    'metadataexporter.LibrarySelections'
   ],
 
   requires: [

diff --git a/.../main-hub/app/model/enaexporter/Sample.js → ...-hub/app/model/metadataexporter/Sample.js b/.../main-hub/app/model/enaexporter/Sample.js → ...-hub/app/model/metadataexporter/Sample.js
@@ -1,4 +1,4 @@
-Ext.define('MainHub.model.enaexporter.Sample', {
+Ext.define('MainHub.model.metadataexporter.Sample', {
   extend: 'MainHub.model.Base',
 
   fields: [

diff --git a/...pp/store/enaexporter/LibrarySelections.js → ...ore/metadataexporter/LibrarySelections.js b/...pp/store/enaexporter/LibrarySelections.js → ...ore/metadataexporter/LibrarySelections.js
@@ -1,4 +1,4 @@
-Ext.define('MainHub.store.enaexporter.LibrarySelections', {
+Ext.define('MainHub.store.metadataexporter.LibrarySelections', {
   extend: 'Ext.data.Store',
   storeId: 'ENALibrarySelections',
 

diff --git a/...b/app/store/enaexporter/LibrarySources.js → .../store/metadataexporter/LibrarySources.js b/...b/app/store/enaexporter/LibrarySources.js → .../store/metadataexporter/LibrarySources.js
@@ -1,4 +1,4 @@
-Ext.define('MainHub.store.enaexporter.LibrarySources', {
+Ext.define('MainHub.store.metadataexporter.LibrarySources', {
   extend: 'Ext.data.Store',
   storeId: 'ENALibrarySources',
 

diff --git a/...main-hub/app/store/enaexporter/Samples.js → ...hub/app/store/metadataexporter/Samples.js b/...main-hub/app/store/enaexporter/Samples.js → ...hub/app/store/metadataexporter/Samples.js
@@ -1,12 +1,12 @@
-Ext.define('MainHub.store.enaexporter.Samples', {
+Ext.define('MainHub.store.metadataexporter.Samples', {
   extend: 'Ext.data.Store',
   storeId: 'ENASamples',
 
   requires: [
-    'MainHub.model.enaexporter.Sample'
+    'MainHub.model.metadataexporter.Sample'
   ],
 
-  model: 'MainHub.model.enaexporter.Sample',
+  model: 'MainHub.model.metadataexporter.Sample',
 
   proxy: {
     type: 'ajax',

diff --git a/...n-hub/app/store/enaexporter/StudyTypes.js → .../app/store/metadataexporter/StudyTypes.js b/...n-hub/app/store/enaexporter/StudyTypes.js → .../app/store/metadataexporter/StudyTypes.js
@@ -1,4 +1,4 @@
-Ext.define('MainHub.store.enaexporter.StudyTypes', {
+Ext.define('MainHub.store.metadataexporter.StudyTypes', {
   extend: 'Ext.data.Store',
   storeId: 'ENAStudyTypes',
 

diff --git a/static/main-hub/app/view/enaexporter/ENAExporterModel.js b/static/main-hub/app/view/enaexporter/ENAExporterModel.js
diff --git a/...n-hub/app/view/enaexporter/ENABaseGrid.js → ...view/metadataexporter/MetadataBaseGrid.js b/...n-hub/app/view/enaexporter/ENABaseGrid.js → ...view/metadataexporter/MetadataBaseGrid.js
@@ -1,6 +1,6 @@
-Ext.define('MainHub.view.enaexporter.ENABaseGrid', {
+Ext.define('MainHub.view.metadataexporter.MetadataBaseGrid', {
   extend: 'Ext.grid.Panel',
-  alias: 'widget.enabasegrid',
+  alias: 'widget.metadatabasegrid',
 
   sortableColumns: false,
   enableColumnMove: false,

diff --git a/...n-hub/app/view/enaexporter/ENAExporter.js → ...view/metadataexporter/MetadataExporter.js b/...n-hub/app/view/enaexporter/ENAExporter.js → ...view/metadataexporter/MetadataExporter.js
@@ -1,19 +1,19 @@
-Ext.define('MainHub.view.enaexporter.ENAExporter', {
+Ext.define('MainHub.view.metadataexporter.MetadataExporter', {
   extend: 'Ext.window.Window',
 
   requires: [
-    'MainHub.view.enaexporter.ENAExporterController',
-    'MainHub.view.enaexporter.ENAExporterModel',
-    'MainHub.view.enaexporter.ENABaseGrid',
-    'MainHub.view.enaexporter.Samples'
+    'MainHub.view.metadataexporter.MetadataExporterController',
+    'MainHub.view.metadataexporter.MetadataExporterModel',
+    'MainHub.view.metadataexporter.MetadataBaseGrid',
+    'MainHub.view.metadataexporter.Samples'
   ],
 
-  controller: 'enaexporter-enaexporter',
+  controller: 'metadataexporter-metadataexporter',
   viewModel: {
-    type: 'enaexporter-enaexporter'
+    type: 'metadataexporter-metadataexporter'
   },
 
-  title: 'ENA Exporter',
+  title: 'Metadata Exporter',
 
   height: 525,
   width: 700,
@@ -94,6 +94,7 @@ Ext.define('MainHub.view.enaexporter.ENAExporter', {
               fieldLabel: 'Galaxy URL',
               emptyText: 'Galaxy URL',
               enableKeyEvents: true,
+              allowBlank: true,
               regex: new RegExp(/^(https?:\/\/.*):?(\d*)\/?(.*)$/),
               regexText: 'Enter a valid Galaxy URL with a protocol.'
             },
@@ -102,6 +103,7 @@ Ext.define('MainHub.view.enaexporter.ENAExporter', {
               itemId: 'galaxy-api-key-input',
               fieldLabel: 'Galaxy API Key',
               emptyText: 'Galaxy API Key',
+              allowBlank: true,
               enableKeyEvents: true
             },
             {
@@ -140,7 +142,7 @@ Ext.define('MainHub.view.enaexporter.ENAExporter', {
         title: 'Samples',
         itemId: 'samples-tab',
         items: [{
-          xtype: 'ena-samples',
+          xtype: 'metadata-samples',
           itemId: 'samples-grid',
           store: 'ENASamples'
         }]

diff --git a/...view/enaexporter/ENAExporterController.js → ...ataexporter/MetadataExporterController.js b/...view/enaexporter/ENAExporterController.js → ...ataexporter/MetadataExporterController.js
@@ -1,6 +1,6 @@
-Ext.define('MainHub.view.enaexporter.ENAExporterController', {
+Ext.define('MainHub.view.metadataexporter.MetadataExporterController', {
   extend: 'Ext.app.ViewController',
-  alias: 'controller.enaexporter-enaexporter',
+  alias: 'controller.metadataexporter-metadataexporter',
 
   config: {
     control: {
@@ -11,9 +11,6 @@ Ext.define('MainHub.view.enaexporter.ENAExporterController', {
       '#galaxy-url-input, #galaxy-api-key-input': {
         keyup: 'saveToLocalStorage'
       },
-      '#tabs': {
-        // tabchange: 'tabChange'
-      },
       '#samples-grid': {
         headercontextmenu: 'showHeaderMenu'
       },
@@ -40,12 +37,6 @@ Ext.define('MainHub.view.enaexporter.ENAExporterController', {
     localStorage.setItem(fld.name, e.target.value);
   },
 
-  // tabChange: function (tp, newTab) {
-  //   tp.up('window').getViewModel().setData({
-  //     createButtonHidden: newTab.itemId === 'general-tab'
-  //   });
-  // },
-
   boxready: function (wnd) {
     var requestId = wnd.request.get('pk');
     var galaxyURLField = wnd.down('form').down('#galaxy-url-input');
@@ -67,7 +58,7 @@ Ext.define('MainHub.view.enaexporter.ENAExporterController', {
 
     // Load samples
     Ext.getStore('ENASamples').reload({
-      url: Ext.String.format('api/ena_exporter/{0}/', requestId)
+      url: Ext.String.format('api/metadata_exporter/{0}/', requestId)
     });
   },
 
@@ -163,7 +154,7 @@ Ext.define('MainHub.view.enaexporter.ENAExporterController', {
     }
 
     Ext.Ajax.request({
-      url: 'api/ena_exporter/get_galaxy_status/',
+      url: 'api/metadata_exporter/get_galaxy_status/',
       timeout: 5000, // 5 seconds
       params: {
         galaxy_url: galaxyURL,
@@ -257,7 +248,7 @@ Ext.define('MainHub.view.enaexporter.ENAExporterController', {
     if (action === 'download') {
       var downloadForm = Ext.create('Ext.form.Panel', { standardSubmit: true });
       downloadForm.submit({
-        url: Ext.String.format('api/ena_exporter/{0}/download/', requestId),
+        url: Ext.String.format('api/metadata_exporter/{0}/download/', requestId),
         params: params
       });
     } else {
@@ -274,7 +265,7 @@ Ext.define('MainHub.view.enaexporter.ENAExporterController', {
 
       wnd.setLoading('Uploading...');
       Ext.Ajax.request({
-        url: Ext.String.format('api/ena_exporter/{0}/{1}/', requestId, action),
+        url: Ext.String.format('api/metadata_exporter/{0}/upload/', requestId),
         params: params,
 
         success: function (response) {

diff --git a/static/main-hub/app/view/metadataexporter/MetadataExporterModel.js b/static/main-hub/app/view/metadataexporter/MetadataExporterModel.js
@@ -0,0 +1,8 @@
+Ext.define('MainHub.view.metadataexporter.MetadataExporterModel', {
+  extend: 'Ext.app.ViewModel',
+  alias: 'viewmodel.metadataexporter-metadataexporter',
+
+  data: {
+    galaxyStatus: 'offline'
+  }
+});
diff --git a/.../main-hub/app/view/enaexporter/Samples.js → ...-hub/app/view/metadataexporter/Samples.js b/.../main-hub/app/view/enaexporter/Samples.js → ...-hub/app/view/metadataexporter/Samples.js
@@ -1,6 +1,6 @@
-Ext.define('MainHub.view.enaexporter.Samples', {
-  extend: 'MainHub.view.enaexporter.ENABaseGrid',
-  alias: 'widget.ena-samples',
+Ext.define('MainHub.view.metadataexporter.Samples', {
+  extend: 'MainHub.view.metadataexporter.MetadataBaseGrid',
+  alias: 'widget.metadata-samples',
 
   border: 0,
 

diff --git a/static/main-hub/app/view/requests/Requests.js b/static/main-hub/app/view/requests/Requests.js
@@ -8,7 +8,7 @@ Ext.define('MainHub.view.requests.Requests', {
     'MainHub.view.requests.RequestWindow',
     'MainHub.view.requests.EmailWindow',
     'MainHub.view.libraries.LibraryWindow',
-    'MainHub.view.enaexporter.ENAExporter'
+    'MainHub.view.metadataexporter.MetadataExporter'
   ],
 
   controller: 'requests',

diff --git a/static/main-hub/app/view/requests/RequestsController.js b/static/main-hub/app/view/requests/RequestsController.js
@@ -104,10 +104,10 @@ Ext.define('MainHub.view.requests.RequestsController', {
         },
         '-',
         {
-          text: 'ENA Exporter',
+          text: 'Metadata Exporter',
           disabled: !record.get('completed'),
           handler: function () {
-            Ext.create('MainHub.view.enaexporter.ENAExporter', {
+            Ext.create('MainHub.view.metadataexporter.MetadataExporter', {
               request: record
             });
           }

diff --git a/wui/api.py b/wui/api.py
@@ -31,7 +31,7 @@
 )
 
 from stats.views import RunStatisticsViewSet, SequencesStatisticsViewSet
-from ena_exporter.views import ENAExporterViewSet
+from metadata_exporter.views import MetadataExporterViewSet
 
 
 router = routers.DefaultRouter()
@@ -73,4 +73,4 @@
 router.register(r'sequences_statistics', SequencesStatisticsViewSet, base_name='sequences-statistics')
 router.register(r'analysis_list', FlowcellAnalysisViewSet, base_name='analysis_list')
 
-router.register(r'ena_exporter', ENAExporterViewSet, base_name='ena_exporter')
+router.register(r'metadata_exporter', MetadataExporterViewSet, base_name='metadata_exporter')
diff --git a/wui/settings/base.py b/wui/settings/base.py
@@ -56,7 +56,7 @@
     'invoicing',
     'usage',
     'stats',
-    'ena_exporter'
+    'metadata_exporter'
 ]
 
 MIDDLEWARE_CLASSES = [