mark index types as obsolete

index_generator/views.py

@@ -20,17 +20,54 @@
     IndexGeneratorLibrarySerializer,
     IndexGeneratorSampleSerializer,
 )
+from library_sample_shared.serializers import IndexTypeSerializer
 from django.conf import settings
 
 Request = apps.get_model('request', 'Request')
 IndexI7 = apps.get_model('library_sample_shared', 'IndexI7')
 IndexI5 = apps.get_model('library_sample_shared', 'IndexI5')
 Library = apps.get_model('library', 'Library')
 Sample = apps.get_model('sample', 'Sample')
+IndexType = apps.get_model('library_sample_shared','IndexType')
 
 logger = logging.getLogger('db')
 
 
+class MoveOtherMixin:
+    """ Move the `Other` option to the end of the returning list. """
+
+    def list(self, request):
+        queryset = self.filter_queryset(self.get_queryset())
+
+        page = self.paginate_queryset(queryset)
+        if page is not None:
+            serializer = self.get_serializer(page, many=True)
+            return self.get_paginated_response(self._get_data(serializer))
+
+        serializer = self.get_serializer(queryset, many=True)
+        return Response(self._get_data(serializer))
+
+    def _get_data(self, serializer):
+        data = serializer.data
+
+        # Move the 'Other' option to the end of the list
+        other_options = sorted([
+            x for x in data if 'Other' in x['name']
+        ], key=lambda x: x['name'])
+
+        for other in other_options:
+            index = data.index(other)
+            data.append(data.pop(index))
+
+        return data
+
+class GeneratorIndexTypeViewSet(MoveOtherMixin, viewsets.ReadOnlyModelViewSet):
+    """ Get the list of index types. """
+    queryset = IndexType.objects.order_by('name')
+    serializer_class = IndexTypeSerializer
+
+
+
 class PoolSizeViewSet(viewsets.ReadOnlyModelViewSet):
     """ Get the list of pool sizes. """
     queryset = PoolSize.objects.all().filter(obsolete=settings.NON_OBSOLETE)

library_sample_shared/admin.py

@@ -64,8 +64,9 @@ def formfield_for_foreignkey(self, db_field, request, **kwargs):
 @admin.register(IndexType)
 class IndexTypeAdmin(admin.ModelAdmin):
     form = IndexTypeForm
-    list_display = ('name', 'index_length', 'is_dual', 'format',)
+    list_display = ('name', 'index_length', 'is_dual', 'format','obsolete_name')
     filter_horizontal = ('indices_i7', 'indices_i5',)
+    actions = ('mark_as_obsolete', 'mark_as_non_obsolete',)
 
     fieldsets = (
         (None, {
@@ -74,6 +75,19 @@ class IndexTypeAdmin(admin.ModelAdmin):
         }),
     )
 
+    def mark_as_obsolete(self,request,queryset):
+        queryset.update(obsolete=settings.OBSOLETE)
+    mark_as_obsolete.short_description = "Mark index type as obsolete"
+
+    def mark_as_non_obsolete(self,request,queryset):
+        queryset.update(obsolete=settings.NON_OBSOLETE)
+    mark_as_non_obsolete.short_description = "Mark index type as non-obsolete"
+
+    def obsolete_name(self,obj):
+
+        return "Non-obsolete" if obj.obsolete==settings.NON_OBSOLETE else "Obsolete"
+    obsolete_name.short_description = "STATUS"
+
     def change_view(self, request, object_id, form_url='', extra_context=None):
         # Display inline when the object has been saved and
         # the format has been set to 'plate'

library_sample_shared/models.py

@@ -125,6 +125,8 @@ class IndexType(models.Model):
         blank=True,
     )
 
+    obsolete = models.PositiveIntegerField("Obsolete", default=1)
+
     class Meta:
         verbose_name = 'Index Type'
         verbose_name_plural = 'Index Types'

library_sample_shared/views.py

@@ -85,7 +85,7 @@ class ConcentrationMethodViewSet(viewsets.ReadOnlyModelViewSet):
 
 class IndexTypeViewSet(MoveOtherMixin, viewsets.ReadOnlyModelViewSet):
     """ Get the list of index types. """
-    queryset = IndexType.objects.order_by('name')
+    queryset = IndexType.objects.filter(obsolete=settings.NON_OBSOLETE).order_by('name')
     serializer_class = IndexTypeSerializer
 
 

static/main-hub/app/Application.js

@@ -43,6 +43,7 @@ Ext.define('MainHub.Application', {
     'incominglibraries.IncomingLibraries',
     'indexgenerator.PoolSizes',
     'indexgenerator.StartCoordinates',
+    'indexgenerator.GeneratorIndexTypes',
     'requests.LibrariesInRequest',
     'indexgenerator.IndexGenerator',
     'librarypreparation.LibraryPreparation',

static/main-hub/app/store/indexgenerator/GeneratorIndexTypes.js

@@ -0,0 +1,27 @@
+Ext.define('MainHub.store.indexgenerator.GeneratorIndexTypes', {
+  extend: 'Ext.data.Store',
+  storeId: 'GeneratorIndexTypes',
+
+  requires: [
+    'MainHub.model.libraries.IndexType'
+  ],
+
+  model: 'MainHub.model.libraries.IndexType',
+
+  proxy: {
+    type: 'ajax',
+    url: 'api/generator_index_types/',
+    timeout: 1000000,
+    pageParam: false,   // to remove param "page"
+    startParam: false,  // to remove param "start"
+    limitParam: false,  // to remove param "limit"
+    noCache: false,     // to remove param "_dc",
+    reader: {
+      type: 'json',
+      rootProperty: 'data',
+      successProperty: 'success'
+    }
+  },
+
+  autoLoad: true
+});

static/main-hub/app/view/indexgenerator/IndexGenerator.js

@@ -122,12 +122,13 @@ Ext.define('MainHub.view.indexgenerator.IndexGenerator', {
               queryMode: 'local',
               displayField: 'name',
               valueField: 'id',
-              store: 'IndexTypes',
+              //store: 'IndexTypes',
+              store: 'GeneratorIndexTypes',
               matchFieldWidth: false,
               forceSelection: true
             },
             renderer: function (value, meta) {
-              var record = Ext.getStore('IndexTypes').findRecord(
+              var record = Ext.getStore('GeneratorIndexTypes').findRecord(
                 'id', value, 0, false, true, true
               );
               var val = '';

wui/api.py

@@ -15,7 +15,7 @@
 from library.views import LibrarySampleTree, LibraryViewSet
 from sample.views import NucleicAcidTypeViewSet, SampleViewSet
 from incoming_libraries.views import IncomingLibrariesViewSet
-from index_generator.views import PoolSizeViewSet, IndexGeneratorViewSet
+from index_generator.views import PoolSizeViewSet, IndexGeneratorViewSet,GeneratorIndexTypeViewSet
 from library_preparation.views import LibraryPreparationViewSet
 from pooling.views import PoolingViewSet
 from flowcell.views import (
@@ -43,6 +43,7 @@
 router.register(r'read_lengths', ReadLengthViewSet, base_name='read-length')
 router.register(r'concentration_methods', ConcentrationMethodViewSet, base_name='concentration-method')
 router.register(r'index_types', IndexTypeViewSet, base_name='index-type')
+router.register(r'generator_index_types', GeneratorIndexTypeViewSet, base_name='generator-index-type')
 router.register(r'indices', IndexViewSet, base_name='index')
 router.register(r'library_protocols', LibraryProtocolViewSet, base_name='library-protocol')
 router.register(r'library_protocols_invoicing', LibraryProtocolInvoicingViewSet, base_name='library-protocol-invoicing')