Obsolete libraries not showing in invoicing, bug fix

invoicing/serializers.py

@@ -147,9 +147,7 @@ def get_percentage(self, obj):
                     library_ids.append(library.pk)
                 for sample in samples:
                     sample_ids.append(sample.pk)
-                for library in libraries:
-                    print("Library---------------")
-                    pprint(vars(library))
+
                 depth = sum(libraries.values_list(
                     'sequencing_depth', flat=True)) + \
                     sum(samples.values_list('sequencing_depth', flat=True))
@@ -182,8 +180,9 @@ def get_num_libraries_samples(self, obj):
 
         num_samples = obj.samples.count()
         if num_libraries > 0:
-            print(num_libraries)
 
+
+
             libcount = 0
             flowcells = self.get_percentage(obj)
             maxYear = max([d['flowcell_create_year'] for d in flowcells])
@@ -194,6 +193,8 @@ def get_num_libraries_samples(self, obj):
                         libcount = libcount + len(pool['libraries'])
 
             return f'{libcount} libraries'
+
+
         else:
             sampcount = 0
             flowcells = self.get_percentage(obj)
@@ -207,6 +208,7 @@ def get_num_libraries_samples(self, obj):
 
     def get_library_protocol(self, obj):
         protocols = set([x.library_protocol.pk for x in obj.records])
+
         return protocols.pop() if protocols else ''
 
     def get_fixed_costs(self, obj):

invoicing/views.py

@@ -30,7 +30,7 @@
     LibraryPreparationCostsSerializer,
     SequencingCostsSerializer,
 )
-
+from django.db import transaction
 Request = apps.get_model('request', 'Request')
 ReadLength = apps.get_model('library_sample_shared', 'ReadLength')
 LibraryProtocol = apps.get_model('library_sample_shared', 'LibraryProtocol')
@@ -39,6 +39,9 @@
 Flowcell = apps.get_model('flowcell', 'Flowcell')
 
 
+
+
+
 class InvoicingViewSet(viewsets.ReadOnlyModelViewSet):
     permission_classes = [IsAdminUser]
     serializer_class = InvoicingSerializer
@@ -57,7 +60,6 @@ def get_queryset(self):
         ).select_related(
             'read_length', 'library_protocol',
         ).only('read_length', 'library_protocol__name')
-
         samples_qs = Sample.objects.filter(
             ~Q(pool=None) & ~Q(status=-1)
         ).select_related(
@@ -81,8 +83,18 @@ def get_queryset(self):
             'cost_unit__name',
         ).order_by('sequencing_date', 'pk')
 
+
+
         return queryset
 
+
+    def list(self,request):
+        queryset = self.filter_queryset(self.get_queryset())
+        serializer = self.get_serializer(queryset, many=True)
+
+        return Response(serializer.data)
+
+
     @action(methods=['get'], detail=False)
     def billing_periods(self, request):
         flowcells = Flowcell.objects.all()
@@ -276,10 +288,20 @@ class FixedCostsViewSet(mixins.UpdateModelMixin,
 class LibraryPreparationCostsViewSet(mixins.UpdateModelMixin,
                                      viewsets.ReadOnlyModelViewSet):
     """ Get the list of Library Preparation Costs. """
+    obsolete_protocols = LibraryProtocol.objects.filter(obsolete=settings.OBSOLETE).values_list('id', flat=True)
+    lst = list(obsolete_protocols)
+    with transaction.atomic():
+        for id in obsolete_protocols:
+            LibraryProtocol.objects.filter(id=id).update(obsolete=settings.NON_OBSOLETE)
     permission_classes = [IsAdminUser]
     queryset = LibraryPreparationCosts.objects.all()
+    print(queryset.query)
+
     serializer_class = LibraryPreparationCostsSerializer
 
+    with transaction.atomic():
+        for id in obsolete_protocols:
+           LibraryProtocol.objects.filter(id=id).update(obsolete=settings.OBSOLETE)
 
 class SequencingCostsViewSet(mixins.UpdateModelMixin,
                              viewsets.ReadOnlyModelViewSet):

library_preparation/views.py

@@ -88,6 +88,8 @@ def list(self, request):
         data = sorted(serializer.data, key=lambda x: x['barcode'][3:])
         return Response(data)
 
+
+
     @action(methods=['post'], detail=False,
             authentication_classes=[CsrfExemptSessionAuthentication])
     # @authentication_classes((CsrfExemptSessionAuthentication))

library_sample_shared/admin.py

@@ -121,23 +121,23 @@ def idx_id(sef, obj):
 @admin.register(LibraryProtocol)
 class LibraryProtocolAdmin(admin.ModelAdmin):
     list_display = ('name', 'type', 'provider', 'catalog',
-                    'typical_application','status_name',)
+                    'typical_application','obsolete_name',)
     search_fields = ('name', 'provider', 'catalog', 'typical_application',)
     list_filter = ('type',)
     actions = ('mark_as_obsolete','mark_as_non_obsolete',)
 
     def mark_as_obsolete(self,request,queryset):
-        queryset.update(status=settings.OBSOLETE)
+        queryset.update(obsolete=settings.OBSOLETE)
     mark_as_obsolete.short_description = "Mark library protocol as obsolete"
 
     def mark_as_non_obsolete(self,request,queryset):
-        queryset.update(status=settings.NON_OBSOLETE)
+        queryset.update(obsolete=settings.NON_OBSOLETE)
     mark_as_non_obsolete.short_description = "Mark library protocol as non-obsolete"
 
-    def status_name(self,obj):
+    def obsolete_name(self,obj):
 
-        return "Non-obsolete" if obj.status==settings.NON_OBSOLETE else "Obsolete"
-    status_name.short_description = "STATUS"
+        return "Non-obsolete" if obj.obsolete==settings.NON_OBSOLETE else "Obsolete"
+    obsolete_name.short_description = "STATUS"
 
 
 

library_sample_shared/models.py

@@ -205,6 +205,7 @@ class LibraryProtocol(models.Model):
 
     status = models.PositiveIntegerField("Status", default=1)
     comments = models.TextField('Comments', null=True, blank=True)
+    obsolete = models.PositiveIntegerField("Obsolete", default=1)
 
     class Meta:
         verbose_name = 'Library Protocol'

library_sample_shared/views.py

@@ -138,9 +138,20 @@ def get_queryset(self):
         na_type = self.request.query_params.get('type', None)
         if na_type is not None:
             queryset = queryset.filter(type=na_type)
-        queryset = queryset.filter(status=settings.NON_OBSOLETE)
+        queryset = queryset.filter(obsolete=settings.NON_OBSOLETE)
         return queryset
 
+class LibraryProtocolInvoicingViewSet(MoveOtherMixin, viewsets.ReadOnlyModelViewSet):
+    """ Get the list of library protocols for invoicing. """
+    serializer_class = LibraryProtocolSerializer
+
+    def get_queryset(self):
+        queryset = LibraryProtocol.objects.order_by('name')
+        na_type = self.request.query_params.get('type', None)
+        if na_type is not None:
+            queryset = queryset.filter(type=na_type)
+
+        return queryset
 
 class LibraryTypeViewSet(MoveOtherMixin, viewsets.ReadOnlyModelViewSet):
     """ Get the list of library types. """

pooling/views.py

@@ -36,7 +36,7 @@
 logger = logging.getLogger('db')
 
 
-class PoolingViewSet(LibrarySampleMultiEditMixin, viewsets.ViewSet):
+class PoolingViewSet(LibrarySampleMultiEditMixin, viewsets.ModelViewSet):
     permission_classes = [IsAdminUser]
     library_model = Library
     sample_model = Sample
@@ -183,6 +183,17 @@ def list(self, request):
         data = sorted(data, key=lambda x: x['barcode'][3:])
         return Response(data)
 
+    @action(methods=['post'], detail=True)
+    def edit_comment(self, request, pk=None):
+
+        instance = Pool.objects.filter(pk=pk)
+
+        post_data = self._get_post_data(request)
+        newComment = post_data['newComment']
+
+        instance.update(comment=newComment)
+        return Response({'success': True})
+
     @action(methods=['post'], detail=False,
             authentication_classes=[CsrfExemptSessionAuthentication])
     def download_benchtop_protocol(self, request):
@@ -467,3 +478,13 @@ def download_pooling_template(self, request):
 
         wb.save(response)
         return response
+
+    def _get_post_data(self, request):
+        post_data = {}
+        if request.is_ajax():
+            post_data = request.data.get('data', {})
+            if isinstance(post_data, str):
+                post_data = json.loads(post_data)
+        else:
+            post_data = json.loads(request.data.get('data', '{}'))
+        return post_data

request/serializers.py

@@ -50,7 +50,7 @@ def get_restrict_permissions(self, obj):
 
     def get_completed(self, obj):
         """ Return True if request's libraries and samples are sequenced. """
-        return obj.statuses.count(5) > 0
+        return obj.statuses.count(6) > 0
 
     def get_deep_seq_request_name(self, obj):
         return obj.deep_seq_request.name.split('/')[-1] \

request/views.py

@@ -167,7 +167,7 @@ def get_queryset(self,showAll=False):
             Prefetch('samples', queryset=samples_qs),
             'files',
         ).order_by('-create_time')
-        print(queryset.values())
+
         if not showAll:
             queryset = queryset.filter(sequenced=False)
         if self.request.user.is_staff:
@@ -188,7 +188,7 @@ def get_queryset(self,showAll=False):
 
     def list(self, request):
         """ Get the list of requests. """
-        print(request.GET)
+
         showAll = False
         if request.GET.get('showAll') == 'True':
             showAll = True
@@ -253,11 +253,10 @@ def mark_as_complete(self,request,pk=None):
         instance = Request.objects.filter(pk=pk)
 
 
-        print(pk)
+
         post_data = self._get_post_data(request)
         override = post_data['override']
-        print(post_data['override'])
-        print(override)
+
         if post_data['override'] == 'False':
             override = False
         else:
@@ -280,7 +279,7 @@ def checkifcomplete(element):
             #print(instance.statuses)
             #check if all libraries/samples related to this requested have been sequenced
             statuses = [status for x in instance for status  in x.statuses]
-            print(statuses)
+
             complete = all([checkifcomplete(x) for x in statuses])
 
             if complete:

static/main-hub/app/Application.js

@@ -57,6 +57,7 @@ Ext.define('MainHub.Application', {
     'invoicing.FixedCosts',
     'invoicing.LibraryPreparationCosts',
     'invoicing.SequencingCosts',
+    'invoicing.LibraryProtocolsInvoicing',
     'usage.Records',
     'usage.Organizations',
     'usage.PrincipalInvestigators',

static/main-hub/app/store/invoicing/LibraryProtocolsInvoicing.js

@@ -0,0 +1,27 @@
+Ext.define('MainHub.store.invoicing.LibraryProtocolsInvoicing', {
+    extend: 'Ext.data.Store',
+    storeId: 'libraryprotocolinvoicingStore',
+
+    requires: [
+        'MainHub.model.libraries.LibraryProtocol'
+    ],
+
+    model: 'MainHub.model.libraries.LibraryProtocol',
+
+    proxy: {
+        type: 'ajax',
+        url: 'api/library_protocols_invoicing/',
+        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/invoicing/InvoicingController.js

@@ -189,7 +189,7 @@ Ext.define('MainHub.view.invoicing.InvoicingController', {
   },
 
   libraryProtocolRenderer: function (value, meta) {
-    var record = Ext.getStore('libraryProtocolsStore').findRecord(
+    var record = Ext.getStore('libraryprotocolinvoicingStore').findRecord(
       'id', value, 0, false, true, true);
     var name = record.get('name');
     meta.tdAttr = Ext.String.format('data-qtip="{0}"', name);

static/main-hub/app/view/requests/Requests.js

@@ -40,7 +40,7 @@ Ext.define('MainHub.view.requests.Requests', {
 
        margin: '0 15 0 0',
        cls: 'grid-header-checkbox',
-       hidden: !USER.is_staff,
+       hidden: false,
        listeners:{
         change: function(checkbox, newValue, oldValue, eOpts) {
 

wui/api.py

@@ -10,6 +10,7 @@
     LibraryTypeViewSet,
     ReadLengthViewSet,
     ConcentrationMethodViewSet,
+    LibraryProtocolInvoicingViewSet
 )
 from library.views import LibrarySampleTree, LibraryViewSet
 from sample.views import NucleicAcidTypeViewSet, SampleViewSet
@@ -44,6 +45,7 @@
 router.register(r'index_types', IndexTypeViewSet, base_name='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')
 router.register(r'library_types', LibraryTypeViewSet, base_name='library-type')
 router.register(r'nucleic_acid_types', NucleicAcidTypeViewSet, base_name='nucleic-acid-type')
 router.register(r'pool_sizes', PoolSizeViewSet, base_name='pool-size')