develop

conf/first_install_tables.json

@@ -20298,7 +20298,7 @@
     "pk": 3,
     "fields": {
         "label": "sample_name",
-        "ontology": "GENEPIO:0001123"
+        "ontology": "NCIT:C70663"
     }
 },
 {   "model": "core.ontologymap",

core/admin.py

@@ -77,7 +77,7 @@ class MoleculePreparationAdmin(admin.ModelAdmin):
         "extraction_type",
         "protocol_used",
         "molecule_extraction_date",
-        "molecule_used_for",
+        "sample_continues_on",
         "reused_number",
     )
     list_filter = ("generated_at",)

core/core_config.py

@@ -32,7 +32,7 @@
 
 # ## Heading values when showing pending samples at handling molecules
 HEADING_FOR_DEFINED_SAMPLES = [
-    "Sample extraction date",
+    "Sample defined date",
     "Sample Code ID",
     "Sample",
     "To be included",
@@ -75,7 +75,7 @@
 HEADING_FOR_SELECTING_MOLECULE_USE = [
     "Sample Name",
     "Extraction Code ID",
-    "Sample continue on",
+    "Sample continues on",
 ]
 
 # ################ PROTOCOL PARAMETER SETTINGS ##############################

core/models.py

@@ -1493,7 +1493,7 @@ class MoleculeUsedFor(models.Model):
     massive_use = models.BooleanField(default=False)
 
     class Meta:
-        db_table = "core_molecule_used_for"
+        db_table = "core_sample_continues_on"
 
     def __str__(self):
         return "%s" % (self.used_for)
@@ -1557,7 +1557,7 @@ class MoleculePreparation(models.Model):
         UserLotCommercialKits, on_delete=models.CASCADE, null=True, blank=True
     )
 
-    molecule_used_for = models.ForeignKey(
+    sample_continues_on = models.ForeignKey(
         MoleculeUsedFor, on_delete=models.CASCADE, null=True, blank=True
     )
 
@@ -1582,10 +1582,10 @@ def get_info_for_display(self):
         molecule_info.append(extraction_date)
         molecule_info.append(self.extraction_type)
         molecule_info.append(self.molecule_type.get_name())
-        if self.molecule_used_for is None:
+        if self.sample_continues_on is None:
             molecule_info.append("Not defined yet")
         else:
-            molecule_info.append(self.molecule_used_for.get_molecule_use_name())
+            molecule_info.append(self.sample_continues_on.get_molecule_use_name())
         molecule_info.append(self.protocol_used.get_name())
         molecule_info.append(self.reused_number)
         return molecule_info
@@ -1629,10 +1629,10 @@ def get_user_lot_kit_obj(self):
         return self.user_lot_kit_id
 
     def set_molecule_use(self, use_for_molecule, app_name):
-        self.molecule_used_for_obj = MoleculeUsedFor.objects.filter(
+        self.sample_continues_on_obj = MoleculeUsedFor.objects.filter(
             used_for__exact=use_for_molecule, apps_name__exact=app_name
         ).last()
-        self.used_for_massive_sequencing = self.molecule_used_for_obj.get_massive()
+        self.used_for_massive_sequencing = self.sample_continues_on_obj.get_massive()
         self.save()
         return self
 

core/utils/samples.py

@@ -706,7 +706,7 @@ def create_table_molecule_pending_use(sample_list, app_name):
     use_type = {}
     use_type["data"] = list(
         core.models.MoleculePreparation.objects.filter(
-            molecule_used_for=None,
+            sample_continues_on=None,
             sample__in=sample_list,
             state__molecule_state_name="assigned_parameters",
         ).values_list("sample__sample_name", "molecule_code_id", "pk")
@@ -1532,9 +1532,10 @@ def get_selection_from_excel_data(data, heading, check_field, field_id):
     excel_data = json.loads(data)
     # Convert excel list-list to dictionary with field_names
     excel_json_data = core.utils.common.jspreadsheet_to_dict(heading, excel_data)
+
     for row in excel_json_data:
         if check_field is not None:
-            if row[check_field] is True:
+            if row[check_field] is not False and row[check_field] != "":
                 selected.append(row[field_id])
                 selected_row.append(row)
         else:
@@ -2085,7 +2086,7 @@ def set_molecule_use(molecule_use_data, app_name):
     }
     for molecule in molecule_use_data:
         molecule_obj = get_molecule_obj_from_id(molecule["m_id"])
-        molecule_obj.set_molecule_use(molecule["Molecule use for"], app_name)
+        molecule_obj.set_molecule_use(molecule["Sample continues on"], app_name)
         sample_obj = molecule_obj.get_sample_obj()
         if molecule_obj.get_used_for_massive():
             sample_obj.set_state("Library preparation")
@@ -2095,7 +2096,7 @@ def set_molecule_use(molecule_use_data, app_name):
             [
                 molecule["Sample Name"],
                 molecule["Extraction Code ID"],
-                molecule["Molecule use for"],
+                molecule["Sample continues on"],
             ]
         )
     return molecule_update