Created Sample verification before import.

src/submissions/backend/db/models/submissions.py

@@ -714,7 +714,6 @@ class BasicSubmission(BaseClass, LogMixin):
         # logger.debug(f"Returning regex: {regex}")
         return regex
 
-
     # NOTE: Polymorphic functions
 
     @classproperty
@@ -1130,13 +1129,13 @@ class BasicSubmission(BaseClass, LogMixin):
                 case date():
                     pass
                 case datetime():
-                    end_date = end_date# + timedelta(days=1)
+                    end_date = end_date  # + timedelta(days=1)
                     # pass
                 case int():
-                    end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date()# \
-                               # + timedelta(days=1)
+                    end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date()  # \
+                    # + timedelta(days=1)
                 case _:
-                    end_date = parse(end_date).date()# + timedelta(days=1)
+                    end_date = parse(end_date).date()  # + timedelta(days=1)
             # end_date = end_date.strftime("%Y-%m-%d")
             start_date = datetime.combine(start_date, datetime.min.time()).strftime("%Y-%m-%d %H:%M:%S.%f")
             end_date = datetime.combine(end_date, datetime.max.time()).strftime("%Y-%m-%d %H:%M:%S.%f")
@@ -1224,10 +1223,11 @@ class BasicSubmission(BaseClass, LogMixin):
         else:
             from frontend.widgets.pop_ups import QuestionAsker
             logger.warning(f"Found existing instance: {instance}, asking to overwrite.")
-        #     code = 1
-        #     msg = "This submission already exists.\nWould you like to overwrite?"
-        # report.add_result(Result(msg=msg, code=code))
-            dlg = QuestionAsker(title="Overwrite?", message="This submission already exists.\nWould you like to overwrite?")
+            #     code = 1
+            #     msg = "This submission already exists.\nWould you like to overwrite?"
+            # report.add_result(Result(msg=msg, code=code))
+            dlg = QuestionAsker(title="Overwrite?",
+                                message="This submission already exists.\nWould you like to overwrite?")
             if dlg.exec():
                 pass
             else:
@@ -1529,10 +1529,23 @@ class BacterialCulture(BasicSubmission):
         main_sheet = xl[lookup_table['sheet']]
         for row in main_sheet.iter_rows(min_row=lookup_table['start_row'], max_row=lookup_table['end_row']):
             idx = row[0].row
-            sample = dict(submitter_id=main_sheet.cell(row=idx, column=lookup_table['sample_columns']['submitter_id']).value)
-            sample['concentration'] = main_sheet.cell(row=idx, column=lookup_table['sample_columns']['concentration']).value
+            sample = dict(
+                submitter_id=main_sheet.cell(row=idx, column=lookup_table['sample_columns']['submitter_id']).value)
+            sample['concentration'] = main_sheet.cell(row=idx,
+                                                      column=lookup_table['sample_columns']['concentration']).value
             yield sample
 
+    def get_provisional_controls(self):
+        if self.controls:
+            provs = (control.sample for control in self.controls)
+        else:
+            regex = re.compile(r"^(ATCC)|(MCS)|(EN)")
+            provs = (sample for sample in self.samples if bool(regex.match(sample.submitter_id)))
+        for prov in provs:
+            prov.submission = self.rsl_plate_num
+            prov.submitted_date = self.submitted_date
+            yield prov
+
 
 class Wastewater(BasicSubmission):
     """
@@ -1827,7 +1840,7 @@ class WastewaterArtic(BasicSubmission):
     artic_date = Column(TIMESTAMP)  #: Date Artic Performed
     ngs_date = Column(TIMESTAMP)  #: Date submission received
     gel_date = Column(TIMESTAMP)  #: Date submission received
-    gel_barcode = Column(String(16)) #: Identifier for the used gel.
+    gel_barcode = Column(String(16))  #: Identifier for the used gel.
 
     __mapper_args__ = dict(polymorphic_identity="Wastewater Artic",
                            polymorphic_load="inline",
@@ -2767,10 +2780,14 @@ class BacterialCultureSample(BasicSample):
         sample = super().to_sub_dict(full_data=full_data)
         sample['name'] = self.submitter_id
         sample['organism'] = self.organism
-        sample['concentration'] = self.concentration
+        try:
+            sample['concentration'] = f"{float(self.concentration):.2f}"
+        except TypeError:
+            sample['concentration'] = 0.0
         if self.control is not None:
             sample['colour'] = [0, 128, 0]
-            target = next((v for k,v in self.control.controltype.targets.items() if k == self.control.subtype), "Not Available")
+            target = next((v for k, v in self.control.controltype.targets.items() if k == self.control.subtype),
+                          "Not Available")
             try:
                 target = ", ".join(target)
             except:

src/submissions/backend/excel/reports.py

@@ -202,19 +202,21 @@ class ConcentrationMaker(ReportArchetype):
         # NOTE: Set page size to zero to override limiting query size.
         self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date,
                                           submission_type_name=submission_type, page_size=0)
-        self.controls = list(itertools.chain.from_iterable([sub.controls for sub in self.subs]))
+        # self.known_controls = list(itertools.chain.from_iterable([sub.controls for sub in self.subs]))
+        self.controls = list(itertools.chain.from_iterable([sub.get_provisional_controls() for sub in self.subs]))
         self.records = [self.build_record(control) for control in self.controls]
         self.df = DataFrame.from_records(self.records)
         self.sheet_name = "Concentration"
 
     @classmethod
-    def build_record(cls, control: IridaControl) -> dict:
-        positive = control.is_positive_control
-        concentration = control.sample.concentration
-        if not concentration:
-            concentration = 0
-        return dict(name=control.name,
-                    submission=str(control.submission.rsl_plate_num), concentration=concentration,
+    def build_record(cls, control) -> dict:
+        positive = not control.submitter_id.lower().startswith("en")
+        try:
+            concentration = float(control.concentration)
+        except (TypeError, ValueError):
+            concentration = 0.0
+        return dict(name=control.submitter_id,
+                    submission=str(control.submission), concentration=concentration,
                     submitted_date=control.submitted_date, positive=positive)
 
 

src/submissions/backend/validators/pydant.py

@@ -195,16 +195,6 @@ class PydSample(BaseModel, extra='allow'):
                 pass
         return value
 
-    def improved_dict(self) -> dict:
-        """
-        Constructs a dictionary consisting of model.fields and model.extras
-
-        Returns:
-            dict: Information dictionary
-        """
-        fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
-        return {k: getattr(self, k) for k in fields}
-
     @report_result
     def to_sql(self, submission: BasicSubmission | str = None) -> Tuple[
         BasicSample, List[SubmissionSampleAssociation], Result | None]:
@@ -1010,6 +1000,18 @@ class PydSubmission(BaseModel, extra='allow'):
             for r in worksheet.rows:
                 c.writerow([cell.value for cell in r])
 
+    @property
+    def sample_list(self) -> List[dict]:
+        samples = []
+        for sample in self.samples:
+            sample = sample.improved_dict()
+            sample['row'] = sample['row'][0]
+            sample['column'] = sample['column'][0]
+            sample['submission_rank'] = sample['submission_rank'][0]
+            samples.append(sample)
+        samples = sorted(samples, key=itemgetter("submission_rank"))
+        return samples
+
 
 class PydContact(BaseModel):
     name: str