Qubit sample results now written to export.

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

@@ -929,7 +929,7 @@ class Procedure(BaseClass):
         logger.info(f"Add Results! {resultstype_name}")
         from backend.managers import results
         results_manager = getattr(results, f"{resultstype_name}Manager")
-        rs = results_manager(procedure=self, parent=obj, fname=Path("C:\\Users\lwark\Documents\Submission_Forms\QubitData_18-09-2025_13-43-53.csv"))
+        rs = results_manager(procedure=self, parent=obj)#, fname=Path("C:\\Users\lwark\Documents\Submission_Forms\QubitData_18-09-2025_13-43-53.csv"))
         procedure = rs.procedure_to_pydantic()
         samples = rs.samples_to_pydantic()
         if procedure:

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

@@ -1926,7 +1926,7 @@ class ProcedureSampleAssociation(BaseClass):
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['sample']}
         output = output['sample'].details_dict()
-        logger.debug(output)
+        # logger.debug(output)
         misc = output['misc_info']
         output.update(relevant)
         output['misc_info'] = misc

src/submissions/backend/excel/parsers/__init__.py

@@ -62,7 +62,7 @@ class DefaultParser(object):
         self.sheet = sheet
         if not start_row:
             start_row = self.__class__.start_row
-        if self.filepath.suffix == ".xslx":
+        if self.filepath.suffix == ".xlsx":
             self.workbook = load_workbook(self.filepath, data_only=True)
             self.worksheet = self.workbook[self.sheet]
         elif self.filepath.suffix == ".csv":

src/submissions/backend/excel/writers/results_writers/__init__.py

@@ -1,6 +1,8 @@
 """
 
 """
+from openpyxl import Workbook
+
 from backend.excel.writers import DefaultKEYVALUEWriter, DefaultTABLEWriter
 from backend.db.models import ProcedureType
 from tools import flatten_list
@@ -16,6 +18,15 @@ class DefaultResultsSampleWriter(DefaultTABLEWriter):
         super().__init__(pydant_obj=pydant_obj, proceduretype=proceduretype, *args, **kwargs)
         self.pydant_obj = flatten_list([sample.results for sample in pydant_obj.sample])
 
+    def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
+                          start_row: int | None = None, *args, **kwargs) -> Workbook:
+        try:
+            self.worksheet = workbook[f"{self.proceduretype.name[:15]} Results"]
+        except KeyError:
+            self.worksheet = workbook.create_sheet(f"{self.proceduretype.name[:15]} Results")
+            # worksheet = workbook[f"{self.proceduretype.name[:15]} Results"]
+        return workbook
+
 
 from .qubit_results_writer import QubitInfoWriter, QubitSampleWriter
 from .pcr_results_writer import PCRInfoWriter, PCRSampleWriter

src/submissions/backend/excel/writers/results_writers/qubit_results_writer.py

@@ -1,16 +1,13 @@
 """
-Writers for PCR results from Design and Analysis Software
+Writers for PCR results from Qubit device
 """
 from __future__ import annotations
 import logging
 from pprint import pformat
-from typing import Generator, TYPE_CHECKING
 from openpyxl import Workbook
 from openpyxl.styles import Alignment
 from . import DefaultResultsInfoWriter, DefaultResultsSampleWriter
-from tools import flatten_list
-if TYPE_CHECKING:
-    from backend.db.models import ProcedureType
+
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -24,16 +21,12 @@ class QubitInfoWriter(DefaultResultsInfoWriter):
 class QubitSampleWriter(DefaultResultsSampleWriter):
 
     def write_to_workbook(self, workbook: Workbook, *args, **kwargs) -> Workbook:
-        try:
-            self.worksheet = workbook[f"{self.proceduretype.name[:15]} Results"]
-        except KeyError:
-            self.worksheet = workbook.create_sheet(f"{self.proceduretype.name[:15]} Results")
-            # worksheet = workbook[f"{self.proceduretype.name[:15]} Results"]
+        workbook = super().write_to_workbook(workbook=workbook, *args, **kwargs)
         header_row = self.proceduretype.allowed_result_methods['Qubit']['sample']['start_row']
         for iii, header in enumerate(self.column_headers, start=1):
-            logger.debug(f"Row: {header_row}, column: {iii}")
+            # logger.debug(f"Row: {header_row}, column: {iii}")
             self.worksheet.cell(row=header_row, column=iii, value=header.replace("_", " ").title())
-        logger.debug(f"Column headers: {self.column_headers}")
+        # logger.debug(f"Column headers: {self.column_headers}")
         for iii, result in enumerate(self.pydant_obj, start = 1):
             row = header_row + iii
             for k, v in result.result.items():
@@ -42,7 +35,7 @@ class QubitSampleWriter(DefaultResultsSampleWriter):
                 except StopIteration:
                     print(f"fail for {k.replace('_', ' ').title()}")
                     continue
-                logger.debug(f"Writing to row: {row}, column {column}")
+                # logger.debug(f"Writing to row: {row}, column {column}")
                 cell = self.worksheet.cell(row=row, column=column)
                 cell.value = v
                 cell.alignment = Alignment(horizontal='left')
@@ -56,6 +49,3 @@ class QubitSampleWriter(DefaultResultsSampleWriter):
             for k, value in result.result.items():
                 output.append(k)
         return sorted(list(set(output)))
-
-
-

src/submissions/backend/managers/__init__.py

@@ -15,7 +15,7 @@ class DefaultManager(object):
 
     def __init__(self, parent, input_object: Path | str | None = None):
         self.parent = parent
-        logger.debug(f"Input object: {pformat(input_object.__dict__)}")
+
         match input_object:
             case str():
                 self.input_object = Path(input_object)

src/submissions/backend/validators/pydant.py

@@ -254,12 +254,12 @@ class PydReagent(PydBaseClass):
         report = Report()
         if self.model_extra is not None:
             self.__dict__.update(self.model_extra)
-        reagent, new = ReagentLot.query_or_create(lot=self.lot, name=self.name)
+        reagentlot, new = ReagentLot.query_or_create(lot=self.lot, name=self.name)
         if new:
-            reagentrole = ReagentRole.query(name=self.reagentrole)
-            reagent.reagentrole = reagentrole
-            reagent.expiry = self.expiry
-        return reagent, report
+            reagent = Reagent.query(name=self.name)
+            reagentlot.reagent = reagent
+            reagentlot.expiry = self.expiry
+        return reagentlot, report
 
 
 class PydSample(PydBaseClass):

src/submissions/frontend/widgets/procedure_creation.py

@@ -56,7 +56,15 @@ class ProcedureCreation(QDialog):
         proceduretype_dict = self.proceduretype.details_dict()
         # NOTE: Add --New-- as an option for reagents.
         for key, value in self.procedure.reagentrole.items():
-            value.append(dict(name="--New--"))
+            try:
+                check = "--New--" in [v['name'] for v in value]
+            except TypeError:
+                try:
+                    check = "--New--" in [v.name for v in value]
+                except (TypeError, AttributeError):
+                    check = True
+            if not check:
+                value.append(dict(name="--New--"))
         if self.procedure.equipment:
             for equipmentrole in proceduretype_dict['equipment']:
                 # NOTE: Check if procedure equipment is present and move to head of the list if so.
@@ -150,6 +158,7 @@ class ProcedureCreation(QDialog):
     def add_new_reagent(self, reagentrole: str, name: str, lot: str, expiry: str):
         from backend.validators.pydant import PydReagent
         expiry = datetime.datetime.strptime(expiry, "%Y-%m-%d")
+        logger.debug(f"{reagentrole}, {name}, {lot}, {expiry}")
         pyd = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
         self.procedure.reagentrole[reagentrole].insert(0, pyd)
         self.set_html()