Fixed bug in adding new reagent during procedure creation.

TODO.md

@@ -1,3 +1,5 @@
+- [ ] Do results writing.
+- [ ] Allow use of multiple tips per process.
 - [x] Add in database objects for rsl_run (submission -> run), procedure (run -> procedure), many more things will likely be associated with procedure.
 - [x] Add in database object for client submission.
 - [ ] Add arbitrary pipette addition to equipment UI.

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

@@ -2,6 +2,8 @@
 All kittype and reagent related models
 """
 from __future__ import annotations
+
+import sys
 import zipfile, logging, re, numpy as np
 from operator import itemgetter
 from pathlib import Path
@@ -593,7 +595,7 @@ class SubmissionType(BaseClass):
         query: Query = cls.__database_session__.query(cls)
         match name:
             case str():
-                logger.debug(f"querying with {name}")
+                # logger.debug(f"querying with {name}")
                 query = query.filter(cls.name == name)
                 limit = 1
             case _:
@@ -927,7 +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:
@@ -982,7 +984,6 @@ class Procedure(BaseClass):
         output['sample'] = active_samples + inactive_samples
         output['reagent'] = [reagent.details_dict() for reagent in output['procedurereagentlotassociation']]
         output['equipment'] = [equipment.details_dict() for equipment in output['procedureequipmentassociation']]
-        # logger.debug(f"equipment: {pformat([item for item in output['equipment']])}")
         output['repeat'] = self.repeat
         output['run'] = self.run.name
         output['excluded'] += self.get_default_info("details_ignore")
@@ -995,7 +996,6 @@ class Procedure(BaseClass):
     def to_pydantic(self, **kwargs):
         from backend.validators.pydant import PydReagent
         output = super().to_pydantic()
-        print(f"Super to_pydantic: {output.equipment}")
         output.sample = [item.to_pydantic() for item in output.proceduresampleassociation]
         reagents = []
         for reagent in output.reagent:

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

@@ -646,7 +646,6 @@ class Run(BaseClass, LogMixin):
                                'permission', "clientsubmission"]
         output['sample_count'] = self.sample_count
         output['clientsubmission'] = self.clientsubmission.name
-        # output['clientlab'] = self.clientsubmission.clientlab
         output['started_date'] = self.started_date
         output['completed_date'] = self.completed_date
         return output
@@ -1852,6 +1851,9 @@ class RunSampleAssociation(BaseClass):
 
 
 class ProcedureSampleAssociation(BaseClass):
+
+    pyd_model_name = "PydSample"
+
     id = Column(INTEGER, unique=True, nullable=False)
     procedure_id = Column(INTEGER, ForeignKey("_procedure.id"), primary_key=True)  #: id of associated procedure
     sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True)  #: id of associated equipment
@@ -1924,12 +1926,13 @@ 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)
         misc = output['misc_info']
         output.update(relevant)
         output['misc_info'] = misc
         output['row'] = self.row
         output['column'] = self.column
-        output['results'] = [result.details_dict() for result in output['results']]
+        output['results'] = [item.details_dict() for item in self.results]
         return output
 
     def to_pydantic(self, **kwargs):

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/__init__.py

@@ -40,7 +40,6 @@ class DefaultWriter(object):
             case x if issubclass(value.__class__, BaseClass):
                 value = value.name
             case x if issubclass(value.__class__, PydBaseClass):
-                logger.warning(f"PydBaseClass: {value}")
                 value = value.name
             case bytes() | list():
                 value = None
@@ -241,6 +240,7 @@ class DefaultTABLEWriter(DefaultWriter):
 
 from .procedure_writers import ProcedureInfoWriter, ProcedureSampleWriter, ProcedureReagentWriter, ProcedureEquipmentWriter
 from .results_writers import (
-    PCRInfoWriter, PCRSampleWriter
+    PCRInfoWriter, PCRSampleWriter,
+    QubitInfoWriter, QubitSampleWriter
 )
 from .clientsubmission_writer import ClientSubmissionInfoWriter, ClientSubmissionSampleWriter

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

@@ -1 +1,32 @@
+"""
+
+"""
+from openpyxl import Workbook
+
+from backend.excel.writers import DefaultKEYVALUEWriter, DefaultTABLEWriter
+from backend.db.models import ProcedureType
+from tools import flatten_list
+
+
+class DefaultResultsInfoWriter(DefaultKEYVALUEWriter):
+
+    pass
+
+class DefaultResultsSampleWriter(DefaultTABLEWriter):
+
+    def __init__(self, pydant_obj, proceduretype: ProcedureType | None = None, *args, **kwargs):
+        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/pcr_results_writer.py

@@ -7,14 +7,15 @@ from pprint import pformat
 from typing import Generator, TYPE_CHECKING
 from openpyxl import Workbook
 from openpyxl.styles import Alignment
-from backend.excel.writers import DefaultKEYVALUEWriter, DefaultTABLEWriter
+# from backend.excel.writers import DefaultKEYVALUEWriter, DefaultTABLEWriter
+from . import DefaultResultsInfoWriter, DefaultResultsSampleWriter
 from tools import flatten_list
 if TYPE_CHECKING:
     from backend.db.models import ProcedureType
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
-class PCRInfoWriter(DefaultKEYVALUEWriter):
+class PCRInfoWriter(DefaultResultsInfoWriter):
 
     start_row = 1
 
@@ -28,7 +29,7 @@ class PCRInfoWriter(DefaultKEYVALUEWriter):
         return workbook
 
 
-class PCRSampleWriter(DefaultTABLEWriter):
+class PCRSampleWriter(DefaultResultsSampleWriter):
 
     def write_to_workbook(self, workbook: Workbook) -> Workbook:
         worksheet = workbook[f"{self.proceduretype.name} Results"]

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

@@ -0,0 +1,51 @@
+"""
+Writers for PCR results from Qubit device
+"""
+from __future__ import annotations
+import logging
+from pprint import pformat
+from openpyxl import Workbook
+from openpyxl.styles import Alignment
+from . import DefaultResultsInfoWriter, DefaultResultsSampleWriter
+
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+class QubitInfoWriter(DefaultResultsInfoWriter):
+
+    def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
+                          start_row: int = 1, *args, **kwargs) -> Workbook:
+        return workbook
+
+
+class QubitSampleWriter(DefaultResultsSampleWriter):
+
+    def write_to_workbook(self, workbook: Workbook, *args, **kwargs) -> Workbook:
+        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}")
+            self.worksheet.cell(row=header_row, column=iii, value=header.replace("_", " ").title())
+        # 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():
+                try:
+                    column = next((col[0].column for col in self.worksheet.iter_cols() if col[0].value == k.replace("_", " ").title()))
+                except StopIteration:
+                    print(f"fail for {k.replace('_', ' ').title()}")
+                    continue
+                # 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')
+        self.worksheet = self.postwrite(self.worksheet)
+        return workbook
+
+    @property
+    def column_headers(self):
+        output = []
+        for result in self.pydant_obj:
+            for k, value in result.result.items():
+                output.append(k)
+        return sorted(list(set(output)))

src/submissions/backend/managers/__init__.py

@@ -2,6 +2,7 @@
 Module for manager defaults.
 """
 import logging
+from pprint import pformat
 from pathlib import Path
 from frontend.widgets.functions import select_open_file
 from tools import get_application_from_parent
@@ -14,6 +15,7 @@ class DefaultManager(object):
 
     def __init__(self, parent, input_object: Path | str | None = None):
         self.parent = parent
+
         match input_object:
             case str():
                 self.input_object = Path(input_object)

src/submissions/backend/managers/procedures.py

@@ -22,6 +22,7 @@ class DefaultProcedureManager(DefaultManager):
         if isinstance(proceduretype, str):
             proceduretype = ProcedureType.query(name=proceduretype)
         self.proceduretype = proceduretype
+        self.procedure = input_object
         super().__init__(parent=parent, input_object=input_object)
 
 
@@ -84,4 +85,8 @@ class DefaultProcedureManager(DefaultManager):
             Writer = getattr(results_writers, f"{result.result_type}InfoWriter")
             res_info_writer = Writer(pydant_obj=result, proceduretype=self.proceduretype)
             workbook = res_info_writer.write_to_workbook(workbook=workbook)
+        for result in self.pyd.sample_results:
+            Writer = getattr(results_writers, f"{result.result_type}SampleWriter")
+            res_sample_writer = Writer(pydant_obj=self.procedure, proceduretype=self.proceduretype)
+            workbook = res_sample_writer.write_to_workbook(workbook=workbook)
         return workbook

src/submissions/backend/managers/results/qubit_results_manager.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING
 from openpyxl.reader.excel import load_workbook
 from backend.db.models import Procedure
 from backend.excel.parsers.results_parsers.qubit_results_parser import QubitSampleParser, QubitInfoParser
-# from backend.excel.writers.results_writers.pcr_results_writer import QubitInfoWriter, QubitSampleWriter
+from backend.excel.writers.results_writers.qubit_results_writer import QubitInfoWriter, QubitSampleWriter
 from . import DefaultResultsManager
 if TYPE_CHECKING:
     from backend.validators.pydant import PydResults
@@ -28,6 +28,6 @@ class QubitManager(DefaultResultsManager):
 
     def write(self):
         workbook = load_workbook(BytesIO(self.procedure.proceduretype.template_file))
-        self.info_writer = PCRInfoWriter(pydant_obj=self.procedure.to_pydantic(), proceduretype=self.procedure.proceduretype)
-        workbook = self.info_writer.write_to_workbook(workbook)
-        self.sample_writer = PCRSampleWriter(pydant_obj=self.procedure.to_pydantic(), proceduretype=self.procedure.proceduretype)
+        self.sample_writer = QubitSampleWriter(pydant_obj=self.procedure.to_pydantic(), proceduretype=self.procedure.proceduretype)
+        workbook = self.sample_writer.write_to_workbook(workbook)
+        return workbook

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):
@@ -268,6 +268,7 @@ class PydSample(PydBaseClass):
     enabled: bool = Field(default=True)
     row: int = Field(default=0)
     column: int = Field(default=0)
+    results: List[PydResults] | PydResults = Field(default=[])
 
     @field_validator("sample_id", mode="before")
     @classmethod
@@ -389,7 +390,6 @@ class PydEquipment(PydBaseClass):
     @field_validator('tips', mode='before')
     @classmethod
     def tips_to_pydantic(cls, value, values):
-        print(f"Value coming into tips: {value}")
         if isinstance(value, GeneratorType):
             value = [item for item in value]
         value = convert_nans_to_nones(value)

src/submissions/frontend/widgets/procedure_creation.py

@@ -56,6 +56,14 @@ 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():
+            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']:
@@ -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()