Code cleanup for managers complete.

src/submissions/backend/managers/__init__.py

@@ -1,8 +1,8 @@
+"""
+Module for manager defaults.
+"""
 import logging
 from pathlib import Path
-from typing import Literal
-
-from backend.db.models import ProcedureType
 from frontend.widgets.functions import select_open_file
 from tools import get_application_from_parent
 from backend.validators.pydant import PydBaseClass
@@ -13,7 +13,6 @@ logger = logging.getLogger(f"submissions.{__name__}")
 class DefaultManager(object):
 
     def __init__(self, parent, input_object: Path | str | None = None):
-        logger.debug(f"FName before correction: {type(input_object)}")
         self.parent = parent
         match input_object:
             case str():
@@ -23,19 +22,15 @@ class DefaultManager(object):
                 self.input_object = input_object
                 self.pyd = self.to_pydantic()
             case x if issubclass(input_object.__class__, PydBaseClass):
-                # logger.debug("Subclass of PydBaseClass")
                 self.pyd = input_object
             case x if issubclass(input_object.__class__, BaseClass):
-                # logger.debug("Subclass of BaseClass")
                 self.pyd = input_object.to_pydantic()
             case _:
                 self.input_object = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
                 self.pyd = self.to_pydantic()
-        # logger.debug(f"FName after correction: {input_object}")
-
 
 
 from .clientsubmissions import DefaultClientSubmissionManager
 from .procedures import DefaultProcedureManager
 from .results import DefaultResultsManager
-from .runs import DefaultRunManager
+from .runs import DefaultRunManager

src/submissions/backend/managers/clientsubmissions.py

@@ -1,9 +1,10 @@
+"""
+Module for manager of ClientSubmission object
+"""
 from __future__ import annotations
-import logging
+import logging, sys
-import sys
 from typing import TYPE_CHECKING
 from pathlib import Path
-from openpyxl.reader.excel import load_workbook
 from openpyxl.workbook import Workbook
 from backend.validators import RSLNamer
 from backend.managers import DefaultManager
@@ -42,24 +43,16 @@ class DefaultClientSubmissionManager(DefaultManager):
         self.sample_parser = ClientSubmissionSampleParser(filepath=self.input_object,
                                                           submissiontype=self.submissiontype,
                                                           start_row=self.info_parser.end_row)
-        logger.debug(self.sample_parser.__dict__)
         self.clientsubmission = self.info_parser.to_pydantic()
         self.clientsubmission.full_batch_size = self.sample_parser.end_row - self.sample_parser.start_row
         self.clientsubmission.sample = self.sample_parser.to_pydantic()
 
         return self.clientsubmission
 
-    # def to_pydantic(self):
-    #     self.clientsubmission = self.info_parser.to_pydantic()
-    #     self.clientsubmission.sample = self.sample_parser.to_pydantic()
-
     def write(self, workbook: Workbook) -> Workbook:
-        # workbook: Workbook = load_workbook(BytesIO(self.submissiontype.template_file))
-
         self.info_writer = ClientSubmissionInfoWriter(pydant_obj=self.pyd)
         assert isinstance(self.info_writer, ClientSubmissionInfoWriter)
-        logger.debug("Attempting write.")
         workbook = self.info_writer.write_to_workbook(workbook)
         self.sample_writer = ClientSubmissionSampleWriter(pydant_obj=self.pyd)
         workbook = self.sample_writer.write_to_workbook(workbook, start_row=self.info_writer.worksheet.max_row + 1)
-        return workbook
+        return workbook

src/submissions/backend/managers/procedures.py

@@ -1,12 +1,10 @@
+"""
+Module for manager of Procedure object.
+"""
 from __future__ import annotations
-import logging
+import logging, sys
-from io import BytesIO
-from pprint import pformat
-
-from openpyxl.reader.excel import load_workbook
 from openpyxl.workbook import Workbook
-
+from backend.managers import DefaultManager
-from backend.managers import DefaultManager, results
 from typing import TYPE_CHECKING
 from pathlib import Path
 from backend.excel.parsers import procedure_parsers
@@ -57,7 +55,6 @@ class DefaultProcedureManager(DefaultManager):
         self.equipment = self.equipment_parser.to_pydantic()
 
     def write(self, workbook: Workbook) -> Workbook:
-        # workbook = load_workbook(BytesIO(self.proceduretype.template_file))
         try:
             info_writer = getattr(procedure_writers, f"{self.proceduretype.name.replace(' ', '')}InfoWriter")
         except AttributeError:
@@ -82,16 +79,9 @@ class DefaultProcedureManager(DefaultManager):
             sample_writer = procedure_writers.ProcedureSampleWriter
         self.sample_writer = sample_writer(pydant_obj=self.pyd)
         workbook = self.sample_writer.write_to_workbook(workbook)
-        # # logger.debug(self.pyd.result)
         # # TODO: Find way to group results by result_type.
         for result in self.pyd.result:
-            logger.debug(f"Writing {result.result_type}")
             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)
-        # # sample_results = [sample.result for sample in self.pyd.sample]
-        # # logger.debug(pformat(self.pyd.sample_results))
-        # Writer = getattr(results_writers, "PCRSampleWriter")
-        # res_sample_writer = Writer(pydant_obj=self.pyd.sample_results, proceduretype=self.proceduretype)
-        # workbook = res_sample_writer.write_to_workbook(workbook=workbook)
         return workbook

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

@@ -1,4 +1,6 @@
-
+"""
+Module for default results manager
+"""
 from __future__ import annotations
 import logging
 from .. import DefaultManager
@@ -7,7 +9,6 @@ from pathlib import Path
 from frontend.widgets.functions import select_open_file
 from tools import get_application_from_parent
 from typing import TYPE_CHECKING, List
-
 if TYPE_CHECKING:
     from backend.validators.pydant import PydResults
 
@@ -17,13 +18,11 @@ logger = logging.getLogger(f"submission.{__name__}")
 class DefaultResultsManager(DefaultManager):
 
     def __init__(self, procedure: Procedure, parent, fname: Path | str | None = None):
-        logger.debug(f"FName before correction: {fname}")
         self.procedure = procedure
         if not fname:
             self.fname = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
         elif isinstance(fname, str):
             self.fname = Path(fname)
-        logger.debug(f"FName after correction: {fname}")
 
     def procedure_to_pydantic(self) -> PydResults:
         info = self.info_parser.to_pydantic()

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

@@ -1,14 +1,12 @@
 """
-
+Module for pcr results from Design and Analysis Studio
 """
 from __future__ import annotations
 import logging
 from io import BytesIO
 from pathlib import Path
-from typing import Tuple, List, TYPE_CHECKING
+from typing import TYPE_CHECKING
-
 from openpyxl.reader.excel import load_workbook
-
 from backend.db.models import Procedure
 from backend.excel.parsers.results_parsers.pcr_results_parser import PCRSampleParser, PCRInfoParser
 from backend.excel.writers.results_writers.pcr_results_writer import PCRInfoWriter, PCRSampleWriter
@@ -33,9 +31,3 @@ class PCRManager(DefaultResultsManager):
         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)
-
-
-
-
-
-

src/submissions/backend/managers/runs.py

@@ -1,13 +1,10 @@
+"""
+Module for managing Runs object
+"""
 from __future__ import annotations
-import logging
+import logging, sys
-from pathlib import Path
 from pprint import pformat
-
-from openpyxl import load_workbook
 from openpyxl.workbook.workbook import Workbook
-from tools import copy_xl_sheet
-
-
 from backend.managers import DefaultManager
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -16,16 +13,11 @@ class DefaultRunManager(DefaultManager):
 
     def write(self) -> Workbook:
         from backend.managers import DefaultClientSubmissionManager, DefaultProcedureManager
-        logger.debug(f"Initializing write")
+        logger.info(f"Initializing write")
         clientsubmission = DefaultClientSubmissionManager(parent=self.parent, input_object=self.pyd.clientsubmission, submissiontype=self.pyd.clientsubmission.submissiontype)
         workbook = Workbook()
         workbook = clientsubmission.write(workbook=workbook)
         for procedure in self.pyd.procedure:
-        #     # logger.debug(f"Running procedure: {pformat(procedure.__dict__)}")
             procedure = DefaultProcedureManager(proceduretype=procedure.proceduretype, parent=self.parent, input_object=procedure)
             workbook: Workbook = procedure.write(workbook=workbook)
-        #     for sheetname in wb.sheetnames:
-        #         source_sheet = wb[sheetname]
-        #         ws = workbook.create_sheet(sheetname)
-        #         copy_xl_sheet(source_sheet, ws)
         return workbook