UPdates to managers.

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

@@ -18,10 +18,8 @@ from sqlalchemy.exc import ArgumentError
 from typing import Any, List, ClassVar
 from pathlib import Path
 from sqlalchemy.orm.relationships import _RelationshipDeclared
-
-from frontend import select_save_file
 from tools import report_result, list_sort_dict
-from backend.excel import writers
+
 
 # NOTE: Load testing environment
 if 'pytest' in sys.modules:
@@ -638,15 +636,19 @@ class BaseClass(Base):
             pass
 
     def export(self, obj, output_filepath: str|Path|None=None):
-        if not hasattr(self, "template_file"):
+        # if not hasattr(self, "template_file"):
-            logger.error(f"Export not implemented for {self.__class__.__name__}")
+        #     logger.error(f"Export not implemented for {self.__class__.__name__}")
-            return
+        #     return
-        pyd = self.to_pydantic()
+        # pyd = self.to_pydantic()
-        if not output_filepath:
+        # if not output_filepath:
-            output_filepath = select_save_file(obj=obj, default_name=pyd.construct_filename(), extension="xlsx")
+        #     from frontend import select_save_file
-        Writer = getattr(writers, f"{self.__class__.__name__}Writer")
+        #     output_filepath = select_save_file(obj=obj, default_name=pyd.construct_filename(), extension="xlsx")
-        writer = Writer(output_filepath=output_filepath, pydant_obj=pyd, range_dict=self.range_dict)
+        # Writer = getattr(writers, f"{self.__class__.__name__}Writer")
-        workbook = writer
+        # writer = Writer(output_filepath=output_filepath, pydant_obj=pyd, range_dict=self.range_dict)
+        # workbook = writer
+        from backend import managers
+        Manager = getattr(managers, f"Default{self.__class__.__name__}")
+        manager = Manager(parent=obj, input_object=self)
 
 
 class LogMixin(Base):

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

@@ -9,15 +9,19 @@ from copy import deepcopy
 from getpass import getuser
 import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys
 from inspect import isclass
+from io import BytesIO
 from zipfile import ZipFile, BadZipfile
 from tempfile import TemporaryDirectory, TemporaryFile
 from operator import itemgetter
 from pprint import pformat
+
+import openpyxl
 from pandas import DataFrame
 from sqlalchemy.ext.hybrid import hybrid_property
 
-from frontend import select_save_file
+from frontend.widgets.functions import select_save_file
-from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin, Procedure, kittype_procedure
+from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin, Procedure, \
+    kittype_procedure
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func, Table, Sequence
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.orm.attributes import flag_modified
@@ -35,10 +39,10 @@ from pathlib import Path
 from jinja2.exceptions import TemplateNotFound
 from jinja2 import Template
 from PIL import Image
+
 if TYPE_CHECKING:
     from backend.db.models.kits import ProcedureType, Procedure
 
-
 logger = logging.getLogger(f"procedure.{__name__}")
 
 
@@ -364,8 +368,10 @@ class ClientSubmission(BaseClass, LogMixin):
 
     def to_pydantic(self, filepath: Path | str | None = None, **kwargs):
         output = super().to_pydantic(filepath=filepath, **kwargs)
+        output.template_file = self.template_file
         return output
 
+
 class Run(BaseClass, LogMixin):
     """
     Object for an entire procedure procedure. Links to client procedure, reagents, equipment, process
@@ -634,7 +640,8 @@ class Run(BaseClass, LogMixin):
         # logger.debug(f"Active samples:{pformat(active_samples)}")
         for sample in active_samples:
             sample['active'] = True
-        inactive_samples = [sample.details_dict() for sample in submission_samples if sample.name not in [s['sample_id'] for s in active_samples]]
+        inactive_samples = [sample.details_dict() for sample in submission_samples if
+                            sample.name not in [s['sample_id'] for s in active_samples]]
         # logger.debug(f"Inactive samples:{pformat(inactive_samples)}")
         for sample in inactive_samples:
             sample['active'] = False
@@ -642,7 +649,8 @@ class Run(BaseClass, LogMixin):
         output['sample'] = active_samples + inactive_samples
         output['procedure'] = [procedure.details_dict() for procedure in output['procedure']]
         output['permission'] = is_power_user()
-        output['excluded'] = ['procedure', "runsampleassociation", 'excluded', 'expanded', 'sample', 'id', 'custom', 'permission']
+        output['excluded'] = ['procedure', "runsampleassociation", 'excluded', 'expanded', 'sample', 'id', 'custom',
+                              'permission']
 
         return output
 
@@ -727,7 +735,8 @@ class Run(BaseClass, LogMixin):
 
     @property
     def sample_dicts(self) -> List[dict]:
-        return [dict(sample_id=assoc.sample.sample_id, row=assoc.row, column=assoc.column, background_color="#6ffe1d") for assoc in self.runsampleassociation]
+        return [dict(sample_id=assoc.sample.sample_id, row=assoc.row, column=assoc.column, background_color="#6ffe1d")
+                for assoc in self.runsampleassociation]
 
     @classmethod
     def make_plate_map(cls, sample_list: list, plate_rows: int = 8, plate_columns=12) -> str:
@@ -1010,7 +1019,6 @@ class Run(BaseClass, LogMixin):
         regex = re.compile(rstring, flags=re.IGNORECASE | re.VERBOSE)
         return regex
 
-
     # NOTE: Query functions
 
     @classmethod
@@ -1190,14 +1198,15 @@ class Run(BaseClass, LogMixin):
         Returns:
             dict: dictionary of functions
         """
-        names = ["Add Procedure", "Edit", "Add Comment", "Show Details", "Delete"]
+        names = ["Add Procedure", "Edit", "Export", "Add Comment", "Show Details", "Delete"]
         output = {item: self.__getattribute__(item.lower().replace(" ", "_")) for item in names}
         logger.debug(output)
         return output
 
     def add_procedure(self, obj, proceduretype_name: str):
         from frontend.widgets.procedure_creation import ProcedureCreation
-        procedure_type = next((proceduretype for proceduretype in self.allowed_procedures if proceduretype.name == proceduretype_name))
+        procedure_type = next(
+            (proceduretype for proceduretype in self.allowed_procedures if proceduretype.name == proceduretype_name))
         logger.debug(f"Got ProcedureType: {procedure_type}")
         dlg = ProcedureCreation(parent=obj, procedure=procedure_type.construct_dummy_procedure(run=self))
         if dlg.exec():
@@ -1280,13 +1289,18 @@ class Run(BaseClass, LogMixin):
             self.save(original=False)
 
     def export(self, obj, output_filepath: str | Path | None = None):
-
+        from backend.excel import writers
         clientsubmission_pyd = self.clientsubmission.to_pydantic()
         if not output_filepath:
-            output_filepath = select_save_file(obj=obj, default_name=clientsubmission_pyd.construct_filename(), extension="xlsx")
+            output_filepath = select_save_file(obj=obj, default_name=self.construct_filename(), extension="xlsx")
         Writer = getattr(writers, "ClientSubmissionWriter")
-        writer = Writer(output_filepath=output_filepath, pydant_obj=pyd, range_dict=self.range_dict)
+        writer = Writer(output_filepath=output_filepath, pydant_obj=clientsubmission_pyd,
-        workbook = writer.
+                        range_dict=self.clientsubmission.range_dict)
+        workbook: openpyxl.Workbook = writer.write_info()
+        workbook.save(filename=output_filepath)
+
+    def construct_filename(self):
+        return f"{self.rsl_plate_number}-{self.clientsubmission.clientlab.name}-{self.clientsubmission.submitter_plate_id}"
 
     def backup(self, obj=None, fname: Path | None = None, full_backup: bool = False):
         """
@@ -1378,10 +1392,12 @@ class Run(BaseClass, LogMixin):
             submission_rank = self.get_submission_rank_of_sample(sample=sample)
             if submission_rank != 0:
                 row, column = plate_dict[submission_rank]
-                ranked_samples.append(dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank, background_color="#6ffe1d"))
+                ranked_samples.append(dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column,
+                                           submission_rank=submission_rank, background_color="#6ffe1d"))
             else:
                 unranked_samples.append(sample)
-        possible_ranks = (item for item in list(plate_dict.keys()) if item not in [sample['submission_rank'] for sample in ranked_samples])
+        possible_ranks = (item for item in list(plate_dict.keys()) if
+                          item not in [sample['submission_rank'] for sample in ranked_samples])
         # logger.debug(possible_ranks)
         # possible_ranks = (plate_dict[idx] for idx in possible_ranks)
         for sample in unranked_samples:
@@ -1391,13 +1407,15 @@ class Run(BaseClass, LogMixin):
                 continue
             row, column = plate_dict[submission_rank]
             ranked_samples.append(
-                dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank,
+                dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column,
+                     submission_rank=submission_rank,
                      background_color="#6ffe1d", enabled=True))
         padded_list = []
         for iii in range(1, proceduretype.total_wells + 1):
             row, column = proceduretype.ranked_plate[iii]
             sample = next((item for item in ranked_samples if item['submission_rank'] == iii),
-                          dict(well_id=f"blank_{iii}", sample_id="", row=row, column=column, submission_rank=iii, background_color="#ffffff", enabled=False)
+                          dict(well_id=f"blank_{iii}", sample_id="", row=row, column=column, submission_rank=iii,
+                               background_color="#ffffff", enabled=False)
                           )
             padded_list.append(sample)
         # logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")
@@ -2126,8 +2144,8 @@ class RunSampleAssociation(BaseClass):
         output['misc_info'] = misc
         return output
 
-class ProcedureSampleAssociation(BaseClass):
 
+class ProcedureSampleAssociation(BaseClass):
     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
@@ -2142,7 +2160,8 @@ class ProcedureSampleAssociation(BaseClass):
     results = relationship("Results", back_populates="sampleprocedureassociation")
 
     @classmethod
-    def query(cls, sample: Sample|str|None=None, procedure: Procedure|str|None=None, limit: int=0, **kwargs):
+    def query(cls, sample: Sample | str | None = None, procedure: Procedure | str | None = None, limit: int = 0,
+              **kwargs):
         query = cls.__database_session__.query(cls)
         match sample:
             case Sample():
@@ -2162,7 +2181,6 @@ class ProcedureSampleAssociation(BaseClass):
             limit = 1
         return cls.execute_query(query=query, limit=limit, **kwargs)
 
-
     def __init__(self, new_id: int | None = None, **kwarg):
         if new_id:
             self.id = new_id
@@ -2170,7 +2188,6 @@ class ProcedureSampleAssociation(BaseClass):
             self.id = self.__class__.autoincrement_id()
         super().__init__(**kwarg)
 
-
     @classmethod
     def autoincrement_id(cls) -> int:
         """
@@ -2195,4 +2212,3 @@ class ProcedureSampleAssociation(BaseClass):
         output['misc_info'] = misc
         output['results'] = [result.details_dict() for result in output['results']]
         return output
-

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

@@ -12,7 +12,7 @@ from openpyxl.reader.excel import load_workbook
 from tools import row_keys
 # from backend.db.models import SubmissionType
 from . import DefaultKEYVALUEParser, DefaultTABLEParser
-from backend.managers import procedures as procedure_managers
+
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -84,9 +84,13 @@ class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
         sheet="Sample List"
     )]
 
-    def __init__(self, filepath: Path | str, *args, **kwargs):
+    def __init__(self, filepath: Path | str, submissiontype:"SubmissionType"|None=None, *args, **kwargs):
         from frontend.widgets.pop_ups import QuestionAsker
+        from backend.managers import procedures as procedure_managers
+        if not submissiontype:
             self.submissiontype = self.retrieve_submissiontype(filepath=filepath)
+        else:
+            self.submissiontype = submissiontype
         if "range_dict" not in kwargs:
             kwargs['range_dict'] = self.submissiontype.info_map
         super().__init__(filepath=filepath, **kwargs)
@@ -118,8 +122,11 @@ class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
         sheet="Sample List"
     )]
 
-    def __init__(self, filepath: Path | str, *args, **kwargs):
+    def __init__(self, filepath: Path | str, submissiontype: "SubmissionType"|None=None, *args, **kwargs):
+        if not submissiontype:
             self.submissiontype = self.retrieve_submissiontype(filepath=filepath)
+        else:
+            self.submissiontype = submissiontype
         if "range_dict" not in kwargs:
             kwargs['range_dict'] = self.submissiontype.sample_map
         super().__init__(filepath=filepath, **kwargs)

src/submissions/backend/managers/__init__.py

@@ -1,22 +1,37 @@
 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
+from backend.db.models import BaseClass
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 class DefaultManager(object):
 
-    def __init__(self, proceduretype: ProcedureType, parent, fname: Path | str | None = None):
+    def __init__(self, parent, input_object: Path | str | None = None):
-        logger.debug(f"FName before correction: {fname}")
+        logger.debug(f"FName before correction: {input_object}")
-        if isinstance(proceduretype, str):
+        # if input_object != "no_file":
-            proceduretype = ProcedureType.query(name=proceduretype)
+        match input_object:
-        self.proceduretype = proceduretype
+            case str():
-        if fname != "no_file":
+                self.input_object = Path(input_object)
-            if not fname:
+                self.pyd = self.parse()
-                self.fname = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
+            case Path():
-            elif isinstance(fname, str):
+                self.input_object = input_object
-                self.fname = Path(fname)
+                self.pyd = self.parse()
-        logger.debug(f"FName after correction: {fname}")
+            case x if issubclass(input_object.__class__, PydBaseClass):
+                self.pyd = input_object
+            case x if issubclass(input_object.__class__, 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.parse()
+        logger.debug(f"FName after correction: {input_object}")
 
+
+from .clientsubmissions import DefaultClientSubmission
+from .procedures import DefaultProcedure
+from.results import DefaultResults

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

@@ -13,28 +13,33 @@ logger = logging.getLogger(f"submissions.{__name__}")
 class DefaultProcedure(DefaultManager):
 
     def __init__(self, proceduretype: "ProcedureType"|str, parent, fname: Path | str | None = None):
+        super().__init__(parent=parent, fname=fname)
+        if isinstance(proceduretype, str):
+            proceduretype = ProcedureType.query(name=proceduretype)
+        self.proceduretype = proceduretype
 
-        super().__init__(proceduretype=proceduretype, parent=parent, fname=fname)
+
+    def parse(self):
         try:
             info_parser = getattr(procedure_parsers, f"{self.proceduretype.name.replace(' ', '')}InfoParser")
         except AttributeError:
             info_parser = procedure_parsers.DefaultInfoParser
-        self.info_parser = info_parser(filepath=fname, proceduretype=proceduretype)
+        self.info_parser = info_parser(filepath=self.fname, proceduretype=self.proceduretype)
         try:
             reagent_parser = getattr(procedure_parsers, f"{self.proceduretype.name.replace(' ', '')}ReagentParser")
         except AttributeError:
             reagent_parser = procedure_parsers.DefaultReagentParser
-        self.reagent_parser = reagent_parser(filepath=fname, proceduretype=proceduretype)
+        self.reagent_parser = reagent_parser(filepath=self.fname, proceduretype=self.proceduretype)
         try:
             sample_parser = getattr(procedure_parsers, f"{self.proceduretype.name.replace(' ', '')}SampleParser")
         except AttributeError:
             sample_parser = procedure_parsers.DefaultSampleParser
-        self.sample_parser = sample_parser(filepath=fname, proceduretype=proceduretype)
+        self.sample_parser = sample_parser(filepath=self.fname, proceduretype=self.proceduretype)
         try:
             equipment_parser = getattr(procedure_parsers, f"{self.proceduretype.name.replace(' ', '')}EquipmentParser")
         except AttributeError:
             equipment_parser = procedure_parsers.DefaultEquipmentParser
-        self.equipment_parser = equipment_parser(filepath=fname, proceduretype=proceduretype)
+        self.equipment_parser = equipment_parser(filepath=self.fname, proceduretype=self.proceduretype)
         self.to_pydantic()
 
     def to_pydantic(self):

src/submissions/backend/validators/pydant.py

@@ -128,6 +128,9 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
         return sql
 
 
+
+
+
 class PydReagent(PydBaseClass):
     lot: str | None
     reagentrole: str | None
@@ -1778,6 +1781,8 @@ class PydClientSubmission(PydBaseClass):
             SubmissionFormWidget: Submission form widget
         """
         from frontend.widgets.submission_widget import ClientSubmissionFormWidget
+        if not samples:
+            samples = self.samples
         return ClientSubmissionFormWidget(parent=parent, clientsubmission=self, samples=samples, disable=disable)
 
     def to_sql(self):
@@ -1804,6 +1809,7 @@ class PydClientSubmission(PydBaseClass):
         return sql
 
 
+
 class PydResults(PydBaseClass, arbitrary_types_allowed=True):
     results: dict = Field(default={})
     results_type: str = Field(default="NA")

src/submissions/frontend/widgets/app.py

@@ -13,7 +13,7 @@ from PyQt6.QtGui import QAction
 from pathlib import Path
 from markdown import markdown
 from pandas import ExcelWriter
-from backend.db.models import Reagent, Sample, ClientSubmission, KitType, Run
+from backend.db.models import Reagent, KitType
 from tools import (
     check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user,
     under_development
@@ -175,6 +175,7 @@ class App(QMainWindow):
         """
         Create a search for sample.
         """
+        from backend.db.models.submissions import Sample
         dlg = SearchBox(self, object_type=Sample, extras=[])
         dlg.exec()
 

src/submissions/frontend/widgets/date_type_picker.py

@@ -2,7 +2,7 @@ from PyQt6.QtWidgets import (
     QVBoxLayout, QDialog, QDialogButtonBox
 )
 from .misc import CheckableComboBox, StartEndDatePicker
-from backend.db import SubmissionType
+from backend.db.models.kits import SubmissionType
 
 
 class DateTypePicker(QDialog):

src/submissions/frontend/widgets/submission_table.py

@@ -11,9 +11,9 @@ from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel, pyqtSlo
 from PyQt6.QtGui import QAction, QCursor, QStandardItemModel, QStandardItem, QIcon, QColor, QContextMenuEvent
 from typing import Dict, List
 
-from backend import Procedure
+# from backend import Procedure
-from backend.db.models import Run, ClientSubmission
+from backend.db.models import Run, ClientSubmission, Procedure
-from tools import Report, Result, report_result
+from tools import Report, Result, report_result, get_application_from_parent
 from .functions import select_open_file
 
 logger = logging.getLogger(f"procedure.{__name__}")
@@ -261,6 +261,7 @@ class SubmissionsTree(QTreeView):
 
     def __init__(self, model, parent=None):
         super(SubmissionsTree, self).__init__(parent)
+        self.app = get_application_from_parent(parent)
         self.total_count = ClientSubmission.__database_session__.query(ClientSubmission).count()
         # self.setIndentation(0)
         self.setExpandsOnDoubleClick(False)

src/submissions/frontend/widgets/submission_widget.py

@@ -6,6 +6,8 @@ from PyQt6.QtWidgets import (
     QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QHBoxLayout, QGridLayout
 )
 from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
+
+from backend.managers import DefaultClientSubmission
 from .functions import select_open_file, select_save_file
 import logging
 from pathlib import Path
@@ -120,25 +122,28 @@ class SubmissionFormContainer(QWidget):
             report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
             return report
         # NOTE: create sheetparser using excel sheet and context from gui
-        try:
+        # try:
-            self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
+        #     self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
-        except PermissionError:
+        # except PermissionError:
-            logger.error(f"Couldn't get permission to access file: {fname}")
+        #     logger.error(f"Couldn't get permission to access file: {fname}")
-            return
+        #     return
-        except AttributeError:
+        # except AttributeError:
-            self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
+        #     self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
-        try:
+        # try:
-            # self.prsr = SheetParser(filepath=fname)
+        #     # self.prsr = SheetParser(filepath=fname)
-            self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
+        #     self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
-        except PermissionError:
+        # except PermissionError:
-            logger.error(f"Couldn't get permission to access file: {fname}")
+        #     logger.error(f"Couldn't get permission to access file: {fname}")
-            return
+        #     return
-        except AttributeError:
+        # except AttributeError:
-            self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
+        #     self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
-        self.pydclientsubmission = self.clientsubmissionparser.to_pydantic()
+
-        self.pydsamples = self.sampleparser.to_pydantic()
+        # self.pydclientsubmission = self.clientsubmissionparser.to_pydantic()
+        # self.pydsamples = self.sampleparser.to_pydantic()
         # logger.debug(f"Samples: {pformat(self.pydclientsubmission.sample)}")
-        checker = SampleChecker(self, "Sample Checker", self.pydsamples)
+        self.clientsubmission_manager = DefaultClientSubmission(parent=self, fname=fname)
+        self.pydclientsubmission = self.clientsubmission_manager.parse()
+        checker = SampleChecker(self, "Sample Checker", self.pydclientsubmission.samples)
         if checker.exec():
             # logger.debug(pformat(self.pydclientsubmission.sample))
             try:
@@ -147,7 +152,7 @@ class SubmissionFormContainer(QWidget):
                 logger.error(f"Got wrong type for {self.pydclientsubmission}: {type(self.pydclientsubmission)}")
                 raise e
             self.form = self.pydclientsubmission.to_form(parent=self)
-            self.form.samples = self.pydsamples
+            # self.form.samples = self.pydsamples
             self.layout().addWidget(self.form)
         else:
             message = "Submission cancelled."