UPdates to managers.

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.db.models import Run, ClientSubmission
-from tools import Report, Result, report_result
+# from backend import Procedure
+from backend.db.models import Run, ClientSubmission, Procedure
+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:
-            self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
-        except PermissionError:
-            logger.error(f"Couldn't get permission to access file: {fname}")
-            return
-        except AttributeError:
-            self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
-        try:
-            # self.prsr = SheetParser(filepath=fname)
-            self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
-        except PermissionError:
-            logger.error(f"Couldn't get permission to access file: {fname}")
-            return
-        except AttributeError:
-            self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
-        self.pydclientsubmission = self.clientsubmissionparser.to_pydantic()
-        self.pydsamples = self.sampleparser.to_pydantic()
+        # try:
+        #     self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
+        # except PermissionError:
+        #     logger.error(f"Couldn't get permission to access file: {fname}")
+        #     return
+        # except AttributeError:
+        #     self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
+        # try:
+        #     # self.prsr = SheetParser(filepath=fname)
+        #     self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
+        # except PermissionError:
+        #     logger.error(f"Couldn't get permission to access file: {fname}")
+        #     return
+        # except AttributeError:
+        #     self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
+
+        # 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."