Pre-code cleanup.

CHANGELOG.md

@@ -1,6 +1,7 @@
 # 202503.05
 
 - Added concentrations chart tab.
+- Saving report xlsx/pdf now inserts report class name in file name.
 
 # 202503.04
 

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

@@ -56,23 +56,23 @@ class BaseClass(Base):
     omni_inheritable = []
     searchables = []
 
-    @classproperty
+    # @classproperty
-    def skip_on_edit(cls):
+    # def skip_on_edit(cls):
-        if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
+    #     if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
-            return True
+    #         return True
-        else:
+    #     else:
-            return False
+    #         return False
 
     @classproperty
     def aliases(cls):
         return [cls.query_alias]
 
-    @classproperty
+    # @classproperty
-    def level(cls):
+    # def level(cls):
-        if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
+    #     if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
-            return 2
+    #         return 2
-        else:
+    #     else:
-            return 1
+    #         return 1
 
     @classproperty
     def query_alias(cls):
@@ -187,8 +187,9 @@ class BaseClass(Base):
         return query.limit(50).all()
 
     @classmethod
-    def results_to_df(cls, objects: list, **kwargs) -> DataFrame:
+    def results_to_df(cls, objects: list|None=None, **kwargs) -> DataFrame:
         """
+        Converts class sub_dicts into a Dataframe for all instances of the class.
 
         Args:
             objects (list): Objects to be converted to dataframe.
@@ -197,6 +198,12 @@ class BaseClass(Base):
         Returns:
             Dataframe
         """
+        if not objects:
+            try:
+                records = [obj.to_sub_dict(**kwargs) for obj in cls.query()]
+            except AttributeError:
+                records = [obj.to_dict(**kwargs) for obj in cls.query(page_size=0)]
+        else:
             try:
                 records = [obj.to_sub_dict(**kwargs) for obj in objects]
             except AttributeError:

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

@@ -262,7 +262,7 @@ class Control(BaseClass):
             try:
                 model = next(subclass for subclass in cls.__subclasses__() if
                              all([hasattr(subclass, attr) for attr in attrs.keys()]))
-            except StopIteration as e:
+            except StopIteration:
                 raise AttributeError(
                     f"Couldn't find existing class/subclass of {cls} with all attributes:\n{pformat(attrs.keys())}")
         return model
@@ -286,6 +286,7 @@ class Control(BaseClass):
         Dummy operation to be overridden by child classes.
 
         Args:
+            parent (QWidget): widget to add chart to.
             chart_settings (dict): settings passed down from chart widget
             ctx (Settings): settings passed down from gui
         """
@@ -663,7 +664,7 @@ class IridaControl(Control):
             return df, previous_dates
         # NOTE: if date was changed, rerun with new date
         else:
-            logger.warning(f"Date check failed, running recursion")
+            logger.warning(f"Date check failed, running recursion.")
             df, previous_dates = cls.check_date(df, item, previous_dates)
             return df, previous_dates
 

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

@@ -31,7 +31,6 @@ from jinja2.exceptions import TemplateNotFound
 from jinja2 import Template
 from PIL import Image
 
-
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
@@ -1584,7 +1583,7 @@ class Wastewater(BasicSubmission):
                     continue
                 thing['tooltip'] = f"Sample Name: {thing['name']}\nWell: {thing['sample_location']}"
                 dummy_samples.append(thing)
-            logger.debug(f"Dummy samples for 24 well: {pformat(dummy_samples)}")
+            # logger.debug(f"Dummy samples for 24 well: {pformat(dummy_samples)}")
             output['origin_plate'] = self.__class__.make_plate_map(sample_list=dummy_samples, plate_rows=4,
                                                                    plate_columns=6)
         # logger.debug(f"PCR info: {output['pcr_info']}")
@@ -2772,7 +2771,12 @@ class BacterialCultureSample(BasicSample):
         sample['concentration'] = self.concentration
         if self.control is not None:
             sample['colour'] = [0, 128, 0]
-            sample['tooltip'] = f"Control: {self.control.controltype.name} - {self.control.controltype.targets}"
+            target = next((v for k,v in self.control.controltype.targets.items() if k == self.control.subtype), "Not Available")
+            try:
+                target = ", ".join(target)
+            except:
+                target = "None"
+            sample['tooltip'] = f"\nControl: {self.control.controltype.name} - {target}"
         return sample
 
 

src/submissions/frontend/visualizations/__init__.py

@@ -134,3 +134,5 @@ class CustomFigure(Figure):
 
 from .irida_charts import IridaFigure
 from .pcr_charts import PCRFigure
+from .concentrations_chart import ConcentrationsChart
+from .turnaround_chart import TurnaroundChart

src/submissions/frontend/widgets/info_tab.py

@@ -60,12 +60,12 @@ class InfoPane(QWidget):
         return abs((d1.year - d2.year) * 12 + d1.month - d2.month)
 
     def save_excel(self):
-        fname = select_save_file(self, default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
+        fname = select_save_file(self, default_name=f"{self.__class__.__name__} Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
         self.report_obj.write_report(fname, obj=self)
 
     def save_pdf(self):
         fname = select_save_file(obj=self,
-                                 default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
+                                 default_name=f"{self.__class__.__name__} Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
                                  extension="pdf")
         save_pdf(obj=self.webview, filename=fname)
 

src/submissions/frontend/widgets/misc.py

@@ -2,13 +2,12 @@
 Contains miscellaneous widgets for frontend functions
 """
 import math
-from datetime import date
 from PyQt6.QtGui import QStandardItem, QIcon
 from PyQt6.QtWidgets import (
     QLabel, QLineEdit, QComboBox, QDateEdit, QPushButton, QWidget,
     QHBoxLayout, QSizePolicy
 )
-from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF
+from PyQt6.QtCore import Qt, QDate, QSize
 from tools import jinja_template_loading
 from backend.db.models import *
 import logging
@@ -18,98 +17,6 @@ logger = logging.getLogger(f"submissions.{__name__}")
 env = jinja_template_loading()
 
 
-# class AddReagentForm(QDialog):
-#     """
-#     dialog to add gather info about new reagent (Defunct)
-#     """
-#
-#     def __init__(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
-#                  reagent_name: str | None = None, kit: str | KitType | None = None) -> None:
-#         super().__init__()
-#         if reagent_name is None:
-#             reagent_name = reagent_role
-#         self.setWindowTitle("Add Reagent")
-#         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
-#         self.buttonBox = QDialogButtonBox(QBtn)
-#         self.buttonBox.accepted.connect(self.accept)
-#         self.buttonBox.rejected.connect(self.reject)
-#         # NOTE: widget to get lot info
-#         self.name_input = QComboBox()
-#         self.name_input.setObjectName("name")
-#         self.name_input.setEditable(True)
-#         self.name_input.setCurrentText(reagent_name)
-#         self.lot_input = QLineEdit()
-#         self.lot_input.setObjectName("lot")
-#         self.lot_input.setText(reagent_lot)
-#         # NOTE: widget to get expiry info
-#         self.expiry_input = QDateEdit(calendarPopup=True)
-#         self.expiry_input.setObjectName('expiry')
-#         # NOTE: if expiry is not passed in from gui, use today
-#         if expiry is None:
-#             logger.warning(f"Did not receive expiry, setting to 1970, 1, 1")
-#             self.expiry_input.setDate(QDate(1970, 1, 1))
-#         else:
-#             try:
-#                 self.expiry_input.setDate(expiry)
-#             except TypeError:
-#                 self.expiry_input.setDate(QDate(1970, 1, 1))
-#         # NOTE: widget to get reagent type info
-#         self.role_input = QComboBox()
-#         self.role_input.setObjectName('role')
-#         if kit:
-#             match kit:
-#                 case str():
-#                     kit = KitType.query(name=kit)
-#                 case _:
-#                     pass
-#             self.role_input.addItems([item.name for item in ReagentRole.query() if kit in item.kit_types])
-#         else:
-#             self.role_input.addItems([item.name for item in ReagentRole.query()])
-#         # NOTE: convert input to user-friendly string?
-#         try:
-#             reagent_role = reagent_role.replace("_", " ").title()
-#         except AttributeError:
-#             reagent_role = None
-#         # NOTE: set parsed reagent type to top of list
-#         index = self.role_input.findText(reagent_role, Qt.MatchFlag.MatchEndsWith)
-#         if index >= 0:
-#             self.role_input.setCurrentIndex(index)
-#         self.layout = QVBoxLayout()
-#         self.layout.addWidget(QLabel("Name:"))
-#         self.layout.addWidget(self.name_input)
-#         self.layout.addWidget(QLabel("Lot:"))
-#         self.layout.addWidget(self.lot_input)
-#         self.layout.addWidget(
-#             QLabel("Expiry:\n(use exact date on reagent.\nEOL will be calculated from kit automatically)")
-#         )
-#         self.layout.addWidget(self.expiry_input)
-#         self.layout.addWidget(QLabel("Type:"))
-#         self.layout.addWidget(self.role_input)
-#         self.layout.addWidget(self.buttonBox)
-#         self.setLayout(self.layout)
-#         self.role_input.currentTextChanged.connect(self.update_names)
-#
-#     def parse_form(self) -> dict:
-#         """
-#         Converts information in form to dict.
-#
-#         Returns:
-#             dict: Output info
-#         """
-#         return dict(name=self.name_input.currentText().strip(),
-#                     lot=self.lot_input.text().strip(),
-#                     expiry=self.expiry_input.date().toPyDate(),
-#                     role=self.role_input.currentText().strip())
-#
-#     def update_names(self):
-#         """
-#         Updates reagent names form field with examples from reagent type
-#         """
-#         self.name_input.clear()
-#         lookup = Reagent.query(role=self.role_input.currentText())
-#         self.name_input.addItems(list(set([item.name for item in lookup])))
-#
-#
 class StartEndDatePicker(QWidget):
     """
     custom widget to pick start and end dates for controls graphs
@@ -135,16 +42,6 @@ class StartEndDatePicker(QWidget):
         return QSize(80, 20)
 
 
-# def save_pdf(obj: QWebEngineView, filename: Path):
-#     page_layout = QPageLayout()
-#     page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
-#     page_layout.setOrientation(QPageLayout.Orientation.Portrait)
-#     page_layout.setMargins(QMarginsF(25, 25, 25, 25))
-#     obj.page().printToPdf(filename.absolute().__str__(), page_layout)
-
-
-# NOTE: subclass
-
 class CheckableComboBox(QComboBox):
     # once there is a checkState set, it is rendered
     # here we assume default Unchecked