Debugged reports.

CHANGELOG.md

@@ -1,3 +1,7 @@
+# 202503.05
+
+- Added concentrations chart tab.
+
 # 202503.04
 
 - Kit editor debugging.

src/submissions/backend/excel/reports.py

@@ -1,6 +1,6 @@
-'''
+"""
 Contains functions for generating summary reports
-'''
+"""
 import itertools
 import sys
 from pprint import pformat
@@ -10,7 +10,7 @@ from pathlib import Path
 from datetime import date
 from typing import Tuple
 from backend.db.models import BasicSubmission, IridaControl
-from tools import jinja_template_loading, get_first_blank_df_row, row_map, ctx
+from tools import jinja_template_loading, get_first_blank_df_row, row_map
 from PyQt6.QtWidgets import QWidget
 from openpyxl.worksheet.worksheet import Worksheet
 
@@ -36,6 +36,7 @@ class ReportArchetype(object):
             filename = Path(filename)
         filename = filename.absolute()
         self.writer = ExcelWriter(filename.with_suffix(".xlsx"), engine='openpyxl')
+        self.df.index += 1
         self.df.to_excel(self.writer, sheet_name=self.sheet_name)
         self.writer.close()
 

src/submissions/backend/validators/omni_gui_objects.py

@@ -22,86 +22,6 @@ class BaseOmni(BaseModel):
     def aliases(cls):
         return cls.class_object.aliases
 
-    # NOTE: Okay, this will not work for editing, since by definition not all attributes will line up.
-    #     def check_all_attributes(self, attributes: dict) -> bool:
-    #         """
-    #         Checks this instance against a dictionary of attributes to determine if they are a match.
-    #
-    #         Args:
-    #             attributes (dict): A dictionary of attributes to be check for equivalence
-    #
-    #         Returns:
-    #             bool: If a single unequivocal value is found will be false, else true.
-    #         """
-    #         logger.debug(f"Incoming attributes: {attributes}")
-    #         for key, value in attributes.items():
-    #             logger.debug(f"Comparing value class: {value.__class__} to omni class")
-    #             if isinstance(value, str):
-    #                 try:
-    #                     check = value.lower() == "none"
-    #                 except AttributeError:
-    #                     continue
-    #                 if check:
-    #                     value = None
-    #             logger.debug(f"Attempting to grab attribute: {key}")
-    #             try:
-    #                 self_value = getattr(self, key)
-    #                 class_attr = getattr(self.class_object, key)
-    #             except AttributeError:
-    #                 continue
-    #             try:
-    #                 logger.debug(f"Check if {self_value.__class__} is subclass of {BaseOmni}")
-    #                 check = issubclass(self_value.__class__, BaseOmni)
-    #             except TypeError as e:
-    #                 logger.error(f"Couldn't check if {self_value.__class__} is subclass of {BaseOmni} due to {e}")
-    #                 check = False
-    #             if check:
-    #                 logger.debug(f"Checking for subclass name.")
-    #                 self_value = self_value.name
-    #             try:
-    #                 logger.debug(f"Check if {value.__class__} is subclass of {BaseOmni}")
-    #                 check = issubclass(value.__class__, BaseOmni)
-    #             except TypeError as e:
-    #                 logger.error(f"Couldn't check if {value.__class__} is subclass of {BaseOmni} due to {e}")
-    #                 check = False
-    #             if check:
-    #                 logger.debug(f"Checking for subclass name.")
-    #                 value = value.name
-    #             logger.debug(f"Self value: {self_value}, class attr: {class_attr} of type: {type(class_attr)}")
-    #             if isinstance(class_attr, property):
-    #                 filter = "property"
-    #             else:
-    #                 filter = class_attr.property
-    #             match filter:
-    #                 case ColumnProperty():
-    #                     match class_attr.type:
-    #                         case INTEGER():
-    #                             if value.lower() == "true":
-    #                                 value = 1
-    #                             elif value.lower() == "false":
-    #                                 value = 0
-    #                             else:
-    #                                 value = int(value)
-    #                         case FLOAT():
-    #                             value = float(value)
-    #                 case "property":
-    #                     pass
-    #                 case _RelationshipDeclared():
-    #                     logger.debug(f"Checking relationship value: {self_value}")
-    #                     try:
-    #                         self_value = self_value.name
-    #                     except AttributeError:
-    #                         pass
-    #                     if class_attr.property.uselist:
-    #                         self_value = self_value.__str__()
-    #             logger.debug(
-    #                 f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
-    #             if self_value != value:
-    #                 output = False
-    #                 logger.debug(f"Value {key} is False, returning.")
-    #                 return output
-    #         return True
-
     def check_all_attributes(self, attributes: dict) -> bool:
         logger.debug(f"Incoming attributes: {attributes}")
         attributes = {k : v for k, v in attributes.items() if k in self.list_searchables.keys()}
@@ -122,7 +42,6 @@ class BaseOmni(BaseModel):
         logger.debug("Everything checks out, these are the same object.")
         return True
 
-
     def __setattr__(self, key, value):
         try:
             class_value = getattr(self.class_object, key)
@@ -395,6 +314,13 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
             return {}
         return value
 
+    @field_validator("required", mode="before")
+    @classmethod
+    def rescue_required_none(cls, value):
+        if not value:
+            value = 1
+        return value
+
     def __init__(self, instance_object: Any, **data):
         super().__init__(**data)
         self.instance_object = instance_object

src/submissions/frontend/visualizations/concentrations_chart.py

@@ -1,5 +1,5 @@
 """
-Construct turnaround time charts
+Construct BC control concentration charts
 """
 from pprint import pformat
 from . import CustomFigure
@@ -21,17 +21,15 @@ class ConcentrationsChart(CustomFigure):
         super().__init__(df=df, modes=modes, settings=settings)
         self.df = df
         self.construct_chart()
-        # if threshold:
-        #     self.add_hline(y=threshold)
         self.update_layout(showlegend=False)
 
     def construct_chart(self, df: pd.DataFrame | None = None):
         if df:
             self.df = df
-        # logger.debug(f"Constructing concentration chart with df:\n{self.df}")
         try:
             self.df = self.df[self.df.concentration.notnull()]
-            self.df = self.df.sort_values(['submitted_date', 'submission'], ascending=[True, True]).reset_index(drop=True)
+            self.df = self.df.sort_values(['submitted_date', 'submission'], ascending=[True, True]).reset_index(
+                drop=True)
             self.df = self.df.reset_index().rename(columns={"index": "idx"})
             # logger.debug(f"DF after changes:\n{self.df}")
             scatter = px.scatter(data_frame=self.df, x='submission', y="concentration",
@@ -41,8 +39,6 @@ class ConcentrationsChart(CustomFigure):
         except (ValueError, AttributeError) as e:
             logger.error(f"Error constructing chart: {e}")
             scatter = px.scatter()
-        # logger.debug(f"Scatter data: {scatter.data}")
-        # self.add_traces(scatter.data)
         # NOTE: For some reason if data is allowed to sort itself it leads to wrong ordering of x axis.
         traces = sorted(scatter.data, key=itemgetter("name"))
         for trace in traces:
@@ -60,6 +56,9 @@ class ConcentrationsChart(CustomFigure):
                 tickmode='array',
                 tickvals=tickvals,
                 ticktext=ticklabels,
+            ),
+            yaxis=dict(
+                rangemode="nonnegative"
             )
         )
         self.update_traces(marker={'size': 15})

src/submissions/frontend/widgets/concentrations.py

@@ -1,7 +1,7 @@
 """
-Pane showing turnaround time summary.
+Pane showing BC control concentrations summary.
 """
-from PyQt6.QtWidgets import QWidget, QPushButton, QComboBox, QLabel
+from PyQt6.QtWidgets import QWidget, QPushButton
 from .info_tab import InfoPane
 from backend.excel.reports import ConcentrationMaker
 from frontend.visualizations.concentrations_chart import ConcentrationsChart
@@ -22,12 +22,6 @@ class Concentrations(InfoPane):
         self.layout.addWidget(self.export_button, 0, 3, 1, 1)
         self.fig = None
         self.report_object = None
-        # self.submission_typer = QComboBox(self)
-        # subs = ["All"] + [item.name for item in SubmissionType.query()]
-        # self.submission_typer.addItems(subs)
-        # self.layout.addWidget(QLabel("Submission Type"), 1, 0, 1, 1)
-        # self.layout.addWidget(self.submission_typer, 1, 1, 1, 3)
-        # self.submission_typer.currentTextChanged.connect(self.update_data)
         self.update_data()
 
     def update_data(self) -> None:
@@ -40,17 +34,6 @@ class Concentrations(InfoPane):
         super().update_data()
         months = self.diff_month(self.start_date, self.end_date)
         chart_settings = dict(start_date=self.start_date, end_date=self.end_date)
-        # if self.submission_typer.currentText() == "All":
-        #     submission_type = None
-        #     subtype_obj = None
-        # else:
-        #     submission_type = self.submission_typer.currentText()
-        #     subtype_obj = SubmissionType.query(name = submission_type)
-        # self.report_obj = ConcentrationMaker(start_date=self.start_date, end_date=self.end_date)#, submission_type=submission_type)
         self.report_obj = ConcentrationMaker(**chart_settings)
-        # if subtype_obj:
-        #     threshold = subtype_obj.defaults['turnaround_time'] + 0.5
-        # else:
-        #     threshold = None
         self.fig = ConcentrationsChart(df=self.report_obj.df, settings=chart_settings, modes=[], months=months)
         self.webview.setHtml(self.fig.html)