Mid-code cleanup

src/submissions/frontend/visualizations/turnaround_chart.py

@@ -11,25 +11,33 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 class TurnaroundChart(CustomFigure):
 
-    def __init__(self, df: pd.DataFrame, modes: list, settings: dict, ytitle: str | None = None,
+    def __init__(self, df: pd.DataFrame, modes: list, settings: dict, threshold: float | None = None,
+                 ytitle: str | None = None,
                  parent: QWidget | None = None,
                  months: int = 6):
         super().__init__(df=df, modes=modes, settings=settings)
+        self.df = df
         try:
             months = int(settings['months'])
         except KeyError:
             months = 6
         # logger.debug(f"DF: {self.df}")
-        self.construct_chart(df=df)
-        self.add_hline(y=3.5)
+        self.construct_chart()
+        if threshold:
+            self.add_hline(y=threshold)
         # self.update_xaxes()
         self.update_layout(showlegend=False)
 
-    def construct_chart(self, df: pd.DataFrame):
+    def construct_chart(self, df: pd.DataFrame | None = None):
+        if df:
+            self.df = df
         # logger.debug(f"PCR df:\n {df}")
-        df = df.sort_values(by=['submitted_date', 'name'])
+        self.df = self.df[self.df.days.notnull()]
+        self.df = self.df.sort_values(['submitted_date', 'name'], ascending=[True, True]).reset_index(drop=True)
+        self.df = self.df.reset_index().rename(columns={"index": "idx"})
+        # logger.debug(f"DF: {self.df}")
         try:
-            scatter = px.scatter(data_frame=df, x='name', y="days",
+            scatter = px.scatter(data_frame=self.df, x='idx', y="days",
                                  hover_data=["name", "submitted_date", "completed_date", "days"],
                                  color="acceptable", color_discrete_map={True: "green", False: "red"}
                                  )
@@ -37,3 +45,12 @@ class TurnaroundChart(CustomFigure):
             scatter = px.scatter()
         self.add_traces(scatter.data)
         self.update_traces(marker={'size': 15})
+        tickvals = self.df['idx'].tolist()
+        ticklabels = self.df['name'].tolist()
+        self.update_layout(
+            xaxis=dict(
+                tickmode='array',
+                tickvals=tickvals,
+                ticktext=ticklabels,
+            )
+        )

src/submissions/frontend/widgets/submission_details.py

@@ -8,7 +8,7 @@ from PyQt6.QtWebChannel import QWebChannel
 from PyQt6.QtCore import Qt, pyqtSlot
 from jinja2 import TemplateNotFound
 from backend.db.models import BasicSubmission, BasicSample, Reagent, KitType
-from tools import is_power_user, jinja_template_loading
+from tools import is_power_user, jinja_template_loading, timezone
 from .functions import select_save_file
 from .misc import save_pdf
 from pathlib import Path
@@ -176,7 +176,8 @@ class SubmissionDetails(QDialog):
         if isinstance(submission, str):
             submission = BasicSubmission.query(rsl_plate_num=submission)
         submission.signed_by = getuser()
-        submission.completed_date = datetime.now().date()
+        submission.completed_date = datetime.now()
+        submission.completed_date.replace(tzinfo=timezone)
         submission.save()
         self.submission_details(submission=self.rsl_plate_num)
 

src/submissions/frontend/widgets/turnaround.py

@@ -1,10 +1,10 @@
 from PyQt6.QtCore import QSignalBlocker
 from PyQt6.QtWebEngineWidgets import QWebEngineView
-from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton, QLabel
+from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton, QLabel, QComboBox
 from .info_tab import InfoPane
 from backend.excel.reports import TurnaroundMaker
 from pandas import DataFrame
-from backend.db import BasicSubmission
+from backend.db import BasicSubmission, SubmissionType
 from frontend.visualizations.turnaround_chart import TurnaroundChart
 import logging
 
@@ -17,6 +17,11 @@ class TurnaroundTime(InfoPane):
         super().__init__(parent)
         self.chart = None
         self.report_object = None
+        self.submission_typer = QComboBox(self)
+        subs = ["Any"] + [item.name for item in SubmissionType.query()]
+        self.submission_typer.addItems(subs)
+        self.layout.addWidget(self.submission_typer, 1, 1, 1, 3)
+        self.submission_typer.currentTextChanged.connect(self.date_changed)
         self.date_changed()
 
     def date_changed(self):
@@ -31,6 +36,16 @@ class TurnaroundTime(InfoPane):
             return
         super().date_changed()
         chart_settings = dict(start_date=self.start_date, end_date=self.end_date)
-        self.report_obj = TurnaroundMaker(start_date=self.start_date, end_date=self.end_date)
-        self.chart = TurnaroundChart(df=self.report_obj.df, settings=chart_settings, modes=[])
+        if self.submission_typer.currentText() == "Any":
+            submission_type = None
+            subtype_obj = None
+        else:
+            submission_type = self.submission_typer.currentText()
+            subtype_obj = SubmissionType.query(name = submission_type)
+        self.report_obj = TurnaroundMaker(start_date=self.start_date, end_date=self.end_date, submission_type=submission_type)
+        if subtype_obj:
+            threshold = subtype_obj.defaults['turnaround_time'] + 0.5
+        else:
+            threshold = None
+        self.chart = TurnaroundChart(df=self.report_obj.df, settings=chart_settings, modes=[], threshold=threshold)
         self.webview.setHtml(self.chart.to_html())