Split Concentration controls on the chart so they are individually selectable.

src/submissions/frontend/widgets/concentrations.py

@@ -7,12 +7,14 @@ from backend.excel.reports import ConcentrationMaker
 from frontend.visualizations.concentrations_chart import ConcentrationsChart
 import logging
 
+
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
 class Concentrations(InfoPane):
 
     def __init__(self, parent: QWidget):
+        from .. import CheckableComboBox
         super().__init__(parent)
         self.save_button = QPushButton("Save Chart", parent=self)
         self.save_button.pressed.connect(self.save_png)
@@ -20,12 +22,14 @@ class Concentrations(InfoPane):
         self.export_button = QPushButton("Save Data", parent=self)
         self.export_button.pressed.connect(self.save_excel)
         self.layout.addWidget(self.export_button, 0, 3, 1, 1)
-        check_label = QLabel("Controls Only")
-        self.all_box = QCheckBox()
-        self.all_box.setChecked(True)
-        self.all_box.checkStateChanged.connect(self.update_data)
-        self.layout.addWidget(check_label, 1, 0, 1, 1)
-        self.layout.addWidget(self.all_box, 1, 1, 1, 1)
+        self.pos_neg = CheckableComboBox(parent=self)
+        self.pos_neg.model().itemChanged.connect(self.update_data)
+        self.pos_neg.setEditable(False)
+        self.pos_neg.addItem("Positive")
+        self.pos_neg.addItem("Negative")
+        self.pos_neg.addItem("Samples", start_checked=False)
+        self.layout.addWidget(QLabel("Control Types"), 1, 0, 1, 1)
+        self.layout.addWidget(self.pos_neg, 1, 1, 1, 1)
         self.fig = None
         self.report_object = None
         self.update_data()
@@ -37,10 +41,14 @@ class Concentrations(InfoPane):
         Returns:
             None
         """
+        include = self.pos_neg.get_checked()
+        # logger.debug(f"Include: {include}")
         super().update_data()
         months = self.diff_month(self.start_date, self.end_date)
         # logger.debug(f"Box checked: {self.all_box.isChecked()}")
-        chart_settings = dict(start_date=self.start_date, end_date=self.end_date, controls_only=self.all_box.isChecked())
+        # chart_settings = dict(start_date=self.start_date, end_date=self.end_date, controls_only=self.all_box.isChecked())
+        chart_settings = dict(start_date=self.start_date, end_date=self.end_date,
+                              include=include)
         self.report_obj = ConcentrationMaker(**chart_settings)
         self.fig = ConcentrationsChart(df=self.report_obj.df, settings=chart_settings, modes=[], months=months)
         self.webview.setHtml(self.fig.html)

src/submissions/frontend/widgets/misc.py

@@ -46,12 +46,15 @@ class CheckableComboBox(QComboBox):
     # once there is a checkState set, it is rendered
     # here we assume default Unchecked
 
-    def addItem(self, item, header: bool = False):
+    def addItem(self, item, header: bool = False, start_checked: bool = True):
         super(CheckableComboBox, self).addItem(item)
         item: QStandardItem = self.model().item(self.count() - 1, 0)
         if not header:
             item.setFlags(Qt.ItemFlag.ItemIsUserCheckable | Qt.ItemFlag.ItemIsEnabled)
-            item.setCheckState(Qt.CheckState.Checked)
+            if start_checked:
+                item.setCheckState(Qt.CheckState.Checked)
+            else:
+                item.setCheckState(Qt.CheckState.Unchecked)
 
     def itemChecked(self, index):
         item = self.model().item(index, 0)
@@ -60,14 +63,18 @@ class CheckableComboBox(QComboBox):
     def changed(self):
         self.updated.emit()
 
+    def get_checked(self):
+        checked = [self.itemText(i) for i in range(self.count()) if self.itemChecked(i)]
+        return checked
+
 
 class Pagifier(QWidget):
 
-    def __init__(self, page_max:int):
+    def __init__(self, page_max: int):
         super().__init__()
         self.page_max = math.ceil(page_max)
         self.page_anchor = 1
-        next = QPushButton(parent=self, icon = QIcon.fromTheme(QIcon.ThemeIcon.GoNext))
+        next = QPushButton(parent=self, icon=QIcon.fromTheme(QIcon.ThemeIcon.GoNext))
         next.pressed.connect(self.increment_page)
         previous = QPushButton(parent=self, icon=QIcon.fromTheme(QIcon.ThemeIcon.GoPrevious))
         previous.pressed.connect(self.decrement_page)

src/submissions/frontend/widgets/submission_details.py

@@ -92,6 +92,7 @@ class SubmissionDetails(QDialog):
         Args:
             sample (str): Submitter Id of the sample.
         """
+        logger.debug(f"Sample details.")
         if isinstance(sample, str):
             sample = BasicSample.query(submitter_id=sample)
         base_dict = sample.to_sub_dict(full_data=True)
@@ -102,6 +103,8 @@ class SubmissionDetails(QDialog):
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
             css = f.read()
         html = template.render(sample=base_dict, css=css)
+        with open(f"{sample.submitter_id}.html", 'w') as f:
+            f.write(html)
         self.webview.setHtml(html)
         self.setWindowTitle(f"Sample Details - {sample.submitter_id}")
 
@@ -114,6 +117,7 @@ class SubmissionDetails(QDialog):
             kit (str | KitType): Name of kit.
             reagent (str | Reagent): Lot number of the reagent
         """
+        logger.debug(f"Reagent details.")
         if isinstance(reagent, str):
             reagent = Reagent.query(lot=reagent)
         if isinstance(kit, str):
@@ -164,6 +168,7 @@ class SubmissionDetails(QDialog):
         Args:
             submission (str | BasicSubmission): Submission of interest.
         """
+        logger.debug(f"Submission details.")
         if isinstance(submission, str):
             submission = BasicSubmission.query(rsl_plate_num=submission)
         self.rsl_plate_num = submission.rsl_plate_num