Updated parsers and chart constructors.

src/submissions/frontend/main_window_functions.py

@@ -35,6 +35,7 @@ from .custom_widgets.pop_ups import AlertPop, QuestionAsker
 from .custom_widgets import ReportDatePicker, ReagentTypeForm
 from .custom_widgets.misc import ImportReagent
 from .visualizations.control_charts import create_charts, construct_html
+import asyncio
 
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -111,11 +112,14 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
                 add_widget = QComboBox()
                 # lookup existing kits by 'submission_type' decided on by sheetparser
                 uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=prsr.sub['submission_type'])]
-                add_widget.addItems(uses)
                 if check_not_nan(prsr.sub[item]):
+                    logger.debug(f"The extraction kit in parser was: {prsr.sub[item]}")
+                    uses.insert(0, uses.pop(uses.index(prsr.sub[item])))
                     obj.ext_kit = prsr.sub[item]
                 else:
-                    obj.ext_kit = add_widget.currentText()
+                    logger.error(f"Couldn't find prsr.sub[extraction_kit]")
+                    obj.ext_kit = uses[0]
+                add_widget.addItems(uses)
             case 'submitted_date':
                 # create label
                 obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
@@ -265,7 +269,7 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
     # reset form
     for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
         item.setParent(None)
-    print(dir(obj))
+    # print(dir(obj))
     if hasattr(obj, 'csv'):
         dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
         if dlg.exec():
@@ -426,6 +430,8 @@ def chart_maker_function(obj:QMainWindow) -> QMainWindow:
         # flatten data to one dimensional list
         data = [item for sublist in data for item in sublist]
         logger.debug(f"Control objects going into df conversion: {data}")
+        if data == []:
+            return obj, dict(status="Critical", message="No data found for controls in given date range.")
         # send to dataframe creator
         df = convert_data_list_to_df(ctx=obj.ctx, input=data, subtype=obj.subtype)
         if obj.subtype == None:

src/submissions/frontend/visualizations/control_charts.py

@@ -39,7 +39,7 @@ def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
             genera.append("")
     df['genus'] = df['genus'].replace({'\*':''}, regex=True).replace({"NaN":"Unknown"})
     df['genera'] = genera
-    df = df.dropna()
+    # df = df.dropna()
     # remove original runs, using reruns if applicable
     df = drop_reruns_from_df(ctx=ctx, df=df)
     # sort by and exclude from
@@ -49,6 +49,7 @@ def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
     # Set descending for any columns that have "{mode}" in the header.
     ascending = [False if item == "target" else True for item in sorts]
     df = df.sort_values(by=sorts, ascending=ascending)
+    logger.debug(df[df.isna().any(axis=1)])
     # actual chart construction is done by
     fig = construct_chart(ctx=ctx, df=df, modes=modes, ytitle=ytitle)
     return fig
@@ -245,6 +246,8 @@ def construct_kraken_chart(settings:dict, df:pd.DataFrame, group_name:str, mode:
         Figure: initial figure with traces for modes
     """    
     df[f'{mode}_count'] = pd.to_numeric(df[f'{mode}_count'],errors='coerce')
+    df = df.groupby('submitted_date')[f'{mode}_count'].nlargest(2)
+    
     # The actual percentage from kraken was off due to exclusion of NaN, recalculating.
     df[f'{mode}_percent'] = 100 * df[f'{mode}_count'] / df.groupby('submitted_date')[f'{mode}_count'].transform('sum')
     modes = settings['modes'][mode]