Missing sample message after Artic parsing.

src/submissions/frontend/custom_widgets/sub_details.py

@@ -114,6 +114,10 @@ class SubmissionsSheet(QTableView):
             del self.data['reagents']
         except KeyError:
             pass
+        try:
+            del self.data['comments']
+        except KeyError:
+            pass
         proxyModel = QSortFilterProxyModel()
         proxyModel.setSourceModel(pandasModel(self.data))
         self.setModel(proxyModel)
@@ -226,11 +230,12 @@ class SubmissionsSheet(QTableView):
                 else:
                     logger.error(f"We had to truncate the number of samples to 94.")
         logger.debug(f"We found {len(dicto)} to hitpick")
-        msg = AlertPop(message=f"We found {len(dicto)} samples to hitpick", status="INFORMATION")
-        msg.exec()
         # convert all samples to dataframe
         df = make_hitpicks(dicto)
-        logger.debug(f"Size of the dataframe: {df.size}")
+        df = df[df.positive != False]
+        logger.debug(f"Size of the dataframe: {df.shape[0]}")
+        msg = AlertPop(message=f"We found {df.shape[0]} samples to hitpick", status="INFORMATION")
+        msg.exec()
         if df.size == 0:
             return
         date = datetime.strftime(datetime.today(), "%Y-%m-%d")
@@ -264,6 +269,7 @@ class SubmissionDetails(QDialog):
         interior.setParent(self)
         # get submision from db
         data = lookup_submission_by_id(ctx=ctx, id=id)
+        logger.debug(f"Submission details data:\n{data.to_dict()}")
         self.base_dict = data.to_dict()
         # don't want id
         del self.base_dict['id']
@@ -308,8 +314,11 @@ class SubmissionDetails(QDialog):
         platemap = make_plate_map(plate_dicto)
         logger.debug(f"platemap: {platemap}")
         image_io = BytesIO()
-        platemap.save(image_io, 'JPEG')
-        platemap.save("test.jpg", 'JPEG')
+        try:
+            platemap.save(image_io, 'JPEG')
+        except AttributeError:
+            logger.error(f"No plate map found for {sub.rsl_plate_num}")
+        # platemap.save("test.jpg", 'JPEG')
         self.base_dict['platemap'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
         logger.debug(self.base_dict)
         html = template.render(sub=self.base_dict)

src/submissions/frontend/main_window_functions.py

@@ -26,7 +26,7 @@ from backend.db.functions import (
     lookup_all_orgs, lookup_kittype_by_use, lookup_kittype_by_name, 
     construct_submission_info, lookup_reagent, store_submission, lookup_submissions_by_date_range, 
     create_kit_from_yaml, create_org_from_yaml, get_control_subtypes, get_all_controls_by_type,
-    lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample
+    lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample, hitpick_plate
 )
 from backend.excel.parser import SheetParser, PCRParser
 from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
@@ -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
+from .visualizations import make_plate_map
 
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -60,6 +61,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
     if prsr.sub['rsl_plate_num'] == None:
         prsr.sub['rsl_plate_num'] = RSLNamer(fname.__str__()).parsed_name
     logger.debug(f"prsr.sub = {prsr.sub}")
+    obj.current_submission_type = prsr.sub['submission_type']
     # destroy any widgets from previous imports
     for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
         item.setParent(None)
@@ -111,7 +113,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
                     uses.insert(0, uses.pop(uses.index(prsr.sub[item])))
                     obj.ext_kit = prsr.sub[item]
                 else:
-                    logger.error(f"Couldn't find prsr.sub[extraction_kit]")
+                    logger.error(f"Couldn't find {prsr.sub['extraction_kit']}")
                     obj.ext_kit = uses[0]
                 add_widget.addItems(uses)
             case 'submitted_date':
@@ -156,6 +158,9 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
     if hasattr(obj, 'ext_kit'):
         obj.kit_integrity_completion()
     logger.debug(f"Imported reagents: {obj.reagents}")
+    if prsr.sample_result != None:
+        msg = AlertPop(message=prsr.sample_result, status="WARNING")
+        msg.exec()
     return obj, result
 
 def kit_reload_function(obj:QMainWindow) -> QMainWindow:
@@ -263,6 +268,7 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
     # reset form
     for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
         item.setParent(None)
+    logger.debug(f"All attributes of obj: {pprint.pprint(obj.__dict__)}")
     if hasattr(obj, 'csv'):
         dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
         if dlg.exec():
@@ -271,6 +277,14 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
                 obj.csv.to_csv(fname.__str__(), index=False)
             except PermissionError:
                 logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
+    try:
+        delattr(obj, "csv")
+    except AttributeError:
+        pass
+    # if obj.current_submission_type == "Bacterial_Culture":
+    #     hitpick = hitpick_plate(base_submission)
+    #     image = make_plate_map(hitpick)
+    #     image.show()
     return obj, result
 
 def generate_report_function(obj:QMainWindow) -> QMainWindow:

src/submissions/frontend/visualizations/plate_map.py

@@ -12,7 +12,7 @@ def make_plate_map(sample_list:list) -> Image:
     Makes a pillow image of a plate from hitpicks 
 
     Args:
-        sample_list (list): list of positive sample dictionaries from the hitpicks
+        sample_list (list): list of sample dictionaries from the hitpicks
 
     Returns:
         Image: Image of the 96 well plate with positive samples in red.
@@ -26,12 +26,17 @@ def make_plate_map(sample_list:list) -> Image:
     except TypeError as e:
         logger.error(f"No samples for this plate. Nothing to do.")
         return None
-    # Make a 8 row, 12 column, 3 color ints array, filled with white by default
+    # Make an 8 row, 12 column, 3 color ints array, filled with white by default
     grid = np.full((8,12,3),255, dtype=np.uint8)
-    # Go through samples and change its row/column to red
+    # Go through samples and change its row/column to red if positive, else blue
     for sample in sample_list:
-        grid[int(sample['row'])-1][int(sample['column'])-1] = [255,0,0]
-    # Create image from the grid
+        logger.debug(f"sample keys: {list(sample.keys())}")
+        if sample['positive']:
+            colour = [255,0,0]
+        else:
+            colour = [0,0,255]
+        grid[int(sample['row'])-1][int(sample['column'])-1] = colour
+    # Create pixel image from the grid and enlarge
     img = Image.fromarray(grid).resize((1200, 800), resample=Image.NEAREST)
     # create a drawer over the image
     draw = ImageDraw.Draw(img)
@@ -58,7 +63,6 @@ def make_plate_map(sample_list:list) -> Image:
     new_img.paste(img, box)
     # create drawer over the new image
     draw = ImageDraw.Draw(new_img)
-    # font = ImageFont.truetype("sans-serif.ttf", 16)
     if check_if_app():
         font_path = Path(sys._MEIPASS).joinpath("files", "resources")
     else: