Improve plate mapping by using layout in submission forms rather than PCR. Pre-moving excel maps to DB.

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 202306.03
+
+- Improve WW plate mapping by using layout in submission forms rather than PCR.
+
 ## 202306.02
 
 - Addition of bacterial plate maps to details export.

TODO.md

@@ -1,4 +1,7 @@
-- [ ] Improve plate mapping by using layout in submission forms rather than PCR.
+- [ ] Move submission types from config.yml into database.
+- [x] Solve bug for plate mapping when two samples of same name are in different rows.
+    - Try importing "L:\Robotics Laboratory Support\Submissions\Wastewater\2023\2023-06-21\RSL-WW-20230621-1.xlsx" for example.
+- [x] Improve plate mapping by using layout in submission forms rather than PCR.
 - [x] Create a method for creation of hitpicking .csvs because of reasons that may or may not exist.
 - [x] Create a method for commenting submissions.
 - [x] Create barcode generator, because of reasons that may or may not exist.

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202306.2b"
+__version__ = "202306.3b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
 

src/submissions/backend/excel/parser.py

@@ -173,6 +173,7 @@ class SheetParser(object):
             elu_map = full.iloc[9:18, 5:]
             elu_map.set_index(elu_map.columns[0], inplace=True)
             elu_map.columns = elu_map.iloc[0]
+            elu_map = elu_map.tail(-1)
             return elu_map
         def parse_reagents(df:pd.DataFrame) -> None:
             """
@@ -274,10 +275,13 @@ class SheetParser(object):
                 for c in df.columns.to_list():
                     logger.debug(f"Checking {ii.name}{c}")
                     if check_not_nan(df.loc[ii.name, int(c)]) and df.loc[ii.name, int(c)] != "EMPTY":
-                        
+                        try:
                             return_list.append(dict(sample_name=re.sub(r"\s?\(.*\)", "", df.loc[ii.name, int(c)]), \
                                                 well=f"{ii.name}{c}",
                                                 artic_plate=self.sub['rsl_plate_num']))
+                        except TypeError as e:
+                            logger.error(f"Got an int for {c}, skipping.")
+                            continue
             logger.debug(f"massaged sample list for {self.sub['rsl_plate_num']}: {pprint.pprint(return_list)}")
             return return_list
         submission_info = self.xl.parse("First Strand", dtype=object)
@@ -355,8 +359,12 @@ class SampleParser(object):
         """        
         def search_df_for_sample(sample_rsl:str):
             logger.debug(f"Attempting to find sample {sample_rsl} in \n {self.elution_map}")
-            print(f"Attempting to find sample {sample_rsl} in \n {self.elution_map}")
+            well = self.elution_map.where(self.elution_map==sample_rsl)
-            well = self.elution_map.where(self.elution_map==sample_rsl).dropna(how='all').dropna(axis=1)
+            # logger.debug(f"Well: {well}")
+            well = well.dropna(how='all').dropna(axis=1, how="all")
+            if well.size > 1:
+                well = well.iloc[0].to_frame().dropna().T
+            logger.debug(f"well {sample_rsl} post processing: {well.size}: {type(well)}, {well.index[0]}, {well.columns[0]}")
             self.elution_map.at[well.index[0], well.columns[0]] = np.nan
             try:
                 col = str(int(well.columns[0]))
@@ -366,6 +374,7 @@ class SampleParser(object):
                 logger.error(f"Problem parsing out column number for {well}:\n {e}")
             return f"{well.index[0]}{col}"
         new_list = []
+        return_val = None
         for sample in self.samples:
             new = WWSample()
             if check_not_nan(sample["Unnamed: 7"]):
@@ -389,9 +398,16 @@ class SampleParser(object):
             # new.site_status = sample['Unnamed: 7']
             new.notes = str(sample['Unnamed: 6']) # previously Unnamed: 8
             new.well_number = sample['Unnamed: 1']
-            new.elution_well = search_df_for_sample(new.rsl_number)
+            elu_well = search_df_for_sample(new.rsl_number)
+            if elu_well != None:
+                new.elution_well = elu_well
+            else:
+                # try:
+                return_val += f"{new.rsl_number}\n"
+                # except TypeError:
+                    # return_val = f"{new.rsl_number}\n"
             new_list.append(new)
-        return None, new_list
+        return return_val, new_list
     
     def parse_wastewater_artic_samples(self) -> Tuple[str|None, list[WWSample]]:
         """

src/submissions/frontend/main_window_functions.py

@@ -61,6 +61,9 @@ 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}")
+    for sample in prsr.sub['samples']:
+        if hasattr(sample, "elution_well"):
+            logger.debug(f"Sample from import: {sample.elution_well}")
     obj.current_submission_type = prsr.sub['submission_type']
     # destroy any widgets from previous imports
     for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):