Missing sample message after Artic parsing.

CHANGELOG.md

@@ -1,3 +1,8 @@
+## 202306.02
+
+- Addition of bacterial plate maps to details export.
+- Change in Artic cost calculation to reflect multiple output plates per submission.
+
 ## 202306.01
 
 - Large scale shake up of import and scraper functions.

TODO.md

@@ -1,4 +1,5 @@
-- [ ] Create a method for creation of hitpicking .csvs because of reasons that may or may not exist.
+- [ ] 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.
 - [x] Move bulk of functions from frontend.__init__ to frontend.functions as __init__ is getting bloated.

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202306.1b"
+__version__ = "202306.2b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
 

src/submissions/backend/db/functions.py

@@ -31,6 +31,7 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
     cursor.execute("PRAGMA foreign_keys=ON")
     cursor.close()
 
+
 def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None|dict:
     """
     Upserts submissions into database
@@ -799,9 +800,21 @@ def lookup_discounts_by_org_and_kit(ctx:dict, kit_id:int, lab_id:int):
         )).all()
 
 def hitpick_plate(submission:models.BasicSubmission, plate_number:int=0) -> list:
+    """
+    Creates a list of sample positions and statuses to be used by plate mapping and csv output to biomek software.
+
+    Args:
+        submission (models.BasicSubmission): Input submission
+        plate_number (int, optional): plate position in the series of selected plates. Defaults to 0.
+
+    Returns:
+        list: list of sample dictionaries.
+    """    
     plate_dicto = []
     for sample in submission.samples:
         # have sample report back its info if it's positive, otherwise, None
+        method_list = [func for func in dir(sample) if callable(getattr(sample, func))]
+        logger.debug(f"Method list of sample: {method_list}")
         samp = sample.to_hitpick()
         if samp == None:
             continue
@@ -811,6 +824,43 @@ def hitpick_plate(submission:models.BasicSubmission, plate_number:int=0) -> list
             # if len(dicto) < 88:
             this_sample = dict(
                 plate_number = plate_number,
+                sample_name = samp['name'],
+                column = samp['col'],
+                row = samp['row'],
+                positive = samp['positive'],
+                plate_name = submission.rsl_plate_num
+            )
+            # append to plate samples
+            plate_dicto.append(this_sample)
+            # append to all samples
+    # image = make_plate_map(plate_dicto)
+    return plate_dicto
+
+def platemap_plate(submission:models.BasicSubmission) -> list:
+    """
+    Depreciated. Replaced by new functionality in hitpick_plate
+
+    Args:
+        submission (models.BasicSubmission): Input submission
+
+    Returns:
+        list: list of sample dictionaries
+    """    
+    plate_dicto = []
+    for sample in submission.samples:
+        # have sample report back its info if it's positive, otherwise, None
+        
+        try:
+            samp = sample.to_platemap()
+        except AttributeError:
+            continue
+        if samp == None:
+            continue
+        else:
+            logger.debug(f"Item name: {samp['name']}")
+            # plate can handle 88 samples to leave column for controls
+            # if len(dicto) < 88:
+            this_sample = dict(
                 sample_name = samp['name'],
                 column = samp['col'],
                 row = samp['row'],

src/submissions/backend/db/models/samples.py

@@ -62,8 +62,10 @@ class WWSample(Base):
         # if well_col > 4:
         #     well
         if self.ct_n1 != None and self.ct_n2 != None:
+            # logger.debug(f"Using well info in name.")
             name = f"{self.ww_sample_full_id}\n\t- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})\n\t- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
         else:
+            # logger.debug(f"NOT using well info in name for: {self.ww_sample_full_id}")
             name = self.ww_sample_full_id
         return {
             "well": self.well_number,
@@ -85,18 +87,23 @@ class WWSample(Base):
         except TypeError as e:
             logger.error(f"Couldn't check positives for {self.rsl_number}. Looks like there isn't PCR data.")
             return None
-        if positive:
-            try:
-                # The first character of the elution well is the row
-                well_row = row_dict[self.elution_well[0]]
-                # The remaining charagers are the columns
-                well_col = self.elution_well[1:]
-            except TypeError as e:
-                logger.error(f"This sample doesn't have elution plate info.")
-                return None
-            return dict(name=self.ww_sample_full_id, row=well_row, col=well_col)
-        else:
-            return None
+        well_row = row_dict[self.elution_well[0]]
+        well_col = self.elution_well[1:]
+        # if positive:
+        #     try:
+        #         # The first character of the elution well is the row
+        #         well_row = row_dict[self.elution_well[0]]
+        #         # The remaining charagers are the columns
+        #         well_col = self.elution_well[1:]
+        #     except TypeError as e:
+        #         logger.error(f"This sample doesn't have elution plate info.")
+        #         return None
+        return dict(name=self.ww_sample_full_id, 
+                    row=well_row, 
+                    col=well_col, 
+                    positive=positive)
+        # else:
+        #     return None
 
 
 class BCSample(Base):
@@ -134,6 +141,23 @@ class BCSample(Base):
             "name": f"{self.sample_id} - ({self.organism})",
         }
 
+    def to_hitpick(self) -> dict|None:
+        """
+        Outputs a dictionary of locations
+
+        Returns:
+            dict: dictionary of sample id, row and column in elution plate
+        """        
+        # dictionary to translate row letters into numbers
+        row_dict = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
+        # if either n1 or n2 is positive, include this sample
+        well_row = row_dict[self.well_number[0]]
+        # The remaining charagers are the columns
+        well_col = self.well_number[1:]
+        return dict(name=self.sample_id, 
+                    row=well_row, 
+                    col=well_col, 
+                    positive=False)
         
 # class ArticSample(Base):
 #     """

src/submissions/backend/db/models/submissions.py

@@ -1,6 +1,7 @@
 '''
 Models for the main submission types.
 '''
+import math
 from . import Base
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT
 from sqlalchemy.orm import relationship
@@ -246,5 +247,24 @@ class WastewaterArtic(BasicSubmission):
     derivative submission type for artic wastewater
     """    
     samples = relationship("WWSample", back_populates="artic_rsl_plate", uselist=True)
-    # Can in use the pcr_info from the wastewater? Cause I can't define pcr_info here due to conflicts with that
+    # Can it use the pcr_info from the wastewater? Cause I can't define pcr_info here due to conflicts with that
+    # Not necessary because we don't get any results for this procedure.
     __mapper_args__ = {"polymorphic_identity": "wastewater_artic", "polymorphic_load": "inline"}
+
+    def calculate_base_cost(self):
+        """
+        This method overrides parent method due to multiple output plates from a single submission
+        """        
+        logger.debug(f"Hello from calculate base cost in WWArtic")
+        try:
+            cols_count_96 = ceil(int(self.sample_count) / 8)
+        except Exception as e:
+            logger.error(f"Column count error: {e}")
+        # Since we have multiple output plates per submission form, the constant cost will have to reflect this.
+        output_plate_count = math.ceil(int(self.sample_count) / 16)
+        logger.debug(f"Looks like we have {output_plate_count} output plates.")
+        const_cost = self.extraction_kit.constant_cost * output_plate_count
+        try:
+            self.run_cost = const_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
+        except Exception as e:
+            logger.error(f"Calculation error: {e}")

src/submissions/backend/excel/parser.py

@@ -3,6 +3,7 @@ contains parser object for pulling values from client generated submission sheet
 '''
 from getpass import getuser
 import math
+import pprint
 from typing import Tuple
 import pandas as pd
 from pathlib import Path
@@ -160,14 +161,19 @@ class SheetParser(object):
         sample_parser = SampleParser(self.ctx, submission_info.iloc[16:112])
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
         logger.debug(f"Parser result: {self.sub}")
-        self.sub['samples'] = sample_parse()
+        self.sample_result, self.sub['samples'] = sample_parse()
 
 
     def parse_wastewater(self) -> None:
         """
         pulls info specific to wastewater sample type
         """        
-
+        def retrieve_elution_map():
+            full = self.xl.parse("Extraction Worksheet")
+            elu_map = full.iloc[9:18, 5:]
+            elu_map.set_index(elu_map.columns[0], inplace=True)
+            elu_map.columns = elu_map.iloc[0]
+            return elu_map
         def parse_reagents(df:pd.DataFrame) -> None:
             """
             Pulls reagents from the bacterial sub-dataframe
@@ -216,9 +222,9 @@ class SheetParser(object):
         parse_reagents(ext_reagent_range)
         parse_reagents(pcr_reagent_range)
         # parse samples
-        sample_parser = SampleParser(self.ctx, submission_info.iloc[16:])
+        sample_parser = SampleParser(self.ctx, submission_info.iloc[16:], elution_map=retrieve_elution_map())
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
-        self.sub['samples'] = sample_parse()
+        self.sample_result, self.sub['samples'] = sample_parse()
         self.sub['csv'] = self.xl.parse("Copy to import file", dtype=object)
 
 
@@ -272,7 +278,7 @@ class SheetParser(object):
                         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']))
-            logger.debug(f"massaged sample list for {self.sub['rsl_plate_num']}: {return_list}")
+            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)
         biomek_info = self.xl.parse("ArticV4 Biomek", dtype=object)
@@ -280,7 +286,7 @@ class SheetParser(object):
         biomek_reagent_range = biomek_info.iloc[60:, 0:3].dropna(how='all')
         self.sub['submitter_plate_num'] = ""
         self.sub['rsl_plate_num'] =  RSLNamer(self.filepath.__str__()).parsed_name
-        self.sub['submitted_date'] = submission_info.iloc[0][2]
+        self.sub['submitted_date'] = biomek_info.iloc[1][1]
         self.sub['submitting_lab'] = "Enterics Wastewater Genomics"
         self.sub['sample_count'] = submission_info.iloc[4][6]
         self.sub['extraction_kit'] = "ArticV4.1"
@@ -290,7 +296,7 @@ class SheetParser(object):
         samples = massage_samples(biomek_info.iloc[22:31, 0:])
         sample_parser = SampleParser(self.ctx, pd.DataFrame.from_records(samples))
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
-        self.sub['samples'] = sample_parse()
+        self.sample_result, self.sub['samples'] = sample_parse()
         
 
 
@@ -299,18 +305,21 @@ class SampleParser(object):
     object to pull data for samples in excel sheet and construct individual sample objects
     """
 
-    def __init__(self, ctx:dict, df:pd.DataFrame) -> None:
+    def __init__(self, ctx:dict, df:pd.DataFrame, elution_map:pd.DataFrame|None=None) -> None:
         """
         convert sample sub-dataframe to dictionary of records
 
         Args:
+            ctx (dict): setting passed down from gui
             df (pd.DataFrame): input sample dataframe
+            elution_map (pd.DataFrame | None, optional): optional map of elution plate. Defaults to None.
         """        
         self.ctx = ctx
         self.samples = df.to_dict("records")
+        self.elution_map = elution_map
 
 
-    def parse_bacterial_culture_samples(self) -> list[BCSample]:
+    def parse_bacterial_culture_samples(self) -> Tuple[str|None, list[BCSample]]:
         """
         construct bacterial culture specific sample objects
 
@@ -334,16 +343,28 @@ class SampleParser(object):
                 not_a_nan = True
             if not_a_nan:
                 new_list.append(new)
-        return new_list
+        return None, new_list
 
 
-    def parse_wastewater_samples(self) -> list[WWSample]:
+    def parse_wastewater_samples(self) -> Tuple[str|None, list[WWSample]]:
         """
         construct wastewater specific sample objects
 
         Returns:
             list[WWSample]: list of sample objects
         """        
+        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).dropna(how='all').dropna(axis=1)
+            self.elution_map.at[well.index[0], well.columns[0]] = np.nan
+            try:
+                col = str(int(well.columns[0]))
+            except ValueError:
+                col = str(well.columns[0])
+            except TypeError as e:
+                logger.error(f"Problem parsing out column number for {well}:\n {e}")
+            return f"{well.index[0]}{col}"
         new_list = []
         for sample in self.samples:
             new = WWSample()
@@ -368,10 +389,11 @@ 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)
             new_list.append(new)
-        return new_list
+        return None, new_list
     
-    def parse_wastewater_artic_samples(self) -> list[WWSample]:
+    def parse_wastewater_artic_samples(self) -> Tuple[str|None, list[WWSample]]:
         """
         The artic samples are the wastewater samples that are to be sequenced
         So we will need to lookup existing ww samples and append Artic well # and plate relation
@@ -380,17 +402,20 @@ class SampleParser(object):
             list[WWSample]: list of wastewater samples to be updated
         """        
         new_list = []
+        missed_samples = []
         for sample in self.samples:
             with self.ctx['database_session'].no_autoflush:
                 instance = lookup_ww_sample_by_ww_sample_num(ctx=self.ctx, sample_number=sample['sample_name'])
             logger.debug(f"Checking: {sample['sample_name']}")
             if instance == None:
                 logger.error(f"Unable to find match for: {sample['sample_name']}")
+                missed_samples.append(sample['sample_name'])
                 continue
             logger.debug(f"Got instance: {instance.ww_sample_full_id}")
             instance.artic_well_number = sample['well']
             new_list.append(instance)
-        return new_list
+        missed_str = "\n\t".join(missed_samples)
+        return f"Could not find matches for the following samples:\n\t {missed_str}", new_list
             
 
 
@@ -472,6 +497,7 @@ class PCRParser(object):
         df = self.parse_general(sheet_name="Results")
         column_names = ["Well", "Well Position", "Omit","Sample","Target","Task"," Reporter","Quencher","Amp Status","Amp Score","Curve Quality","Result Quality Issues","Cq","Cq Confidence","Cq Mean","Cq SD","Auto Threshold","Threshold", "Auto Baseline", "Baseline Start", "Baseline End"]
         self.samples_df = df.iloc[23:][0:]
+        logger.debug(f"Dataframe of PCR results:\n\t{self.samples_df}")
         self.samples_df.columns = column_names
         logger.debug(f"Samples columns: {self.samples_df.columns}")
         well_call_df = self.xl.parse(sheet_name="Well Call").iloc[24:][0:].iloc[:,-1:]
@@ -488,7 +514,7 @@ class PCRParser(object):
                 sample_obj = dict(
                     sample = row['Sample'],
                     plate_rsl = self.plate_num,
-                    elution_well = row['Well Position']
+                    # elution_well = row['Well Position']
                 )
             logger.debug(f"Got sample obj: {sample_obj}") 
             # logger.debug(f"row: {row}")

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:

src/submissions/tools/__init__.py

@@ -261,3 +261,4 @@ def massage_common_reagents(reagent_name:str):
     reagent_name = reagent_name.replace("µ", "u")
     return reagent_name
         
+