Commit pre-refactor for code cleanup.

src/submissions/backend/excel/parser.py

@@ -7,6 +7,7 @@ import re
 import numpy as np
 from datetime import date
 import uuid
+from frontend.functions import check_not_nan
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -59,7 +60,8 @@ class SheetParser(object):
     def _parse_unknown(self) -> None:
         """
         Dummy function to handle unknown excel structures
-        """        
+        """    
+        logger.error(f"Unknown excel workbook structure. Cannot parse.")    
         self.sub = None
     
 
@@ -96,11 +98,11 @@ class SheetParser(object):
                 if ii == 11:
                     continue
                 logger.debug(f"Running reagent parse for {row[1]} with type {type(row[1])} and value: {row[2]} with type {type(row[2])}")
-                try:
-                    check = not np.isnan(row[1])
-                except TypeError:
-                    check = True
-                if not isinstance(row[2], float) and check:
+                # try:
+                #     check = not np.isnan(row[1])
+                # except TypeError:
+                #     check = True
+                if not isinstance(row[2], float) and check_not_nan(row[1]):
                     # must be prefixed with 'lot_' to be recognized by gui
                     try:
                         reagent_type = row[1].replace(' ', '_').lower().strip()
@@ -114,7 +116,18 @@ class SheetParser(object):
                         logger.debug(f"Couldn't upperize {row[2]}, must be a number")
                         output_var = row[2]
                     logger.debug(f"Output variable is {output_var}")
-                    self.sub[f"lot_{reagent_type}"] = output_var
+                    # self.sub[f"lot_{reagent_type}"] = output_var
+                    # update 2023-02-10 to above allowing generation of expiry date in adding reagent to db.
+                    logger.debug(f"Expiry date for imported reagent: {row[3]}")
+                    try:
+                        check = not np.isnan(row[3])
+                    except TypeError:
+                        check = True
+                    if check:
+                        expiry = row[3].date()
+                    else:
+                        expiry = date.today()
+                    self.sub[f"lot_{reagent_type}"] = {'lot':output_var, 'exp':expiry}
 
         submission_info = self._parse_generic("Sample List")
         # iloc is [row][column] and the first row is set as header row so -2

src/submissions/backend/excel/reports.py

@@ -33,7 +33,9 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
     # put submissions with the same lab together
     df = df.sort_values("Submitting Lab")
     # aggregate cost and sample count columns
-    df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Cost': ['sum', 'count'], 'Sample Count':['sum']})
+    df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Extraction Kit':'count', 'Cost': 'sum', 'Sample Count':'sum'})
+    df2 = df2.rename(columns={"Extraction Kit": 'Kit Count'})
+    logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
     # apply formating to cost column
     # df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')] = df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')].applymap('${:,.2f}'.format)
     return df2
@@ -54,11 +56,14 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
     """    
     old_lab = ""
     output = []
+    logger.debug(f"Report DataFrame: {df}")
     for ii, row in enumerate(df.iterrows()):
         row = [item for item in row]
+        logger.debug(f"Row: {row}")
+        
         lab = row[0][0]
         logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
-        kit = dict(name=row[0][1], cost=row[1][('Cost', 'sum')], plate_count=int(row[1][('Cost', 'count')]), sample_count=int(row[1][('Sample Count', 'sum')]))
+        kit = dict(name=row[0][1], cost=row[1]['Cost'], plate_count=int(row[1]['Kit Count']), sample_count=int(row[1]['Sample Count']))
         if lab == old_lab:
             output[ii-1]['kits'].append(kit)
             output[ii-1]['total_cost'] += kit['cost']