Better xlsx reports

src/submissions/__init__.py

@@ -1,4 +1,4 @@
 # __init__.py
 
 # Version of the realpython-reader package
-__version__ = "1.1.2"
+__version__ = "1.2.1"

src/submissions/backend/db/__init__.py

@@ -2,16 +2,14 @@ from . import models
 import pandas as pd
 import sqlalchemy.exc
 import sqlite3
-# from sqlalchemy.exc import IntegrityError, OperationalError
-# from sqlite3 import IntegrityError, OperationalError
 import logging
 from datetime import date, datetime, timedelta
 from sqlalchemy import and_
 import uuid
-import base64
+# import base64
 from sqlalchemy import JSON
 import json
-from dateutil.relativedelta import relativedelta
+# from dateutil.relativedelta import relativedelta
 from getpass import getuser
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -94,11 +92,14 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
     instance = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
     msg = "This submission already exists.\nWould you like to overwrite?"
     # get model based on submission type converted above
+    logger.debug(f"Looking at models for submission type: {query}")
     model = getattr(models, query)
+    logger.debug(f"We've got the model: {type(model)}")
     info_dict['submission_type'] = info_dict['submission_type'].replace(" ", "_").lower()
     # if query return nothing, ie doesn't already exist in db
     if instance == None:
         instance = model()
+        logger.debug(f"Submission doesn't exist yet, creating new instance: {instance}")
         msg = None
     for item in info_dict:
         logger.debug(f"Setting {item} to {info_dict[item]}")
@@ -133,11 +134,11 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
             logger.debug(f"Could not set attribute: {item} to {info_dict[item]}")
             continue
         # calculate cost of the run: immutable cost + mutable times number of columns
-        try:
-            instance.run_cost = instance.extraction_kit.immutable_cost + (instance.extraction_kit.mutable_cost * ((instance.sample_count / 8)/12))
-        except TypeError:
-            logger.debug(f"Looks like that kit doesn't have cost breakdown yet, using full plate cost.")
-            instance.run_cost = instance.extraction_kit.cost_per_run
+    try:
+        instance.run_cost = instance.extraction_kit.immutable_cost + (instance.extraction_kit.mutable_cost * ((instance.sample_count / 8)/12))
+    except (TypeError, AttributeError):
+        logger.debug(f"Looks like that kit doesn't have cost breakdown yet, using full plate cost.")
+        instance.run_cost = instance.extraction_kit.cost_per_run
     logger.debug(f"Constructed instance: {instance.to_string()}")
     logger.debug(msg)
     return instance, {'message':msg}

src/submissions/frontend/__init__.py

@@ -15,9 +15,12 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
 from pathlib import Path
 import plotly
 import pandas as pd
+from openpyxl.utils import get_column_letter
+from openpyxl.styles import NamedStyle
 from xhtml2pdf import pisa
 # import plotly.express as px
 import yaml
+import pprint
 
 from backend.excel.parser import SheetParser
 from backend.excel.reports import convert_control_by_mode, convert_data_list_to_df
@@ -35,7 +38,7 @@ import difflib
 from datetime import date
 from frontend.visualizations.charts import create_charts
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(f'submissions.{__name__}')
 logger.info("Hello, I am a logger")
 
 class App(QMainWindow):
@@ -64,6 +67,7 @@ class App(QMainWindow):
         self._connectActions()
         self.controls_getter()
         self.show()
+        
 
     def _createMenuBar(self):
         """
@@ -261,10 +265,11 @@ class App(QMainWindow):
                     logger.debug("Will not add reagent.")
             if wanted_reagent != None:
                 parsed_reagents.append(wanted_reagent)
-                logger.debug(info)
+                # logger.debug(info)
         # move samples into preliminary submission dict
         info['samples'] = self.samples
         # construct submission object
+        logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
         base_submission, output = construct_submission_info(ctx=self.ctx, info_dict=info)
         # check output message for issues
         if output['message'] != None:
@@ -376,7 +381,31 @@ class App(QMainWindow):
             # df.to_excel(fname, engine='openpyxl')
             with open(fname, "w+b") as f:
                 pisa.CreatePDF(html, dest=f)
-            df.to_excel(fname.with_suffix(".xlsx"), engine='openpyxl')       
+            writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
+            df.to_excel(writer, sheet_name="Report") 
+            worksheet = writer.sheets['Report']
+            for idx, col in enumerate(df):  # loop through all columns
+                series = df[col]
+                max_len = max((
+                    series.astype(str).map(len).max(),  # len of largest item
+                    len(str(series.name))  # len of column name/header
+                    )) + 20  # adding a little extra space
+                try:
+                    worksheet.column_dimensions[get_column_letter(idx)].width = max_len 
+                except ValueError:
+                    pass
+                # set_column(idx, idx, max_len)  # set column width
+            # colu = worksheet.column_dimensions["C"]
+            # style = NamedStyle(name="custom_currency", number_format='Currency')
+            for cell in worksheet['C']:
+                # try:
+                #     check = int(cell.row)
+                # except TypeError:
+                #     continue
+                if cell.row > 3:
+                    cell.style = 'Currency'
+            writer.close()
+                  
 
             
             

src/submissions/templates/submission_details.txt

@@ -1,7 +1,7 @@
 {# template for constructing submission details #}
 
 {% for key, value in sub.items() if key != 'reagents' and key != 'samples' %}
-{{ key }}: {{ value }}
+{% if key=='Cost' %} {{ key }}: {{ "${:,.2f}".format(value) }} {% else %} {{ key }}: {{ value }} {% endif %}
 {% endfor %}
 Reagents:
 {% for item in sub['reagents'] %}