Commit before bringing in pydantic

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 202307.01
+
+- Moved parser to metadata based recognition of submission type.
+
 ## 202306.03
 
 - Improve WW plate mapping by using layout in submission forms rather than PCR.

TODO.md

@@ -1,4 +1,5 @@
-- [ ] Move submission types from config.yml into database.
+- [ ] Migrate the parser.sub dictionary to pydantic models.
+- [x] Move type_decider to metadata based method rather than excel map.
 - [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.

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202306.3b"
+__version__ = "202307.1b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
 
@@ -25,6 +25,7 @@ class bcolors:
 # set out the workflow I've imagined for creating new submission types.
 # First of all, you will need to write new parsing methods in backend.excel.parser to pull information out of the submission form
 # for the submission itself as well as for any samples you can pull out of that same workbook.
+# The workbooks no longer need a sheet map, but they do need their submission type put in the categories metadata of the client excel template.
 # Second, you will have to update the model in backend.db.models.submissions and provide a new polymorph to the BasicSubmission object.
 # The BSO should hold the majority of the general info.
 # You can also update any of the parsers to pull out any custom info you need, like enforcing RSL plate numbers, scraping PCR results, etc.

src/submissions/backend/excel/parser.py

@@ -2,7 +2,6 @@
 contains parser object for pulling values from client generated submission sheets.
 '''
 from getpass import getuser
-import math
 import pprint
 from typing import Tuple
 import pandas as pd
@@ -44,6 +43,7 @@ class SheetParser(object):
             except ValueError as e:
                 logger.error(f"Incorrect value: {e}")
                 self.xl = None
+        # TODO: replace OrderedDict with pydantic BaseModel
         self.sub = OrderedDict()
         # make decision about type of sample we have
         self.sub['submission_type'] = self.type_decider()
@@ -58,14 +58,22 @@ class SheetParser(object):
         Returns:
             str: submission type name
         """        
-        try:
-            for type in self.ctx['submission_types']:
-                if self.xl.sheet_names == self.ctx['submission_types'][type]['excel_map']:
-                    return type.title()
-            return "Unknown"
-        except Exception as e:
-            logger.warning(f"We were unable to parse the submission type due to: {e}")
-            return "Unknown"
+        # Check metadata for category, return first category
+        if self.xl.book.properties.category != None:
+            categories = [item.strip().title() for item in self.xl.book.properties.category.split(";")]
+            return categories[0].replace(" ", "_")
+        else:
+            # This code is going to be depreciated once there is full adoption of the client sheets
+            # with updated metadata
+            try:
+                for type in self.ctx['submission_types']:
+                    # This gets the *first* submission type that matches the sheet names in the workbook 
+                    if self.xl.sheet_names == self.ctx['submission_types'][type]['excel_map']:
+                        return type.title()
+                return "Unknown"
+            except Exception as e:
+                logger.warning(f"We were unable to parse the submission type due to: {e}")
+                return "Unknown"
 
 
     def parse_unknown(self) -> None:

src/submissions/backend/excel/reports.py

@@ -9,7 +9,6 @@ import sys
 from pathlib import Path
 import re
 from tools import check_if_app
-import asyncio
 
 logger = logging.getLogger(f"submissions.{__name__}")
 

src/submissions/frontend/main_window_functions.py

@@ -18,7 +18,7 @@ from backend.db.models import *
 import logging
 from PyQt6.QtWidgets import (
     QMainWindow, QLabel, QWidget, QPushButton, QFileDialog,
-    QLineEdit, QMessageBox, QComboBox, QDateEdit
+    QLineEdit, QComboBox, QDateEdit
 )
 from .all_window_functions import extract_form_info, select_open_file, select_save_file
 from PyQt6.QtCore import QSignalBlocker
@@ -26,16 +26,15 @@ 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, hitpick_plate
+    lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample
 )
 from backend.excel.parser import SheetParser, PCRParser
 from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
 from tools import RSLNamer, check_not_nan, check_kit_integrity
 from .custom_widgets.pop_ups import AlertPop, QuestionAsker
-from .custom_widgets import ReportDatePicker, ReagentTypeForm
+from .custom_widgets import ReportDatePicker
 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__}")