Everything working pretty well.

TODO.md

@@ -1,3 +1,4 @@
+- [ ] Create Tips ... *sigh*.
 - [x] Create platemap image from html for export to pdf.
 - [x] Move plate map maker to submission.
 - [x] Finish Equipment Parser (add in regex to id asset_number)

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202402.2b"
+__version__ = "202402.3b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2024, Government of Canada"
 

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

@@ -4,10 +4,10 @@ All kit and reagent related models
 from __future__ import annotations
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
 from sqlalchemy.orm import relationship, validates, Query
-from sqlalchemy.ext.associationproxy import association_proxy, AssociationProxy
+from sqlalchemy.ext.associationproxy import association_proxy
 from datetime import date
 import logging, re
-from tools import check_authorization, setup_lookup, Report, Result, Settings
+from tools import check_authorization, setup_lookup, Report, Result
 from typing import List
 from pandas import ExcelFile
 from pathlib import Path
@@ -921,23 +921,32 @@ class SubmissionReagentAssociation(BaseClass):
         from . import BasicSubmission
         query: Query = cls.__database_session__.query(cls)
         match reagent:
-            case Reagent():
+            case Reagent() | str():
                 # logger.debug(f"Lookup SubmissionReagentAssociation by reagent Reagent {reagent}")
+                if isinstance(reagent, str):
+                    reagent = Reagent.query(lot_number=reagent)
                 query = query.filter(cls.reagent==reagent)
-            case str():
+            # case str():
-                # logger.debug(f"Lookup SubmissionReagentAssociation by reagent str {reagent}")
+            #     logger.debug(f"Lookup SubmissionReagentAssociation by reagent str {reagent}")
-                query = query.join(Reagent).filter(Reagent.lot==reagent)
+                
+            #     query = query.filter(cls.reagent==reagent)
+            #     logger.debug(f"Result: {query.all()}")
             case _:
                 pass
         match submission:
-            case BasicSubmission():
+            case BasicSubmission() | str():
+                if isinstance(submission, str):
+                    submission = BasicSubmission.query(rsl_number=submission)
                 # logger.debug(f"Lookup SubmissionReagentAssociation by submission BasicSubmission {submission}")
                 query = query.filter(cls.submission==submission)
-            case str():
+            # case str():
-                # logger.debug(f"Lookup SubmissionReagentAssociation by submission str {submission}")
+            #     logger.debug(f"Lookup SubmissionReagentAssociation by submission str {submission}")
-                query = query.join(BasicSubmission).filter(BasicSubmission.rsl_plate_num==submission)
+            #     submission = BasicSubmission.query(rsl_number=submission)
+            #     query = query.filter(cls.submission==submission)
+            #     logger.debug(f"Result: {query.all()}")
             case int():
                 # logger.debug(f"Lookup SubmissionReagentAssociation by submission id {submission}")
+                submission = BasicSubmission.query(id=submission)                
                 query = query.join(BasicSubmission).filter(BasicSubmission.id==submission)
             case _:
                 pass

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

@@ -338,7 +338,7 @@ class BasicSubmission(BaseClass):
         logger.debug(f"Got {len(subs)} submissions.")
         df = pd.DataFrame.from_records(subs)
         # Exclude sub information
-        for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', 'equipment']:
+        for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', 'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number']:
             try:
                 df = df.drop(item, axis=1)
             except:
@@ -1068,7 +1068,21 @@ class BacterialCulture(BasicSubmission):
             outstr = re.sub(r"BC(\d{6})", r"BC-\1", outstr, flags=re.IGNORECASE)
         except (AttributeError, TypeError) as e:
             outstr = RSLNamer.construct_new_plate_name(data=data)
-        return outstr
+        try:
+            plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
+            # logger.debug(f"Plate number is: {plate_number}")
+        except AttributeError as e:
+            plate_number = "1"
+        outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
+        # logger.debug(f"After addition of plate number the plate name is: {outstr}")
+        try:
+            repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
+            if repeat == None:
+                repeat = "1"
+        except AttributeError as e:
+            repeat = ""
+        return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
+        # return outstr
 
     @classmethod
     def get_regex(cls) -> str:
@@ -1078,7 +1092,7 @@ class BacterialCulture(BasicSubmission):
         Returns:
             str: string for regex construction
         """        
-        return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\s]|$)?R?\d?)?)"
+        return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
     
     @classmethod
     def filename_template(cls):
@@ -1244,7 +1258,7 @@ class Wastewater(BasicSubmission):
         Returns:
             str: String for regex construction
         """        
-        return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\s]|$)?R?\d?)?)"
+        return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
   
     @classmethod
     def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]:

src/submissions/backend/excel/parser.py

@@ -601,5 +601,3 @@ class PCRParser(object):
         self.pcr['plugin'] = df.iloc[19][1]
         self.pcr['exported_on'] = df.iloc[20][1]
         self.pcr['imported_by'] = getuser()
-
-    

src/submissions/backend/excel/reports.py

@@ -32,7 +32,6 @@ def make_report_xlsx(records:list[dict]) -> Tuple[DataFrame, DataFrame]:
     df = df.sort_values(['Submitting Lab', "Submitted Date"])
     return df, df2
 
-
 def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
     
     """
@@ -74,7 +73,6 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
     html = temp.render(input=dicto)
     return html
 
-
 def convert_data_list_to_df(input:list[dict], subtype:str|None=None) -> DataFrame:
     """
     Convert list of control records to dataframe
@@ -104,7 +102,6 @@ def convert_data_list_to_df(input:list[dict], subtype:str|None=None) -> DataFram
     df = df_column_renamer(df=df)
     return df
 
-
 def df_column_renamer(df:DataFrame) -> DataFrame:
     """
     Ad hoc function I created to clarify some fields
@@ -123,7 +120,6 @@ def df_column_renamer(df:DataFrame) -> DataFrame:
         "kraken_percent":"kraken2_read_percent_(top_50)"
     })
 
-
 def displace_date(df:DataFrame) -> DataFrame:
     """
     This function serves to split samples that were submitted on the same date by incrementing dates.
@@ -182,7 +178,6 @@ def check_date(df:DataFrame, item:dict, previous_dates:list) -> Tuple[DataFrame,
         df, previous_dates = check_date(df, item, previous_dates)
         return df, previous_dates
                 
-
 def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
     """
     get all unique values in a dataframe column by name
@@ -196,7 +191,6 @@ def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
     """    
     return sorted(df[column_name].unique())
 
-
 def drop_reruns_from_df(ctx:Settings, df: DataFrame) -> DataFrame:
     """
     Removes semi-duplicates from dataframe after finding sequencing repeats.

src/submissions/backend/validators/__init__.py

@@ -133,10 +133,10 @@ class RSLNamer(object):
             else:
                 today = data['submitted_date']
         else:
-            today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", data['rsl_plate_num'])
             try:
+                today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", data['rsl_plate_num'])
                 today = parse(today.group())
-            except AttributeError:
+            except (AttributeError, KeyError):
                 today = datetime.now()
         if "rsl_plate_num" in data.keys():
             plate_number = data['rsl_plate_num'].split("-")[-1][0]

src/submissions/backend/validators/pydant.py

@@ -642,7 +642,14 @@ class PydSubmission(BaseModel, extra='allow'):
                 new_item = {}
                 new_item['type'] = k
                 new_item['location'] = excel_map['info'][k]
-                new_item['value'] = v['value']
+                match k:
+                    case "comment":
+                        if v['value'] is not None:
+                            new_item['value'] = "--".join([comment['text'] for comment in v['value']])
+                        else:
+                            new_item['value'] = None
+                    case _:
+                        new_item['value'] = v['value']
                 new_info.append(new_item)
             except KeyError:
                 logger.error(f"Unable to fill in {k}, not found in relevant info.")

src/submissions/frontend/widgets/__init__.py

@@ -10,4 +10,8 @@ from .submission_table import *
 from .submission_widget import *
 from .controls_chart import *
 from .kit_creator import *
+from .submission_details import *
+from .equipment_usage import *
+from .gel_checker import *
+from .submission_type_creator import *
 from .app import App

src/submissions/frontend/widgets/equipment_usage.py

@@ -80,7 +80,6 @@ class EquipmentUsage(QDialog):
             for object in self.parent().findChildren(QCheckBox):
                 object.setChecked(self.check.isChecked())
 
-# TODO: Figure out how this is working again
 class RoleComboBox(QWidget):
 
     def __init__(self, parent, role:PydEquipmentRole, used:list) -> None:

src/submissions/frontend/widgets/gel_checker.py

@@ -1,12 +1,12 @@
 """
 Gel box for artic quality control
 """
-from PyQt6.QtWidgets import *
+from PyQt6.QtWidgets import (QWidget, QDialog, QGridLayout,
-from PyQt6.QtWidgets import QWidget
+                             QLabel, QLineEdit, QDialogButtonBox
+                             )
 import numpy as np
 import pyqtgraph as pg
-from PyQt6.QtGui import *
+from PyQt6.QtGui import QIcon
-from PyQt6.QtCore import *
 from PIL import Image
 import numpy as np
 import logging

src/submissions/frontend/widgets/submission_details.py

@@ -60,7 +60,6 @@ class SubmissionDetails(QDialog):
         btn.setFixedWidth(900)
         btn.clicked.connect(self.export)
 
-           
     def export(self):
         """
         Renders submission to html, then creates and saves .pdf file to user selected file.

src/submissions/tools.py

@@ -9,7 +9,7 @@ import pandas as pd
 from jinja2 import Environment, FileSystemLoader
 from logging import handlers
 from pathlib import Path
-from sqlalchemy.orm import Query, Session
+from sqlalchemy.orm import Session
 from sqlalchemy import create_engine
 from pydantic import field_validator, BaseModel, Field
 from pydantic_settings import BaseSettings, SettingsConfigDict