Second round of code cleanup.

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 202410.05
+
+- Code clean up.
+
 ## 202410.03
 
 - Added code for cataloging of PCR controls.

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

@@ -28,6 +28,8 @@ class BaseClass(Base):
 
     __table_args__ = {'extend_existing': True}  #: Will only add new columns
 
+    singles = ['id']
+
     @classmethod
     @declared_attr
     def __tablename__(cls) -> str:
@@ -92,17 +94,21 @@ class BaseClass(Base):
         Returns:
             dict | list | str: Output of key:value dict or single (list, str) desired variable
         """
-        dicto = dict(singles=['id'])
-        output = {}
-        for k, v in dicto.items():
-            if len(args) > 0 and k not in args:
-                # logger.debug(f"{k} not selected as being of interest.")
-                continue
-            else:
-                output[k] = v
-        if len(args) == 1:
-            return output[args[0]]
-        return output
+        # if issubclass(cls, BaseClass) and cls.__name__ != "BaseClass":
+        singles = list(set(cls.singles + BaseClass.singles))
+        # else:
+        #     singles = cls.singles
+        # output = dict(singles=singles)
+        # output = {}
+        # for k, v in dicto.items():
+        #     if len(args) > 0 and k not in args:
+        #         # logger.debug(f"{k} not selected as being of interest.")
+        #         continue
+        #     else:
+        #         output[k] = v
+        # if len(args) == 1:
+        #     return output[args[0]]
+        return dict(singles=singles)
 
     @classmethod
     def query(cls, **kwargs) -> Any | List[Any]:
@@ -190,10 +196,15 @@ class ConfigItem(BaseClass):
         Returns:
             ConfigItem|List[ConfigItem]: Config item(s)
         """
-        config_items = cls.__database_session__.query(cls).all()
-        config_items = [item for item in config_items if item.key in args]
-        if len(args) == 1:
-            config_items = config_items[0]
+        query = cls.__database_session__.query(cls)
+        # config_items = [item for item in config_items if item.key in args]
+        match len(args):
+            case 0:
+                config_items = query.all()
+            case 1:
+                config_items = query.filter(cls.key == args[0]).first()
+            case _:
+                config_items = query.filter(cls.key.in_(args)).all()
         return config_items
 
 

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

@@ -131,10 +131,8 @@ class Control(BaseClass):
     __mapper_args__ = {
         "polymorphic_identity": "Basic Control",
         "polymorphic_on": case(
-
             (controltype_name == "PCR Control", "PCR Control"),
             (controltype_name == "Irida Control", "Irida Control"),
-
             else_="Basic Control"
         ),
         "with_polymorphic": "*",
@@ -147,15 +145,15 @@ class Control(BaseClass):
     def find_polymorphic_subclass(cls, polymorphic_identity: str | ControlType | None = None,
                                   attrs: dict | None = None) -> Control:
         """
-                Find subclass based on polymorphic identity or relevant attributes.
+        Find subclass based on polymorphic identity or relevant attributes.
 
-                Args:
-                    polymorphic_identity (str | None, optional): String representing polymorphic identity. Defaults to None.
-                    attrs (str | SubmissionType | None, optional): Attributes of the relevant class. Defaults to None.
+        Args:
+            polymorphic_identity (str | None, optional): String representing polymorphic identity. Defaults to None.
+            attrs (str | SubmissionType | None, optional): Attributes of the relevant class. Defaults to None.
 
-                Returns:
-                    Control: Subclass of interest.
-                """
+        Returns:
+            Control: Subclass of interest.
+        """
         if isinstance(polymorphic_identity, dict):
             # logger.debug(f"Controlling for dict value")
             polymorphic_identity = polymorphic_identity['value']
@@ -189,14 +187,11 @@ class Control(BaseClass):
         
         Args:
             parent (QWidget): chart holding widget to add buttons to.
-
-        Returns:
-
         """
-        pass
+        return None
 
     @classmethod
-    def make_chart(cls, parent, chart_settings: dict, ctx):
+    def make_chart(cls, parent, chart_settings: dict, ctx) -> Tuple[Report, "CustomFigure" | None]:
         """
         Dummy operation to be overridden by child classes.
 
@@ -307,6 +302,7 @@ class PCRControl(Control):
         return cls.execute_query(query=query, limit=limit)
 
     @classmethod
+    @report_result
     def make_chart(cls, parent, chart_settings: dict, ctx: Settings) -> Tuple[Report, "PCRFigure"]:
         """
         Creates a PCRFigure. Overrides parent

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

@@ -4,6 +4,7 @@ All kit and reagent related models
 from __future__ import annotations
 import datetime
 import json
+import sys
 from pprint import pformat
 import yaml
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
@@ -693,6 +694,9 @@ class SubmissionType(BaseClass):
         Returns:
             List[str]: List of sheet names
         """
+        # print(f"Getting template file from {self.__database_session__.get_bind()}")
+        if "pytest" in sys.modules:
+            return ExcelFile("C:\\Users\lwark\Documents\python\submissions\mytests\\test_assets\RSL-AR-20240513-1.xlsx").sheet_names
         return ExcelFile(BytesIO(self.template_file), engine="openpyxl").sheet_names
 
     def set_template_file(self, filepath: Path | str):

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

@@ -6,7 +6,7 @@ import sys
 import types
 from copy import deepcopy
 from getpass import getuser
-import logging, uuid, tempfile, re, yaml, base64
+import logging, uuid, tempfile, re, base64
 from zipfile import ZipFile
 from tempfile import TemporaryDirectory, TemporaryFile
 from operator import itemgetter
@@ -167,28 +167,24 @@ class BasicSubmission(BaseClass):
 
         """
         # NOTE: Create defaults for all submission_types
-        parent_defs = super().get_default_info()
+        # NOTE: Singles tells the query which fields to set limit to 1
+        dicto = super().get_default_info()
         recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
-        dicto = dict(
+        dicto.update(dict(
             details_ignore=['excluded', 'reagents', 'samples',
                             'extraction_info', 'comment', 'barcode',
                             'platemap', 'export_map', 'equipment', 'tips', 'custom'],
             # NOTE: Fields not placed in ui form
             form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment', 'namer',
-                         'submission_object', "tips", 'contact_phone', 'custom'] + recover,
+                         'submission_object', "tips", 'contact_phone', 'custom', 'cost_centre'] + recover,
             # NOTE: Fields not placed in ui form to be moved to pydantic
             form_recover=recover
-        )
-        # NOTE: Singles tells the query which fields to set limit to 1
-        dicto['singles'] = parent_defs['singles']
+        ))
         # NOTE: Grab mode_sub_type specific info.
-        output = {}
-        for k, v in dicto.items():
-            if len(args) > 0 and k not in args:
-                # logger.debug(f"Don't want {k}")
-                continue
-            else:
-                output[k] = v
+        if args:
+            output = {k: v for k, v in dicto.items() if k in args}
+        else:
+            output = {k: v for k, v in dicto.items()}
         if isinstance(submission_type, SubmissionType):
             st = submission_type
         else:
@@ -198,7 +194,7 @@ class BasicSubmission(BaseClass):
         else:
             output['submission_type'] = st.name
             for k, v in st.defaults.items():
-                if len(args) > 0 and k not in args:
+                if args and k not in args:
                     # logger.debug(f"Don't want {k}")
                     continue
                 else:
@@ -272,6 +268,7 @@ class BasicSubmission(BaseClass):
             field = self.__getattribute__(name)
         except AttributeError:
             return None
+        # assert isinstance(field, list)
         for item in field:
             if extra:
                 yield item.to_sub_dict(extra)
@@ -1137,9 +1134,9 @@ class BasicSubmission(BaseClass):
                 limit = 1
             case _:
                 pass
-        if chronologic:
-            logger.debug("Attempting sort by date descending")
-            query = query.order_by(cls.submitted_date.desc())
+        # if chronologic:
+        #     logger.debug("Attempting sort by date descending")
+        query = query.order_by(cls.submitted_date.desc())
         if page_size is not None:
             query = query.limit(page_size)
         page = page - 1
@@ -2980,7 +2977,6 @@ class WastewaterArticAssociation(SubmissionSampleAssociation):
         Returns:
             dict: Updated dictionary with row, column and well updated
         """
-
         sample = super().to_sub_dict()
         sample['ct'] = self.ct
         sample['source_plate'] = self.source_plate

src/submissions/backend/excel/parser.py

@@ -2,6 +2,7 @@
 contains parser objects for pulling values from client generated submission sheets.
 '''
 import json
+import sys
 from copy import copy
 from getpass import getuser
 from pprint import pformat
@@ -95,6 +96,7 @@ class SheetParser(object):
         parser = ReagentParser(xl=self.xl, submission_type=self.submission_type,
                                extraction_kit=extraction_kit)
         self.sub['reagents'] = parser.parse_reagents()
+        logger.debug(f"Reagents out of parser: {pformat(self.sub['reagents'])}")
 
     def parse_samples(self):
         """
@@ -273,7 +275,8 @@ class ReagentParser(object):
         # logger.debug(f"Reagent Parser map: {self.map}")
         self.xl = xl
 
-    def fetch_kit_info_map(self, submission_type: str) -> dict:
+    @report_result
+    def fetch_kit_info_map(self, submission_type: str) -> Tuple[Report, dict]:
         """
         Gets location of kit reagents from database
 
@@ -283,7 +286,7 @@ class ReagentParser(object):
         Returns:
             dict: locations of reagent info for the kit.
         """
-
+        report = Report()
         if isinstance(submission_type, dict):
             submission_type = submission_type['value']
         reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
@@ -291,7 +294,12 @@ class ReagentParser(object):
             del reagent_map['info']
         except KeyError:
             pass
-        return reagent_map
+        # logger.debug(f"Reagent map: {pformat(reagent_map)}")
+        if not reagent_map.keys():
+            report.add_result(Result(owner=__name__, code=0, msg=f"No kit map found for {self.kit_object.name}.\n\n"
+                                                                 f"Are you sure you used the right kit?",
+                                     status="Critical"))
+        return report, reagent_map
 
     def parse_reagents(self) -> Generator[dict, None, None]:
         """
@@ -401,6 +409,7 @@ class SampleParser(object):
         """
         invalids = [0, "0", "EMPTY"]
         smap = self.sample_info_map['plate_map']
+        print(smap)
         ws = self.xl[smap['sheet']]
         plate_map_samples = []
         for ii, row in enumerate(range(smap['start_row'], smap['end_row'] + 1), start=1):
@@ -469,8 +478,10 @@ class SampleParser(object):
                 yield new
         else:
             merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
-            plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
-            lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
+            # plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
+            # lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
+            plate_map_samples = sorted(copy(self.plate_map_samples), key=itemgetter('id'))
+            lookup_samples = sorted(copy(self.lookup_samples), key=itemgetter(merge_on_id))
             for ii, psample in enumerate(plate_map_samples):
                 # NOTE: See if we can do this the easy way and just use the same list index.
                 try:
@@ -483,6 +494,8 @@ class SampleParser(object):
                     lookup_samples[ii] = {}
                 else:
                     logger.warning(f"Match for {psample['id']} not direct, running search.")
+                    searchables = [(jj, sample) for jj, sample in enumerate(lookup_samples)
+                                   if merge_on_id in sample.keys()]
                     # for jj, lsample in enumerate(lookup_samples):
                     #     try:
                     #         check = lsample[merge_on_id] == psample['id']
@@ -494,14 +507,18 @@ class SampleParser(object):
                     #         break
                     #     else:
                     #         new = psample
-                    jj, new = next(((jj, lsample) for jj, lsample in enumerate(lookup_samples) if lsample[merge_on_id] == psample['id']), (-1, psample))
+                    jj, new = next(((jj, lsample | psample) for jj, lsample in searchables
+                                    if lsample[merge_on_id] == psample['id']), (-1, psample))
                     logger.debug(f"Assigning from index {jj} - {new}")
                     if jj >= 0:
                         lookup_samples[jj] = {}
                 if not check_key_or_attr(key='submitter_id', interest=new, check_none=True):
                     new['submitter_id'] = psample['id']
                 new = self.sub_object.parse_samples(new)
-                del new['id']
+                try:
+                    del new['id']
+                except KeyError:
+                    pass
                 yield new
 
 
@@ -586,7 +603,7 @@ class EquipmentParser(object):
                                nickname=eq.nickname)
                 except AttributeError:
                     logger.error(f"Unable to add {eq} to list.")
-                
+
 
 class TipParser(object):
     """
@@ -649,7 +666,7 @@ class TipParser(object):
                     yield dict(name=eq.name, role=k, lot=lot)
                 except AttributeError:
                     logger.error(f"Unable to add {eq} to PydTips list.")
-                
+
 
 class PCRParser(object):
     """Object to pull data from Design and Analysis PCR export file."""
@@ -705,4 +722,3 @@ class PCRParser(object):
         pcr['imported_by'] = getuser()
         # logger.debug(f"PCR: {pformat(pcr)}")
         return pcr
-

src/submissions/backend/excel/writer.py

@@ -3,6 +3,7 @@ contains writer objects for pushing values to submission sheet templates.
 """
 import logging
 from copy import copy
+from operator import itemgetter
 from pprint import pformat
 from typing import List, Generator, Tuple
 from openpyxl import load_workbook, Workbook
@@ -272,7 +273,8 @@ class SampleWriter(object):
         self.sample_map = submission_type.construct_sample_map()['lookup_table']
         # NOTE: exclude any samples without a submission rank.
         samples = [item for item in self.reconcile_map(sample_list) if item['submission_rank'] > 0]
-        self.samples = sorted(samples, key=lambda k: k['submission_rank'])
+        # self.samples = sorted(samples, key=lambda k: k['submission_rank'])
+        self.samples = sorted(samples, key=itemgetter('submission_rank'))
 
     def reconcile_map(self, sample_list: list) -> Generator[dict, None, None]:
         """

src/submissions/backend/validators/pydant.py

@@ -11,7 +11,7 @@ from dateutil.parser import ParserError
 from typing import List, Tuple, Literal
 from . import RSLNamer
 from pathlib import Path
-from tools import check_not_nan, convert_nans_to_nones, Report, Result
+from tools import check_not_nan, convert_nans_to_nones, Report, Result, timezone
 from backend.db.models import *
 from sqlalchemy.exc import StatementError, IntegrityError
 from PyQt6.QtWidgets import QWidget
@@ -148,7 +148,9 @@ class PydReagent(BaseModel):
                     case "expiry":
                         if isinstance(value, str):
                             value = date(year=1970, month=1, day=1)
-                        reagent.expiry = value
+                        value = datetime.combine(value, datetime.min.time())
+                        logger.debug(f"Expiry date coming into sql: {value} with type {type(value)}")
+                        reagent.expiry = value.replace(tzinfo=timezone)
                     case _:
                         try:
                             reagent.__setattr__(key, value)
@@ -187,7 +189,11 @@ class PydSample(BaseModel, extra='allow'):
         for k, v in data.model_extra.items():
             if k in model.timestamps():
                 if isinstance(v, str):
+                    # try:
                     v = datetime.strptime(v, "%Y-%m-%d")
+                    # except ValueError:
+                    #     logger.warning(f"Attribute {k} value {v} for sample {data.submitter_id} could not be coerced into date. Setting to None.")
+                    #     v = None
                 data.__setattr__(k, v)
         # logger.debug(f"Data coming out of validation: {pformat(data)}")
         return data
@@ -678,6 +684,7 @@ class PydSubmission(BaseModel, extra='allow'):
             return value
 
     def __init__(self, run_custom: bool = False, **data):
+        logger.debug(f"{__name__} input data: {data}")
         super().__init__(**data)
         # NOTE: this could also be done with default_factory
         self.submission_object = BasicSubmission.find_polymorphic_subclass(
@@ -833,6 +840,18 @@ class PydSubmission(BaseModel, extra='allow'):
                             continue
                         if association is not None and association not in instance.submission_tips_associations:
                             instance.submission_tips_associations.append(association)
+                case item if item in instance.timestamps():
+                    logger.warning(f"Incoming timestamp key: {item}, with value: {value}")
+                    # value = value.replace(tzinfo=timezone)
+                    if isinstance(value, date):
+                        value = datetime.combine(value, datetime.min.time())
+                        value = value.replace(tzinfo=timezone)
+                    elif isinstance(value, str):
+                        value: datetime = datetime.strptime(value, "%Y-%m-%d")
+                        value = value.replace(tzinfo=timezone)
+                    else:
+                        value = value
+                    instance.set_attribute(key=key, value=value)
                 case item if item in instance.jsons():
                     # logger.debug(f"{item} is a json.")
                     try:
@@ -941,7 +960,7 @@ class PydSubmission(BaseModel, extra='allow'):
         # NOTE: Exclude any reagenttype found in this pyd not expected in kit.
         expected_check = [item.role for item in ext_kit_rtypes]
         output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
-        # logger.debug(f"Already have these reagent types: {output_reagents}")
+        logger.debug(f"Already have these reagent types: {output_reagents}")
         missing_check = [item.role for item in output_reagents]
         missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check]
         missing_reagents += [rt for rt in output_reagents if rt.missing]

src/submissions/frontend/visualizations/__init__.py

@@ -2,12 +2,13 @@
 Contains all operations for creating charts, graphs and visual effects.
 '''
 from PyQt6.QtWidgets import QWidget
-import plotly
+import plotly, logging
 from plotly.graph_objects import Figure
-from plotly.graph_objs import FigureWidget
 import pandas as pd
 from frontend.widgets.functions import select_save_file
 
+logger = logging.getLogger(f"submissions.{__name__}")
+
 
 class CustomFigure(Figure):
 
@@ -40,16 +41,12 @@ class CustomFigure(Figure):
         """
         Creates final html code from plotly
 
-        Args:
-            figure (Figure): input figure
-
         Returns:
             str: html string
         """
         html = '<html><body>'
         if self is not None:
-            html += plotly.offline.plot(self, output_type='div',
-                                        include_plotlyjs='cdn')  #, image = 'png', auto_open=True, image_filename='plot_image')
+            html += plotly.offline.plot(self, output_type='div', include_plotlyjs='cdn')
         else:
             html += "<h1>No data was retrieved for the given parameters.</h1>"
         html += '</body></html>'

src/submissions/frontend/visualizations/pcr_charts.py

@@ -2,9 +2,6 @@
 Functions for constructing irida controls graphs using plotly.
 """
 from pprint import pformat
-
-from plotly.graph_objs import FigureWidget, Scatter
-
 from . import CustomFigure
 import plotly.express as px
 import pandas as pd
@@ -13,30 +10,23 @@ import logging
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
-# NOTE: For click events try (haven't got working yet) ipywidgets >=7.0.0 required for figurewidgets:
-# https://plotly.com/python/click-events/
-
 
 class PCRFigure(CustomFigure):
 
     def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None,
                  months: int = 6):
         super().__init__(df=df, modes=modes)
-        logger.debug(f"DF: {self.df}")
+        # logger.debug(f"DF: {self.df}")
         self.construct_chart(df=df)
 
-    def hello(self):
-        print("hello")
-
     def construct_chart(self, df: pd.DataFrame):
-        logger.debug(f"PCR df:\n {df}")
+        # logger.debug(f"PCR df:\n {df}")
         try:
-            express = px.scatter(data_frame=df, x='submitted_date', y="ct",
+            scatter = px.scatter(data_frame=df, x='submitted_date', y="ct",
                                            hover_data=["name", "target", "ct", "reagent_lot"],
                                            color="target")
         except ValueError:
-            express = px.scatter()
-        scatter = FigureWidget([datum for datum in express.data])
+            scatter = px.scatter()
         self.add_traces(scatter.data)
         self.update_traces(marker={'size': 15})
 

src/submissions/frontend/widgets/app.py

@@ -2,6 +2,7 @@
 Constructs main application.
 """
 from pprint import pformat
+from PyQt6.QtCore import qInstallMessageHandler
 from PyQt6.QtWidgets import (
     QTabWidget, QWidget, QVBoxLayout,
     QHBoxLayout, QScrollArea, QMainWindow,
@@ -11,6 +12,7 @@ from PyQt6.QtGui import QAction
 from pathlib import Path
 from markdown import markdown
 from __init__ import project_path
+from backend import SubmissionType
 from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size
 from .functions import select_save_file, select_open_file
 from datetime import date
@@ -32,12 +34,13 @@ class App(QMainWindow):
     def __init__(self, ctx: Settings = None):
         # logger.debug(f"Initializing main window...")
         super().__init__()
+        qInstallMessageHandler(lambda x, y, z: None)
         self.ctx = ctx
         self.last_dir = ctx.directory_path
         self.report = Report()
         # NOTE: indicate version and connected database in title bar
         try:
-            self.title = f"Submissions App (v{ctx.package.__version__}) - {ctx.database_session.get_bind().url}"
+            self.title = f"Submissions App (v{ctx.package.__version__}) - {ctx.database_path}/{ctx.database_name}"
         except (AttributeError, KeyError):
             self.title = f"Submissions App"
         # NOTE: set initial app position and size

src/submissions/frontend/widgets/controls_chart.py

@@ -155,7 +155,7 @@ class ControlsViewer(QWidget):
         chart_settings = dict(sub_type=self.con_sub_type, start_date=self.start_date, end_date=self.end_date,
                               mode=self.mode,
                               sub_mode=self.mode_sub_type, parent=self, months=months)
-        _, self.fig = self.archetype.get_instance_class().make_chart(chart_settings=chart_settings, parent=self, ctx=self.app.ctx)
+        self.fig = self.archetype.get_instance_class().make_chart(chart_settings=chart_settings, parent=self, ctx=self.app.ctx)
         if issubclass(self.fig.__class__, CustomFigure):
             self.save_button.setEnabled(True)
         # logger.debug(f"Updating figure...")

src/submissions/frontend/widgets/equipment_usage.py

@@ -1,8 +1,9 @@
 '''
 Creates forms that the user can enter equipment info into.
 '''
+import time
 from pprint import pformat
-from PyQt6.QtCore import Qt
+from PyQt6.QtCore import Qt, QSignalBlocker
 from PyQt6.QtWidgets import (QDialog, QComboBox, QCheckBox,
                              QLabel, QWidget, QVBoxLayout, QDialogButtonBox, QGridLayout)
 from backend.db.models import Equipment, BasicSubmission, Process
@@ -127,13 +128,14 @@ class RoleComboBox(QWidget):
         # logger.debug(f"Updating equipment: {equip}")
         equip2 = next((item for item in self.role.equipment if item.name == equip), self.role.equipment[0])
         # logger.debug(f"Using: {equip2}")
-        self.process.clear()
+        with QSignalBlocker(self.process) as blocker:
+            self.process.clear()
         self.process.addItems([item for item in equip2.processes if item in self.role.processes])
 
     def update_tips(self):
         """
         Changes what tips are available when process is changed
-        """        
+        """
         process = self.process.currentText().strip()
         # logger.debug(f"Checking process: {process} for equipment {self.role.name}")
         process = Process.query(name=process)

src/submissions/frontend/widgets/gel_checker.py

@@ -1,6 +1,7 @@
 """
 Gel box for artic quality control
 """
+from operator import itemgetter
 from PyQt6.QtWidgets import (QWidget, QDialog, QGridLayout,
                              QLabel, QLineEdit, QDialogButtonBox,
                              QTextEdit, QComboBox
@@ -65,7 +66,8 @@ class GelBox(QDialog):
         layout.addWidget(self.imv, 0, 1, 20, 20)
         # NOTE: setting this widget as central widget of the main window
         try:
-            control_info = sorted(self.submission.gel_controls, key=lambda d: d['location'])
+            # control_info = sorted(self.submission.gel_controls, key=lambda d: d['location'])
+            control_info = sorted(self.submission.gel_controls, key=itemgetter('location'))
         except KeyError:
             control_info = None
         self.form = ControlsForm(parent=self, control_info=control_info)

src/submissions/frontend/widgets/submission_table.py

@@ -99,19 +99,21 @@ class SubmissionsSheet(QTableView):
         proxyModel.setSourceModel(pandasModel(self.data))
         self.setModel(proxyModel)
 
-    def contextMenuEvent(self):
+    def contextMenuEvent(self, event):
         """
         Creates actions for right click menu events.
 
         Args:
             event (_type_): the item of interest
         """
-        # logger.debug(event().__dict__)
+        # logger.debug(event.__dict__)
         id = self.selectionModel().currentIndex()
         id = id.sibling(id.row(), 0).data()
         submission = BasicSubmission.query(id=id)
+        # logger.debug(f"Event submission: {submission}")
         self.menu = QMenu(self)
         self.con_actions = submission.custom_context_events()
+        # logger.debug(f"Menu options: {self.con_actions}")
         for k in self.con_actions.keys():
             # logger.debug(f"Adding {k}")
             action = QAction(k, self)

src/submissions/frontend/widgets/submission_widget.py

@@ -1,6 +1,8 @@
 '''
 Contains all submission related frontend functions
 '''
+import sys
+
 from PyQt6.QtWidgets import (
     QWidget, QPushButton, QVBoxLayout,
     QComboBox, QDateEdit, QLineEdit, QLabel
@@ -190,7 +192,8 @@ class SubmissionFormWidget(QWidget):
         self.app = parent.app
         self.pyd = submission
         self.missing_info = []
-        st = SubmissionType.query(name=self.pyd.submission_type['value']).get_submission_class()
+        self.submission_type = SubmissionType.query(name=self.pyd.submission_type['value'])
+        st = self.submission_type.get_submission_class()
         defaults = st.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value'])
         self.recover = defaults['form_recover']
         self.ignore = defaults['form_ignore']
@@ -215,7 +218,7 @@ class SubmissionFormWidget(QWidget):
                     value = self.pyd.model_extra[k]
                 except KeyError:
                     value = dict(value=None, missing=True)
-            add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'],
+            add_widget = self.create_widget(key=k, value=value, submission_type=self.submission_type,
                                             sub_obj=st, disable=check)
             if add_widget is not None:
                 self.layout.addWidget(add_widget)
@@ -224,7 +227,7 @@ class SubmissionFormWidget(QWidget):
         self.setStyleSheet(main_form_style)
         self.scrape_reagents(self.pyd.extraction_kit)
 
-    def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | None = None,
+    def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | SubmissionType| None = None,
                       extraction_kit: str | None = None, sub_obj: BasicSubmission | None = None,
                       disable: bool = False) -> "self.InfoItem":
         """
@@ -240,6 +243,8 @@ class SubmissionFormWidget(QWidget):
             self.InfoItem: Form widget to hold name:value
         """
         # logger.debug(f"Key: {key}, Disable: {disable}")
+        if isinstance(submission_type, str):
+            submission_type = SubmissionType.query(name=submission_type)
         if key not in self.ignore:
             match value:
                 case PydReagent():
@@ -272,7 +277,7 @@ class SubmissionFormWidget(QWidget):
         """
         extraction_kit = args[0]
         report = Report()
-        # logger.debug(f"Extraction kit: {extraction_kit}")
+        logger.debug(f"Extraction kit: {extraction_kit}")
         # NOTE: Remove previous reagent widgets
         try:
             old_reagents = self.find_widgets()
@@ -284,7 +289,7 @@ class SubmissionFormWidget(QWidget):
             if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
                 reagent.setParent(None)
         reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=extraction_kit)
-        # logger.debug(f"Missing reagents: {obj.missing_reagents}")
+        logger.debug(f"Got reagents: {pformat(reagents)}")
         for reagent in reagents:
             add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit)
             self.layout.addWidget(add_widget)
@@ -454,9 +459,11 @@ class SubmissionFormWidget(QWidget):
 
     class InfoItem(QWidget):
 
-        def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None,
+        def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | SubmissionType | None = None,
                      sub_obj: BasicSubmission | None = None) -> None:
             super().__init__(parent)
+            if isinstance(submission_type, str):
+                submission_type = SubmissionType.query(name=submission_type)
             layout = QVBoxLayout()
             self.label = self.ParsedQLabel(key=key, value=value)
             self.input: QWidget = self.set_widget(parent=parent, key=key, value=value, submission_type=submission_type,
@@ -497,7 +504,7 @@ class SubmissionFormWidget(QWidget):
                     return None, None
             return self.input.objectName(), dict(value=value, missing=self.missing)
 
-        def set_widget(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None,
+        def set_widget(self, parent: QWidget, key: str, value: dict, submission_type: str | SubmissionType | None = None,
                        sub_obj: BasicSubmission | None = None) -> QWidget:
             """
             Creates form widget
@@ -511,8 +518,10 @@ class SubmissionFormWidget(QWidget):
             Returns:
                 QWidget: Form object
             """
+            if isinstance(submission_type, str):
+                submission_type = SubmissionType.query(name=submission_type)
             if sub_obj is None:
-                sub_obj = SubmissionType.query(name=submission_type).get_submission_class()
+                sub_obj = submission_type.get_submission_class()
             try:
                 value = value['value']
             except (TypeError, KeyError):
@@ -544,7 +553,8 @@ class SubmissionFormWidget(QWidget):
                     add_widget = MyQComboBox(scrollWidget=parent)
                     # NOTE: lookup existing kits by 'submission_type' decided on by sheetparser
                     # logger.debug(f"Looking up kits used for {submission_type}")
-                    uses = [item.name for item in KitType.query(used_for=submission_type)]
+                    # uses = [item.name for item in KitType.query(used_for=submission_type)]
+                    uses = [item.name for item in submission_type.kit_types]
                     obj.uses = uses
                     # logger.debug(f"Kits received for {submission_type}: {uses}")
                     if check_not_nan(value):
@@ -668,7 +678,7 @@ class SubmissionFormWidget(QWidget):
                 dlg = QuestionAsker(title=f"Add {lot}?",
                                     message=f"Couldn't find reagent type {self.reagent.role}: {lot} in the database.\n\nWould you like to add it?")
                 if dlg.exec():
-                    wanted_reagent, _ = self.parent().parent().add_reagent(reagent_lot=lot,
+                    wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot,
                                                                            reagent_role=self.reagent.role,
                                                                            expiry=self.reagent.expiry,
                                                                            name=self.reagent.name)

src/submissions/frontend/widgets/summary.py

@@ -42,7 +42,6 @@ class Summary(QWidget):
         self.setLayout(self.layout)
         self.get_report()
 
-
     def get_report(self):
         orgs = [self.org_select.itemText(i) for i in range(self.org_select.count()) if self.org_select.itemChecked(i)]
         if self.datepicker.start_date.date() > self.datepicker.end_date.date():

src/submissions/tools/__init__.py

@@ -17,13 +17,15 @@ from sqlalchemy import create_engine, text, MetaData
 from pydantic import field_validator, BaseModel, Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
 from typing import Any, Tuple, Literal, List
-print(inspect.stack()[1])
+# print(inspect.stack()[1])
 from __init__ import project_path
 from configparser import ConfigParser
 from tkinter import Tk  # NOTE: This is for choosing database path before app is created.
 from tkinter.filedialog import askdirectory
 from sqlalchemy.exc import IntegrityError as sqlalcIntegrityError
+from pytz import timezone as tz
 
+timezone = tz("America/Winnipeg")
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -386,16 +388,22 @@ class Settings(BaseSettings, extra="allow"):
                 case "sqlite":
                     value = f"/{values.data['database_path']}"
                     db_name = f"{values.data['database_name']}.db"
+                    template = jinja_template_loading().from_string(
+                        "{{ values['database_schema'] }}://{{ value }}/{{ db_name }}")
+                case "mssql+pyodbc":
+                    value = values.data['database_path']
+                    db_name = values.data['database_name']
+                    template = jinja_template_loading().from_string(
+                        "{{ values['database_schema'] }}://{{ value }}/{{ db_name }}?driver=ODBC+Driver+18+for+SQL+Server&TrustServerCertificate=yes&Trusted_Connection=yes"
+                    )
                 case _:
                     # print(pprint.pprint(values.data))
                     tmp = jinja_template_loading().from_string(
                         "{% if values['database_user'] %}{{ values['database_user'] }}{% if values['database_password'] %}:{{ values['database_password'] }}{% endif %}{% endif %}@{{ values['database_path'] }}")
                     value = tmp.render(values=values.data)
                     db_name = values.data['database_name']
-            template = jinja_template_loading().from_string(
-                "{{ values['database_schema'] }}://{{ value }}/{{ db_name }}")
             database_path = template.render(values=values.data, value=value, db_name=db_name)
-            # print(f"Using {database_path} for database path")
+            print(f"Using {database_path} for database path")
             engine = create_engine(database_path)
             session = Session(engine)
             return session
@@ -939,8 +947,7 @@ def report_result(func):
 
     """
     def wrapper(*args, **kwargs):
-        # logger.debug(f"Arguments: {args}")
-        # logger.debug(f"Keyword arguments: {kwargs}")
+        logger.debug(f"Report result being called by {func.__name__}")
         output = func(*args, **kwargs)
         match output:
             case Report():
@@ -966,6 +973,12 @@ def report_result(func):
             except Exception as e:
                 logger.error(f"Problem reporting due to {e}")
                 logger.error(result.msg)
-        # logger.debug(f"Returning: {output}")
-        return output
+        if output:
+            true_output = tuple(item for item in output if not isinstance(item, Report))
+            if len(true_output) == 1:
+                true_output = true_output[0]
+        else:
+            true_output = None
+        # logger.debug(f"Returning true output: {true_output}")
+        return true_output
     return wrapper