Allow for grabbing of single kit if only one exists for submission type.

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

@@ -683,6 +683,11 @@ class SubmissionType(BaseClass):
         """
         return f"<SubmissionType({self.name})>"
 
+    @classmethod
+    def retrieve_template_file(cls):
+        submission_type = cls.query(name="Bacterial Culture")
+        return submission_type.template_file
+
     def get_template_file_sheets(self) -> List[str]:
         logger.debug(f"Submission type to get sheets for: {self.name}")
         """
@@ -779,6 +784,12 @@ class SubmissionType(BaseClass):
                 tmap = {}
             yield item.tip_role.name, tmap
 
+    def get_default_kit(self) -> KitType | None:
+        if len(self.kit_types) == 1:
+            return self.kit_types[0]
+        else:
+            return None
+
     def get_equipment(self, extraction_kit: str | KitType | None = None) -> Generator['PydEquipmentRole', None, None]:
         """
         Returns PydEquipmentRole of all equipment associated with this SubmissionType

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

@@ -8,7 +8,7 @@ from pprint import pformat
 from sqlalchemy import Column, String, INTEGER, ForeignKey, Table
 from sqlalchemy.orm import relationship, Query
 from . import Base, BaseClass
-from tools import check_authorization, setup_lookup
+from tools import check_authorization, setup_lookup, yaml_regex_creator
 from typing import List
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -88,6 +88,7 @@ class Organization(BaseClass):
         Returns:
 
         """
+        yaml.add_constructor("!regex", yaml_regex_creator)
         if isinstance(filepath, str):
             filepath = Path(filepath)
         if not filepath.exists():
@@ -97,7 +98,7 @@ class Organization(BaseClass):
             if filepath.suffix == ".json":
                 import_dict = json.load(fp=f)
             elif filepath.suffix == ".yml":
-                import_dict = yaml.safe_load(stream=f)
+                import_dict = yaml.load(stream=f, Loader=yaml.Loader)
             else:
                 raise Exception(f"Filetype {filepath.suffix} not supported.")
         data = import_dict['orgs']

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

@@ -1038,7 +1038,7 @@ class BasicSubmission(BaseClass):
               chronologic: bool = False,
               limit: int = 0,
               page: int = 1,
-              page_size: int = 250,
+              page_size: None | int = 250,
               **kwargs
               ) -> BasicSubmission | List[BasicSubmission]:
         """
@@ -1059,6 +1059,7 @@ class BasicSubmission(BaseClass):
         """
         # logger.debug(f"Incoming kwargs: {kwargs}")
         # NOTE: if you go back to using 'model' change the appropriate cls to model in the query filters
+        # logger.debug(f"Page size: {page_size}")
         if submission_type is not None:
             model = cls.find_polymorphic_subclass(polymorphic_identity=submission_type)
         elif len(kwargs) > 0:
@@ -1139,7 +1140,7 @@ class BasicSubmission(BaseClass):
         # if chronologic:
         #     logger.debug("Attempting sort by date descending")
         query = query.order_by(cls.submitted_date.desc())
-        if page_size is not None:
+        if page_size > 0:
             query = query.limit(page_size)
         page = page - 1
         if page is not None:

src/submissions/backend/excel/parser.py

@@ -96,7 +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'])}")
+        # logger.debug(f"Reagents out of parser: {pformat(self.sub['reagents'])}")
 
     def parse_samples(self):
         """
@@ -273,11 +273,11 @@ class ReagentParser(object):
         self.kit_object = KitType.query(name=extraction_kit)
         logger.debug(f"Got extraction kit object: {self.kit_object}")
         self.map = self.fetch_kit_info_map(submission_type=submission_type)
-        # logger.debug(f"Reagent Parser map: {self.map}")
+        logger.debug(f"Reagent Parser map: {self.map}")
         self.xl = xl
 
     @report_result
-    def fetch_kit_info_map(self, submission_type: str|SubmissionType) -> Tuple[Report, dict]:
+    def fetch_kit_info_map(self, submission_type: str | SubmissionType) -> Tuple[Report, dict]:
         """
         Gets location of kit reagents from database
 
@@ -296,15 +296,24 @@ class ReagentParser(object):
         except KeyError:
             pass
         # logger.debug(f"Reagent map: {pformat(reagent_map)}")
+        # NOTE: If reagent map is empty, maybe the wrong kit was given, check if there's only one kit for that submission type and use it if so.
         if not reagent_map.keys():
-            try:
+            temp_kit_object = self.submission_type_obj.get_default_kit()
-                ext_kit_loc = self.submission_type_obj.info_map['extraction_kit']['read'][0]
+            if temp_kit_object:
-                location_string = f"Sheet: {ext_kit_loc['sheet']}, Row: {ext_kit_loc['row']}, Column: {ext_kit_loc['column']}?"
+                self.kit_object = temp_kit_object
-            except:
+                reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
-                location_string = ""
+                logger.warning(f"Attempting to salvage {self.kit_object} with default kit map: {reagent_map}")
-            report.add_result(Result(owner=__name__, code=0, msg=f"No kit map found for {self.kit_object.name}.\n\n"
+            if not reagent_map.keys():
-                                                                 f"Are you sure you put the right kit in:\n\n{location_string}?",
+                logger.error(f"Still no reagent map, displaying error.")
-                                     status="Critical"))
+                try:
+                    ext_kit_loc = self.submission_type_obj.info_map['extraction_kit']['read'][0]
+                    location_string = f"Sheet: {ext_kit_loc['sheet']}, Row: {ext_kit_loc['row']}, Column: {ext_kit_loc['column']}?"
+                except (IndexError, KeyError):
+                    location_string = ""
+                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 put the right kit in:\n\n{location_string}?",
+                                         status="Critical"))
         return report, reagent_map
 
     def parse_reagents(self) -> Generator[dict, None, None]:
@@ -317,7 +326,7 @@ class ReagentParser(object):
         for sheet in self.xl.sheetnames:
             ws = self.xl[sheet]
             relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']}
-            # logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
+            logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
             if relevant == {}:
                 continue
             for item in relevant:

src/submissions/backend/excel/reports.py

@@ -18,10 +18,12 @@ env = jinja_template_loading()
 
 class ReportMaker(object):
 
-    def __init__(self, start_date: date, end_date: date, organizations:list|None=None):
+    def __init__(self, start_date: date, end_date: date, organizations: list | None = None):
         self.start_date = start_date
         self.end_date = end_date
-        self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date)
+        # NOTE: Set page size to zero to override limiting query size.
+        self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date, page_size=0)
+        # logger.debug(f"Number of subs returned: {len(self.subs)}")
         if organizations is not None:
             self.subs = [sub for sub in self.subs if sub.submitting_lab.name in organizations]
         self.detailed_df, self.summary_df = self.make_report_xlsx()
@@ -46,6 +48,7 @@ class ReportMaker(object):
         # logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
         df = df.drop('id', axis=1)
         df = df.sort_values(['submitting_lab', "submitted_date"])
+        logger.debug(f"Details dataframe:\n{df2}")
         return df, df2
 
     def make_report_html(self, df: DataFrame) -> str:
@@ -97,7 +100,7 @@ class ReportMaker(object):
         Args:
             filename (Path | str): Basename of output file
             obj (QWidget | None, optional): Parent object. Defaults to None.
-        """        
+        """
         if isinstance(filename, str):
             filename = Path(filename)
         filename = filename.absolute()
@@ -111,7 +114,7 @@ class ReportMaker(object):
     def fix_up_xl(self):
         """
         Handles formatting of xl file, mediocrely.
-        """        
+        """
         # logger.debug(f"Updating worksheet")
         worksheet: Worksheet = self.writer.sheets['Report']
         for idx, col in enumerate(self.summary_df, start=1):  # NOTE: loop through all columns
@@ -134,5 +137,3 @@ class ReportMaker(object):
         for cell in worksheet['D']:
             if cell.row > 1:
                 cell.style = 'Currency'
-
-

src/submissions/backend/excel/writer.py

@@ -51,6 +51,9 @@ class SheetWriter(object):
         #     except Exception as e:
         #         logger.error(f"Couldn't open workbook due to {e}")
         template = self.submission_type.template_file
+        if not template:
+            logger.error(f"No template file found, falling back to Bacterial Culture")
+            template = SubmissionType.retrieve_template_file()
         workbook = load_workbook(BytesIO(template))
         # self.workbook = workbook
         self.xl = workbook

src/submissions/frontend/widgets/app.py

@@ -1,6 +1,7 @@
 """
 Constructs main application.
 """
+import os
 from pprint import pformat
 from PyQt6.QtCore import qInstallMessageHandler
 from PyQt6.QtWidgets import (
@@ -213,7 +214,7 @@ class App(QMainWindow):
             None
         """
         if check_if_app():
-            yaml_path = Path(sys._MEIPASS).joinpath("resources", "viral_culture.yml")
+            yaml_path = Path(sys._MEIPASS).joinpath("files", "resources", "viral_culture.yml")
         else:
             yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
         fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")

src/submissions/frontend/widgets/submission_widget.py

@@ -225,7 +225,8 @@ class SubmissionFormWidget(QWidget):
             if k == "extraction_kit":
                 add_widget.input.currentTextChanged.connect(self.scrape_reagents)
         self.setStyleSheet(main_form_style)
-        self.scrape_reagents(self.pyd.extraction_kit)
+        # self.scrape_reagents(self.pyd.extraction_kit)
+        self.scrape_reagents(self.extraction_kit)
 
     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,
@@ -275,9 +276,9 @@ class SubmissionFormWidget(QWidget):
         Returns:
             Tuple[QMainWindow, dict]: Updated application and result
         """
-        extraction_kit = args[0]
+        self.extraction_kit = args[0]
         report = Report()
-        logger.debug(f"Extraction kit: {extraction_kit}")
+        logger.debug(f"Extraction kit: {self.extraction_kit}")
         # NOTE: Remove previous reagent widgets
         try:
             old_reagents = self.find_widgets()
@@ -288,10 +289,11 @@ class SubmissionFormWidget(QWidget):
         for reagent in old_reagents:
             if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
                 reagent.setParent(None)
-        reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=extraction_kit)
+        reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit)
         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)
+            # add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit)
+            add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.extraction_kit)
             self.layout.addWidget(add_widget)
         report.add_result(integrity_report)
         # logger.debug(f"Outgoing report: {report.results}")
@@ -569,6 +571,7 @@ class SubmissionFormWidget(QWidget):
                         obj.ext_kit = uses[0]
                     add_widget.addItems(uses)
                     add_widget.setToolTip("Select extraction kit.")
+                    parent.extraction_kit = add_widget.currentText()
                 case 'submission_category':
                     add_widget = MyQComboBox(scrollWidget=parent)
                     cats = ['Diagnostic', "Surveillance", "Research"]

src/submissions/frontend/widgets/summary.py

@@ -56,6 +56,7 @@ class Summary(QWidget):
         # NOTE: convert to python useable date objects
         self.start_date = self.datepicker.start_date.date().toPyDate()
         self.end_date = self.datepicker.end_date.date().toPyDate()
+        logger.debug(f"Getting report from {self.start_date} to {self.end_date} using {orgs}")
         self.report_obj = ReportMaker(start_date=self.start_date, end_date=self.end_date, organizations=orgs)
         self.webview.setHtml(self.report_obj.html)
         if self.report_obj.subs: