Converted client manager to new Omni pydantic version.

CHANGELOG.md

@@ -1,5 +1,6 @@
 # 202504.01
 
+- Added in method to backup submissions to xlsx (partly).
 - Added in checkbox to use all samples in Concentrations tab (very slow).
 
 # 202503.05

TODO.md

@@ -1,4 +1,4 @@
-- [ ] Change "Manage Organizations" to the Pydantic version.
+- [x] Change "Manage Organizations" to the Pydantic version.
 - [x] Can my "to_dict", "to_sub_dict", "to_pydantic" methods be rewritten as properties?
 - [ ] Stop displacing date on Irida controls and just do what Turnaround time does.
 - [x] Get Manager window working for KitType, maybe SubmissionType

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

@@ -60,28 +60,26 @@ class BaseClass(Base):
         try:
             return f"<{self.__class__.__name__}({self.name})>"
         except AttributeError:
-            return f"<{self.__class__.__name__}(Unknown)>"
+            return f"<{self.__class__.__name__}(Name Unavailable)>"
-
-    # @classproperty
-    # def skip_on_edit(cls):
-    #     if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
-    #         return True
-    #     else:
-    #         return False
 
     @classproperty
-    def aliases(cls):
+    def aliases(cls) -> List[str]:
+        """
+        List of other names this class might be known by.
+
+        Returns:
+            List[str]: List of names
+        """
         return [cls.query_alias]
 
-    # @classproperty
-    # def level(cls):
-    #     if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
-    #         return 2
-    #     else:
-    #         return 1
-
     @classproperty
-    def query_alias(cls):
+    def query_alias(cls) -> str:
+        """
+        What to query this class as.
+
+        Returns:
+            str: query name
+        """
         return cls.__name__.lower()
 
     @classmethod
@@ -153,21 +151,23 @@ class BaseClass(Base):
         return dict(singles=singles)
 
     @classmethod
-    def find_regular_subclass(cls, name: str = "") -> Any:
+    def find_regular_subclass(cls, name: str|None = None) -> Any:
         """
-
         Args:
             name (str): name of subclass of interest.
 
         Returns:
-            Any: Subclass of this object
+            Any: Subclass of this object.
-
         """
+        if name:
             if " " in name:
                 search = name.title().replace(" ", "")
             else:
                 search = name
             return next((item for item in cls.__subclasses__() if item.__name__ == search), cls)
+        else:
+            return cls.__subclasses__()
+
 
     @classmethod
     def fuzzy_search(cls, **kwargs) -> List[Any]:
@@ -193,7 +193,7 @@ class BaseClass(Base):
         return query.limit(50).all()
 
     @classmethod
-    def results_to_df(cls, objects: list|None=None, **kwargs) -> DataFrame:
+    def results_to_df(cls, objects: list | None = None, **kwargs) -> DataFrame:
         """
         Converts class sub_dicts into a Dataframe for all instances of the class.
 
@@ -395,7 +395,8 @@ class BaseClass(Base):
             if check:
                 logger.debug(f"Checking for subclass name.")
                 self_value = self_value.name
-            logger.debug(f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
+            logger.debug(
+                f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
             if self_value != value:
                 output = False
                 logger.debug(f"Value {key} is False, returning.")

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

@@ -425,17 +425,23 @@ class IridaControl(Control):
             kraken = self.kraken
         except TypeError:
             kraken = {}
+        try:
             kraken_cnt_total = sum([item['kraken_count'] for item in kraken.values()])
+        except AttributeError:
+            kraken_cnt_total = 0
+        try:
             new_kraken = [dict(name=key, kraken_count=value['kraken_count'],
                            kraken_percent=f"{value['kraken_count'] / kraken_cnt_total:0.2%}",
                            target=key in self.controltype.targets)
                       for key, value in kraken.items()]
-        new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)
+            new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)[0:10]
+        except (AttributeError, ZeroDivisionError):
+            new_kraken = []
         output = dict(
             name=self.name,
             type=self.controltype.name,
             targets=", ".join(self.targets),
-            kraken=new_kraken[0:10]
+            kraken=new_kraken
         )
         return output
 

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

@@ -10,7 +10,7 @@ from sqlalchemy.ext.hybrid import hybrid_property
 from sqlalchemy.orm import relationship, Query
 from . import Base, BaseClass
 from tools import check_authorization, setup_lookup, yaml_regex_creator
-from typing import List
+from typing import List, Tuple
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -123,6 +123,20 @@ class Organization(BaseClass):
                 organ.contacts.append(cont)
             organ.save()
 
+    def to_omni(self, expand: bool = False):
+        from backend.validators.omni_gui_objects import OmniOrganization
+        if self.cost_centre:
+            cost_centre = self.cost_centre
+        else:
+            cost_centre = "NA"
+        if self.name:
+            name = self.name
+        else:
+            name = "NA"
+        return OmniOrganization(instance_object=self,
+                                name=name, cost_centre=cost_centre,
+                                contact=[item.to_omni() for item in self.contacts])
+
 
 class Contact(BaseClass):
     """
@@ -144,6 +158,20 @@ class Contact(BaseClass):
     def searchables(cls):
         return []
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[Contact, bool]:
+        new = False
+        disallowed = []
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = cls()
+            new = True
+        for k, v in sanitized_kwargs.items():
+            setattr(instance, k, v)
+        logger.info(f"Instance from contact query or create: {instance}")
+        return instance, new
+
     @classmethod
     @setup_lookup
     def query(cls,
@@ -195,3 +223,22 @@ class Contact(BaseClass):
     def to_pydantic(self) -> "PydContact":
         from backend.validators import PydContact
         return PydContact(name=self.name, email=self.email, phone=self.phone)
+
+    def to_omni(self, expand: bool = False):
+        from backend.validators.omni_gui_objects import OmniContact
+        if self.email:
+            email = self.email
+        else:
+            email = "NA"
+        if self.name:
+            name = self.name
+        else:
+            name = "NA"
+        if self.phone:
+            phone = self.phone
+        else:
+            phone = "NA"
+        return OmniContact(instance_object=self,
+                                name=name, email=email,
+                                phone=phone)
+

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

@@ -3,6 +3,7 @@ Models for the main submission and sample types.
 """
 from __future__ import annotations
 
+import itertools
 import pickle
 from copy import deepcopy
 from getpass import getuser
@@ -12,6 +13,8 @@ from zipfile import ZipFile, BadZipfile
 from tempfile import TemporaryDirectory, TemporaryFile
 from operator import itemgetter
 from pprint import pformat
+
+from pandas import DataFrame
 from sqlalchemy.ext.hybrid import hybrid_property
 from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin, SubmissionReagentAssociation
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func
@@ -287,6 +290,7 @@ class BasicSubmission(BaseClass, LogMixin):
         Constructs dictionary used in submissions summary
 
         Args:
+            expand (bool, optional): indicates if generators to be expanded. Defaults to False.
             report (bool, optional): indicates if to be used for a report. Defaults to False.
             full_data (bool, optional): indicates if sample dicts to be constructed. Defaults to False.
             backup (bool, optional): passed to adjust_to_dict_samples. Defaults to False.
@@ -393,6 +397,33 @@ class BasicSubmission(BaseClass, LogMixin):
             output["completed_date"] = self.completed_date
         return output
 
+    @classmethod
+    def archive_submissions(cls, start_date: date | datetime | str | int | None = None,
+                            end_date: date | datetime | str | int | None = None,
+                            submissiontype: List[str] | None = None):
+        if submissiontype:
+            if isinstance(submissiontype, str):
+                submissiontype = [submissiontype]
+            query_out = []
+            for sub_type in submissiontype:
+                subs = cls.query(page_size=0, start_date=start_date, end_date=end_date, submissiontype=sub_type)
+                # logger.debug(f"Sub results: {subs}")
+                query_out.append(subs)
+            query_out = list(itertools.chain.from_iterable(query_out))
+        else:
+            query_out = cls.query(page_size=0, start_date=start_date, end_date=end_date)
+        records = []
+        for sub in query_out:
+            output = sub.to_dict(full_data=True)
+            for k, v in output.items():
+                if isinstance(v, types.GeneratorType):
+                    output[k] = [item for item in v]
+            records.append(output)
+        df = DataFrame.from_records(records)
+        df.sort_values(by="id", inplace=True)
+        df.set_index("id", inplace=True)
+        return df
+
     @property
     def column_count(self) -> int:
         """
@@ -590,61 +621,18 @@ class BasicSubmission(BaseClass, LogMixin):
             except AttributeError as e:
                 logger.error(f"Could not set {self} attribute {key} to {value} due to \n{e}")
 
-    # def update_subsampassoc(self, sample: BasicSample, input_dict: dict) -> SubmissionSampleAssociation:
-    #     """
-    #     Update a joined submission sample association.
-    #
-    #     Args:
-    #         sample (BasicSample): Associated sample.
-    #         input_dict (dict): values to be updated
-    #
-    #     Returns:
-    #         SubmissionSampleAssociation: Updated association
-    #     """
-    #     try:
-    #         logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
-    #         assoc = next((item for item in self.submission_sample_associations
-    #                      if item.sample == sample and
-    #                      item.row == input_dict['row'] and
-    #                      item.column == input_dict['column']))
-    #         logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
-    #     except StopIteration:
-    #         report = Report()
-    #         report.add_result(
-    #             Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
-    #         return report
-    #     for k, v in input_dict.items():
-    #         try:
-    #             # logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
-    #             setattr(assoc, k, v)
-    #             # NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
-    #         except AttributeError:
-    #             logger.error(f"Can't set {k} to {v}")
-    #     return assoc
-
     def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
         """
         Update a joined submission sample association.
 
         Args:
-            sample (BasicSample): Associated sample.
+            assoc (SubmissionSampleAssociation): Sample association to be updated.
-            input_dict (dict): values to be updated
+            input_dict (dict): updated values to insert.
 
         Returns:
             SubmissionSampleAssociation: Updated association
         """
-        # try:
+        # NOTE: No longer searches for association here, done in caller function
-        #     logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
-        #     assoc = next((item for item in self.submission_sample_associations
-        #                  if item.sample == sample and
-        #                  item.row == input_dict['row'] and
-        #                  item.column == input_dict['column']))
-        #     logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
-        # except StopIteration:
-        #     report = Report()
-        #     report.add_result(
-        #         Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
-        #     return report
         for k, v in input_dict.items():
             try:
                 # logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
@@ -771,8 +759,8 @@ class BasicSubmission(BaseClass, LogMixin):
         return regex
 
     @classmethod
-    def find_polymorphic_subclass(cls, polymorphic_identity: str | SubmissionType | None = None,
+    def find_polymorphic_subclass(cls, polymorphic_identity: str | SubmissionType | list | None = None,
-                                  attrs: dict | None = None) -> BasicSubmission:
+                                  attrs: dict | None = None) -> BasicSubmission | List[BasicSubmission]:
         """
         Find subclass based on polymorphic identity or relevant attributes.
 
@@ -795,6 +783,13 @@ class BasicSubmission(BaseClass, LogMixin):
                 except Exception as e:
                     logger.error(
                         f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
+            case list():
+                output = []
+                for identity in polymorphic_identity:
+                    if isinstance(identity, SubmissionType):
+                        identity = polymorphic_identity.name
+                    output.append(cls.__mapper__.polymorphic_map[identity].class_)
+                return output
             case _:
                 pass
         if attrs and any([not hasattr(cls, attr) for attr in attrs.keys()]):
@@ -1855,18 +1850,6 @@ class Wastewater(BasicSubmission):
             result = assoc.save()
             if result:
                 report.add_result(result)
-        # for sample in self.samples:
-        #     logger.debug(f"Checking pcr_samples for {sample.rsl_number}, {sample.ww_full_sample_id}")
-        #     try:
-        #         # NOTE: Fix for ENs which have no rsl_number...
-        #         sample_dict = next(item for item in pcr_samples if item['sample'] == sample.rsl_number)
-        #         logger.debug(f"Found sample {sample_dict} at index {pcr_samples.index(sample_dict)}: {pcr_samples[pcr_samples.index(sample_dict)]}")
-        #     except StopIteration:
-        #         logger.error(f"Couldn't find {sample} in the Parser samples")
-        #         continue
-        #     assoc = self.update_subsampassoc(sample=sample, input_dict=sample_dict)
-        #     result = assoc.save()
-        #     report.add_result(result)
         controltype = ControlType.query(name="PCR Control")
         submitted_date = datetime.strptime(" ".join(parser.pcr_info['run_start_date/time'].split(" ")[:-1]),
                                            "%Y-%m-%d %I:%M:%S %p")
@@ -1880,35 +1863,6 @@ class Wastewater(BasicSubmission):
             new_control.save()
         return report
 
-    # def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
-    #     """
-    #     Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
-    #
-    #     Args:
-    #         sample (BasicSample): Associated sample.
-    #         input_dict (dict): values to be updated
-    #
-    #     Returns:
-    #         SubmissionSampleAssociation: Updated association
-    #     """
-    #     # logger.debug(f"Input dict: {pformat(input_dict)}")
-    #     #
-    #     assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
-    #     # targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
-    #     # assert 0 < len(targets) <= 2
-    #     # for k, v in targets.items():
-    #     #     # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
-    #     #     # update_key = f"ct_n{i}"
-    #     #     current_value = getattr(assoc, k)
-    #     #     logger.debug(f"Current value came back as: {current_value}")
-    #     #     if current_value is None:
-    #     #         setattr(assoc, k, v)
-    #     #     else:
-    #     #         logger.debug(f"Have a value already, {current_value}... skipping.")
-    #     if assoc.column == 3:
-    #         logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
-    #     return assoc
-
 
 class WastewaterArtic(BasicSubmission):
     """
@@ -2196,14 +2150,14 @@ class WastewaterArtic(BasicSubmission):
         # logger.debug(processed)
         # NOTE: Remove brackets at end
         processed = re.sub(r"\(.*\)$", "", processed).strip()
-        logger.debug(processed)
+        # logger.debug(processed)
         processed = re.sub(r"-RPT", "", processed, flags=re.IGNORECASE)
         # NOTE: Remove any non-R letters at end.
         processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
-        logger.debug(processed)
+        # logger.debug(processed)
         # NOTE: Remove trailing '-' if any
         processed = processed.strip("-")
-        logger.debug(processed)
+        # logger.debug(processed)
         try:
             plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
             processed = rreplace(processed, plate_num, "")
@@ -2221,20 +2175,20 @@ class WastewaterArtic(BasicSubmission):
             plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num)
         except AttributeError:
             logger.error(f"Problem re-evaluating plate number for {processed}")
-        logger.debug(processed)
+        # logger.debug(processed)
         # NOTE: Remove any redundant -digits
         processed = re.sub(r"-\d$", "", processed)
-        logger.debug(processed)
+        # logger.debug(processed)
         day = re.search(r"\d{2}$", processed).group()
         processed = rreplace(processed, day, "")
-        logger.debug(processed)
+        # logger.debug(processed)
         month = re.search(r"\d{2}$", processed).group()
         processed = rreplace(processed, month, "")
         processed = processed.replace("--", "")
-        logger.debug(processed)
+        # logger.debug(processed)
         year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
         year = f"20{year}"
-        logger.debug(processed)
+        # logger.debug(processed)
         final_en_name = f"PBS{year}{month}{day}-{plate_num}"
         return final_en_name
 
@@ -2881,7 +2835,7 @@ class BacterialCultureSample(BasicSample):
         sample['organism'] = self.organism
         try:
             sample['concentration'] = f"{float(self.concentration):.2f}"
-        except TypeError:
+        except (TypeError, ValueError):
             sample['concentration'] = 0.0
         if self.control is not None:
             sample['colour'] = [0, 128, 0]

src/submissions/backend/validators/omni_gui_objects.py

@@ -593,3 +593,57 @@ class OmniKitType(BaseOmni):
         for item in kit.kit_reagentrole_associations:
             logger.debug(f"KTRRassoc: {item.__dict__}")
         return kit
+
+
+class OmniOrganization(BaseOmni):
+
+    class_object: ClassVar[Any] = Organization
+
+    name: str = Field(default="", description="property")
+    cost_centre: str = Field(default="", description="property")
+    # TODO: add in List[OmniContacts]
+    contact: List[str] | List[OmniContact] = Field(default=[], description="relationship", title="Contact")
+
+    def __init__(self, instance_object: Any, **data):
+        logger.debug(f"Incoming data: {data}")
+        super().__init__(**data)
+        self.instance_object = instance_object
+
+    def to_dataframe_dict(self):
+        return dict(
+            name=self.name,
+            cost_centre=self.cost_centre,
+            contacts=self.contact
+        )
+
+
+class OmniContact(BaseOmni):
+
+    class_object: ClassVar[Any] = Contact
+
+    name: str = Field(default="", description="property")
+    email: str = Field(default="", description="property")
+    phone: str = Field(default="", description="property")
+
+    @property
+    def list_searchables(self):
+        return dict(name=self.name, email=self.email)
+
+    def __init__(self, instance_object: Any, **data):
+        super().__init__(**data)
+        self.instance_object = instance_object
+
+    def to_dataframe_dict(self):
+        return dict(
+            name=self.name,
+            email=self.email,
+            phone=self.phone
+        )
+
+    def to_sql(self):
+        contact, is_new = Contact.query_or_create(name=self.name, email=self.email, phone=self.phone)
+        if is_new:
+            logger.debug(f"New contact made: {contact}")
+        else:
+            logger.debug(f"Contact retrieved: {contact}")
+        return contact

src/submissions/frontend/widgets/app.py

@@ -9,17 +9,19 @@ from PyQt6.QtWidgets import (
     QHBoxLayout, QScrollArea, QMainWindow,
     QToolBar
 )
-# import pickle
 from PyQt6.QtGui import QAction
 from pathlib import Path
 from markdown import markdown
+from pandas import ExcelWriter
 from __init__ import project_path
-from backend import SubmissionType, Reagent, BasicSample, Organization, KitType
+from backend import SubmissionType, Reagent, BasicSample, Organization, KitType, BasicSubmission
 from tools import (
-    check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user, under_development
+    check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user,
+    under_development
 )
-from .functions import select_save_file, select_open_file
+from .date_type_picker import DateTypePicker
-from .pop_ups import HTMLPop, AlertPop
+from .functions import select_save_file
+from .pop_ups import HTMLPop
 from .misc import Pagifier
 from .submission_table import SubmissionsSheet
 from .submission_widget import SubmissionFormContainer
@@ -80,7 +82,7 @@ class App(QMainWindow):
         helpMenu.addAction(self.docsAction)
         helpMenu.addAction(self.githubAction)
         fileMenu.addAction(self.importAction)
-        # fileMenu.addAction(self.yamlExportAction)
+        fileMenu.addAction(self.archiveSubmissionsAction)
         # fileMenu.addAction(self.yamlImportAction)
         methodsMenu.addAction(self.searchSample)
         maintenanceMenu.addAction(self.joinExtractionAction)
@@ -112,8 +114,7 @@ class App(QMainWindow):
         self.docsAction = QAction("&Docs", self)
         self.searchSample = QAction("Search Sample", self)
         self.githubAction = QAction("Github", self)
-        # self.yamlExportAction = QAction("Export Type Example", self)
+        self.archiveSubmissionsAction = QAction("Submissions to Excel", self)
-        # self.yamlImportAction = QAction("Import Type Template", self)
         self.editReagentAction = QAction("Edit Reagent", self)
         self.manageOrgsAction = QAction("Manage Clients", self)
         self.manageKitsAction = QAction("Manage Kits", self)
@@ -130,8 +131,7 @@ class App(QMainWindow):
         self.docsAction.triggered.connect(self.openDocs)
         self.searchSample.triggered.connect(self.runSampleSearch)
         self.githubAction.triggered.connect(self.openGithub)
-        # self.yamlExportAction.triggered.connect(self.export_ST_yaml)
+        self.archiveSubmissionsAction.triggered.connect(self.submissions_to_excel)
-        # self.yamlImportAction.triggered.connect(self.import_ST_yaml)
         self.table_widget.pager.current_page.textChanged.connect(self.update_data)
         self.editReagentAction.triggered.connect(self.edit_reagent)
         self.manageOrgsAction.triggered.connect(self.manage_orgs)
@@ -186,60 +186,18 @@ class App(QMainWindow):
         dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="role")])
         dlg.exec()
 
-    # def export_ST_yaml(self):
-    #     """
-    #     Copies submission type yaml to file system for editing and remport
-    #
-    #     Returns:
-    #         None
-    #     """
-    #     if check_if_app():
-    #         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")
-    #     shutil.copyfile(yaml_path, fname)
-
-    # @check_authorization
-    # def import_ST_yaml(self, *args, **kwargs):
-    #     """
-    #     Imports a yml form into a submission type.
-    #
-    #     Args:
-    #         *args ():
-    #         **kwargs ():
-    #
-    #     Returns:
-    #
-    #     """
-    #     fname = select_open_file(obj=self, file_extension="yml")
-    #     if not fname:
-    #         logger.info(f"Import cancelled.")
-    #         return
-    #     ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
-    #     ap.exec()
-    #     st = SubmissionType.import_from_json(filepath=fname)
-    #     if st:
-    #         # NOTE: Do not delete the print statement below.
-    #         choice = input("Save the above submission type? [y/N]: ")
-    #         if choice.lower() == "y":
-    #             pass
-    #         else:
-    #             logger.warning("Save of submission type cancelled.")
-
     def update_data(self):
         self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
 
     # TODO: Change this to the Pydantic version.
     def manage_orgs(self):
         from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
-        dlg = ManagerWindow(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
+        # dlg = ManagerWindow(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
+        dlg = ManagerWindowPyd(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
         if dlg.exec():
             new_org = dlg.parse_form()
             new_org.save()
-            # logger.debug(new_org.__dict__)
 
-    @under_development
     def manage_kits(self, *args, **kwargs):
         from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
         dlg = ManagerWindowPyd(parent=self, object_type=KitType, extras=[], add_edit='edit', managers=set())
@@ -252,6 +210,17 @@ class App(QMainWindow):
             assert isinstance(sql, KitType)
             sql.save()
 
+    @under_development
+    def submissions_to_excel(self, *args, **kwargs):
+        dlg = DateTypePicker(self)
+        if dlg.exec():
+            output = dlg.parse_form()
+            df = BasicSubmission.archive_submissions(**output)
+            filepath = select_save_file(self, f"Submissions {output['start_date']}-{output['end_date']}", "xlsx")
+            writer = ExcelWriter(filepath, "openpyxl")
+            df.to_excel(writer)
+            writer.close()
+
 
 class AddSubForm(QWidget):
 

src/submissions/frontend/widgets/date_type_picker.py

@@ -0,0 +1,36 @@
+from PyQt6.QtWidgets import (
+    QLabel, QVBoxLayout, QDialog,
+    QDialogButtonBox, QMessageBox, QComboBox
+)
+from .misc import CheckableComboBox, StartEndDatePicker
+from backend.db import SubmissionType
+
+
+class DateTypePicker(QDialog):
+    
+    def __init__(self, parent):
+        super().__init__(parent)
+        self.layout = QVBoxLayout()
+        self.setFixedWidth(500)
+        self.typepicker = CheckableComboBox(parent=self)
+        self.typepicker.setEditable(False)
+        self.typepicker.addItem("Select", header=True)
+        for org in [org.name for org in SubmissionType.query()]:
+            self.typepicker.addItem(org)
+        self.datepicker = StartEndDatePicker(-180)
+        self.layout.addWidget(self.typepicker)
+        self.layout.addWidget(self.datepicker)
+        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+        self.buttonBox = QDialogButtonBox(QBtn)
+        self.buttonBox.accepted.connect(self.accept)
+        self.buttonBox.rejected.connect(self.reject)
+        self.layout.addWidget(self.buttonBox)
+        self.setLayout(self.layout)
+
+    def parse_form(self):
+        sub_types = [self.typepicker.itemText(i) for i in range(self.typepicker.count()) if self.typepicker.itemChecked(i)]
+        start_date = self.datepicker.start_date.date().toPyDate()
+        end_date = self.datepicker.end_date.date().toPyDate()
+        return dict(submissiontype=sub_types, start_date=start_date, end_date=end_date)
+
+

src/submissions/frontend/widgets/omni_manager_pydant.py

@@ -269,6 +269,7 @@ class EditRelationship(QWidget):
         from backend.db import models
         super().__init__(parent)
         self.class_object = getattr(models, class_object)
+        logger.debug(f"Attempt value: {value}")
         # logger.debug(f"Class object: {self.class_object}")
         self.setParent(parent)
         # logger.debug(f"Edit relationship class_object: {self.class_object}")
@@ -388,7 +389,7 @@ class EditRelationship(QWidget):
         """
         sets data in model
         """
-        # logger.debug(f"Self.data: {self.data}")
+        logger.debug(f"Self.data: {self.data}")
         try:
             records = [item.to_dataframe_dict() for item in self.data]
         except AttributeError:

src/submissions/resources/viral_culture.json

@@ -1,429 +0,0 @@
-{
-    "name": "Viral Culture",
-    "defaults": {
-            "abbreviation": "VE",
-            "details_ignore": [
-            ],
-            "form_ignore": [
-                "cost_centre"
-            ],
-            "regex": "(?P<Viral_Culture>RSL(?:-|_)?VE(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)?\\d?([^_0123456789\\sA-QS-Z]|$)?R?\\d?)?)",
-            "sample_type": "Basic Sample"
-        },
-    "info": {
-        "comment": {
-            "read": [
-                {
-                    "column": 2,
-                    "row": 34,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "contact": {
-            "read": [
-                {
-                    "column": 2,
-                    "row": 4,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "contact_phone": {
-            "read": [],
-            "write": [
-                {
-                    "column": 2,
-                    "row": 5,
-                    "sheet": "Sample List"
-                }
-            ]
-        },
-        "cost_centre": {
-            "read": [
-                {
-                    "column": 2,
-                    "row": 6,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "custom": {},
-        "extraction_kit": {
-            "read": [
-                {
-                    "column": 4,
-                    "row": 5,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "rsl_plate_num": {
-            "read": [
-                {
-                    "column": 2,
-                    "row": 13,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "sample_count": {
-            "read": [
-                {
-                    "column": 4,
-                    "row": 4,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "signed_by": {
-            "read": [],
-            "write": [
-                {
-                    "column": 2,
-                    "row": 15,
-                    "sheet": "Sample List"
-                }
-            ]
-        },
-        "submission_category": {
-            "read": [
-                {
-                    "column": 4,
-                    "row": 6,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "submission_type": {
-            "read": [
-                {
-                    "column": 4,
-                    "row": 3,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "submitted_date": {
-            "read": [
-                {
-                    "column": 2,
-                    "row": 3,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "submitter_plate_num": {
-            "read": [
-                {
-                    "column": 2,
-                    "row": 2,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "submitting_lab": {
-            "read": [
-                {
-                    "column": 4,
-                    "row": 2,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        },
-        "technician": {
-            "read": [
-                {
-                    "column": 2,
-                    "row": 14,
-                    "sheet": "Sample List"
-                }
-            ],
-            "write": []
-        }
-    },
-    "samples": {
-        "lookup_table": {
-            "end_row": 132,
-            "merge_on_id": "submitter_id",
-            "sample_columns": {
-                "column": 6,
-                "concentration": 4,
-                "organism": 3,
-                "row": 5,
-                "submitter_id": 2
-            },
-            "sheet": "Sample List",
-            "start_row": 37
-        },
-        "plate_map": {
-            "end_column": 13,
-            "end_row": 14,
-            "sheet": "Plate Map",
-            "start_column": 2,
-            "start_row": 7
-        }
-    },
-    "kits": [
-        {
-            "constant_cost": 0.00,
-            "mutable_cost_column": 0.00,
-            "mutable_cost_sample": 0.00,
-            "kit_type": {
-                "name": "MagMAX-96 Viral RNA Isolation Kit",
-                "reagent roles": [
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 19
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 19
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 19
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "Wash Solution 1 (MagMAX-96 Viral)",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 20
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 20
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 20
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "Wash Solution 2 (MagMAX-96 Viral)",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 21
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 21
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 21
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "Lysis/Binding Solution (MagMAX-96 Viral)",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 22
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 22
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 22
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "RNA Binding Beads (MagMAX-96 Viral)",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 23
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 23
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 23
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "Lysis/Binding Enhancer (MagMAX-96 Viral)",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 24
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 24
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 24
-                        },
-                        "sheet": "Sample List",
-                        "required": 0,
-                        "role": "Bacterial-Lysis Buffer",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 25
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 25
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 25
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "Elution Buffer (MagMAX-96 Viral)",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 30
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 30
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 30
-                        },
-                        "sheet": "Sample List",
-                        "required": 0,
-                        "role": "Bacterial-Positive Control",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 31
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 31
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 31
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "Bead Plate",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 28
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 28
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 28
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "Isopropanol",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 29
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 29
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 29
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "Ethanol",
-                        "extension_of_life": 0
-                    },
-                    {
-                        "expiry": {
-                            "column": 4,
-                            "row": 32
-                        },
-                        "lot": {
-                            "column": 3,
-                            "row": 32
-                        },
-                        "name": {
-                            "column": 2,
-                            "row": 32
-                        },
-                        "sheet": "Sample List",
-                        "required": 1,
-                        "role": "Carrier RNA",
-                        "extension_of_life": 0
-                    }
-                ],
-                "equipment roles": [
-                    {
-                        "static": 0,
-                        "role": "Extractor",
-                        "processes": [
-                            "OBT_M4029_KFF_v1.0"
-                        ]
-                    },
-                    {
-                        "static": 1,
-                        "role": "Momentum - Extraction",
-                        "processes": [
-                            "Omega_MagBind_Universal_VarCol"
-                        ]
-                    },
-                    {
-                        "static": 1,
-                        "role": "Liquid Handler",
-                        "processes": [
-                            "Bacterial_Core_Submission"
-                        ]
-                    }
-                ]
-            }
-        }       
-    ]
-}

src/submissions/resources/viral_culture.yml

@@ -1,339 +0,0 @@
-name: &NAME Viral Culture
-# The defaults section helps us with some parsing and writing functions
-defaults:
-#    The abbreviation gets put in the RSL-{abbreviation}-20XXXXXX-1 plate name
-    abbreviation: &ABBREV VE
-#    Details ignore tells us what to leave out of the details view.
-#    For basic submissions this is typically and empty list or '[]'
-#    To add entries, remove [] and add list entries preceded by dashes (see 'form_ignore' as an example)
-    details_ignore: []
-#    Form ignore tells us what to leave out of the form created when importing the submission.
-#    It is in list format. Each entry is preceded by a dash.
-    form_ignore:
-    - cost_centre
-    sample_type: Basic Sample
-    #    The regex is used to identify a submission type by its file name, example: RSL-WW-20240924-1R1
-    #    By default the regex will be programmatically constructed using the submission type name and abbreviation
-    #    https://stackoverflow.com/a/23212501
-    regex: !regex [*NAME, *ABBREV]
-# The info section holds a map of where submission info can be located  in the submission form.
-# For example, below the 'comment' field is found on the 'Sample List' tab in column 2 of tow 34.
-# 'read' is a list of where the info can be parsed from, write is a list of where it will be written to.
-# By default, items in the 'read' list will be appended to the 'write' list.
-# These fields are common to all submissions. Without programming changes, at present no new fields can be added.
-info:
-    comment:
-        read:
-        -   column: 2
-            row: 34
-            sheet: Sample List
-        write: []
-    contact:
-        read:
-        -   column: 2
-            row: 4
-            sheet: Sample List
-        write: []
-    contact_phone:
-        read: []
-        write:
-        -   column: 2
-            row: 5
-            sheet: Sample List
-    cost_centre:
-        read:
-        -   column: 2
-            row: 6
-            sheet: Sample List
-        write: []
-#    The 'custom' field is currently under development and will allow parsing, storage and writing of new fields in
-#    generic submission types.
-#    Examples of the types of fields are given below.
-    custom: {
-      #        The 'cell' type will read a single cell from the excel sheet and write it to the same cell as well as
-      #        any specified in the write list.
-      #        "test cell": {
-      #            "read": {
-      #                "column": 3,
-      #                "row": 1,
-      #                "sheet": "Plate Map"
-      #            },
-      #            "type": "cell",
-      #            "write": [{
-      #                      "column": 8,
-      #                      "row": 8,
-      #                      "sheet": "Sample List"
-      #                    }]
-      #        },
-      #        The 'range' type will read a group of cells, store them as a list of values, row and column integers
-      #        and write to that range.
-      #        "test range": {
-      #             "sheet": "First Strand",
-      #             "start_row": 1,
-      #             "end_row":9,
-      #             "start_column": 1,
-      #             "end_column": 5
-      #        }
-    }
-    extraction_kit:
-        read:
-        -   column: 4
-            row: 5
-            sheet: Sample List
-        write: []
-    rsl_plate_num:
-        read:
-        -   column: 2
-            row: 13
-            sheet: Sample List
-        write: []
-    sample_count:
-        read:
-        -   column: 4
-            row: 4
-            sheet: Sample List
-        write: []
-    signed_by:
-        read: []
-        write:
-        -   column: 2
-            row: 15
-            sheet: Sample List
-    submission_category:
-        read:
-        -   column: 4
-            row: 6
-            sheet: Sample List
-        write: []
-    submission_type:
-        read:
-        -   column: 4
-            row: 3
-            sheet: Sample List
-        write: []
-    submitted_date:
-        read:
-        -   column: 2
-            row: 3
-            sheet: Sample List
-        write: []
-    submitter_plate_num:
-        read:
-        -   column: 2
-            row: 2
-            sheet: Sample List
-        write: []
-    submitting_lab:
-        read:
-        -   column: 4
-            row: 2
-            sheet: Sample List
-        write: []
-    technician:
-        read:
-        -   column: 2
-            row: 14
-            sheet: Sample List
-        write: []
-# The 'kits' field holds reagents, equipment and tips information. It's a list of kit_type objects.
-kits:
--   kit_type:
-        name: MagMAX-96 Viral RNA Isolation Kit
-        equipment roles:
-        -   role: Extractor
-            processes:
-            - OBT_M4029_KFF_v1.0
-            static: 0
-        -   processes:
-            - Omega_MagBind_Universal_VarCol
-            role: Momentum - Extraction
-            static: 1
-        -   processes:
-            - Bacterial_Core_Submission
-            role: Liquid Handler
-            static: 1
-        reagent roles:
-        -   expiry:
-                column: 4
-                row: 19
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 19
-            name:
-                column: 2
-                row: 19
-            required: 1
-            role: Wash Solution 1 (MagMAX-96 Viral)
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 20
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 20
-            name:
-                column: 2
-                row: 20
-            required: 1
-            role: Wash Solution 2 (MagMAX-96 Viral)
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 21
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 21
-            name:
-                column: 2
-                row: 21
-            required: 1
-            role: Lysis/Binding Solution (MagMAX-96 Viral)
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 22
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 22
-            name:
-                column: 2
-                row: 22
-            required: 1
-            role: RNA Binding Beads (MagMAX-96 Viral)
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 23
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 23
-            name:
-                column: 2
-                row: 23
-            required: 1
-            role: Lysis/Binding Enhancer (MagMAX-96 Viral)
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 24
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 24
-            name:
-                column: 2
-                row: 24
-            required: 0
-            role: Bacterial-Lysis Buffer
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 25
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 25
-            name:
-                column: 2
-                row: 25
-            required: 1
-            role: Elution Buffer (MagMAX-96 Viral)
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 30
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 30
-            name:
-                column: 2
-                row: 30
-            required: 0
-            role: Bacterial-Positive Control
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 31
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 31
-            name:
-                column: 2
-                row: 31
-            required: 0
-            role: Bead Plate
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 28
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 28
-            name:
-                column: 2
-                row: 28
-            required: 1
-            role: Isopropanol
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 29
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 29
-            name:
-                column: 2
-                row: 29
-            required: 1
-            role: Ethanol
-            sheet: Sample List
-        -   expiry:
-                column: 4
-                row: 32
-            extension_of_life: 0
-            lot:
-                column: 3
-                row: 32
-            name:
-                column: 2
-                row: 32
-            required: 1
-            role: Carrier RNA
-            sheet: Sample List
-    constant_cost: 0.0
-    mutable_cost_column: 0.0
-    mutable_cost_sample: 0.0
-samples:
-    lookup_table:
-        end_row: 132
-        merge_on_id: submitter_id
-        sample_columns:
-            column: 6
-            concentration: 4
-            organism: 3
-            row: 5
-            submitter_id: 2
-        sheet: Sample List
-        start_row: 37
-    plate_map:
-        end_column: 13
-        end_row: 14
-        sheet: Plate Map
-        start_column: 2
-        start_row: 7
-orgs:
-    - name: IRVC-Genomics
-      cost_centre: xxx
-      contacts:
-          - name: Ruimin Gao
-            phone: (204) 789-5078
-            email: Ruimin.Gao@phac-aspc.gc.ca