Created Sample verification before import.

2025-03-27 15:02:18 -05:00
parent f215972b9d
commit e355aee5de
9 changed files with 179 additions and 416 deletions
--- a/src/submissions/backend/db/models/submissions.py
+++ b/src/submissions/backend/db/models/submissions.py
@@ -714,7 +714,6 @@ class BasicSubmission(BaseClass, LogMixin):
        # logger.debug(f"Returning regex: {regex}")
        return regex

-
    # NOTE: Polymorphic functions

    @classproperty
@@ -1130,13 +1129,13 @@ class BasicSubmission(BaseClass, LogMixin):
                case date():
                    pass
                case datetime():
-                    end_date = end_date# + timedelta(days=1)
+                    end_date = end_date  # + timedelta(days=1)
                    # pass
                case int():
-                    end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date()# \
-                               # + timedelta(days=1)
+                    end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date()  # \
+                    # + timedelta(days=1)
                case _:
-                    end_date = parse(end_date).date()# + timedelta(days=1)
+                    end_date = parse(end_date).date()  # + timedelta(days=1)
            # end_date = end_date.strftime("%Y-%m-%d")
            start_date = datetime.combine(start_date, datetime.min.time()).strftime("%Y-%m-%d %H:%M:%S.%f")
            end_date = datetime.combine(end_date, datetime.max.time()).strftime("%Y-%m-%d %H:%M:%S.%f")
@@ -1224,10 +1223,11 @@ class BasicSubmission(BaseClass, LogMixin):
        else:
            from frontend.widgets.pop_ups import QuestionAsker
            logger.warning(f"Found existing instance: {instance}, asking to overwrite.")
-        #     code = 1
-        #     msg = "This submission already exists.\nWould you like to overwrite?"
-        # report.add_result(Result(msg=msg, code=code))
-            dlg = QuestionAsker(title="Overwrite?", message="This submission already exists.\nWould you like to overwrite?")
+            #     code = 1
+            #     msg = "This submission already exists.\nWould you like to overwrite?"
+            # report.add_result(Result(msg=msg, code=code))
+            dlg = QuestionAsker(title="Overwrite?",
+                                message="This submission already exists.\nWould you like to overwrite?")
            if dlg.exec():
                pass
            else:
@@ -1529,10 +1529,23 @@ class BacterialCulture(BasicSubmission):
        main_sheet = xl[lookup_table['sheet']]
        for row in main_sheet.iter_rows(min_row=lookup_table['start_row'], max_row=lookup_table['end_row']):
            idx = row[0].row
-            sample = dict(submitter_id=main_sheet.cell(row=idx, column=lookup_table['sample_columns']['submitter_id']).value)
-            sample['concentration'] = main_sheet.cell(row=idx, column=lookup_table['sample_columns']['concentration']).value
+            sample = dict(
+                submitter_id=main_sheet.cell(row=idx, column=lookup_table['sample_columns']['submitter_id']).value)
+            sample['concentration'] = main_sheet.cell(row=idx,
+                                                      column=lookup_table['sample_columns']['concentration']).value
            yield sample

+    def get_provisional_controls(self):
+        if self.controls:
+            provs = (control.sample for control in self.controls)
+        else:
+            regex = re.compile(r"^(ATCC)|(MCS)|(EN)")
+            provs = (sample for sample in self.samples if bool(regex.match(sample.submitter_id)))
+        for prov in provs:
+            prov.submission = self.rsl_plate_num
+            prov.submitted_date = self.submitted_date
+            yield prov
+

 class Wastewater(BasicSubmission):
    """
@@ -1827,7 +1840,7 @@ class WastewaterArtic(BasicSubmission):
    artic_date = Column(TIMESTAMP)  #: Date Artic Performed
    ngs_date = Column(TIMESTAMP)  #: Date submission received
    gel_date = Column(TIMESTAMP)  #: Date submission received
-    gel_barcode = Column(String(16)) #: Identifier for the used gel.
+    gel_barcode = Column(String(16))  #: Identifier for the used gel.

    __mapper_args__ = dict(polymorphic_identity="Wastewater Artic",
                           polymorphic_load="inline",
@@ -2767,10 +2780,14 @@ class BacterialCultureSample(BasicSample):
        sample = super().to_sub_dict(full_data=full_data)
        sample['name'] = self.submitter_id
        sample['organism'] = self.organism
-        sample['concentration'] = self.concentration
+        try:
+            sample['concentration'] = f"{float(self.concentration):.2f}"
+        except TypeError:
+            sample['concentration'] = 0.0
        if self.control is not None:
            sample['colour'] = [0, 128, 0]
-            target = next((v for k,v in self.control.controltype.targets.items() if k == self.control.subtype), "Not Available")
+            target = next((v for k, v in self.control.controltype.targets.items() if k == self.control.subtype),
+                          "Not Available")
            try:
                target = ", ".join(target)
            except:
--- a/src/submissions/backend/excel/reports.py
+++ b/src/submissions/backend/excel/reports.py
@@ -202,19 +202,21 @@ class ConcentrationMaker(ReportArchetype):
        # NOTE: Set page size to zero to override limiting query size.
        self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date,
                                          submission_type_name=submission_type, page_size=0)
-        self.controls = list(itertools.chain.from_iterable([sub.controls for sub in self.subs]))
+        # self.known_controls = list(itertools.chain.from_iterable([sub.controls for sub in self.subs]))
+        self.controls = list(itertools.chain.from_iterable([sub.get_provisional_controls() for sub in self.subs]))
        self.records = [self.build_record(control) for control in self.controls]
        self.df = DataFrame.from_records(self.records)
        self.sheet_name = "Concentration"

    @classmethod
-    def build_record(cls, control: IridaControl) -> dict:
-        positive = control.is_positive_control
-        concentration = control.sample.concentration
-        if not concentration:
-            concentration = 0
-        return dict(name=control.name,
-                    submission=str(control.submission.rsl_plate_num), concentration=concentration,
+    def build_record(cls, control) -> dict:
+        positive = not control.submitter_id.lower().startswith("en")
+        try:
+            concentration = float(control.concentration)
+        except (TypeError, ValueError):
+            concentration = 0.0
+        return dict(name=control.submitter_id,
+                    submission=str(control.submission), concentration=concentration,
                    submitted_date=control.submitted_date, positive=positive)


--- a/src/submissions/backend/validators/pydant.py
+++ b/src/submissions/backend/validators/pydant.py
@@ -195,16 +195,6 @@ class PydSample(BaseModel, extra='allow'):
                pass
        return value

-    def improved_dict(self) -> dict:
-        """
-        Constructs a dictionary consisting of model.fields and model.extras
-
-        Returns:
-            dict: Information dictionary
-        """
-        fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
-        return {k: getattr(self, k) for k in fields}
-
    @report_result
    def to_sql(self, submission: BasicSubmission | str = None) -> Tuple[
        BasicSample, List[SubmissionSampleAssociation], Result | None]:
@@ -1010,6 +1000,18 @@ class PydSubmission(BaseModel, extra='allow'):
            for r in worksheet.rows:
                c.writerow([cell.value for cell in r])

+    @property
+    def sample_list(self) -> List[dict]:
+        samples = []
+        for sample in self.samples:
+            sample = sample.improved_dict()
+            sample['row'] = sample['row'][0]
+            sample['column'] = sample['column'][0]
+            sample['submission_rank'] = sample['submission_rank'][0]
+            samples.append(sample)
+        samples = sorted(samples, key=itemgetter("submission_rank"))
+        return samples
+

 class PydContact(BaseModel):
    name: str
--- a/src/submissions/frontend/widgets/sample_checker.py
+++ b/src/submissions/frontend/widgets/sample_checker.py
@@ -0,0 +1,67 @@
+
+import logging
+from pathlib import Path
+from typing import List
+
+from PyQt6.QtCore import Qt, pyqtSlot
+from PyQt6.QtWebChannel import QWebChannel
+from PyQt6.QtWebEngineWidgets import QWebEngineView
+from PyQt6.QtWidgets import (QDialog, QPushButton, QVBoxLayout,
+                             QDialogButtonBox, QTextEdit, QGridLayout)
+
+from backend.validators import PydSubmission
+from tools import get_application_from_parent, jinja_template_loading
+
+env = jinja_template_loading()
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+class SampleChecker(QDialog):
+
+    def __init__(self, parent, title:str, pyd: PydSubmission):
+        super().__init__(parent)
+        self.pyd = pyd
+        self.setWindowTitle(title)
+        self.app = get_application_from_parent(parent)
+        self.webview = QWebEngineView(parent=self)
+        self.webview.setMinimumSize(900, 500)
+        self.webview.setMaximumWidth(900)
+        self.layout = QGridLayout()
+        self.layout.addWidget(self.webview, 0, 0, 10, 10)
+        # NOTE: setup channel
+        self.channel = QWebChannel()
+        self.channel.registerObject('backend', self)
+        # NOTE: Used to maintain javascript functions.
+        # self.webview.page().setWebChannel(self.channel)
+        template = env.get_template("sample_checker.html")
+        template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
+        with open(template_path.joinpath("css", "styles.css"), "r") as f:
+            css = f.read()
+        html = template.render(samples=pyd.sample_list, css=css)
+        self.webview.setHtml(html)
+        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, 11, 9, 1, 1, alignment=Qt.AlignmentFlag.AlignRight)
+        self.setLayout(self.layout)
+        self.webview.page().setWebChannel(self.channel)
+
+    @pyqtSlot(str, str, str)
+    def text_changed(self, submission_rank: str, key: str, new_value: str):
+        logger.debug(f"Name: {submission_rank}, Key: {key}, Value: {new_value}")
+        match key:
+            case "row" | "column":
+                value = [new_value]
+            case _:
+                value = new_value
+        try:
+            item = next((sample for sample in self.pyd.samples if int(submission_rank) in sample.submission_rank))
+        except StopIteration:
+            logger.error(f"Unable to find sample {submission_rank}")
+        item.__setattr__(key, value)
+
+
+
+
+
--- a/src/submissions/frontend/widgets/submission_widget.py
+++ b/src/submissions/frontend/widgets/submission_widget.py
@@ -22,6 +22,8 @@ from .omni_add_edit import AddEdit
 from typing import List, Tuple
 from datetime import date

+from .sample_checker import SampleChecker
+
 logger = logging.getLogger(f"submissions.{__name__}")


@@ -135,8 +137,16 @@ class SubmissionFormContainer(QWidget):
        except AttributeError:
            self.prsr = SheetParser(filepath=fname)
        self.pyd = self.prsr.to_pydantic()
-        self.form = self.pyd.to_form(parent=self)
-        self.layout().addWidget(self.form)
+        # logger.debug(f"Samples: {pformat(self.pyd.samples)}")
+        checker = SampleChecker(self, "Sample Checker", self.pyd)
+        if checker.exec():
+            logger.debug(pformat(self.pyd.samples))
+            self.form = self.pyd.to_form(parent=self)
+            self.layout().addWidget(self.form)
+        else:
+            message = "Submission cancelled."
+            logger.warning(message)
+            report.add_result(Result(msg=message, owner=self.__class__.__name__, status="Warning"))
        return report

    @report_result
--- a/src/submissions/templates/css/styles.css
+++ b/src/submissions/templates/css/styles.css
@@ -39,3 +39,5 @@
  text-decoration-color: #ff33ff;
  cursor: pointer;
 }
+
+
--- a/src/submissions/templates/sample_checker.html
+++ b/src/submissions/templates/sample_checker.html
@@ -0,0 +1,44 @@
+{% extends "details.html" %}
+<head>
+    {% block head %}
+    {{ super() }}
+    <title>Sample Checker</title>
+    {% endblock %}
+</head>
+<body>
+    {% block body %}
+    <h2><u>Sample Checker</u></h2>
+    <br>
+    <p>Take a moment to verify sample names.</p>
+    <br>
+    <form>
+        &emsp;&emsp;Submitter ID&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Row&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp; Column<br/>
+        {% for sample in samples %}
+            {{ '%02d' % sample['submission_rank'] }}
+            <input type="text" id="{{ sample['submission_rank'] }}_id" name="submitter_id" value="{{ sample['submitter_id'] }}" size="40">
+            <input type="number" id="{{ sample['submission_rank'] }}_row" name="row" value="{{ sample['row'] }}" size="5", min="1">
+            <input type="number" id="{{ sample['submission_rank'] }}_col" name="column" value="{{ sample['column'] }}" size="5", min="1">
+            <br/>
+        {% endfor %}
+    </form>
+    {% endblock %}
+</body>
+<script>
+  {% block script %}
+  {{ super() }}
+  {% for sample in samples %}
+  document.getElementById("{{ sample['submission_rank'] }}_id").addEventListener("input", function(){
+      backend.text_changed("{{ sample['submission_rank'] }}", this.name, this.value);
+  });
+  document.getElementById("{{ sample['submission_rank'] }}_row").addEventListener("input", function(){
+      backend.text_changed("{{ sample['submission_rank'] }}", this.name, this.value);
+  });
+  document.getElementById("{{ sample['submission_rank'] }}_column").addEventListener("input", function(){
+      backend.text_changed("{{ sample['submission_rank'] }}", this.name, this.value);
+  });
+  {% endfor %}
+  document.addEventListener('DOMContentLoaded', function() {
+          backend.activate_export(false);
+      }, false);
+  {% endblock %}
+</script>
--- a/src/submissions/tools/init.py
+++ b/src/submissions/tools/init.py
@@ -259,388 +259,6 @@ def timer(func):
    return wrapper


-# Settings
-
-# class Settings(BaseSettings, extra="allow"):
-#     """
-#     Pydantic model to hold settings
-#
-#     Raises:
-#         FileNotFoundError: Error if database not found.
-#
-#     """
-#     database_schema: str | None = None
-#     directory_path: Path | None = None
-#     database_user: str | None = None
-#     database_password: str | None = None
-#     database_name: str | None = None
-#     database_path: Path | str | None = None
-#     backup_path: Path | str | None = None
-#     submission_types: dict | None = None
-#     database_session: Session | None = None
-#     package: Any | None = None
-#     logging_enabled: bool = Field(default=False)
-#
-#     model_config = SettingsConfigDict(env_file_encoding='utf-8')
-#
-#     # model_config = SettingsConfigDict(yaml_file="C:\\Users\lwark\AppData\Local\submissions\config\config.yml",
-#     #                                   yaml_file_encoding='utf-8')
-#
-#     # @classmethod
-#     # def settings_customise_sources(
-#     #         cls,
-#     #         settings_cls: type[BaseSettings],
-#     #         init_settings: PydanticBaseSettingsSource,
-#     #         env_settings: PydanticBaseSettingsSource,
-#     #         dotenv_settings: PydanticBaseSettingsSource,
-#     #         file_secret_settings: PydanticBaseSettingsSource,
-#     # ) -> tuple[PydanticBaseSettingsSource, ...]:
-#     #     return (
-#     #         YamlConfigSettingsSource(settings_cls),
-#     #         init_settings,
-#     #         env_settings,
-#     #         dotenv_settings,
-#     #         file_secret_settings,
-#     #     )
-#
-#     @field_validator('database_schema', mode="before")
-#     @classmethod
-#     def set_schema(cls, value):
-#         if value is None:
-#             if check_if_app():
-#                 alembic_path = Path(sys._MEIPASS).joinpath("files", "alembic.ini")
-#             else:
-#                 alembic_path = project_path.joinpath("alembic.ini")
-#             value = cls.get_alembic_db_path(alembic_path=alembic_path, mode='schema')
-#         if value is None:
-#             value = "sqlite"
-#         return value
-#
-#     @field_validator('backup_path', mode="before")
-#     @classmethod
-#     def set_backup_path(cls, value, values):
-#         match value:
-#             case str():
-#                 value = Path(value)
-#             case None:
-#                 value = values.data['directory_path'].joinpath("Database backups")
-#         if not value.exists():
-#             try:
-#                 value.mkdir(parents=True)
-#             except OSError:
-#                 value = Path(askdirectory(title="Directory for backups."))
-#         return value
-#
-#     @field_validator('directory_path', mode="before")
-#     @classmethod
-#     def ensure_directory_exists(cls, value, values):
-#         if value is None:
-#             match values.data['database_schema']:
-#                 case "sqlite":
-#                     if check_if_app():
-#                         alembic_path = Path(sys._MEIPASS).joinpath("files", "alembic.ini")
-#                     else:
-#                         alembic_path = project_path.joinpath("alembic.ini")
-#                     value = cls.get_alembic_db_path(alembic_path=alembic_path, mode='path').parent
-#                 case _:
-#                     Tk().withdraw()  # we don't want a full GUI, so keep the root window from appearing
-#                     value = Path(askdirectory(
-#                         title="Select directory for DB storage"))  # show an "Open" dialog box and return the path to the selected file
-#         if isinstance(value, str):
-#             value = Path(value)
-#         try:
-#             check = value.exists()
-#         except AttributeError:
-#             check = False
-#         if not check:
-#             value.mkdir(exist_ok=True)
-#         return value
-#
-#     @field_validator('database_path', mode="before")
-#     @classmethod
-#     def ensure_database_exists(cls, value, values):
-#         match values.data['database_schema']:
-#             case "sqlite":
-#                 if value is None:
-#                     value = values.data['directory_path']
-#                 if isinstance(value, str):
-#                     value = Path(value)
-#             case _:
-#                 if value is None:
-#                     if check_if_app():
-#                         alembic_path = Path(sys._MEIPASS).joinpath("files", "alembic.ini")
-#                     else:
-#                         alembic_path = project_path.joinpath("alembic.ini")
-#                     value = cls.get_alembic_db_path(alembic_path=alembic_path, mode='path').parent
-#         return value
-#
-#     @field_validator('database_name', mode='before')
-#     @classmethod
-#     def get_database_name(cls, value):
-#         if value is None:
-#             if check_if_app():
-#                 alembic_path = Path(sys._MEIPASS).joinpath("files", "alembic.ini")
-#             else:
-#                 alembic_path = project_path.joinpath("alembic.ini")
-#             value = cls.get_alembic_db_path(alembic_path=alembic_path, mode='path').stem
-#         return value
-#
-#     @field_validator("database_user", mode='before')
-#     @classmethod
-#     def get_user(cls, value):
-#         if value is None:
-#             if check_if_app():
-#                 alembic_path = Path(sys._MEIPASS).joinpath("files", "alembic.ini")
-#             else:
-#                 alembic_path = project_path.joinpath("alembic.ini")
-#             value = cls.get_alembic_db_path(alembic_path=alembic_path, mode='user')
-#         return value
-#
-#     @field_validator("database_password", mode='before')
-#     @classmethod
-#     def get_pass(cls, value):
-#         if value is None:
-#             if check_if_app():
-#                 alembic_path = Path(sys._MEIPASS).joinpath("files", "alembic.ini")
-#             else:
-#                 alembic_path = project_path.joinpath("alembic.ini")
-#             value = cls.get_alembic_db_path(alembic_path=alembic_path, mode='pass')
-#         return value
-#
-#     @field_validator('database_session', mode="before")
-#     @classmethod
-#     def create_database_session(cls, value, values):
-#         if value is not None:
-#             return value
-#         else:
-#             match values.data['database_schema']:
-#                 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 _:
-#                     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']
-#             database_path = template.render(values=values.data, value=value, db_name=db_name)
-#             print(f"Using {database_path} for database path")
-#             engine = create_engine(database_path)
-#             session = Session(engine)
-#             return session
-#
-#     @field_validator('package', mode="before")
-#     @classmethod
-#     def import_package(cls, value):
-#         import __init__ as package
-#         if value is None:
-#             return package
-#
-#     def __init__(self, *args, **kwargs):
-#         super().__init__(*args, **kwargs)
-#
-#         self.set_from_db()
-#         self.set_scripts()
-#
-#     def set_from_db(self):
-#         if 'pytest' in sys.modules:
-#             output = dict(power_users=['lwark', 'styson', 'ruwang'],
-#                           startup_scripts=dict(hello=None),
-#                           teardown_scripts=dict(goodbye=None)
-#                           )
-#         else:
-#             session = self.database_session
-#             metadata = MetaData()
-#             try:
-#                 metadata.reflect(bind=session.get_bind())
-#             except AttributeError as e:
-#                 print(f"Error getting tables: {e}")
-#                 return
-#             if "_configitem" not in metadata.tables.keys():
-#                 print(f"Couldn't find _configitems in {metadata.tables.keys()}.")
-#                 return
-#             config_items = session.execute(text("SELECT * FROM _configitem")).all()
-#             output = {}
-#             for item in config_items:
-#                 try:
-#                     output[item[1]] = json.loads(item[2])
-#                 except (JSONDecodeError, TypeError):
-#                     output[item[1]] = item[2]
-#         for k, v in output.items():
-#             if not hasattr(self, k):
-#                 self.__setattr__(k, v)
-#
-#     def set_scripts(self):
-#         """
-#         Imports all functions from "scripts" folder, adding them to ctx scripts
-#         """
-#         if check_if_app():
-#             p = Path(sys._MEIPASS).joinpath("files", "scripts")
-#         else:
-#             p = Path(__file__).parents[2].joinpath("scripts").absolute()
-#         if p.__str__() not in sys.path:
-#             sys.path.append(p.__str__())
-#         # NOTE: Get all .py files that don't have __ in them.
-#         modules = p.glob("[!__]*.py")
-#         for module in modules:
-#             mod = importlib.import_module(module.stem)
-#             for function in getmembers(mod, isfunction):
-#                 name = function[0]
-#                 func = function[1]
-#                 # NOTE: assign function based on its name being in config: startup/teardown
-#                 # NOTE: scripts must be registered using {name: Null} in the database
-#                 if name in self.startup_scripts.keys():
-#                     self.startup_scripts[name] = func
-#                 if name in self.teardown_scripts.keys():
-#                     self.teardown_scripts[name] = func
-#
-#     @timer
-#     def run_startup(self):
-#         """
-#         Runs startup scripts.
-#         """
-#         for script in self.startup_scripts.values():
-#             try:
-#                 logger.info(f"Running startup script: {script.__name__}")
-#                 thread = Thread(target=script, args=(ctx,))
-#                 thread.start()
-#             except AttributeError:
-#                 logger.error(f"Couldn't run startup script: {script}")
-#
-#     @timer
-#     def run_teardown(self):
-#         """
-#         Runs teardown scripts.
-#         """
-#         for script in self.teardown_scripts.values():
-#             try:
-#                 logger.info(f"Running teardown script: {script.__name__}")
-#                 thread = Thread(target=script, args=(ctx,))
-#                 thread.start()
-#             except AttributeError:
-#                 logger.error(f"Couldn't run teardown script: {script}")
-#
-#     @classmethod
-#     def get_alembic_db_path(cls, alembic_path, mode=Literal['path', 'schema', 'user', 'pass']) -> Path | str:
-#         c = ConfigParser()
-#         c.read(alembic_path)
-#         url = c['alembic']['sqlalchemy.url']
-#         match mode:
-#             case 'path':
-#                 path = re.sub(r"^.*//", "", url)
-#                 path = re.sub(r"^.*@", "", path)
-#                 return Path(path)
-#             case "schema":
-#                 return url[:url.index(":")]
-#             case "user":
-#                 url = re.sub(r"^.*//", "", url)
-#                 try:
-#                     return url[:url.index("@")].split(":")[0]
-#                 except (IndexError, ValueError) as e:
-#                     return None
-#             case "pass":
-#                 url = re.sub(r"^.*//", "", url)
-#                 try:
-#                     return url[:url.index("@")].split(":")[1]
-#                 except (IndexError, ValueError) as e:
-#                     return None
-#
-#     def save(self, settings_path: Path):
-#         if not settings_path.exists():
-#             dicto = {}
-#             for k, v in self.__dict__.items():
-#                 if k in ['package', 'database_session', 'submission_types']:
-#                     continue
-#                 match v:
-#                     case Path():
-#                         if v.is_dir():
-#                             v = v.absolute().__str__()
-#                         elif v.is_file():
-#                             v = v.parent.absolute().__str__()
-#                         else:
-#                             v = v.__str__()
-#                     case _:
-#                         pass
-#                 dicto[k] = v
-#             with open(settings_path, 'w') as f:
-#                 yaml.dump(dicto, f)
-#
-#
-# def get_config(settings_path: Path | str | None = None) -> Settings:
-#     """
-#     Get configuration settings from path or default if blank.
-#
-#     Args:
-#         settings_path (Path | str | None, optional): Path to config.yml Defaults to None.
-#         override (dict | None, optional): dictionary of settings to be used instead of file. Defaults to None.
-#
-#     Returns:
-#         Settings: Pydantic settings object
-#     """
-#     if isinstance(settings_path, str):
-#         settings_path = Path(settings_path)
-#
-#     # NOTE: custom pyyaml constructor to join fields
-#     def join(loader, node):
-#         seq = loader.construct_sequence(node)
-#         return ''.join([str(i) for i in seq])
-#     # NOTE: register the tag handler
-#     yaml.add_constructor('!join', join)
-#     # NOTE: make directories
-#     try:
-#         CONFIGDIR.mkdir(parents=True)
-#     except FileExistsError:
-#         logger.warning(f"Config directory {CONFIGDIR} already exists.")
-#     try:
-#         LOGDIR.mkdir(parents=True)
-#     except FileExistsError:
-#         logger.warning(f"Logging directory {LOGDIR} already exists.")
-#     # NOTE: if user hasn't defined config path in cli args
-#     if settings_path is None:
-#         # NOTE: Check user .config/submissions directory
-#         if CONFIGDIR.joinpath("config.yml").exists():
-#             settings_path = CONFIGDIR.joinpath("config.yml")
-#         # NOTE: Check user .submissions directory
-#         elif Path.home().joinpath(".submissions", "config.yml").exists():
-#             settings_path = Path.home().joinpath(".submissions", "config.yml")
-#         # NOTE: finally look in the local config
-#         else:
-#             if check_if_app():
-#                 settings_path = Path(sys._MEIPASS).joinpath("files", "config.yml")
-#             else:
-#                 settings_path = project_path.joinpath('src', 'config.yml')
-#             with open(settings_path, "r") as dset:
-#                 default_settings = yaml.load(dset, Loader=yaml.Loader)
-#             # NOTE: Tell program we need to copy the config.yml to the user directory
-#             # NOTE: copy settings to config directory
-#             settings = Settings(**default_settings)
-#             settings.save(settings_path=CONFIGDIR.joinpath("config.yml"))
-#             return settings
-#     else:
-#         # NOTE: check if user defined path is directory
-#         if settings_path.is_dir():
-#             settings_path = settings_path.joinpath("config.yml")
-#         # NOTE: check if user defined path is file
-#         elif settings_path.is_file():
-#             settings_path = settings_path
-#         else:
-#             logger.error("No config.yml file found. Writing to directory.")
-#             with open(settings_path, "r") as dset:
-#                 default_settings = yaml.load(dset, Loader=yaml.Loader)
-#             settings = Settings(**default_settings)
-#             settings.save(settings_path=settings_path)
-#     with open(settings_path, "r") as stream:
-#         settings = yaml.load(stream, Loader=yaml.Loader)
-#     return Settings(**settings)
-#
-
 def check_if_app() -> bool:
    """
    Checks if the program is running from pyinstaller compiled