Plate map in procedure details.

CHANGELOG.md

@@ -1,3 +1,7 @@
+# 202509.02
+
+- First Useable updated version.
+
 # 202504.04
 
 - Added html links for equipment/processes/tips.

src/submissions/backend/__init__.py

@@ -1,6 +1,32 @@
-'''
+"""
 Contains database, validators and excel operations.
-'''
+"""
-from .db import *
+from .db import (
-from .excel import *
+    set_sqlite_pragma,
-from .validators import *
+    LogMixin, ConfigItem,
+    AuditLog,
+    ControlType, Control,
+    ClientLab, Contact,
+    ReagentRole, Reagent, ReagentLot, Discount, SubmissionType, ProcedureType, Procedure, ProcedureTypeReagentRoleAssociation,
+    ProcedureReagentLotAssociation, EquipmentRole, Equipment, EquipmentRoleEquipmentAssociation, Process, ProcessVersion,
+    Tips, TipsLot, ProcedureEquipmentAssociation,
+    ProcedureTypeEquipmentRoleAssociation, Results,
+    ClientSubmission, Run, Sample, ClientSubmissionSampleAssociation, RunSampleAssociation, ProcedureSampleAssociation,
+    update_log
+)
+from .excel import (
+    DefaultParser, DefaultKEYVALUEParser, DefaultTABLEParser, ProcedureInfoParser, ProcedureSampleParser,
+    ProcedureReagentParser, ProcedureEquipmentParser, DefaultResultsInfoParser, DefaultResultsSampleParser,
+    PCRSampleParser, PCRInfoParser, ClientSubmissionSampleParser, ClientSubmissionInfoParser, PCRInfoParser,
+    PCRSampleParser,
+    DefaultWriter, DefaultKEYVALUEWriter, DefaultTABLEWriter,
+    ProcedureInfoWriter, ProcedureSampleWriter, ProcedureReagentWriter, ProcedureEquipmentWriter,
+    PCRInfoWriter, PCRSampleWriter,
+    ClientSubmissionInfoWriter, ClientSubmissionSampleWriter,
+    ReportArchetype, ReportMaker, TurnaroundMaker, ConcentrationMaker, ChartReportMaker
+)
+from .validators import (
+    DefaultNamer, ClientSubmissionNamer, RSLNamer,
+    PydRun, PydContact, PydClientLab, PydSample, PydReagent, PydReagentRole, PydEquipment, PydEquipmentRole, PydTips,
+    PydProcess, PydElastic, PydClientSubmission, PydProcedure, PydResults, PydReagentLot
+)

src/submissions/backend/db/__init__.py

@@ -1,9 +1,14 @@
 """
 All database related operations.
 """
+from datetime import datetime
+from getpass import getuser
 from sqlalchemy import event, inspect
 from sqlalchemy.engine import Engine
 from tools import ctx
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
 
 
 @event.listens_for(Engine, "connect")
@@ -22,14 +27,23 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
         execution_phrase = "PRAGMA foreign_keys=ON"
         print(f"Executing '{execution_phrase}' in sql.")
     else:
-        # print("Nothing to execute, returning")
         cursor.close()
         return
     cursor.execute(execution_phrase)
     cursor.close()
 
 
-from .models import *
+from .models import (
+    LogMixin, ConfigItem,
+    AuditLog,
+    ReagentRole, Reagent, ReagentLot, Discount, SubmissionType, ProcedureType, Procedure, ProcedureTypeReagentRoleAssociation,
+    ProcedureReagentLotAssociation, EquipmentRole, Equipment, EquipmentRoleEquipmentAssociation, Process, ProcessVersion,
+    Tips, TipsLot, ProcedureEquipmentAssociation,
+    ProcedureTypeEquipmentRoleAssociation, Results,
+    ClientSubmission, Run, Sample, ClientSubmissionSampleAssociation, RunSampleAssociation, ProcedureSampleAssociation,
+    ControlType, Control,
+    ClientLab, Contact
+)
 
 
 def update_log(mapper, connection, target):
@@ -55,9 +69,6 @@ def update_log(mapper, connection, target):
             continue
         added = [str(item) for item in hist.added]
         # NOTE: Attributes left out to save space
-        # if attr.key in ['artic_technician', 'clientsubmissionsampleassociation', 'submission_reagent_associations',
-        #                 'submission_equipment_associations', 'submission_tips_associations', 'contact_id', 'gel_info',
-        #                 'gel_controls', 'source_plates']:
         if attr.key in LogMixin.tracking_exclusion:
             continue
         deleted = [str(item) for item in hist.deleted]

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

@@ -2,11 +2,14 @@
 Contains all models for sqlalchemy
 """
 from __future__ import annotations
-import sys, logging, json
+import sys, logging, json, inspect
+from datetime import datetime, date
+from pprint import pformat
 from dateutil.parser import parse
+from jinja2 import TemplateNotFound, Template
 from pandas import DataFrame
 from pydantic import BaseModel
-from sqlalchemy import Column, INTEGER, String, JSON
+from sqlalchemy import Column, INTEGER, String, JSON, TIMESTAMP
 from sqlalchemy.ext.associationproxy import AssociationProxy
 from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session, InstrumentedAttribute, ColumnProperty
 from sqlalchemy.ext.declarative import declared_attr
@@ -15,7 +18,7 @@ from sqlalchemy.exc import ArgumentError
 from typing import Any, List, ClassVar
 from pathlib import Path
 from sqlalchemy.orm.relationships import _RelationshipDeclared
-from tools import report_result, list_sort_dict
+from tools import report_result, list_sort_dict, jinja_template_loading, Report, Result, ctx
 
 # NOTE: Load testing environment
 if 'pytest' in sys.modules:
@@ -36,10 +39,6 @@ class BaseClass(Base):
     __table_args__ = {'extend_existing': True}  #: NOTE Will only add new columns
 
     singles = ['id']
-    # omni_removes = ["id", 'run', "omnigui_class_dict", "omnigui_instance_dict"]
-    # omni_sort = ["name"]
-    # omni_inheritable = []
-    searchables = []
 
     _misc_info = Column(JSON)
 
@@ -49,7 +48,9 @@ class BaseClass(Base):
         except AttributeError:
             return f"<{self.__class__.__name__}(Name Unavailable)>"
 
-    @classproperty
+    # @classproperty
+    @classmethod
+    @declared_attr
     def aliases(cls) -> List[str]:
         """
         List of other names this class might be known by.
@@ -59,7 +60,8 @@ class BaseClass(Base):
         """
         return [cls.query_alias]
 
-    @classproperty
+    @classmethod
+    @declared_attr
     def query_alias(cls) -> str:
         """
         What to query this class as.
@@ -89,10 +91,6 @@ class BaseClass(Base):
         Returns:
             Session: DB session from ctx settings.
         """
-        if 'pytest' not in sys.modules:
-            from tools import ctx
-        else:
-            from test_settings import ctx
         return ctx.database_session
 
     @classmethod
@@ -104,10 +102,6 @@ class BaseClass(Base):
         Returns:
             Path: Location of the Submissions directory in Settings object
         """
-        if 'pytest' not in sys.modules:
-            from tools import ctx
-        else:
-            from test_settings import ctx
         return ctx.directory_path
 
     @classmethod
@@ -119,17 +113,15 @@ class BaseClass(Base):
         Returns:
             Path: Location of the Submissions backup directory in Settings object
         """
-        if 'pytest' not in sys.modules:
-            from tools import ctx
-        else:
-            from test_settings import ctx
         return ctx.backup_path
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self._misc_info = dict()
 
-    @classproperty
+    # @classproperty
+    @classmethod
+    @declared_attr
     def jsons(cls) -> List[str]:
         """
         Get list of JSON db columns
@@ -142,7 +134,9 @@ class BaseClass(Base):
         except AttributeError:
             return []
 
-    @classproperty
+    # @classproperty
+    @classmethod
+    @declared_attr
     def timestamps(cls) -> List[str]:
         """
         Get list of TIMESTAMP columns
@@ -155,6 +149,30 @@ class BaseClass(Base):
         except AttributeError:
             return []
 
+    @classmethod
+    def get_omni_sort(cls):
+        output = [item[0] for item in inspect.getmembers(cls, lambda a: not (inspect.isroutine(a)))
+                  if isinstance(item[1], InstrumentedAttribute)]  # and not isinstance(item[1].property, _RelationshipDeclared)]
+        output = [item for item in output if item not in ['_misc_info']]
+        return output
+
+    @classmethod
+    def get_searchables(cls):
+        output = []
+        for item in inspect.getmembers(cls, lambda a: not (inspect.isroutine(a))):
+            if item[0] in ["_misc_info"]:
+                continue
+            if not isinstance(item[1], InstrumentedAttribute):
+                continue
+            if not isinstance(item[1].property, ColumnProperty):
+                continue
+            if len(item[1].foreign_keys) > 0:
+                continue
+            if item[1].type.__class__.__name__ not in ["String"]:
+                continue
+            output.append(item[0])
+        return output
+
     @classmethod
     def get_default_info(cls, *args) -> dict | list | str:
         """
@@ -164,8 +182,7 @@ class BaseClass(Base):
             dict | list | str: Output of key:value dict or single (list, str) desired variable
         """
         # NOTE: singles is a list of fields that need to be limited to 1 result.
-        singles = list(set(cls.singles + BaseClass.singles))
+        return dict(singles=list(set(cls.singles + BaseClass.singles)))
-        return dict(singles=singles)
 
     @classmethod
     def find_regular_subclass(cls, name: str | None = None) -> Any:
@@ -222,14 +239,15 @@ class BaseClass(Base):
         """
         if not objects:
             try:
-                records = [obj.details_dict(**kwargs) for obj in cls.query()]
+                q = cls.query()
             except AttributeError:
-                records = [obj.details_dict(**kwargs) for obj in cls.query(page_size=0)]
+                q = cls.query(page_size=0)
         else:
-            try:
+            q = objects
-                records = [obj.to_sub_dict(**kwargs) for obj in objects]
+        records = []
-            except AttributeError:
+        for obj in q:
-                records = [{k: v['instance_attr'] for k, v in obj.omnigui_instance_dict.items()} for obj in objects]
+            dicto = obj.details_dict(**kwargs)
+            records.append({key: value for key, value in dicto.items() if key not in dicto['excluded']})
         return DataFrame.from_records(records)
 
     @classmethod
@@ -237,10 +255,8 @@ class BaseClass(Base):
         new = False
         allowed = [k for k, v in cls.__dict__.items() if
                    isinstance(v, InstrumentedAttribute) or isinstance(v, hybrid_property)]
-        # and not isinstance(v.property, _RelationshipDeclared)]
         sanitized_kwargs = {k: v for k, v in kwargs.items() if k in allowed}
         outside_kwargs = {k: v for k, v in kwargs.items() if k not in allowed}
-        logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
         instance = cls.query(limit=1, **sanitized_kwargs)
         if not instance or isinstance(instance, list):
             instance = cls()
@@ -254,8 +270,6 @@ class BaseClass(Base):
                 from backend.validators.pydant import PydBaseClass
                 if issubclass(v.__class__, PydBaseClass):
                     setattr(instance, k, v.to_sql())
-                # else:
-                #     logger.error(f"Could not set {k} due to {e}")
         instance._misc_info.update(outside_kwargs)
         # logger.info(f"Instance from query or create: {instance}, new: {new}")
         return instance, new
@@ -286,17 +300,10 @@ class BaseClass(Base):
         Returns:
             Any | List[Any]: Single result if limit = 1 or List if other.
         """
-        # logger.debug(f"Kwargs: {kwargs}")
-        # if model is None:
-        #     model = cls
-        # logger.debug(f"Model: {model}")
         if query is None:
             query: Query = cls.__database_session__.query(cls)
-        # else:
-        #     logger.debug(f"Incoming query: {query}")
         singles = cls.get_default_info('singles')
         for k, v in kwargs.items():
-            # logger.info(f"Using key: {k} with value: {v} against {cls}")
             try:
                 attr = getattr(cls, k)
             except (ArgumentError, AttributeError) as e:
@@ -308,13 +315,11 @@ class BaseClass(Base):
             except AttributeError:
                 check = False
             if check:
-                logger.debug("Got uselist")
                 try:
                     query = query.filter(attr.contains(v))
                 except ArgumentError:
                     continue
             else:
-                # logger.debug("Single item.")
                 try:
                     query = query.filter(attr == v)
                 except ArgumentError:
@@ -354,9 +359,6 @@ class BaseClass(Base):
         try:
             self.__database_session__.add(self)
             self.__database_session__.commit()
-        # except sqlalchemy.exc.IntegrityError as i:
-        #     logger.error(f"Integrity error saving {self} due to: {i}")
-        #     logger.error(pformat(self.__dict__))
         except Exception as e:
             logger.critical(f"Problem saving {self} due to: {e}")
             logger.error(f"Error message: {type(e)}")
@@ -374,16 +376,14 @@ class BaseClass(Base):
             dict: Dictionary of object minus _sa_instance_state with id at the front.
         """
         dicto = {key: dict(class_attr=getattr(self.__class__, key), instance_attr=getattr(self, key))
-                 for key in dir(self.__class__) if
+                 for key in self.get_omni_sort()}
-                 isinstance(getattr(self.__class__, key), InstrumentedAttribute) and key not in self.omni_removes
-                 }
         for k, v in dicto.items():
             try:
                 v['instance_attr'] = v['instance_attr'].name
             except AttributeError:
                 continue
         try:
-            dicto = list_sort_dict(input_dict=dicto, sort_list=self.__class__.omni_sort)
+            dicto = list_sort_dict(input_dict=dicto, sort_list=self.__class__.get_omni_sort())
         except TypeError as e:
             logger.error(f"Could not sort {self.__class__.__name__} by list due to :{e}")
         try:
@@ -392,7 +392,9 @@ class BaseClass(Base):
             pass
         return dicto
 
-    @classproperty
+    # @classproperty
+    @classmethod
+    @declared_attr
     def pydantic_model(cls) -> BaseModel:
         """
         Gets the pydantic model corresponding to this object.
@@ -405,10 +407,15 @@ class BaseClass(Base):
             model = getattr(pydant, f"Pyd{cls.__name__}")
         except AttributeError:
             logger.warning(f"Couldn't get {cls.__name__} pydantic model.")
-            return pydant.PydElastic
+            try:
+                model = getattr(pydant, f"Pyd{cls.pyd_model_name}")
+            except AttributeError:
+                return pydant.PydElastic
         return model
 
-    @classproperty
+    # @classproperty
+    @classmethod
+    @declared_attr
     def add_edit_tooltips(cls) -> dict:
         """
         Gets tooltips for Omni-add-edit
@@ -418,7 +425,9 @@ class BaseClass(Base):
         """
         return dict()
 
-    @classproperty
+    # @classproperty
+    @classmethod
+    @declared_attr
     def details_template(cls) -> Template:
         """
         Get the details jinja template for the correct class
@@ -434,7 +443,7 @@ class BaseClass(Base):
         try:
             template = env.get_template(temp_name)
         except TemplateNotFound as e:
-            #     logger.error(f"Couldn't find template {e}")
+            # logger.error(f"Couldn't find template {e}")
             template = env.get_template("details.html")
         return template
 
@@ -448,14 +457,11 @@ class BaseClass(Base):
         Returns:
             bool: If a single unequivocal value is found will be false, else true.
         """
-        # logger.debug(f"Incoming attributes: {attributes}")
         for key, value in attributes.items():
             if value.lower() == "none":
                 value = None
-            # logger.debug(f"Attempting to grab attribute: {key}")
             self_value = getattr(self, key)
             class_attr = getattr(self.__class__, key)
-            # logger.debug(f"Self value: {self_value}, class attr: {class_attr} of type: {type(class_attr)}")
             if isinstance(class_attr, property):
                 filter = "property"
             else:
@@ -475,7 +481,6 @@ class BaseClass(Base):
                 case "property":
                     pass
                 case _RelationshipDeclared():
-                    # logger.debug(f"Checking {self_value}")
                     try:
                         self_value = self_value.name
                     except AttributeError:
@@ -483,18 +488,14 @@ class BaseClass(Base):
                     if class_attr.property.uselist:
                         self_value = self_value.__str__()
             try:
-                # logger.debug(f"Check if {self_value.__class__} is subclass of {self.__class__}")
                 check = issubclass(self_value.__class__, self.__class__)
             except TypeError as e:
                 logger.error(f"Couldn't check if {self_value.__class__} is subclass of {self.__class__} due to {e}")
                 check = False
             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)}")
             if self_value != value:
                 output = False
-                # logger.debug(f"Value {key} is False, returning.")
                 return output
         return True
 
@@ -502,17 +503,14 @@ class BaseClass(Base):
         """
         Custom dunder method to handle potential list relationship issues.
         """
-        # logger.debug(f"Attempting to set: {key} to {value}")
         if key.startswith("_"):
             return super().__setattr__(key, value)
-        # try:
         check = not hasattr(self, key)
-        # except:
-        #     return
         if check:
             try:
                 value = json.dumps(value)
-            except TypeError:
+            except TypeError as e:
+                logger.error(f"Error json dumping value: {e}")
                 value = str(value)
             try:
                 self._misc_info.update({key: value})
@@ -524,27 +522,20 @@ class BaseClass(Base):
         except AttributeError:
             return super().__setattr__(key, value)
         if isinstance(field_type, InstrumentedAttribute):
-            # logger.debug(f"{key} is an InstrumentedAttribute.")
             match field_type.property:
                 case ColumnProperty():
-                    # logger.debug(f"Setting ColumnProperty to {value}")
                     return super().__setattr__(key, value)
                 case _RelationshipDeclared():
-                    # logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
                     if field_type.property.uselist:
-                        # logger.debug(f"Setting with uselist")
                         existing = self.__getattribute__(key)
                         # NOTE: This is causing problems with removal of items from lists. Have to overhaul it.
                         if existing is not None:
-                            logger.debug(f"{key} Existing: {existing}, incoming: {value}")
                             if isinstance(value, list):
-                                # value = existing + value
                                 value = value
                             else:
                                 value = existing + [value]
                         else:
                             if isinstance(value, list):
-                                # value = value
                                 pass
                             else:
                                 value = [value]
@@ -552,7 +543,6 @@ class BaseClass(Base):
                             value = list(set(value))
                         except TypeError:
                             pass
-                        # logger.debug(f"Final value for {key}: {value}")
                         return super().__setattr__(key, value)
                     else:
                         if isinstance(value, list):
@@ -573,7 +563,10 @@ class BaseClass(Base):
                 case _:
                     return super().__setattr__(key, value)
         else:
-            return super().__setattr__(key, value)
+            try:
+                return super().__setattr__(key, value)
+            except AttributeError:
+                raise AttributeError(f"Can't set {key} to {value}")
 
     def delete(self, **kwargs):
         logger.error(f"Delete has not been implemented for {self.__class__.__name__}")
@@ -608,7 +601,6 @@ class BaseClass(Base):
 
         relevant = {k: v for k, v in self.__class__.__dict__.items() if
                     isinstance(v, InstrumentedAttribute) or isinstance(v, AssociationProxy)}
-        # output = OrderedDict()
         output = dict(excluded=["excluded", "misc_info", "_misc_info", "id"])
         for k, v in relevant.items():
             try:
@@ -621,15 +613,14 @@ class BaseClass(Base):
                 value = getattr(self, k)
             except AttributeError:
                 continue
-            # try:
+            match value:
-            #     logger.debug(f"Setting {k} to {value} for details dict.")
+                case str():
-            # except AttributeError as e:
+                    value = value.strip('\"')
-            #     logger.error(f"Can't log {k} value due to {type(e)}")
+                case _:
-            #     continue
+                    pass
             output[k.strip("_")] = value
         if self._misc_info:
             for key, value in self._misc_info.items():
-                # logger.debug(f"Misc info key {key}")
                 output[key] = value
         return output
 
@@ -664,33 +655,20 @@ class BaseClass(Base):
         from backend.validators import pydant
         if not pyd_model_name:
             pyd_model_name = f"Pyd{self.__class__.__name__}"
-        logger.debug(f"Looking for pydant model {pyd_model_name}")
+        logger.info(f"Looking for pydant model {pyd_model_name}")
         try:
             pyd = getattr(pydant, pyd_model_name)
         except AttributeError:
             raise AttributeError(f"Could not get pydantic class {pyd_model_name}")
-        # logger.debug(f"Kwargs: {kwargs}")
-        # logger.debug(f"Dict: {pformat(self.details_dict())}")
         return pyd(**self.details_dict(**kwargs))
 
     def show_details(self, obj):
-        logger.debug("Show Details")
         from frontend.widgets.submission_details import SubmissionDetails
         dlg = SubmissionDetails(parent=obj, sub=self)
         if dlg.exec():
             pass
 
     def export(self, obj, output_filepath: str | Path | None = None):
-        # if not hasattr(self, "template_file"):
-        #     logger.error(f"Export not implemented for {self.__class__.__name__}")
-        #     return
-        # pyd = self.to_pydantic()
-        # if not output_filepath:
-        #     from frontend import select_save_file
-        #     output_filepath = select_save_file(obj=obj, default_name=pyd.construct_filename(), extension="xlsx")
-        # Writer = getattr(writers, f"{self.__class__.__name__}Writer")
-        # writer = Writer(output_filepath=output_filepath, pydant_obj=pyd, range_dict=self.range_dict)
-        # workbook = writer
         from backend import managers
         Manager = getattr(managers, f"Default{self.__class__.__name__}")
         manager = Manager(parent=obj, input_object=self)
@@ -749,12 +727,20 @@ class ConfigItem(BaseClass):
         return config_items
 
 
-from .controls import *
 # NOTE: import order must go: orgs, kittype, run due to circular import issues
-from .organizations import *
-from .procedures import *
-from .submissions import *
 from .audit import AuditLog
+from .organizations import (
+    ClientLab, Contact, BaseClass # NOTE: For some reason I  need to import BaseClass at this point for queries to work.
+)
+from .procedures import (
+    ReagentRole, Reagent, ReagentLot, Discount, SubmissionType, ProcedureType, Procedure, ProcedureTypeReagentRoleAssociation,
+    ProcedureReagentLotAssociation, EquipmentRole, Equipment, EquipmentRoleEquipmentAssociation, Process, ProcessVersion,
+    Tips, TipsLot, ProcedureEquipmentAssociation, ProcedureTypeEquipmentRoleAssociation, Results
+)
+from .submissions import (
+    ClientSubmission, Run, Sample, ClientSubmissionSampleAssociation, RunSampleAssociation, ProcedureSampleAssociation
+)
+from .controls import ControlType, Control
 
 # NOTE: Add a creator to the procedure for reagent association. Assigned here due to circular import constraints.
 # https://docs.sqlalchemy.org/en/20/orm/extensions/associationproxy.html#sqlalchemy.ext.associationproxy.association_proxy.params.creator

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

@@ -11,6 +11,7 @@ import logging
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
+# NOTE: Need a seperate base for this.
 Base: DeclarativeMeta = declarative_base()
 
 class AuditLog(Base):
@@ -18,10 +19,10 @@ class AuditLog(Base):
     __tablename__ = "_auditlog"
 
     id = Column(INTEGER, primary_key=True, autoincrement=True)  #: primary key
-    user = Column(String(64))
+    user = Column(String(64)) #: The user who made the change
-    time = Column(TIMESTAMP)
+    time = Column(TIMESTAMP) #: When the change was made
-    object = Column(String(64))
+    object = Column(String(64)) #: What was changed
-    changes = Column(JSON)
+    changes = Column(JSON) #: List of changes that were made
 
     def __repr__(self):
         return f"<{self.object}: {self.user} @ {self.time}>"

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

@@ -2,17 +2,13 @@
 All control related models.
 """
 from __future__ import annotations
-import itertools
 from pprint import pformat
-from PyQt6.QtWidgets import QWidget, QCheckBox, QLabel
+from PyQt6.QtWidgets import QWidget
-from pandas import DataFrame
+from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, case
-from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, case, FLOAT
+from sqlalchemy.orm import relationship, Query
-from sqlalchemy.orm import relationship, Query, validates
 import logging, re
-from operator import itemgetter
 from . import BaseClass
-from tools import setup_lookup, report_result, Result, Report, Settings, get_unique_values_in_df_column, super_splitter, \
+from tools import setup_lookup, Report, Settings, super_splitter
-    flatten_list, timer
 from datetime import date, datetime, timedelta
 from typing import List, Literal, Tuple, Generator
 from re import Pattern
@@ -131,16 +127,6 @@ class Control(BaseClass):
     procedure = relationship("Procedure", back_populates="control",
                               foreign_keys=[procedure_id])  #: parent procedure
 
-    # __mapper_args__ = {
-    #     "polymorphic_identity": "Basic Control",
-    #     "polymorphic_on": case(
-    #         (controltype_name == "PCR Control", "PCR Control"),
-    #         (controltype_name == "Irida Control", "Irida Control"),
-    #         else_="Basic Control"
-    #     ),
-    #     "with_polymorphic": "*",
-    # }
-
     def __repr__(self) -> str:
         return f"<{self.controltype_name}({self.name})>"
 
@@ -282,450 +268,3 @@ class Control(BaseClass):
     def delete(self):
         self.__database_session__.delete(self)
         self.__database_session__.commit()
-
-
-# class PCRControl(Control):
-#     """
-#     Class made to hold info from Design & Analysis software.
-#     """
-#
-#     id = Column(INTEGER, ForeignKey('_control.id'), primary_key=True)
-#     subtype = Column(String(16))  #: PC or NC
-#     target = Column(String(16))  #: N1, N2, etc.
-#     ct = Column(FLOAT)  #: PCR result
-#     reagent_lot = Column(String(64), ForeignKey("_reagent.lot", ondelete="SET NULL",
-#                                                 name="fk_reagent_lot"))
-#     reagent = relationship("Reagent", foreign_keys=reagent_lot)  #: reagent used for this control
-#
-#     __mapper_args__ = dict(polymorphic_identity="PCR Control",
-#                            polymorphic_load="inline",
-#                            inherit_condition=(id == Control.id))
-#
-#     def to_sub_dict(self) -> dict:
-#         """
-#         Creates dictionary of fields for this object.
-#
-#         Returns:
-#             dict: Output dict of name, ct, subtype, target, reagent_lot and submitted_date
-#         """
-#         return dict(
-#             name=self.name,
-#             ct=self.ct,
-#             subtype=self.subtype,
-#             target=self.target,
-#             reagent_lot=self.reagent_lot,
-#             submitted_date=self.submitted_date.date()
-#         )
-#
-#     @classmethod
-#     @report_result
-#     def make_chart(cls, parent, chart_settings: dict, ctx: Settings) -> Tuple[Report, "PCRFigure"]:
-#         """
-#         Creates a PCRFigure. Overrides parent
-#
-#         Args:
-#             parent (__type__): Widget to contain the chart.
-#             chart_settings (dict): settings passed down from chart widget
-#             ctx (Settings): settings passed down from gui. Not used here.
-#
-#         Returns:
-#             Tuple[Report, "PCRFigure"]: Report of status and resulting figure.
-#         """
-#         from frontend.visualizations.pcr_charts import PCRFigure
-#         parent.mode_typer.clear()
-#         parent.mode_typer.setEnabled(False)
-#         report = Report()
-#         control = cls.query(proceduretype=chart_settings['submissiontype'], start_date=chart_settings['start_date'],
-#                              end_date=chart_settings['end_date'])
-#         data = [control.to_sub_dict() for control in control]
-#         df = DataFrame.from_records(data)
-#         # NOTE: Get all PCR control with ct over 0
-#         try:
-#             df = df[df.ct > 0.0]
-#         except AttributeError:
-#             df = df
-#         fig = PCRFigure(df=df, modes=[], settings=chart_settings)
-#         return report, fig
-#
-#     def to_pydantic(self):
-#         from backend.validators import PydPCRControl
-#         return PydPCRControl(**self.to_sub_dict(),
-#                              controltype_name=self.controltype_name,
-#                              clientsubmission_id=self.clientsubmission_id)
-#
-#
-# class IridaControl(Control):
-#     subtyping_allowed = ['kraken']
-#
-#     id = Column(INTEGER, ForeignKey('_control.id'), primary_key=True)
-#     contains = Column(JSON)  #: unstructured hashes in contains.tsv for each organism
-#     matches = Column(JSON)  #: unstructured hashes in matches.tsv for each organism
-#     kraken = Column(JSON)  #: unstructured output from kraken_report
-#     subtype = Column(String(16), nullable=False)  #: EN-NOS, MCS-NOS, etc
-#     refseq_version = Column(String(16))  #: version of refseq used in fastq parsing
-#     kraken2_version = Column(String(16))  #: version of kraken2 used in fastq parsing
-#     kraken2_db_version = Column(String(32))  #: folder name of kraken2 db
-#     sample_id = Column(INTEGER,
-#                        ForeignKey("_basicsample.id", ondelete="SET NULL", name="cont_BCS_id"))  #: sample id key
-#
-#     __mapper_args__ = dict(polymorphic_identity="Irida Control",
-#                            polymorphic_load="inline",
-#                            inherit_condition=(id == Control.id))
-#
-#     @property
-#     def targets(self):
-#         if self.controltype.targets:
-#             return list(itertools.chain.from_iterable([value for key, value in self.controltype.targets.items()
-#                                                        if key == self.subtype]))
-#         else:
-#             return ["None"]
-#
-#     @validates("subtype")
-#     def enforce_subtype_literals(self, key: str, value: str) -> str:
-#         """
-#         Validates submissiontype field with acceptable values
-#
-#         Args:
-#             key (str): Field name
-#             value (str): Field Value
-#
-#         Raises:
-#             KeyError: Raised if value is not in the acceptable list.
-#
-#         Returns:
-#             str: Validated string.
-#         """
-#         acceptables = ['ATCC49226', 'ATCC49619', 'EN-NOS', "EN-SSTI", "MCS-NOS", "MCS-SSTI", "SN-NOS", "SN-SSTI"]
-#         if value.upper() not in acceptables:
-#             raise KeyError(f"Sub-type must be in {acceptables}")
-#         return value
-#
-#     def to_sub_dict(self) -> dict:
-#         """
-#             Converts object into convenient dictionary for use in procedure summary
-#
-#             Returns:
-#                 dict: output dictionary containing: Name, Type, Targets, Top Kraken results
-#             """
-#         try:
-#             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)[0:10]
-#         except (AttributeError, ZeroDivisionError):
-#             new_kraken = []
-#         output = dict(
-#             name=self.name,
-#             type=self.controltype.name,
-#             targets=", ".join(self.targets),
-#             kraken=new_kraken
-#         )
-#         return output
-#
-#     def convert_by_mode(self, control_sub_type: str, mode: Literal['kraken', 'matches', 'contains'],
-#                         consolidate: bool = False) -> Generator[dict, None, None]:
-#         """
-#         split this instance into analysis types ('kraken', 'matches', 'contains') for control graphs
-#
-#         Args:
-#             consolidate (bool): whether to merge all off-target genera. Defaults to False
-#             control_sub_type (str): control subtype, 'MCS-NOS', etc.
-#             mode (Literal['kraken', 'matches', 'contains']): analysis type, 'contains', etc.
-#
-#         Returns:
-#             List[dict]: list of records
-#         """
-#         try:
-#             data = self.__getattribute__(mode)
-#         except TypeError:
-#             data = {}
-#         if data is None:
-#             data = {}
-#         # NOTE: Data truncation and consolidation.
-#         if "kraken" in mode:
-#             data = {k: v for k, v in sorted(data.items(), key=lambda d: d[1][f"{mode}_count"], reverse=True)[:50]}
-#         else:
-#             if consolidate:
-#                 on_tar = {k: v for k, v in data.items() if k.strip("*") in self.controltype.targets[control_sub_type]}
-#                 off_tar = sum(v[f'{mode}_ratio'] for k, v in data.items() if
-#                               k.strip("*") not in self.controltype.targets[control_sub_type])
-#                 on_tar['Off-target'] = {f"{mode}_ratio": off_tar}
-#                 data = on_tar
-#         for genus in data:
-#             _dict = dict(
-#                 name=self.name,
-#                 submitted_date=self.submitted_date,
-#                 genus=genus,
-#                 target='Target' if genus.strip("*") in self.controltype.targets[control_sub_type] else "Off-target"
-#             )
-#             for key in data[genus]:
-#                 _dict[key] = data[genus][key]
-#             yield _dict
-#
-#     @classproperty
-#     def modes(cls) -> List[str]:
-#         """
-#         Get all control modes from database
-#
-#         Returns:
-#             List[str]: List of control mode names.
-#         """
-#         try:
-#             cols = [item.name for item in list(cls.__table__.columns) if isinstance(item.type, JSON)]
-#         except AttributeError as e:
-#             logger.error(f"Failed to get available modes from db: {e}")
-#             cols = []
-#         return cols
-#
-#     @classmethod
-#     def make_parent_buttons(cls, parent: QWidget) -> None:
-#         """
-#         Creates buttons for controlling
-#
-#         Args:
-#             parent (QWidget): chart holding widget to add buttons to.
-#
-#         """
-#         super().make_parent_buttons(parent=parent)
-#         rows = parent.layout.rowCount() - 2
-#         # NOTE: check box for consolidating off-target items
-#         checker = QCheckBox(parent)
-#         checker.setChecked(True)
-#         checker.setObjectName("irida_check")
-#         checker.setToolTip("Pools off-target genera to save time.")
-#         parent.layout.addWidget(QLabel("Consolidate Off-targets"), rows, 0, 1, 1)
-#         parent.layout.addWidget(checker, rows, 1, 1, 2)
-#         checker.checkStateChanged.connect(parent.update_data)
-#
-#     @classmethod
-#     @report_result
-#     def make_chart(cls, chart_settings: dict, parent, ctx) -> Tuple[Report, "IridaFigure" | None]:
-#         """
-#         Creates a IridaFigure. Overrides parent
-#
-#         Args:
-#             parent (__type__): Widget to contain the chart.
-#             chart_settings (dict): settings passed down from chart widget
-#             ctx (Settings): settings passed down from gui.
-#
-#         Returns:
-#             Tuple[Report, "IridaFigure"]: Report of status and resulting figure.
-#         """
-#         from frontend.visualizations import IridaFigure
-#         try:
-#             checker = parent.findChild(QCheckBox, name="irida_check")
-#             if chart_settings['mode'] == "kraken":
-#                 checker.setEnabled(False)
-#                 checker.setChecked(False)
-#             else:
-#                 checker.setEnabled(True)
-#             consolidate = checker.isChecked()
-#         except AttributeError:
-#             consolidate = False
-#         report = Report()
-#         control = cls.query(subtype=chart_settings['submissiontype'], start_date=chart_settings['start_date'],
-#                              end_date=chart_settings['end_date'])
-#         if not control:
-#             report.add_result(Result(status="Critical", msg="No control found in given date range."))
-#             return report, None
-#         # NOTE: change each control to list of dictionaries
-#         data = [control.convert_by_mode(control_sub_type=chart_settings['submissiontype'], mode=chart_settings['mode'],
-#                                         consolidate=consolidate) for
-#                 control in control]
-#         # NOTE: flatten data to one dimensional list
-#         # data = [item for sublist in data for item in sublist]
-#         data = flatten_list(data)
-#         if not data:
-#             report.add_result(Result(status="Critical", msg="No data found for control in given date range."))
-#             return report, None
-#         df = cls.convert_data_list_to_df(input_df=data, sub_mode=chart_settings['sub_mode'])
-#         if chart_settings['sub_mode'] is None:
-#             title = chart_settings['sub_mode']
-#         else:
-#             title = f"{chart_settings['mode']} - {chart_settings['sub_mode']}"
-#         # NOTE: send dataframe to chart maker
-#         df, modes = cls.prep_df(ctx=ctx, df=df)
-#         fig = IridaFigure(df=df, ytitle=title, modes=modes, parent=parent,
-#                           settings=chart_settings)
-#         return report, fig
-#
-#     @classmethod
-#     def convert_data_list_to_df(cls, input_df: list[dict], sub_mode) -> DataFrame:
-#         """
-#         Convert list of control records to dataframe
-#
-#         Args:
-#             input_df (list[dict]): list of dictionaries containing records
-#             sub_mode (str | None, optional): submissiontype of procedure type. Defaults to None.
-#
-#         Returns:
-#             DataFrame: dataframe of control
-#         """
-#         df = DataFrame.from_records(input_df)
-#         safe = ['name', 'submitted_date', 'genus', 'target']
-#         for column in df.columns:
-#             if column not in safe:
-#                 if sub_mode is not None and column != sub_mode:
-#                     continue
-#                 else:
-#                     safe.append(column)
-#             if "percent" in column:
-#                 try:
-#                     count_col = next(item for item in df.columns if "count" in item)
-#                 except StopIteration:
-#                     continue
-#                 # NOTE: The actual percentage from kraken was off due to exclusion of NaN, recalculating.
-#                 df[column] = 100 * df[count_col] / df.groupby('name')[count_col].transform('sum')
-#         df = df[[c for c in df.columns if c in safe]]
-#         # NOTE: move date of sample submitted on same date as previous ahead one.
-#         df = cls.displace_date(df=df)
-#         # NOTE: ad hoc method to make data labels more accurate.
-#         df = cls.df_column_renamer(df=df)
-#         return df
-#
-#     @classmethod
-#     def df_column_renamer(cls, df: DataFrame) -> DataFrame:
-#         """
-#         Ad hoc function I created to clarify some fields
-#
-#         Args:
-#             df (DataFrame): input dataframe
-#
-#         Returns:
-#             DataFrame: dataframe with 'clarified' column names
-#         """
-#         df = df[df.columns.drop(list(df.filter(regex='_hashes')))]
-#         return df.rename(columns={
-#             "contains_ratio": "contains_shared_hashes_ratio",
-#             "matches_ratio": "matches_shared_hashes_ratio",
-#             "kraken_count": "kraken2_read_count_(top_50)",
-#             "kraken_percent": "kraken2_read_percent_(top_50)"
-#         })
-#
-#     @classmethod
-#     def displace_date(cls, df: DataFrame) -> DataFrame:
-#         """
-#         This function serves to split sample that were submitted on the same date by incrementing dates.
-#         It will shift the date forward by one day if it is the same day as an existing date in a list.
-#
-#         Args:
-#             df (DataFrame): input dataframe composed of control records
-#
-#         Returns:
-#             DataFrame: output dataframe with dates incremented.
-#         """
-#         # NOTE: get submitted dates for each control
-#         dict_list = [dict(name=item, date=df[df.name == item].iloc[0]['submitted_date']) for item in
-#                      sorted(df['name'].unique())]
-#         previous_dates = set()
-#         for item in dict_list:
-#             df, previous_dates = cls.check_date(df=df, item=item, previous_dates=previous_dates)
-#         return df
-#
-#     @classmethod
-#     def check_date(cls, df: DataFrame, item: dict, previous_dates: set) -> Tuple[DataFrame, list]:
-#         """
-#         Checks if an items date is already present in df and adjusts df accordingly
-#
-#         Args:
-#             df (DataFrame): input dataframe
-#             item (dict): control for checking
-#             previous_dates (list): list of dates found in previous control
-#
-#         Returns:
-#             Tuple[DataFrame, list]: Output dataframe and appended list of previous dates
-#         """
-#         try:
-#             check = item['date'] in previous_dates
-#         except IndexError:
-#             check = False
-#         previous_dates.add(item['date'])
-#         if check:
-#             # NOTE: get df locations where name == item name
-#             mask = df['name'] == item['name']
-#             # NOTE: increment date in dataframe
-#             df.loc[mask, 'submitted_date'] = df.loc[mask, 'submitted_date'].apply(lambda x: x + timedelta(days=1))
-#             item['date'] += timedelta(days=1)
-#             passed = False
-#         else:
-#             passed = True
-#         # NOTE: if procedure didn't lead to changed date, return values
-#         if passed:
-#             return df, previous_dates
-#         # NOTE: if date was changed, rerun with new date
-#         else:
-#             logger.warning(f"Date check failed, running recursion.")
-#             df, previous_dates = cls.check_date(df, item, previous_dates)
-#             return df, previous_dates
-#
-#     @classmethod
-#     def prep_df(cls, ctx: Settings, df: DataFrame) -> Tuple[DataFrame | None, list]:
-#         """
-#         Constructs figures based on parsed pandas dataframe.
-#
-#         Args:
-#             ctx (Settings): settings passed down from gui
-#             df (pd.DataFrame): input dataframe
-#             ytitle (str | None, optional): title for the y-axis. Defaults to None.
-#
-#         Returns:
-#             Figure: Plotly figure
-#         """
-#         # NOTE: converts starred genera to normal and splits off list of starred
-#         if df.empty:
-#             return None, []
-#         df['genus'] = df['genus'].replace({'\*': ''}, regex=True).replace({"NaN": "Unknown"})
-#         df['genera'] = [item[-1] if item and item[-1] == "*" else "" for item in df['genus'].to_list()]
-#         # NOTE: remove original run, using reruns if applicable
-#         df = cls.drop_reruns_from_df(ctx=ctx, df=df)
-#         # NOTE: sort by and exclude from
-#         sorts = ['submitted_date', "target", "genus"]
-#         exclude = ['name', 'genera']
-#         modes = [item for item in df.columns if item not in sorts and item not in exclude]
-#         # NOTE: Set descending for any columns that have "{mode}" in the header.
-#         ascending = [False if item == "target" else True for item in sorts]
-#         df = df.sort_values(by=sorts, ascending=ascending)
-#         # NOTE: actual chart construction is done by
-#         return df, modes
-#
-#     @classmethod
-#     def drop_reruns_from_df(cls, ctx: Settings, df: DataFrame) -> DataFrame:
-#         """
-#         Removes semi-duplicates from dataframe after finding sequencing repeats.
-#
-#         Args:
-#             ctx (Settings): settings passed from gui
-#             df (DataFrame): initial dataframe
-#
-#         Returns:
-#             DataFrame: dataframe with originals removed in favour of repeats.
-#         """
-#         if 'rerun_regex' in ctx.model_extra:
-#             sample_names = get_unique_values_in_df_column(df, column_name="name")
-#             rerun_regex = re.compile(fr"{ctx.rerun_regex}")
-#             exclude = [re.sub(rerun_regex, "", sample) for sample in sample_names if rerun_regex.search(sample)]
-#             df = df[~df.name.isin(exclude)]
-#         return df
-#
-#     def to_pydantic(self) -> "PydIridaControl":
-#         """
-#         Constructs a pydantic version of this object.
-#
-#         Returns:
-#             PydIridaControl: This object as a pydantic model.
-#         """
-#         from backend.validators import PydIridaControl
-#         return PydIridaControl(**self.__dict__)
-#
-#     @property
-#     def is_positive_control(self):
-#         return not self.subtype.lower().startswith("en")

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

@@ -3,21 +3,19 @@ All client organization related models.
 '''
 from __future__ import annotations
 import logging
-from pathlib import Path
-from pprint import pformat
 from sqlalchemy import Column, String, INTEGER, ForeignKey, Table
-from sqlalchemy.ext.hybrid import hybrid_property
+from sqlalchemy.orm import relationship, Query, declared_attr
-from sqlalchemy.orm import relationship, Query
+from . import BaseClass
-from . import Base, BaseClass
 from tools import check_authorization, setup_lookup
-from typing import List, Tuple
+from typing import List
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 # table containing clientlab/contact relationship
 clientlab_contact = Table(
     "_clientlab_contact",
-    Base.metadata,
+    # Base.metadata,
+    BaseClass.__base__.metadata,
     Column("clientlab_id", INTEGER, ForeignKey("_clientlab.id")),
     Column("contact_id", INTEGER, ForeignKey("_contact.id")),
     extend_existing=True
@@ -31,7 +29,7 @@ class ClientLab(BaseClass):
 
     id = Column(INTEGER, primary_key=True)  #: primary key
     name = Column(String(64))  #: clientlab name
-    clientsubmission = relationship("ClientSubmission", back_populates="clientlab")  #: procedure this clientlab has submitted
+    clientsubmission = relationship("ClientSubmission", back_populates="clientlab")  #: submission this clientlab has submitted
     cost_centre = Column(String())  #: cost centre used by org for payment
     contact = relationship("Contact", back_populates="clientlab",
                            secondary=clientlab_contact)  #: contact involved with this org
@@ -47,6 +45,7 @@ class ClientLab(BaseClass):
         Lookup clientlabs in the database by a number of parameters.
 
         Args:
+            id (int | None, optional): id integer of the clientlab. Defaults to None.
             name (str | None, optional): Name of the clientlab. Defaults to None.
             limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
 
@@ -100,24 +99,12 @@ class Contact(BaseClass):
                              secondary=clientlab_contact)  #: relationship to joined clientlab
     clientsubmission = relationship("ClientSubmission", back_populates="contact")  #: procedure this contact has submitted
 
-    @classproperty
+    # @classproperty
+    @classmethod
+    @declared_attr
     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,
@@ -131,6 +118,7 @@ class Contact(BaseClass):
         Lookup contact in the database by a number of parameters.
 
         Args:
+            id (int | None, optional): id integer of the contact. Defaults to None.
             name (str | None, optional): Name of the contact. Defaults to None.
             email (str | None, optional): Email of the contact. Defaults to None.
             phone (str | None, optional): Phone number of the contact. Defaults to None.

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

@@ -2,43 +2,26 @@
 Models for the main procedure and sample types.
 """
 from __future__ import annotations
-
-import itertools
-import pickle
-from copy import deepcopy
 from getpass import getuser
-import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys
+import logging, tempfile, re, numpy as np, pandas as pd, types, sys, itertools
 from inspect import isclass
-from io import BytesIO
+from zipfile import BadZipfile
-from zipfile import ZipFile, BadZipfile
-from tempfile import TemporaryDirectory, TemporaryFile
 from operator import itemgetter
 from pprint import pformat
-
-import openpyxl
 from pandas import DataFrame
 from sqlalchemy.ext.hybrid import hybrid_property
-
 from frontend.widgets.functions import select_save_file
-from . import Base, BaseClass, Reagent, SubmissionType, ClientLab, Contact, LogMixin, Procedure
+from . import BaseClass, SubmissionType, ClientLab, Contact, LogMixin, Procedure
-from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func, Table, Sequence
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func
-from sqlalchemy.orm import relationship, validates, Query
+from sqlalchemy.orm import relationship, Query, declared_attr
 from sqlalchemy.orm.attributes import flag_modified
 from sqlalchemy.ext.associationproxy import association_proxy
-from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError, \
+from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError
-    ArgumentError
 from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
-from openpyxl import Workbook
+from tools import setup_lookup, jinja_template_loading, create_holidays_for_year, check_dictionary_inclusion_equality, is_power_user
-from openpyxl.drawing.image import Image as OpenpyxlImage
-from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
-    report_result, create_holidays_for_year, check_dictionary_inclusion_equality, is_power_user
 from datetime import datetime, date
-from typing import List, Any, Tuple, Literal, Generator, Type, TYPE_CHECKING
+from typing import List, Literal, Generator, TYPE_CHECKING
 from pathlib import Path
-from jinja2.exceptions import TemplateNotFound
-from jinja2 import Template
-from PIL import Image
-
 if TYPE_CHECKING:
     from backend.db.models.procedures import ProcedureType, Procedure
 
@@ -51,21 +34,21 @@ class ClientSubmission(BaseClass, LogMixin):
     """
 
     id = Column(INTEGER, primary_key=True)  #: primary key
-    submitter_plate_id = Column(String(127), unique=True)  #: The number given to the procedure by the submitting lab
+    submitter_plate_id = Column(String(127), unique=True)  #: The number given to the submission by the submitting lab
-    submitted_date = Column(TIMESTAMP)  #: Date procedure received
+    submitted_date = Column(TIMESTAMP)  #: Date submission received
     clientlab = relationship("ClientLab", back_populates="clientsubmission")  #: client org
     clientlab_id = Column(INTEGER, ForeignKey("_clientlab.id", ondelete="SET NULL",
                                               name="fk_BS_sublab_id"))  #: client lab id from _organizations
-    submission_category = Column(String(64))
+    submission_category = Column(String(64))  #: i.e. Surveillance
     sample_count = Column(INTEGER)  #: Number of sample in the procedure
     full_batch_size = Column(INTEGER)  #: Number of wells in provided plate. 0 if no plate.
-    comment = Column(JSON)
+    comment = Column(JSON)  #: comment objects from users.
     run = relationship("Run", back_populates="clientsubmission")  #: many-to-one relationship
-    contact = relationship("Contact", back_populates="clientsubmission")  #: client org
+    contact = relationship("Contact", back_populates="clientsubmission")  #: contact representing submitting lab.
     contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
-                                            name="fk_BS_contact_id"))  #: client lab id from _organizations
+                                            name="fk_BS_contact_id"))  #: contact id from _organizations
     submissiontype_name = Column(String, ForeignKey("_submissiontype.name", ondelete="SET NULL",
-                                                    name="fk_BS_subtype_name"))  #: name of joined procedure type
+                                                    name="fk_BS_subtype_name"))  #: name of joined submission type
     submissiontype = relationship("SubmissionType", back_populates="clientsubmission")  #: archetype of this procedure
     cost_centre = Column(
         String(64))  #: Permanent storage of used cost centre in case organization field changed in the future.
@@ -93,7 +76,7 @@ class ClientSubmission(BaseClass, LogMixin):
     @setup_lookup
     def query(cls,
               submissiontype: str | SubmissionType | None = None,
-              submissiontype_name: str | None = None,
+              # submissiontype_name: str | None = None,
               id: int | str | None = None,
               submitter_plate_id: str | None = None,
               start_date: date | datetime | str | int | None = None,
@@ -108,7 +91,7 @@ class ClientSubmission(BaseClass, LogMixin):
         Lookup procedure based on a number of parameters. Overrides parent.
 
         Args:
-            submission_type (str | models.SubmissionType | None, optional): Submission type of interest. Defaults to None.
+            submissiontype (str | models.SubmissionType | None, optional): Submission type of interest. Defaults to None.
             id (int | str | None, optional): Submission id in the database (limits results to 1). Defaults to None.
             rsl_plate_number (str | None, optional): Submission name in the database (limits results to 1). Defaults to None.
             start_date (date | str | int | None, optional): Beginning date to search by. Defaults to None.
@@ -133,7 +116,6 @@ class ClientSubmission(BaseClass, LogMixin):
         if start_date is not None:
             start_date = cls.rectify_query_date(start_date)
             end_date = cls.rectify_query_date(end_date, eod=True)
-            logger.debug(f"Start date: {start_date}, end date: {end_date}")
             query = query.filter(cls.submitted_date.between(start_date, end_date))
         # NOTE: by rsl number (returns only a single value)
         match submitter_plate_id:
@@ -142,9 +124,11 @@ class ClientSubmission(BaseClass, LogMixin):
                 limit = 1
             case _:
                 pass
-        match submissiontype_name:
+        match submissiontype:
+            case SubmissionType():
+                query = query.filter(cls.submissiontype == submissiontype)
             case str():
-                query = query.filter(cls.submissiontype_name == submissiontype_name)
+                query = query.filter(cls.submissiontype_name == submissiontype)
             case _:
                 pass
         # NOTE: by id (returns only a single value)
@@ -157,7 +141,6 @@ class ClientSubmission(BaseClass, LogMixin):
                 limit = 1
             case _:
                 pass
-        # query = query.order_by(cls.submitted_date.desc())
         # NOTE: Split query results into pages of size {page_size}
         if page_size > 0 and limit == 0:
             limit = page_size
@@ -249,11 +232,8 @@ class ClientSubmission(BaseClass, LogMixin):
         if report:
             return output
         if full_data:
-            # dicto, _ = self.kittype.construct_xl_map_for_use(self.proceduretype)
-            # sample = self.generate_associations(name="clientsubmissionsampleassociation")
             samples = None
             runs = [item.to_dict(full_data=True) for item in self.run]
-            # custom = self.custom
         else:
             samples = None
             custom = None
@@ -280,7 +260,6 @@ class ClientSubmission(BaseClass, LogMixin):
         output["comment"] = comments
         output["contact"] = contact
         output["contact_phone"] = contact_phone
-        # output["custom"] = custom
         output["run"] = runs
         output['name'] = self.name
         return output
@@ -291,7 +270,6 @@ class ClientSubmission(BaseClass, LogMixin):
         except AssertionError:
             logger.warning(f"Converting {sample} to sql.")
             sample = sample.to_sql()
-        # logger.debug(sample.__dict__)
         try:
             row = sample._misc_info['row']
         except (KeyError, AttributeError):
@@ -300,7 +278,6 @@ class ClientSubmission(BaseClass, LogMixin):
             column = sample._misc_info['column']
         except KeyError:
             column = 0
-        # logger.debug(f"Sample: {sample}")
         submission_rank = sample._misc_info['submission_rank']
         if sample in self.sample:
             return
@@ -311,7 +288,6 @@ class ClientSubmission(BaseClass, LogMixin):
             row=row,
             column=column
         )
-        # assoc.save()
         return assoc
 
     @property
@@ -326,20 +302,16 @@ class ClientSubmission(BaseClass, LogMixin):
         return {item: self.__getattribute__(item.lower().replace(" ", "_")) for item in names}
 
     def add_run(self, obj):
-        logger.debug("Add Run")
         from frontend.widgets.sample_checker import SampleChecker
         samples = [sample.to_pydantic() for sample in self.clientsubmissionsampleassociation]
         checker = SampleChecker(parent=None, title="Create Run", samples=samples, clientsubmission=self)
         if checker.exec():
             run = Run(clientsubmission=self, rsl_plate_number=checker.rsl_plate_number)
             active_samples = [sample for sample in samples if sample.enabled]
-            logger.debug(active_samples)
             for sample in active_samples:
                 sample = sample.to_sql()
-                logger.debug(f"Sample: {sample.id}")
                 if sample not in run.sample:
                     assoc = run.add_sample(sample)
-                    # assoc.save()
             run.save()
         else:
             logger.warning("Run cancelled.")
@@ -351,13 +323,6 @@ class ClientSubmission(BaseClass, LogMixin):
     def add_comment(self, obj):
         logger.debug("Add Comment")
 
-    # def show_details(self, obj):
-    #     logger.debug("Show Details")
-    #     from frontend.widgets.submission_details import SubmissionDetails
-    #     dlg = SubmissionDetails(parent=obj, sub=self)
-    #     if dlg.exec():
-    #         pass
-
     def details_dict(self, **kwargs):
         output = super().details_dict(**kwargs)
         output['clientlab'] = output['clientlab'].details_dict()
@@ -377,7 +342,6 @@ class ClientSubmission(BaseClass, LogMixin):
 
     def to_pydantic(self, filepath: Path | str | None = None, **kwargs):
         output = super().to_pydantic(filepath=filepath, **kwargs)
-        # output.template_file = self.template_file
         return output
 
 
@@ -389,18 +353,16 @@ class Run(BaseClass, LogMixin):
     id = Column(INTEGER, primary_key=True)  #: primary key
     rsl_plate_number = Column(String(32), unique=True, nullable=False)  #: RSL name (e.g. RSL-22-0012)
     clientsubmission_id = Column(INTEGER, ForeignKey("_clientsubmission.id", ondelete="SET NULL",
-                                                     name="fk_BS_clientsub_id"))  #: client lab id from _organizations)
+                                                     name="fk_BS_clientsub_id"))  #: id of parent clientsubmission
-    clientsubmission = relationship("ClientSubmission", back_populates="run")
+    clientsubmission = relationship("ClientSubmission", back_populates="run")  #: parent clientsubmission
     _started_date = Column(TIMESTAMP)  #: Date this procedure was started.
     run_cost = Column(
         FLOAT(2))  #: total cost of running the plate. Set from constant and mutable kittype costs at time of creation.
     signed_by = Column(String(32))  #: user name of person who submitted the procedure to the database.
     comment = Column(JSON)  #: user notes
-    custom = Column(JSON)
+    custom = Column(JSON)  #: unknown
-
+    _completed_date = Column(TIMESTAMP)  #: Date this procedure was finished.
-    _completed_date = Column(TIMESTAMP)
+    procedure = relationship("Procedure", back_populates="run", uselist=True)  #: children procedures
-
-    procedure = relationship("Procedure", back_populates="run", uselist=True)
 
     runsampleassociation = relationship(
         "RunSampleAssociation",
@@ -412,20 +374,6 @@ class Run(BaseClass, LogMixin):
                                "sample", creator=lambda sample: RunSampleAssociation(
             sample=sample))  #: Association proxy to ClientSubmissionSampleAssociation.sample
 
-    # NOTE: Allows for subclassing into ex. BacterialCulture, Wastewater, etc.
-    # __mapper_args__ = {
-    #     "polymorphic_identity": "Basic Submission",
-    #     "polymorphic_on": case(
-    #
-    #         (submissiontype_name == "Wastewater", "Wastewater"),
-    #         (submissiontype_name == "Wastewater Artic", "Wastewater Artic"),
-    #         (submissiontype_name == "Bacterial Culture", "Bacterial Culture"),
-    #
-    #         else_="Basic Submission"
-    #     ),
-    #     "with_polymorphic": "*",
-    # }
-
     def __repr__(self) -> str:
         return f"<Submission({self.name})>"
 
@@ -505,13 +453,14 @@ class Run(BaseClass, LogMixin):
             output = {k: v for k, v in dicto.items() if k in args}
         else:
             output = {k: v for k, v in dicto.items()}
-        logger.debug(f"Submission type for get default info: {submissiontype}")
+        # logger.debug(f"Submission type for get default info: {submissiontype}")
         if isinstance(submissiontype, SubmissionType):
             st = submissiontype
         else:
             st = cls.get_submission_type(submissiontype)
         if st is None:
-            logger.error("No default info for Run.")
+            # logger.error("No default info for Run.")
+            pass
         else:
             output['submissiontype'] = st.name
             for k, v in st.defaults.items():
@@ -556,7 +505,6 @@ class Run(BaseClass, LogMixin):
             case SubmissionType():
                 return submissiontype
             case _:
-                # return SubmissionType.query(cls.__mapper_args__['polymorphic_identity'])
                 return None
 
     @classmethod
@@ -697,7 +645,7 @@ class Run(BaseClass, LogMixin):
                                'permission', "clientsubmission"]
         output['sample_count'] = self.sample_count
         output['clientsubmission'] = self.clientsubmission.name
-        output['clientlab'] = self.clientsubmission.clientlab
+        # output['clientlab'] = self.clientsubmission.clientlab
         output['started_date'] = self.started_date
         output['completed_date'] = self.completed_date
         return output
@@ -712,14 +660,12 @@ class Run(BaseClass, LogMixin):
             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: {run}")
                 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)
             output = sub.details_dict()
             for k, v in output.items():
                 if isinstance(v, types.GeneratorType):
@@ -746,29 +692,6 @@ class Run(BaseClass, LogMixin):
         Calculates cost of the plate
         """
         # NOTE: Calculate number of columns based on largest column number
-        # try:
-        #     cols_count_96 = self.column_count
-        # except Exception as e:
-        #     logger.error(f"Column count error: {e}")
-        # # NOTE: Get kittype associated with this procedure
-        # # logger.debug(f"Checking associations with procedure type: {self.submissiontype_name}")
-        # assoc = next((item for item in self.kittype.kit_submissiontype_associations if
-        #               item.proceduretype == self.submission_type),
-        #              None)
-        # # logger.debug(f"Got association: {assoc}")
-        # # NOTE: If every individual cost is 0 this is probably an old plate.
-        # if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]):
-        #     try:
-        #         self.run_cost = self.kittype.cost_per_run
-        #     except Exception as e:
-        #         logger.error(f"Calculation error: {e}")
-        # else:
-        #     try:
-        #         self.run_cost = assoc.constant_cost + (assoc.mutable_cost_column * cols_count_96) + (
-        #                 assoc.mutable_cost_sample * int(self.sample_count))
-        #     except Exception as e:
-        #         logger.error(f"Calculation error: {e}")
-        # self.run_cost = round(self.run_cost, 2)
         pass
 
     @property
@@ -802,7 +725,6 @@ class Run(BaseClass, LogMixin):
         """
         rows = range(1, plate_rows + 1)
         columns = range(1, plate_columns + 1)
-        # logger.debug(f"sample list for plate map: {pformat(sample_list)}")
         # NOTE: An overly complicated list comprehension create a list of sample locations
         # NOTE: next will return a blank cell if no value found for row/column
         output_samples = [next((item for item in sample_list if item['row'] == row and item['column'] == column),
@@ -841,7 +763,6 @@ class Run(BaseClass, LogMixin):
             pd.DataFrame: Pandas Dataframe of all relevant procedure
         """
         # NOTE: use lookup function to create list of dicts
-        # subs = [item.to_dict() for item in
         subs = [item.details_dict() for item in
                 cls.query(submissiontype=submission_type, limit=limit, chronologic=chronologic, page=page,
                           page_size=page_size)]
@@ -872,8 +793,6 @@ class Run(BaseClass, LogMixin):
             value (_type_): value of attribute
         """
         match key:
-            # case "kittype":
-            #     field_value = KitType.query(name=value)
             case "clientlab":
                 field_value = ClientLab.query(name=value)
             case "contact":
@@ -900,13 +819,11 @@ class Run(BaseClass, LogMixin):
                         existing = value
                     case _:
                         existing = self.__getattribute__(key)
-                        logger.debug(f"Existing value is {pformat(existing)}")
                         if value in ['', 'null', None]:
                             logger.error(f"No value given, not setting.")
                             return
                         if existing is None:
                             existing = []
-                        # if value in existing:
                         if check_dictionary_inclusion_equality(existing, value):
                             logger.warning("Value already exists. Preventing duplicate addition.")
                             return
@@ -955,17 +872,6 @@ class Run(BaseClass, LogMixin):
                 pass
         return assoc
 
-    # def update_reagentassoc(self, reagent: Reagent, role: str):
-    #     # NOTE: get the first reagent assoc that fills the given reagentrole.
-    #     try:
-    #         assoc = next(item for item in self.submission_reagent_associations if
-    #                      item.reagent and role in [role.name for role in item.reagent.equipmentrole])
-    #         assoc.reagent = reagent
-    #     except StopIteration as e:
-    #         logger.error(f"Association for {role} not found, creating new association.")
-    #         assoc = ProcedureReagentAssociation(procedure=self, reagent=reagent)
-    #         self.submission_reagent_associations.append(assoc)
-
     def to_pydantic(self, backup: bool = False) -> "PydSubmission":
         """
         Converts this instance into a PydSubmission
@@ -973,7 +879,7 @@ class Run(BaseClass, LogMixin):
         Returns:
             PydSubmission: converted object.
         """
-        from backend.validators import PydRun
+        from backend.validators import PydClientSubmission, PydRun
         dicto = self.details_dict(full_data=True, backup=backup)
         new_dict = {}
         for key, value in dicto.items():
@@ -1028,7 +934,6 @@ class Run(BaseClass, LogMixin):
         Returns:
             str: String from which regex will be compiled.
         """
-        # logger.debug(f"Class for regex: {cls}")
         try:
             regex = cls.get_submission_type(submission_type).defaults['regex']
         except AttributeError as e:
@@ -1038,12 +943,12 @@ class Run(BaseClass, LogMixin):
             regex = re.compile(rf"{regex}", flags=re.IGNORECASE | re.VERBOSE)
         except re.error as e:
             regex = cls.construct_regex()
-        # logger.debug(f"Returning regex: {regex}")
         return regex
 
     # NOTE: Polymorphic functions
 
-    @classproperty
+    @classmethod
+    @declared_attr
     def regex(cls) -> re.Pattern:
         """
         Constructs catchall regex.
@@ -1089,15 +994,6 @@ class Run(BaseClass, LogMixin):
         Returns:
             models.Run | List[models.Run]: Run(s) of interest
         """
-        # from ... import RunReagentAssociation
-        # NOTE: if you go back to using 'model' change the appropriate cls to model in the query filters
-        # if submissiontype is not None:
-        #     model = cls.find_polymorphic_subclass(polymorphic_identity=submissiontype)
-        # elif len(kwargs) > 0:
-        #     # NOTE: find the subclass containing the relevant attributes
-        #     model = cls.find_polymorphic_subclass(attrs=kwargs)
-        # else:
-        #     model = cls
         query: Query = cls.__database_session__.query(cls)
         if start_date is not None and end_date is None:
             logger.warning(f"Start date with no end date, using today.")
@@ -1107,38 +1003,8 @@ class Run(BaseClass, LogMixin):
             start_date = cls.__database_session__.query(cls, func.min(cls.submitted_date)).first()[1]
             logger.warning(f"End date with no start date, using first procedure date: {start_date}")
         if start_date is not None:
-            # match start_date:
-            #     case date():
-            #         pass
-            #     case datetime():
-            #         start_date = start_date.date()
-            #     case int():
-            #         start_date = datetime.fromordinal(
-            #             datetime(1900, 1, 1).toordinal() + start_date - 2).date()
-            #     case _:
-            #         start_date = parse(start_date).date()
-            # # start_date = start_date.strftime("%Y-%m-%d")
-            # match end_date:
-            #     case date():
-            #         pass
-            #     case datetime():
-            #         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)
-            #     case _:
-            #         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")
-            # # if start_date == end_date:
-            # #     start_date = start_date.strftime("%Y-%m-%d %H:%M:%S.%f")
-            # #     query = query.filter(model.submitted_date == start_date)
-            # # else:
             start_date = cls.rectify_query_date(start_date)
             end_date = cls.rectify_query_date(end_date, eod=True)
-            logger.debug(f"Start date: {start_date}, end date: {end_date}")
             query = query.join(ClientSubmission).filter(ClientSubmission.submitted_date.between(start_date, end_date))
         # NOTE: by rsl number (returns only a single value)
         match name:
@@ -1164,7 +1030,6 @@ class Run(BaseClass, LogMixin):
                 limit = 1
             case _:
                 pass
-        # query = query.order_by(cls.submitted_date.desc())
         # NOTE: Split query results into pages of size {page_size}
         if page_size > 0:
             query = query.limit(page_size)
@@ -1173,58 +1038,6 @@ class Run(BaseClass, LogMixin):
             query = query.offset(page * page_size)
         return cls.execute_query(query=query, limit=limit, **kwargs)
 
-    # @classmethod
-    # def query_or_create(cls, submissiontype: str | SubmissionType | None = None, **kwargs) -> Run:
-    #     """
-    #     Returns object from db if exists, else, creates new. Due to need for user input, doesn't see much use ATM.
-    #
-    #     Args:
-    #         submissiontype (str | SubmissionType | None, optional): Submission type to be created. Defaults to None.
-    #
-    #     Raises:
-    #         ValueError: Raised if no kwargs passed.
-    #         ValueError: Raised if disallowed key is passed.
-    #
-    #     Returns:
-    #         cls: A Run subclass instance.
-    #     """
-    #     code = 0
-    #     msg = ""
-    #     report = Report()
-    #     disallowed = ["id"]
-    #     if kwargs == {}:
-    #         raise ValueError("Need to narrow down query or the first available instance will be returned.")
-    #     sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
-    #     instance = cls.query(submissiontype=submissiontype, limit=1, **sanitized_kwargs)
-    #     if instance is None:
-    #         used_class = cls.find_polymorphic_subclass(attrs=kwargs, polymorphic_identity=submissiontype)
-    #         instance = used_class(**sanitized_kwargs)
-    #         match submissiontype:
-    #             case str():
-    #                 submissiontype = SubmissionType.query(name=submissiontype)
-    #             case _:
-    #                 pass
-    #         instance.proceduretype = submissiontype
-    #         instance.submissiontype_name = submissiontype.name
-    #         if "submitted_date" not in kwargs.keys():
-    #             instance.submitted_date = date.today()
-    #     else:
-    #         from frontend.widgets.pop_ups import QuestionAsker
-    #         logger.warning(f"Found existing instance: {instance}, asking to overwrite.")
-    #         #     code = 1
-    #         #     msg = "This procedure already exists.\nWould you like to overwrite?"
-    #         # report.add_result(Result(msg=msg, code=code))
-    #         dlg = QuestionAsker(title="Overwrite?",
-    #                             message="This procedure already exists.\nWould you like to overwrite?")
-    #         if dlg.exec():
-    #             pass
-    #         else:
-    #             code = 1
-    #             msg = "This procedure already exists.\nWould you like to overwrite?"
-    #             report.add_result(Result(msg=msg, code=code))
-    #             return None, report
-    #     return instance, report
-
     # NOTE: Custom context events for the ui
 
     @property
@@ -1237,18 +1050,15 @@ class Run(BaseClass, LogMixin):
         """
         names = ["Add Procedure", "Edit", "Export", "Add Comment", "Show Details", "Delete"]
         output = {item: self.__getattribute__(item.lower().replace(" ", "_")) for item in names}
-        logger.debug(output)
         return output
 
     def add_procedure(self, obj, proceduretype_name: str):
         from frontend.widgets.procedure_creation import ProcedureCreation
         procedure_type: ProcedureType = next(
             (proceduretype for proceduretype in self.allowed_procedures if proceduretype.name == proceduretype_name))
-        logger.debug(f"Got ProcedureType: {procedure_type}")
         dlg = ProcedureCreation(parent=obj, procedure=procedure_type.construct_dummy_procedure(run=self))
         if dlg.exec():
             sql, _ = dlg.return_sql(new=True)
-            # sys.exit(pformat(sql.__dict__))
             sql.save()
         obj.set_data()
 
@@ -1282,18 +1092,6 @@ class Run(BaseClass, LogMixin):
             except AttributeError:
                 logger.error("App will not refresh data at this time.")
 
-    # def show_details(self, obj):
-    #     """
-    #     Creates Widget for showing procedure details.
-    #
-    #     Args:
-    #         obj (Widget): Parent widget
-    #     """
-    #     from frontend.widgets.submission_details import SubmissionDetails
-    #     dlg = SubmissionDetails(parent=obj, sub=self)
-    #     if dlg.exec():
-    #         pass
-
     def edit(self, obj):
         """
         Return procedure to form widget for updating
@@ -1315,7 +1113,6 @@ class Run(BaseClass, LogMixin):
         Args:
             obj (_type_): parent widget
         """
-        logger.debug(obj)
         from frontend.widgets.submission_details import SubmissionComment
         dlg = SubmissionComment(parent=obj, submission=self)
         if dlg.exec():
@@ -1437,8 +1234,6 @@ class Run(BaseClass, LogMixin):
                 unranked_samples.append(sample)
         possible_ranks = (item for item in list(plate_dict.keys()) if
                           item not in [sample['submission_rank'] for sample in ranked_samples])
-        # logger.debug(possible_ranks)
-        # possible_ranks = (plate_dict[idx] for idx in possible_ranks)
         for sample in unranked_samples:
             try:
                 submission_rank = next(possible_ranks)
@@ -1457,17 +1252,9 @@ class Run(BaseClass, LogMixin):
                                background_color="#ffffff", enabled=False)
                           )
             padded_list.append(sample)
-        # logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")
         return list(sorted(padded_list, key=itemgetter('submission_rank')))
 
 
-# class SampleType(BaseClass):
-#     id = Column(INTEGER, primary_key=True)  #: primary key
-#     name = Column(String(64), nullable=False, unique=True)  #: identification from submitter
-#
-#     sample = relationship("Sample", back_populates="sampletype", uselist=True)
-
-
 # NOTE: Sample Classes
 
 class Sample(BaseClass, LogMixin):
@@ -1477,11 +1264,7 @@ class Sample(BaseClass, LogMixin):
 
     id = Column(INTEGER, primary_key=True)  #: primary key
     sample_id = Column(String(64), nullable=False, unique=True)  #: identification from submitter
-    # sampletype_id = Column(INTEGER, ForeignKey("_sampletype.id", ondelete="SET NULL",
+    control = relationship("Control", back_populates="sample", uselist=False)  #: Control function this sample fills.
-    #                                            name="fk_SAMP_sampletype_id"))
-    # sampletype = relationship("SampleType", back_populates="sample")
-    # misc_info = Column(JSON)
-    control = relationship("Control", back_populates="sample", uselist=False)
 
     sampleclientsubmissionassociation = relationship(
         "ClientSubmissionSampleAssociation",
@@ -1515,7 +1298,8 @@ class Sample(BaseClass, LogMixin):
     def __repr__(self) -> str:
         return f"<Sample({self.sample_id})>"
 
-    @classproperty
+    @classmethod
+    @declared_attr
     def searchables(cls):
         return [dict(label="Submitter ID", field="sample_id")]
 
@@ -1529,13 +1313,8 @@ class Sample(BaseClass, LogMixin):
         Returns:
             dict: submitter id and sample type and linked procedure if full data
         """
-        # try:
-        #     sample_type = self.sampletype.name
-        # except AttributeError:
-        #     sample_type = "NA"
         sample = dict(
             sample_id=self.sample_id
-            # sampletype=sample_type
         )
         if full_data:
             sample['clientsubmission'] = sorted([item.to_sub_dict() for item in self.sampleclientsubmissionassociation],
@@ -1563,7 +1342,6 @@ class Sample(BaseClass, LogMixin):
     @setup_lookup
     def query(cls,
               sample_id: str | None = None,
-              # sampletype: str | SampleType | None = None,
               limit: int = 0,
               **kwargs
               ) -> Sample | List[Sample]:
@@ -1578,13 +1356,6 @@ class Sample(BaseClass, LogMixin):
             models.Sample|List[models.Sample]: Sample(s) of interest.
         """
         query = cls.__database_session__.query(cls)
-        # match sampletype:
-        #     case str():
-        #         query = query.join(SampleType).filter(SampleType.name == sampletype)
-        #     case SampleType():
-        #         query = query.filter(cls.sampletype == sampletype)
-        #     case _:
-        #         pass
         match sample_id:
             case str():
                 query = query.filter(cls.sample_id == sample_id)
@@ -1593,38 +1364,6 @@ class Sample(BaseClass, LogMixin):
                 pass
         return cls.execute_query(query=query, limit=limit, **kwargs)
 
-    # @classmethod
-    # def fuzzy_search(cls,
-    #                  sampletype: str | Sample | None = None,
-    #                  **kwargs
-    #                  ) -> List[Sample]:
-    #     """
-    #     Allows for fuzzy search of sample.
-    #
-    #     Args:
-    #         sampletype (str | BasicSample | None, optional): Type of sample. Defaults to None.
-    #
-    #     Returns:
-    #         List[Sample]: List of sample that match kwarg search parameters.
-    #     """
-    #     query: Query = cls.__database_session__.query(cls)
-    #     match sampletype:
-    #         case str():
-    #             query = query.join(SampleType).filter(SampleType.name == sampletype)
-    #         case SampleType():
-    #             query = query.filter(cls.sampletype == sampletype)
-    #         case _:
-    #             pass
-    #     for k, v in kwargs.items():
-    #         search = f"%{v}%"
-    #         try:
-    #             attr = getattr(cls, k)
-    #             # NOTE: the secret sauce is in attr.like
-    #             query = query.filter(attr.like(search))
-    #         except (ArgumentError, AttributeError) as e:
-    #             logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
-    #     return query.limit(50).all()
-
     def delete(self):
         raise AttributeError(f"Delete not implemented for {self.__class__}")
 
@@ -1686,12 +1425,9 @@ class ClientSubmissionSampleAssociation(BaseClass):
     DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
     """
 
-    # id = Column(INTEGER, unique=True, nullable=False, autoincrement=True)  #: id to be used for inheriting purposes
     sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True)  #: id of associated sample
     clientsubmission_id = Column(INTEGER, ForeignKey("_clientsubmission.id"),
-                                 primary_key=True)  #: id of associated procedure
+                                 primary_key=True)  #: id of associated client submission
-    # row = Column(INTEGER)
-    # column = Column(INTEGER)
     submission_rank = Column(INTEGER, primary_key=True, default=0)  #: Location in sample list
     # NOTE: reference to the Submission object
     clientsubmission = relationship("ClientSubmission",
@@ -1708,10 +1444,6 @@ class ClientSubmissionSampleAssociation(BaseClass):
         self.row = row
         self.column = column
         self.submission_rank = submission_rank
-        # if id is not None:
-        #     self.id = id
-        # else:
-        #     self.id = self.__class__.autoincrement_id()
         for k, v in kwargs.items():
             try:
                 self.__setattr__(k, v)
@@ -1735,13 +1467,6 @@ class ClientSubmissionSampleAssociation(BaseClass):
         # NOTE: Get associated sample info
         sample = self.sample.to_sub_dict()
         sample['sample_id'] = self.sample.sample_id
-        # sample['row'] = self.row
-        # sample['column'] = self.column
-        # try:
-        #     sample['well'] = f"{row_map[self.row]}{self.column}"
-        # except (KeyError, AttributeError) as e:
-        #     logger.error(f"Unable to find row {self.row} in row_map.")
-        #     sample['Well'] = None
         sample['plate_name'] = self.clientsubmission.submitter_plate_id
         sample['positive'] = False
         sample['submitted_date'] = self.clientsubmission.submitted_date
@@ -1752,10 +1477,8 @@ class ClientSubmissionSampleAssociation(BaseClass):
         output = super().details_dict()
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['sample']}
-        # logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
         output = output['sample'].details_dict()
         misc = output['misc_info']
-        # # logger.debug(f"Output from sample: {pformat(output)}")
         output.update(relevant)
         output['misc_info'] = misc
         return output
@@ -1798,48 +1521,6 @@ class ClientSubmissionSampleAssociation(BaseClass):
         sample.update(dict(Name=self.sample.sample_id[:10], tooltip=tooltip_text, background_color=background))
         return sample
 
-    # @classmethod
-    # def autoincrement_id(cls) -> int:
-    #     """
-    #     Increments the association id automatically
-    #
-    #     Returns:
-    #         int: incremented id
-    #     """
-    #     if cls.__name__ == "ClientSubmissionSampleAssociation":
-    #         model = cls
-    #     else:
-    #         model = next((base for base in cls.__bases__ if base.__name__ == "ClientSubmissionSampleAssociation"),
-    #                      ClientSubmissionSampleAssociation)
-    #     try:
-    #         return max([item.id for item in model.query()]) + 1
-    #     except ValueError as e:
-    #         logger.error(f"Problem incrementing id: {e}")
-    #         return 1
-
-    # @classmethod
-    # def find_polymorphic_subclass(cls, polymorphic_identity: str | None = None) -> ClientSubmissionSampleAssociation:
-    #     """
-    #     Retrieves subclasses of ClientSubmissionSampleAssociation based on type name.
-    #
-    #     Args:
-    #         polymorphic_identity (str | None, optional): Name of subclass fed to polymorphic identity. Defaults to None.
-    #
-    #     Returns:
-    #         ClientSubmissionSampleAssociation: Subclass of interest.
-    #     """
-    #     if isinstance(polymorphic_identity, dict):
-    #         polymorphic_identity = polymorphic_identity['value']
-    #     if polymorphic_identity is None:
-    #         model = cls
-    #     else:
-    #         try:
-    #             model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
-    #         except Exception as e:
-    #             logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
-    #             model = cls
-    #     return model
-
     @classmethod
     @setup_lookup
     def query(cls,
@@ -1857,12 +1538,14 @@ class ClientSubmissionSampleAssociation(BaseClass):
         Lookup junction of Submission and Sample in the database
 
         Args:
-            run (models.Run | str | None, optional): Submission of interest. Defaults to None.
+            clientsubmission (models.ClientSubmission | str | None, optional): Submission of interest. Defaults to None.
+            exclude_submission_type ( str | None, optional): Name of submissiontype to exclude. Defaults to None.
             sample (models.Sample | str | None, optional): Sample of interest. Defaults to None.
             row (int, optional): Row of the sample location on procedure plate. Defaults to 0.
             column (int, optional): Column of the sample location on the procedure plate. Defaults to 0.
             limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
             chronologic (bool, optional): Return results in chronologic order. Defaults to False.
+            reverse (bool, optional): Whether or not to reverse order of list. Defaults to False.
 
         Returns:
             models.ClientSubmissionSampleAssociation|List[models.ClientSubmissionSampleAssociation]: Junction(s) of interest
@@ -1960,12 +1643,8 @@ class RunSampleAssociation(BaseClass):
     DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
     """
 
-    # id = Column(INTEGER, unique=True, nullable=False)  #: id to be used for inheriting purposes
     sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True)  #: id of associated sample
     run_id = Column(INTEGER, ForeignKey("_run.id"), primary_key=True)  #: id of associated procedure
-    # row = Column(INTEGER)  #: row on the 96 well plate
-    # column = Column(INTEGER)  #: column on the 96 well plate
-    # misc_info = Column(JSON)
 
     # NOTE: reference to the Submission object
 
@@ -2003,13 +1682,6 @@ class RunSampleAssociation(BaseClass):
         # NOTE: Get associated sample info
         sample = self.sample.to_sub_dict()
         sample['name'] = self.sample.sample_id
-        # sample['row'] = self.row
-        # sample['column'] = self.column
-        # try:
-        #     sample['well'] = f"{row_map[self.row]}{self.column}"
-        # except KeyError as e:
-        #     logger.error(f"Unable to find row {self.row} in row_map.")
-        #     sample['Well'] = None
         sample['plate_name'] = self.run.rsl_plate_number
         sample['positive'] = False
         return sample
@@ -2070,11 +1742,13 @@ class RunSampleAssociation(BaseClass):
 
         Args:
             run (models.Run | str | None, optional): Submission of interest. Defaults to None.
+            exclude_submission_type ( str | None, optional): Name of submissiontype to exclude. Defaults to None.
             sample (models.Sample | str | None, optional): Sample of interest. Defaults to None.
             row (int, optional): Row of the sample location on procedure plate. Defaults to 0.
             column (int, optional): Column of the sample location on the procedure plate. Defaults to 0.
             limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
             chronologic (bool, optional): Return results in chronologic order. Defaults to False.
+            reverse (bool, optional): Whether or not to reverse order of list. Defaults to False.
 
         Returns:
             models.ClientSubmissionSampleAssociation|List[models.ClientSubmissionSampleAssociation]: Junction(s) of interest
@@ -2169,13 +1843,10 @@ class RunSampleAssociation(BaseClass):
         output = super().details_dict()
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['sample']}
-        # logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
         output = output['sample'].details_dict()
         misc = output['misc_info']
-        # logger.debug(f"Output from sample: {pformat(output)}")
         output.update(relevant)
         output['misc_info'] = misc
-
         return output
 
 
@@ -2192,7 +1863,7 @@ class ProcedureSampleAssociation(BaseClass):
 
     sample = relationship(Sample, back_populates="sampleprocedureassociation")  #: associated equipment
 
-    results = relationship("Results", back_populates="sampleprocedureassociation")
+    results = relationship("Results", back_populates="sampleprocedureassociation")  #: associated results
 
     @classmethod
     def query(cls, sample: Sample | str | None = None, procedure: Procedure | str | None = None, limit: int = 0,
@@ -2242,12 +1913,11 @@ class ProcedureSampleAssociation(BaseClass):
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['sample']}
         output = output['sample'].details_dict()
-        logger.debug(f"Output: {pformat(output)}")
-        logger.debug(f"Relevant: {pformat(relevant)}")
-        # relevant['submission_rank'] = output['misc_info']['submission_rank']
         misc = output['misc_info']
         output.update(relevant)
         output['misc_info'] = misc
+        output['row'] = self.row
+        output['column'] = self.column
         output['results'] = [result.details_dict() for result in output['results']]
         return output
 

src/submissions/backend/excel/__init__.py

@@ -1,8 +1,18 @@
-'''
+"""
 Contains pandas and openpyxl convenience functions for interacting with excel workbooks
-'''
+"""
 
-# from .parser import *
+from .parsers import (
-from backend.excel.parsers.clientsubmission_parser import ClientSubmissionInfoParser, ClientSubmissionSampleParser
+    DefaultParser, DefaultKEYVALUEParser, DefaultTABLEParser,
-# from .reports import *
+    ProcedureInfoParser, ProcedureSampleParser, ProcedureReagentParser, ProcedureEquipmentParser,
-# from .writer import *
+    DefaultResultsInfoParser, DefaultResultsSampleParser, PCRSampleParser, PCRInfoParser,
+    ClientSubmissionSampleParser, ClientSubmissionInfoParser,
+    PCRInfoParser, PCRSampleParser
+)
+from .writers import (
+    DefaultWriter, DefaultKEYVALUEWriter, DefaultTABLEWriter,
+    ProcedureInfoWriter, ProcedureSampleWriter, ProcedureReagentWriter, ProcedureEquipmentWriter,
+    PCRInfoWriter, PCRSampleWriter,
+    ClientSubmissionInfoWriter, ClientSubmissionSampleWriter
+)
+from .reports import ReportArchetype, ReportMaker, TurnaroundMaker, ConcentrationMaker, ChartReportMaker

src/submissions/backend/excel/parsers/__init__.py

@@ -1,5 +1,5 @@
 """
-
+Default Parser archetypes.
 """
 from __future__ import annotations
 import logging, re
@@ -43,7 +43,8 @@ class DefaultParser(object):
             *args ():
             **kwargs ():
         """
-        logger.debug(f"\n\nHello from {self.__class__.__name__}\n\n")
+        logger.info(f"\n\nHello from {self.__class__.__name__}\n\n")
+        self.filepath = filepath
         self.proceduretype = proceduretype
         try:
             self._pyd_object = getattr(pydant,
@@ -61,10 +62,8 @@ class DefaultParser(object):
         self.worksheet = self.workbook[self.sheet]
         self.start_row = self.delineate_start_row(start_row=start_row)
         self.end_row = self.delineate_end_row(start_row=self.start_row)
-        logger.debug(f"Start row: {self.start_row}, End row: {self.end_row}")
 
     def to_pydantic(self):
-        # data = {key: value['value'] for key, value in self.parsed_info.items()}
         data = self.parsed_info
         data['filepath'] = self.filepath
         return self._pyd_object(**data)
@@ -100,7 +99,6 @@ class DefaultKEYVALUEParser(DefaultParser):
         rows = range(self.start_row, self.end_row)
         for row in rows:
             check_row = [item for item in self.worksheet.rows][row-1]
-            logger.debug(f"Checking row {row-1}, {check_row} for merged cells.")
             if any([isinstance(cell, MergedCell) for cell in check_row]):
                 continue
             key = self.worksheet.cell(row, 1).value
@@ -110,9 +108,7 @@ class DefaultKEYVALUEParser(DefaultParser):
                 key = key.lower().replace(":", "").strip().replace(" ", "_")
                 value = self.worksheet.cell(row, 2).value
                 missing = False if value else True
-                # location_map = dict(row=row, key_column=1, value_column=2, sheet=self.worksheet.title)
                 value = dict(value=value, missing=missing)#, location=location_map)
-                logger.debug(f"Yielding {value} for {key}")
                 yield key, value
 
 
@@ -123,7 +119,6 @@ class DefaultTABLEParser(DefaultParser):
 
     @property
     def parsed_info(self) -> Generator[dict, None, None]:
-        logger.debug(f"creating dataframe from {self.start_row} to {self.end_row}")
         df = DataFrame(
             [item for item in self.worksheet.values][self.start_row - 1:self.end_row - 1])
         df.columns = df.iloc[0]
@@ -131,12 +126,10 @@ class DefaultTABLEParser(DefaultParser):
         df = df.dropna(axis=1, how='all')
         for ii, row in enumerate(df.iterrows()):
             output = {}
-            # for key, value in row[1].to_dict().items():
+            for key, value in row[1].to_dict().items():
-            for key, value in row[1].details_dict().items():
                 if isinstance(key, str):
                     key = key.lower().replace(" ", "_")
                     key = re.sub(r"_(\(.*\)|#)", "", key)
-                # logger.debug(f"Row {ii} values: {key}: {value}")
                 output[key] = value
             yield output
 
@@ -144,5 +137,10 @@ class DefaultTABLEParser(DefaultParser):
         return [self._pyd_object(**output) for output in self.parsed_info]
 
 
+from .procedure_parsers import ProcedureInfoParser, ProcedureSampleParser, ProcedureReagentParser, ProcedureEquipmentParser
+from .results_parsers import (
+    DefaultResultsInfoParser, DefaultResultsSampleParser,
+    PCRSampleParser, PCRInfoParser
+)
 from .clientsubmission_parser import ClientSubmissionSampleParser, ClientSubmissionInfoParser
-from backend.excel.parsers.results_parsers.pcr_results_parser import PCRInfoParser, PCRSampleParser
+from .results_parsers.pcr_results_parser import PCRInfoParser, PCRSampleParser

src/submissions/backend/excel/parsers/clientsubmission_parser.py

@@ -1,11 +1,11 @@
 """
-
+Module for clientsubmission parsing
 """
 from __future__ import annotations
 import logging
 from pathlib import Path
 from string import ascii_lowercase
-from typing import Generator, TYPE_CHECKING, Literal
+from typing import Generator, TYPE_CHECKING
 from openpyxl.reader.excel import load_workbook
 from tools import row_keys
 from . import DefaultKEYVALUEParser, DefaultTABLEParser
@@ -122,20 +122,6 @@ class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
         else:
             self.submissiontype = submissiontype
         super().__init__(filepath=filepath, sheet="Client Info", start_row=1, **kwargs)
-        # NOTE: move to the manager class.
-        # allowed_procedure_types = [item.name for item in self.submissiontype.proceduretype]
-        # for name in allowed_procedure_types:
-        #     if name in self.workbook.sheetnames:
-        #         # TODO: check if run with name already exists
-        #         add_run = QuestionAsker(title="Add Run?", message="We've detected a sheet corresponding to an associated procedure type.\nWould you like to add a new run?")
-        #         if add_run.accepted:
-        #         # NOTE: recruit parser.
-        #             try:
-        #                 manager = getattr(procedure_managers, name)
-        #             except AttributeError:
-        #                 manager = procedure_managers.DefaultManager
-        #             self.manager = manager(proceduretype=name)
-        #         pass
 
     @property
     def parsed_info(self):
@@ -144,13 +130,11 @@ class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
             output['clientlab'] = output['client_lab']
         except KeyError:
             pass
-        # output['submissiontype'] = dict(value=self.submissiontype.name.title())
         try:
             output['submissiontype'] = output['submission_type']
             output['submissiontype']['value'] = self.submissiontype.name.title()
         except KeyError:
             pass
-        logger.debug(f"Data: {output}")
         return output
 
 
@@ -173,8 +157,6 @@ class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
     def parsed_info(self) -> Generator[dict, None, None]:
         output = super().parsed_info
         for ii, sample in enumerate(output, start=1):
-            # logger.debug(f"Parsed info sample: {sample}")
-
             if isinstance(sample["row"], str) and sample["row"].lower() in ascii_lowercase[0:8]:
                 try:
                     sample["row"] = row_keys[sample["row"]]
@@ -184,5 +166,4 @@ class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
             yield sample
 
     def to_pydantic(self):
-        logger.debug(f"Attempting to pydantify: {self._pyd_object}")
         return [self._pyd_object(**sample) for sample in self.parsed_info if sample['sample_id']]

src/submissions/backend/excel/parsers/procedure_parsers/__init__.py

@@ -8,6 +8,13 @@ if TYPE_CHECKING:
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
+"""
+TODO
+
+- range dicts should hopefully not be necessary in this type of parser. Hopefully all procedure parsers are the same.
+"""
+
+
 class ProcedureInfoParser(DefaultKEYVALUEParser):
 
     default_range_dict = [dict(

src/submissions/backend/excel/parsers/results_parsers/pcr_results_parser.py

@@ -1,5 +1,5 @@
 """
-
+Parser for pcr results from Design and Analysis Studio
 """
 from __future__ import annotations
 import logging
@@ -15,7 +15,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 class PCRInfoParser(DefaultResultsInfoParser):
 
-    def __init__(self, filepath: Path | str, sheet: str | None = None, start_row: int = 1, procedure=None, **kwargs):
+    def __init__(self, filepath: Path | str, procedure=None, **kwargs):
         self.results_type = "PCR"
         self.procedure = procedure
         super().__init__(filepath=filepath, proceduretype=self.procedure.proceduretype)

src/submissions/backend/excel/reports.py

@@ -7,10 +7,8 @@ from pandas import DataFrame, ExcelWriter
 from pathlib import Path
 from datetime import date
 from typing import Tuple, List
-
-# from backend import Procedure
 from backend.db.models import Procedure, Run
-from tools import jinja_template_loading, get_first_blank_df_row, row_map, flatten_list
+from tools import jinja_template_loading, get_first_blank_df_row, row_map, flatten_list, ctx
 from PyQt6.QtWidgets import QWidget
 from openpyxl.worksheet.worksheet import Worksheet
 
@@ -47,7 +45,6 @@ class ReportMaker(object):
         self.start_date = start_date
         self.end_date = end_date
         # NOTE: Set page size to zero to override limiting query size.
-        # self.runs = Run.query(start_date=start_date, end_date=end_date, page_size=0)
         self.procedures = Procedure.query(start_date=start_date, end_date=end_date, page_size=0)
         if organizations is not None:
             self.procedures = [procedure for procedure in self.procedures if procedure.run.clientsubmission.clientlab.name in organizations]
@@ -63,9 +60,7 @@ class ReportMaker(object):
         """
         if not self.procedures:
             return DataFrame(), DataFrame()
-        # df = DataFrame.from_records([item.to_dict(report=True) for item in self.runs])
         df = DataFrame.from_records([item.details_dict() for item in self.procedures])
-        logger.debug(df.columns)
         # NOTE: put procedure with the same lab together
         df = df.sort_values("clientlab")
         # NOTE: aggregate cost and sample count columns
@@ -178,10 +173,6 @@ class TurnaroundMaker(ReportArchetype):
         Returns:
 
         """
-        if 'pytest' not in sys.modules:
-            from tools import ctx
-        else:
-            from test_settings import ctx
         days = sub.turnaround_time
         try:
             tat = sub.get_default_info("turnaround_time")
@@ -203,14 +194,12 @@ class TurnaroundMaker(ReportArchetype):
 class ConcentrationMaker(ReportArchetype):
 
     def __init__(self, start_date: date, end_date: date, submission_type: str = "Bacterial Culture",
-                 # controls_only: bool = True):
                  include: List[str] = []):
         self.start_date = start_date
         self.end_date = end_date
         # NOTE: Set page size to zero to override limiting query size.
         self.subs = Run.query(start_date=start_date, end_date=end_date,
                                    submissiontype_name=submission_type, page_size=0)
-        # self.sample = flatten_list([sub.get_provisional_controls(controls_only=controls_only) for sub in self.run])
         try:
             self.samples = flatten_list([sub.get_provisional_controls(include=include) for sub in self.subs])
         except AttributeError:

src/submissions/backend/excel/writers/__init__.py

@@ -1,11 +1,12 @@
+"""
+Module for default excel writers
+"""
+from __future__ import annotations
 import logging, sys
 from datetime import datetime, date
 from pprint import pformat
-from types import NoneType
 from typing import Any, Literal
-
 from openpyxl.styles import Alignment, PatternFill
-from openpyxl.utils import get_column_letter
 from openpyxl.workbook.workbook import Workbook
 from openpyxl.worksheet.worksheet import Worksheet
 from pandas import DataFrame
@@ -39,15 +40,14 @@ class DefaultWriter(object):
             case x if issubclass(value.__class__, BaseClass):
                 value = value.name
             case x if issubclass(value.__class__, PydBaseClass):
+                logger.warning(f"PydBaseClass: {value}")
                 value = value.name
             case bytes() | list():
                 value = None
             case datetime() | date():
                 value = value.strftime("%Y-%m-%d")
-
             case _:
                 value = str(value)
-        # logger.debug(f"Returning value: {value}")
         return value
 
     @classmethod
@@ -60,7 +60,6 @@ class DefaultWriter(object):
 
     def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
                           start_row: int | None = None, *args, **kwargs):
-        logger.debug(f"Writing to workbook with {self.__class__.__name__}")
         if not start_row:
             try:
                 start_row = self.__class__.start_row
@@ -81,14 +80,19 @@ class DefaultWriter(object):
         self.worksheet = self.prewrite(self.worksheet, start_row=start_row)
         self.start_row = self.delineate_start_row(start_row=start_row)
         self.end_row = self.delineate_end_row(start_row=start_row)
-        logger.debug(f"{self.__class__.__name__} Start row: {self.start_row}, end row: {self.end_row}")
         return workbook
 
-    def delineate_start_row(self, start_row: int = 1):
+    def delineate_start_row(self, start_row: int = 1) -> int:
-        logger.debug(f"Attempting to find start row from {start_row}")
+        """
+        Gets the first black row.
+        Args:
+            start_row (int): row to start looking at.
+
+        Returns:
+            int
+        """
         for iii, row in enumerate(self.worksheet.iter_rows(min_row=start_row), start=start_row):
             if all([item.value is None for item in row]):
-                logger.debug(f"Returning {iii} for start row.")
                 return iii
         if self.worksheet.max_row == 1:
             return self.worksheet.max_row + 1
@@ -109,7 +113,7 @@ class DefaultWriter(object):
                 if len(str(cell.value)) > setlen:
                     setlen = len(str(cell.value))
             set_col_width = setlen + 5
-            # Setting the column width
+            # Note: Setting the column width
             worksheet.column_dimensions[column].width = set_col_width
         return worksheet
 
@@ -130,7 +134,6 @@ class DefaultKEYVALUEWriter(DefaultWriter):
 
     @classmethod
     def check_location(cls, locations: list, sheet: str):
-        logger.debug(f"Checking for location against {sheet}")
         return any([item['sheet'] == sheet for item in locations])
 
     def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
@@ -164,7 +167,8 @@ class DefaultTABLEWriter(DefaultWriter):
         return row_count
 
     def delineate_end_row(self, start_row: int = 1) -> int:
-        return start_row + len(self.pydant_obj) + 1
+        end_row = start_row + len(self.pydant_obj) + 1
+        return end_row
 
     def pad_samples_to_length(self, row_count,
                               mode: Literal["submission", "procedure"] = "submission"):  #, column_names):
@@ -193,7 +197,6 @@ class DefaultTABLEWriter(DefaultWriter):
                           start_row: int | None = None, *args, **kwargs) -> Workbook:
         workbook = super().write_to_workbook(workbook=workbook, sheet=sheet, start_row=start_row, *args, **kwargs)
         self.header_list = self.sort_header_row(list(set(flatten_list([item.fields for item in self.pydant_obj]))))
-        logger.debug(f"Header row: {self.header_list}")
         self.worksheet = self.write_header_row(worksheet=self.worksheet)
         for iii, object in enumerate(self.pydant_obj, start=1):
             write_row = self.start_row + iii
@@ -219,7 +222,6 @@ class DefaultTABLEWriter(DefaultWriter):
     @classmethod
     def sort_header_row(cls, header_list: list) -> list:
         output = []
-        logger.debug(cls.exclude)
         for item in cls.header_order:
             if item in [header for header in header_list if header not in cls.exclude]:
                 output.append(header_list.pop(header_list.index(item)))
@@ -237,4 +239,8 @@ class DefaultTABLEWriter(DefaultWriter):
         return worksheet
 
 
+from .procedure_writers import ProcedureInfoWriter, ProcedureSampleWriter, ProcedureReagentWriter, ProcedureEquipmentWriter
+from .results_writers import (
+    PCRInfoWriter, PCRSampleWriter
+)
 from .clientsubmission_writer import ClientSubmissionInfoWriter, ClientSubmissionSampleWriter

src/submissions/backend/excel/writers/clientsubmission_writer.py

@@ -1,3 +1,6 @@
+"""
+Module for ClientSubmission writing
+"""
 from __future__ import annotations
 import logging
 from pprint import pformat
@@ -17,10 +20,8 @@ class ClientSubmissionInfoWriter(DefaultKEYVALUEWriter):
 
     def __init__(self, pydant_obj, *args, **kwargs):
         super().__init__(pydant_obj=pydant_obj, *args, **kwargs)
-        logger.debug(f"{self.__class__.__name__} recruited!")
 
     def prewrite(self, worksheet: Worksheet, start_row: int) -> Worksheet:
-        # worksheet.merge_cells(start_row=start_row, start_column=1, end_row=start_row, end_column=4)
         worksheet.cell(row=start_row, column=1, value="Submitter Info")
         worksheet.cell(row=start_row, column=1).alignment = Alignment(horizontal="center")
         return worksheet

src/submissions/backend/excel/writers/procedure_writers/__init__.py

@@ -1,14 +1,11 @@
+"""
+Default writers for procedures.
+"""
 from __future__ import annotations
-import logging
+import logging, sys
-import sys
 from pprint import pformat
-
 from openpyxl.workbook import Workbook
-
 from backend.excel.writers import DefaultKEYVALUEWriter, DefaultTABLEWriter
-from typing import TYPE_CHECKING
-if TYPE_CHECKING:
-    from backend.db.models import ProcedureType
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -18,38 +15,31 @@ class ProcedureInfoWriter(DefaultKEYVALUEWriter):
     header_order = []
     exclude = ['control', 'equipment', 'excluded', 'id', 'misc_info', 'plate_map', 'possible_kits',
                'procedureequipmentassociation', 'procedurereagentassociation', 'proceduresampleassociation', 'proceduretipsassociation', 'reagent',
-               'reagentrole', 'results', 'sample', 'tips']
+               'reagentrole', 'results', 'sample', 'tips', 'reagentlot']
 
     def __init__(self, pydant_obj, *args, **kwargs):
-
         super().__init__(pydant_obj=pydant_obj, *args, **kwargs)
-
         self.fill_dictionary = {k: v for k, v in self.fill_dictionary.items() if k not in self.__class__.exclude}
-        # logger.debug(pformat(self.fill_dictionary))
-        # for rng in self.range_dict:
-        #     if "sheet" not in rng or rng['sheet'] == "":
-        #         rng['sheet'] = f"{pydant_obj.proceduretype.name} Quality"
 
     def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
                           start_row: int = 1, *args, **kwargs) -> Workbook:
-        workbook = super().write_to_workbook(workbook=workbook, sheet=f"{self.pydant_obj.proceduretype.name} Quality")
+        workbook = super().write_to_workbook(workbook=workbook, sheet=f"{self.pydant_obj.proceduretype.name[:20]} Quality")
         return workbook
 
 
 class ProcedureReagentWriter(DefaultTABLEWriter):
 
-    exclude = ["id", "comments", "missing"]
+    exclude = ["id", "comments", "missing", "active", "name"]
-    header_order = ["reagentrole", "name", "lot", "expiry"]
+    header_order = ["reagentrole", "reagent_name", "lot", "expiry"]
 
     def __init__(self, pydant_obj, *args, **kwargs):
         super().__init__(pydant_obj=pydant_obj, *args, **kwargs)
-        self.sheet = f"{self.pydant_obj.proceduretype.name} Quality"
+        self.sheet = f"{self.pydant_obj.proceduretype.name[:20]} Quality"
         self.pydant_obj = self.pydant_obj.reagent
 
     def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
                           start_row: int = 1, *args, **kwargs) -> Workbook:
-        logger.debug(self.pydant_obj)
+        workbook = super().write_to_workbook(workbook=workbook, sheet=self.sheet, start_row=start_row)
-        workbook = super().write_to_workbook(workbook=workbook, sheet=self.sheet)
         return workbook
 
 
@@ -60,13 +50,12 @@ class ProcedureEquipmentWriter(DefaultTABLEWriter):
 
     def __init__(self, pydant_obj, range_dict: dict | None = None, *args, **kwargs):
         super().__init__(pydant_obj=pydant_obj, range_dict=range_dict, *args, **kwargs)
-        self.sheet = f"{self.pydant_obj.proceduretype.name} Quality"
+        self.sheet = f"{self.pydant_obj.proceduretype.name[:20]} Quality"
         self.pydant_obj = self.pydant_obj.equipment
 
     def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
                           start_row: int = 1, *args, **kwargs) -> Workbook:
-        logger.debug(self.pydant_obj)
+        workbook = super().write_to_workbook(workbook=workbook, sheet=self.sheet, start_row=start_row)
-        workbook = super().write_to_workbook(workbook=workbook, sheet=self.sheet)
         return workbook
 
 
@@ -77,12 +66,10 @@ class ProcedureSampleWriter(DefaultTABLEWriter):
 
     def __init__(self, pydant_obj, range_dict: dict | None = None, *args, **kwargs):
         super().__init__(pydant_obj=pydant_obj, range_dict=range_dict, *args, **kwargs)
-        self.sheet = f"{self.pydant_obj.proceduretype.name} Quality"
+        self.sheet = f"{self.pydant_obj.proceduretype.name[:20]} Quality"
-        # self.pydant_obj = self.pydant_obj.sample
         self.pydant_obj = self.pad_samples_to_length(row_count=pydant_obj.max_sample_rank, mode="procedure")
 
     def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
                           start_row: int = 1, *args, **kwargs) -> Workbook:
-        logger.debug(self.pydant_obj)
+        workbook = super().write_to_workbook(workbook=workbook, sheet=self.sheet, start_row=start_row)
-        workbook = super().write_to_workbook(workbook=workbook, sheet=self.sheet)
         return workbook

src/submissions/backend/excel/writers/results_writers/pcr_results_writer.py

@@ -1,12 +1,12 @@
+"""
+Writers for PCR results from Design and Analysis Software
+"""
 from __future__ import annotations
 import logging
-from pathlib import Path
 from pprint import pformat
 from typing import Generator, TYPE_CHECKING
-
 from openpyxl import Workbook
 from openpyxl.styles import Alignment
-
 from backend.excel.writers import DefaultKEYVALUEWriter, DefaultTABLEWriter
 from tools import flatten_list
 if TYPE_CHECKING:
@@ -21,26 +21,10 @@ class PCRInfoWriter(DefaultKEYVALUEWriter):
     def __init__(self, pydant_obj, proceduretype: "ProcedureType" | None = None, *args, **kwargs):
         super().__init__(pydant_obj=pydant_obj, proceduretype=proceduretype, *args, **kwargs)
         self.fill_dictionary = self.pydant_obj.improved_dict()['result']
-        logger.debug(pformat(self.fill_dictionary))
 
     def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
                           start_row: int | None = None, *args, **kwargs) -> Workbook:
         workbook = super().write_to_workbook(workbook=workbook, sheet=f"{self.proceduretype.name} Results")
-    #     if not start_row:
-    #         try:
-    #             start_row = self.__class__.start_row
-    #         except AttributeError as e:
-    #             logger.error(f"Couldn't get start row due to {e}")
-    #             start_row = 1
-    #     # worksheet = workbook[f"{self.proceduretype.name} Results"]
-    #     self.worksheet = workbook.create_sheet(f"{self.proceduretype.name} Results")
-    #     self.worksheet = self.prewrite(self.worksheet, start_row=start_row)
-    #     # self.start_row = self.delineate_start_row(start_row=start_row)
-    #     # self.end_row = self.delineate_end_row(start_row=start_row)
-    #     # for key, value in self.fill_dictionary['result'].items():
-    #     #     # logger.debug(f"Filling in {key} with {value}")
-    #     #     self.worksheet.cell(value['location']['row'], value['location']['key_column'], value=key.replace("_", " ").title())
-    #     #     self.worksheet.cell(value['location']['row'], value['location']['value_column'], value=value['value'])
         return workbook
 
 
@@ -56,7 +40,6 @@ class PCRSampleWriter(DefaultTABLEWriter):
             columns.append((iii, header))
         columns = sorted(columns, key=lambda x: x[0])
         columns = proto_columns + columns
-        # logger.debug(columns)
         all_results = flatten_list([[item for item in self.rearrange_results(result)] for result in self.pydant_obj])
         if len(all_results) > 0 :
             worksheet.cell(row=header_row, column=1, value="Sample")
@@ -83,21 +66,10 @@ class PCRSampleWriter(DefaultTABLEWriter):
     def column_headers(self):
         output = []
         for item in self.pydant_obj:
-            # logger.debug(item)
             dicto: dict = item.result
             for value in dicto.values():
                 if not isinstance(value, dict):
-                    # logger.debug(f"Will not include {value} in column headers.")
                     continue
                 for key in value.keys():
                     output.append(key)
         return sorted(list(set(output)))
-
-
-
-
-
-
-
-
-

src/submissions/backend/managers/__init__.py

@@ -1,8 +1,8 @@
+"""
+Module for manager defaults.
+"""
 import logging
 from pathlib import Path
-from typing import Literal
-
-from backend.db.models import ProcedureType
 from frontend.widgets.functions import select_open_file
 from tools import get_application_from_parent
 from backend.validators.pydant import PydBaseClass
@@ -13,7 +13,6 @@ logger = logging.getLogger(f"submissions.{__name__}")
 class DefaultManager(object):
 
     def __init__(self, parent, input_object: Path | str | None = None):
-        logger.debug(f"FName before correction: {type(input_object)}")
         self.parent = parent
         match input_object:
             case str():
@@ -23,19 +22,15 @@ class DefaultManager(object):
                 self.input_object = input_object
                 self.pyd = self.to_pydantic()
             case x if issubclass(input_object.__class__, PydBaseClass):
-                # logger.debug("Subclass of PydBaseClass")
                 self.pyd = input_object
             case x if issubclass(input_object.__class__, BaseClass):
-                # logger.debug("Subclass of BaseClass")
                 self.pyd = input_object.to_pydantic()
             case _:
                 self.input_object = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
                 self.pyd = self.to_pydantic()
-        # logger.debug(f"FName after correction: {input_object}")
-
 
 
 from .clientsubmissions import DefaultClientSubmissionManager
 from .procedures import DefaultProcedureManager
 from .results import DefaultResultsManager
-from .runs import DefaultRunManager
+from .runs import DefaultRunManager

src/submissions/backend/managers/clientsubmissions.py

@@ -1,9 +1,10 @@
+"""
+Module for manager of ClientSubmission object
+"""
 from __future__ import annotations
-import logging
+import logging, sys
-import sys
 from typing import TYPE_CHECKING
 from pathlib import Path
-from openpyxl.reader.excel import load_workbook
 from openpyxl.workbook import Workbook
 from backend.validators import RSLNamer
 from backend.managers import DefaultManager
@@ -42,24 +43,16 @@ class DefaultClientSubmissionManager(DefaultManager):
         self.sample_parser = ClientSubmissionSampleParser(filepath=self.input_object,
                                                           submissiontype=self.submissiontype,
                                                           start_row=self.info_parser.end_row)
-        logger.debug(self.sample_parser.__dict__)
         self.clientsubmission = self.info_parser.to_pydantic()
         self.clientsubmission.full_batch_size = self.sample_parser.end_row - self.sample_parser.start_row
         self.clientsubmission.sample = self.sample_parser.to_pydantic()
 
         return self.clientsubmission
 
-    # def to_pydantic(self):
-    #     self.clientsubmission = self.info_parser.to_pydantic()
-    #     self.clientsubmission.sample = self.sample_parser.to_pydantic()
-
     def write(self, workbook: Workbook) -> Workbook:
-        # workbook: Workbook = load_workbook(BytesIO(self.submissiontype.template_file))
-
         self.info_writer = ClientSubmissionInfoWriter(pydant_obj=self.pyd)
         assert isinstance(self.info_writer, ClientSubmissionInfoWriter)
-        logger.debug("Attempting write.")
         workbook = self.info_writer.write_to_workbook(workbook)
         self.sample_writer = ClientSubmissionSampleWriter(pydant_obj=self.pyd)
         workbook = self.sample_writer.write_to_workbook(workbook, start_row=self.info_writer.worksheet.max_row + 1)
-        return workbook
+        return workbook

src/submissions/backend/managers/procedures.py

@@ -1,12 +1,10 @@
+"""
+Module for manager of Procedure object.
+"""
 from __future__ import annotations
-import logging
+import logging, sys
-from io import BytesIO
-from pprint import pformat
-
-from openpyxl.reader.excel import load_workbook
 from openpyxl.workbook import Workbook
-
+from backend.managers import DefaultManager
-from backend.managers import DefaultManager, results
 from typing import TYPE_CHECKING
 from pathlib import Path
 from backend.excel.parsers import procedure_parsers
@@ -57,7 +55,6 @@ class DefaultProcedureManager(DefaultManager):
         self.equipment = self.equipment_parser.to_pydantic()
 
     def write(self, workbook: Workbook) -> Workbook:
-        # workbook = load_workbook(BytesIO(self.proceduretype.template_file))
         try:
             info_writer = getattr(procedure_writers, f"{self.proceduretype.name.replace(' ', '')}InfoWriter")
         except AttributeError:
@@ -69,29 +66,22 @@ class DefaultProcedureManager(DefaultManager):
         except AttributeError:
             reagent_writer = procedure_writers.ProcedureReagentWriter
         self.reagent_writer = reagent_writer(pydant_obj=self.pyd)
-        workbook = self.reagent_writer.write_to_workbook(workbook)
+        workbook = self.reagent_writer.write_to_workbook(workbook, start_row=self.info_writer.end_row)
         try:
             equipment_writer = getattr(procedure_writers, f"{self.proceduretype.name.replace(' ', '')}EquipmentWriter")
         except AttributeError:
             equipment_writer = procedure_writers.ProcedureEquipmentWriter
         self.equipment_writer = equipment_writer(pydant_obj=self.pyd)
-        workbook = self.equipment_writer.write_to_workbook(workbook)
+        workbook = self.equipment_writer.write_to_workbook(workbook, start_row=self.reagent_writer.end_row)
         try:
             sample_writer = getattr(procedure_writers, f"{self.proceduretype.name.replace(' ', '')}SampleWriter")
         except AttributeError:
             sample_writer = procedure_writers.ProcedureSampleWriter
         self.sample_writer = sample_writer(pydant_obj=self.pyd)
-        workbook = self.sample_writer.write_to_workbook(workbook)
+        workbook = self.sample_writer.write_to_workbook(workbook, start_row=self.equipment_writer.end_row)
-        # # logger.debug(self.pyd.result)
         # # TODO: Find way to group results by result_type.
         for result in self.pyd.result:
-            logger.debug(f"Writing {result.result_type}")
             Writer = getattr(results_writers, f"{result.result_type}InfoWriter")
             res_info_writer = Writer(pydant_obj=result, proceduretype=self.proceduretype)
             workbook = res_info_writer.write_to_workbook(workbook=workbook)
-        # # sample_results = [sample.result for sample in self.pyd.sample]
-        # # logger.debug(pformat(self.pyd.sample_results))
-        # Writer = getattr(results_writers, "PCRSampleWriter")
-        # res_sample_writer = Writer(pydant_obj=self.pyd.sample_results, proceduretype=self.proceduretype)
-        # workbook = res_sample_writer.write_to_workbook(workbook=workbook)
         return workbook

src/submissions/backend/managers/results/__init__.py

@@ -1,4 +1,6 @@
-
+"""
+Module for default results manager
+"""
 from __future__ import annotations
 import logging
 from .. import DefaultManager
@@ -7,7 +9,6 @@ from pathlib import Path
 from frontend.widgets.functions import select_open_file
 from tools import get_application_from_parent
 from typing import TYPE_CHECKING, List
-
 if TYPE_CHECKING:
     from backend.validators.pydant import PydResults
 
@@ -17,13 +18,11 @@ logger = logging.getLogger(f"submission.{__name__}")
 class DefaultResultsManager(DefaultManager):
 
     def __init__(self, procedure: Procedure, parent, fname: Path | str | None = None):
-        logger.debug(f"FName before correction: {fname}")
         self.procedure = procedure
         if not fname:
             self.fname = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
         elif isinstance(fname, str):
             self.fname = Path(fname)
-        logger.debug(f"FName after correction: {fname}")
 
     def procedure_to_pydantic(self) -> PydResults:
         info = self.info_parser.to_pydantic()

src/submissions/backend/managers/results/pcr_results_manager.py

@@ -1,14 +1,12 @@
 """
-
+Module for pcr results from Design and Analysis Studio
 """
 from __future__ import annotations
 import logging
 from io import BytesIO
 from pathlib import Path
-from typing import Tuple, List, TYPE_CHECKING
+from typing import TYPE_CHECKING
-
 from openpyxl.reader.excel import load_workbook
-
 from backend.db.models import Procedure
 from backend.excel.parsers.results_parsers.pcr_results_parser import PCRSampleParser, PCRInfoParser
 from backend.excel.writers.results_writers.pcr_results_writer import PCRInfoWriter, PCRSampleWriter
@@ -33,9 +31,3 @@ class PCRManager(DefaultResultsManager):
         self.info_writer = PCRInfoWriter(pydant_obj=self.procedure.to_pydantic(), proceduretype=self.procedure.proceduretype)
         workbook = self.info_writer.write_to_workbook(workbook)
         self.sample_writer = PCRSampleWriter(pydant_obj=self.procedure.to_pydantic(), proceduretype=self.procedure.proceduretype)
-
-
-
-
-
-

src/submissions/backend/managers/runs.py

@@ -1,13 +1,10 @@
+"""
+Module for managing Runs object
+"""
 from __future__ import annotations
-import logging
+import logging, sys
-from pathlib import Path
 from pprint import pformat
-
-from openpyxl import load_workbook
 from openpyxl.workbook.workbook import Workbook
-from tools import copy_xl_sheet
-
-
 from backend.managers import DefaultManager
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -16,16 +13,11 @@ class DefaultRunManager(DefaultManager):
 
     def write(self) -> Workbook:
         from backend.managers import DefaultClientSubmissionManager, DefaultProcedureManager
-        logger.debug(f"Initializing write")
+        logger.info(f"Initializing write")
         clientsubmission = DefaultClientSubmissionManager(parent=self.parent, input_object=self.pyd.clientsubmission, submissiontype=self.pyd.clientsubmission.submissiontype)
         workbook = Workbook()
         workbook = clientsubmission.write(workbook=workbook)
         for procedure in self.pyd.procedure:
-        #     # logger.debug(f"Running procedure: {pformat(procedure.__dict__)}")
             procedure = DefaultProcedureManager(proceduretype=procedure.proceduretype, parent=self.parent, input_object=procedure)
             workbook: Workbook = procedure.write(workbook=workbook)
-        #     for sheetname in wb.sheetnames:
-        #         source_sheet = wb[sheetname]
-        #         ws = workbook.create_sheet(sheetname)
-        #         copy_xl_sheet(source_sheet, ws)
         return workbook

src/submissions/backend/validators/__init__.py

@@ -48,8 +48,6 @@ class ClientSubmissionNamer(DefaultNamer):
         if not sub_type:
             logger.warning(f"Getting submissiontype from regex failed, using default submissiontype.")
             sub_type = SubmissionType.query(name="Default")
-        logger.debug(f"Submission Type: {sub_type}")
-        sys.exit()
         return sub_type
 
     def get_subtype_from_regex(self) -> SubmissionType:
@@ -84,9 +82,6 @@ class ClientSubmissionNamer(DefaultNamer):
         return sub_type
 
 
-
-
-
 class RSLNamer(object):
     """
     Object that will enforce proper formatting on RSL plate names.
@@ -98,17 +93,10 @@ class RSLNamer(object):
         self.submission_type = submission_type
         if not self.submission_type:
             self.submission_type = self.retrieve_submission_type(filename=filename)
-        # logger.info(f"got submission type: {self.submission_type}")
         if self.submission_type:
-            # self.sub_object = BasicRun.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
             self.sub_object = SubmissionType.query(name=self.submission_type['name'], limit=1)
             self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(
                 submission_type=self.submission_type))
-            # if not data:
-            #     data = dict(submission_type=self.submission_type)
-            # if "proceduretype" not in data.keys():
-            #     data['proceduretype'] = self.submission_type
-            # self.parsed_name = self.sub_object.enforce_name(instr=self.parsed_name, data=data)
             logger.info(f"Parsed name: {self.parsed_name}")
 
     @classmethod
@@ -227,7 +215,6 @@ class RSLNamer(object):
         Returns:
             str: Output filename
         """
-        logger.debug(data)
         if "submitted_date" in data.keys():
             if isinstance(data['submitted_date'], dict):
                 if data['submitted_date']['value'] is not None:
@@ -244,13 +231,8 @@ class RSLNamer(object):
                 today = datetime.now()
         if isinstance(today, str):
             today = datetime.strptime(today, "%Y-%m-%d")
-        # if "name" in data.keys():
-        #     logger.debug(f"Found name: {data['name']}")
-        #     plate_number = data['name'].split("-")[-1][0]
-        # else:
         previous = Run.query(start_date=today, end_date=today, submissiontype=data['submissiontype'])
         plate_number = len(previous) + 1
-        logger.debug(f"Using plate number: {plate_number}")
         return f"RSL-{data['abbreviation']}-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}-{plate_number}"
 
     @classmethod
@@ -283,5 +265,7 @@ class RSLNamer(object):
             return ""
 
 
-from .pydant import PydRun, PydKitType, PydContact, PydOrganization, PydSample, PydReagent, PydReagentRole, \
+from .pydant import (
-    PydEquipment, PydEquipmentRole, PydTips, PydProcess, PydElastic, PydClientSubmission, PydProcedure, PydResults
+    PydRun, PydContact, PydClientLab, PydSample, PydReagent, PydReagentRole, PydEquipment, PydEquipmentRole, PydTips,
+    PydProcess, PydElastic, PydClientSubmission, PydProcedure, PydResults, PydReagentLot
+)

src/submissions/frontend/__init__.py

@@ -1,5 +1,32 @@
-'''
+"""
 Constructs main application.
-'''
+"""
-from .widgets import *
+from .widgets import (
-from .visualizations import *
+    pandasModel,
+    App,
+    Concentrations,
+    ControlsViewer,
+    DateTypePicker,
+    EquipmentUsage, RoleComboBox,
+    select_open_file, select_save_file, save_pdf,
+    GelBox, ControlsForm,
+    InfoPane,
+    StartEndDatePicker, CheckableComboBox, Pagifier,
+    AddEdit, EditProperty,
+    SearchBox, SearchResults, FieldSearch,
+    QuestionAsker, AlertPop, HTMLPop, ObjectSelector,
+    ProcedureCreation,
+    SampleChecker,
+    SubmissionDetails, SubmissionComment,
+    SubmissionsTree, ClientSubmissionRunModel,
+    MyQComboBox, MyQDateEdit, SubmissionFormContainer, SubmissionFormWidget, ClientSubmissionFormWidget,
+    Summary,
+    TurnaroundMaker
+)
+from .visualizations import (
+    CustomFigure,
+    IridaFigure,
+    PCRFigure,
+    ConcentrationsChart,
+    TurnaroundChart
+)

src/submissions/frontend/visualizations/__init__.py

@@ -1,10 +1,9 @@
-'''
+"""
 Contains all operations for creating charts, graphs and visual effects.
-'''
+"""
 from datetime import timedelta, date
 from pathlib import Path
 from typing import Generator
-
 import plotly
 from PyQt6.QtWidgets import QWidget
 import pandas as pd, logging
@@ -128,13 +127,10 @@ class CustomFigure(Figure):
         html = f'<html><body>'
         if self is not None:
             # NOTE: Just cannot get this load from string to freaking work.
-            # html += self.to_html(include_plotlyjs='cdn', full_html=False)
             html += plotly.offline.plot(self, output_type='div', include_plotlyjs="cdn")
         else:
             html += "<h1>No data was retrieved for the given parameters.</h1>"
         html += '</body></html>'
-        # with open("test.html", "w", encoding="utf-8") as f:
-        #     f.write(html)
         return html
 
 

src/submissions/frontend/visualizations/concentrations_chart.py

@@ -3,10 +3,9 @@ Construct BC control concentration charts
 """
 from pprint import pformat
 from . import CustomFigure
-import plotly.express as px
+import logging, sys, plotly.express as px
 import pandas as pd
 from PyQt6.QtWidgets import QWidget
-import logging
 from operator import itemgetter
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -31,13 +30,12 @@ class ConcentrationsChart(CustomFigure):
             self.df = self.df.sort_values(['submitted_date', 'procedure'], ascending=[True, True]).reset_index(
                 drop=True)
             self.df = self.df.reset_index().rename(columns={"index": "idx"})
-            # logger.debug(f"DF after changes:\n{self.df}")
             scatter = px.scatter(data_frame=self.df, x='procedure', y="concentration",
                                  hover_data=["name", "procedure", "submitted_date", "concentration"],
                                  color="positive", color_discrete_map={"positive": "red", "negative": "green", "sample":"orange"}
                                  )
         except (ValueError, AttributeError) as e:
-            logger.error(f"Error constructing chart: {e}")
+            # logger.error(f"Error constructing chart: {e}")
             scatter = px.scatter()
         # NOTE: For some reason if data is allowed to sort itself it leads to wrong ordering of x axis.
         traces = sorted(scatter.data, key=itemgetter("name"))

src/submissions/frontend/visualizations/irida_charts.py

@@ -3,11 +3,9 @@ Functions for constructing irida control graphs using plotly.
 """
 from datetime import date
 from pprint import pformat
-import plotly.express as px
+import logging, plotly.express as px, pandas as pd
-import pandas as pd
 from PyQt6.QtWidgets import QWidget
 from . import CustomFigure
-import logging
 from tools import get_unique_values_in_df_column
 
 logger = logging.getLogger(f"submissions.{__name__}")

src/submissions/frontend/widgets/__init__.py

@@ -1,20 +1,71 @@
 """
 Contains all custom generated PyQT6 derivative widgets.
 """
+from PyQt6.QtCore import QAbstractTableModel, Qt
+
+
+class pandasModel(QAbstractTableModel):
+    """
+    pandas model for inserting summary sheet into gui
+    NOTE: Copied from Stack Overflow. I have no idea how it actually works.
+    """
+
+    def __init__(self, data) -> None:
+        QAbstractTableModel.__init__(self)
+        self._data = data
+
+    def rowCount(self, parent=None) -> int:
+        """
+        does what it says
+
+        Args:
+            parent (_type_, optional): _description_. Defaults to None.
+
+        Returns:
+            int: number of rows in data
+        """
+        return self._data.shape[0]
+
+    def columnCount(self, parent=None) -> int:
+        """
+        does what it says
+
+        Args:
+            parent (_type_, optional): _description_. Defaults to None.
+
+        Returns:
+            int: number of columns in data
+        """
+        return self._data.shape[1]
+
+    def data(self, index, role=Qt.ItemDataRole.DisplayRole) -> str | None:
+        if index.isValid():
+            if role == Qt.ItemDataRole.DisplayRole:
+                return str(self._data.iloc[index.row(), index.column()])
+        return None
+
+    def headerData(self, col, orientation, role):
+        if orientation == Qt.Orientation.Horizontal and role == Qt.ItemDataRole.DisplayRole:
+            return self._data.columns[col]
+        return None
+
 
 from .app import App
-from .controls_chart import *
+from .concentrations import Concentrations
-from .equipment_usage import *
+from .controls_chart import ControlsViewer
-from .functions import *
+from .date_type_picker import DateTypePicker
-from .gel_checker import *
+from .equipment_usage import EquipmentUsage, RoleComboBox
-from .info_tab import *
+from .functions import select_open_file, select_save_file, save_pdf
-from .misc import *
+from .gel_checker import GelBox, ControlsForm
-from .omni_search import *
+from .info_tab import InfoPane
-from .pop_ups import *
+from .misc import StartEndDatePicker, CheckableComboBox, Pagifier
-from .submission_details import *
+from .omni_add_edit import AddEdit, EditProperty
-from .submission_table import *
+from .omni_search import SearchBox, SearchResults, FieldSearch
-from .submission_widget import *
+from .pop_ups import QuestionAsker, AlertPop, HTMLPop, ObjectSelector
-from .summary import *
+from .procedure_creation import ProcedureCreation
-from .turnaround import *
+from .sample_checker import SampleChecker
-from .omni_add_edit import *
+from .submission_details import SubmissionDetails, SubmissionComment
-from .omni_manager_pydant import *
+from .submission_table import SubmissionsTree, ClientSubmissionRunModel
+from .submission_widget import MyQComboBox, MyQDateEdit, SubmissionFormContainer, SubmissionFormWidget, ClientSubmissionFormWidget
+from .summary import Summary
+from .turnaround import TurnaroundMaker

src/submissions/frontend/widgets/app.py

@@ -13,7 +13,7 @@ from PyQt6.QtGui import QAction
 from pathlib import Path
 from markdown import markdown
 from pandas import ExcelWriter
-from backend.db.models import Reagent
+# from backend.db.models import ReagentLot
 from tools import (
     check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user,
     under_development
@@ -22,9 +22,8 @@ from .date_type_picker import DateTypePicker
 from .functions import select_save_file
 from .pop_ups import HTMLPop
 from .misc import Pagifier
-from .submission_table import SubmissionsSheet, SubmissionsTree, ClientSubmissionRunModel
+from .submission_table import SubmissionsTree, ClientSubmissionRunModel
 from .submission_widget import SubmissionFormContainer
-from .controls_chart import ControlsViewer
 from .summary import Summary
 from .turnaround import TurnaroundTime
 from .concentrations import Concentrations
@@ -132,7 +131,7 @@ class App(QMainWindow):
         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)
-        self.manageKitsAction.triggered.connect(self.manage_kits)
+        # self.manageKitsAction.triggered.connect(self.manage_kits)
 
     def showAbout(self):
         """
@@ -181,7 +180,8 @@ class App(QMainWindow):
 
     @check_authorization
     def edit_reagent(self, *args, **kwargs):
-        dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="reagentrole")])
+        from backend.db.models import ReagentLot
+        dlg = SearchBox(parent=self, object_type=ReagentLot, extras=ReagentLot.get_searchables())
         dlg.exec()
 
     def update_data(self):
@@ -195,24 +195,23 @@ class App(QMainWindow):
             new_org = dlg.parse_form()
             new_org.save()
 
-    def manage_kits(self, *args, **kwargs):
+    # def manage_kits(self, *args, **kwargs):
-        from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
+    #     from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
-        dlg = ManagerWindowPyd(parent=self, object_type=KitType, extras=[], add_edit='edit', managers=set())
+    #     dlg = ManagerWindowPyd(parent=self, object_type=KitType, extras=[], add_edit='edit', managers=set())
-        if dlg.exec():
+    #     if dlg.exec():
-            # logger.debug("\n\nBeginning parsing\n\n")
+    #         output = dlg.parse_form()
-            output = dlg.parse_form()
+    #         sql = output.to_sql()
-            # logger.debug(f"Kit output: {pformat(output.__dict__)}")
+    #         assert isinstance(sql, KitType)
-            # logger.debug("\n\nBeginning transformation\n\n")
+    #         sql.save()
-            sql = output.to_sql()
-            assert isinstance(sql, KitType)
-            sql.save()
 
     @under_development
     def submissions_to_excel(self, *args, **kwargs):
+        from backend.db.models import Run
         dlg = DateTypePicker(self)
         if dlg.exec():
             output = dlg.parse_form()
-            df = BasicRun.archive_submissions(**output)
+            # TODO: Move to ClientSubmissions
+            df = Run.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)
@@ -254,7 +253,6 @@ class AddSubForm(QWidget):
         self.sheetwidget = QWidget(self)
         self.sheetlayout = QVBoxLayout(self)
         self.sheetwidget.setLayout(self.sheetlayout)
-        # self.sub_wid = SubmissionsSheet(parent=parent)
         self.sub_wid = SubmissionsTree(parent=parent, model=ClientSubmissionRunModel(self))
         self.pager = Pagifier(page_max=self.sub_wid.total_count / page_size)
         self.sheetlayout.addWidget(self.sub_wid)
@@ -265,12 +263,10 @@ class AddSubForm(QWidget):
         self.tab1.layout.addWidget(self.interior)
         self.tab1.layout.addWidget(self.sheetwidget)
         self.tab2.layout = QVBoxLayout(self)
-        # self.irida_viewer = ControlsViewer(self, archetype="Irida Control")
         self.irida_viewer = None
         self.tab2.layout.addWidget(self.irida_viewer)
         self.tab2.setLayout(self.tab2.layout)
         self.tab3.layout = QVBoxLayout(self)
-        # self.pcr_viewer = ControlsViewer(self, archetype="PCR Control")
         self.pcr_viewer = None
         self.tab3.layout.addWidget(self.pcr_viewer)
         self.tab3.setLayout(self.tab3.layout)

src/submissions/frontend/widgets/concentrations.py

@@ -43,10 +43,8 @@ class Concentrations(InfoPane):
             None
         """
         include = self.pos_neg.get_checked()
-        # logger.debug(f"Include: {include}")
         super().update_data()
         months = self.diff_month(self.start_date, self.end_date)
-        # logger.debug(f"Box checked: {self.all_box.isChecked()}")
         chart_settings = dict(start_date=self.start_date, end_date=self.end_date,
                               include=include)
         self.report_obj = ConcentrationMaker(**chart_settings)

src/submissions/frontend/widgets/controls_chart.py

@@ -108,7 +108,6 @@ class ControlsViewer(InfoPane):
             parent=self,
             months=months
         )
-        # logger.debug(f"Chart settings: {chart_settings}")
         self.fig = self.archetype.instance_class.make_chart(chart_settings=chart_settings, parent=self, ctx=self.app.ctx)
         self.report_obj = ChartReportMaker(df=self.fig.df, sheet_name=self.archetype.name)
         if issubclass(self.fig.__class__, CustomFigure):

src/submissions/frontend/widgets/date_type_picker.py

@@ -1,13 +1,19 @@
+"""
+
+"""
 from PyQt6.QtWidgets import (
     QVBoxLayout, QDialog, QDialogButtonBox
 )
 from .misc import CheckableComboBox, StartEndDatePicker
-from backend.db.models.procedures import SubmissionType
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
 
 
 class DateTypePicker(QDialog):
     
     def __init__(self, parent):
+        from backend.db.models.procedures import SubmissionType
         super().__init__(parent)
         self.layout = QVBoxLayout()
         self.setFixedWidth(500)
@@ -27,10 +33,7 @@ class DateTypePicker(QDialog):
         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)]
         sub_types = self.typepicker.get_checked()
         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/equipment_usage.py

@@ -1,91 +1,97 @@
-'''
+"""
 Creates forms that the user can enter equipment info into.
-'''
+"""
+import sys, logging
 from pprint import pformat
-from PyQt6.QtCore import Qt, QSignalBlocker
-from PyQt6.QtWidgets import (
-    QDialog, QComboBox, QCheckBox, QLabel, QWidget, QVBoxLayout, QDialogButtonBox, QGridLayout
-)
-from backend.db.models import Equipment, Run, Process, Procedure
-from backend.validators.pydant import PydEquipment, PydEquipmentRole, PydTips
-import logging
 from typing import Generator
+from PyQt6.QtCore import Qt, pyqtSlot, QSignalBlocker
+from PyQt6.QtWebChannel import QWebChannel
+from PyQt6.QtWebEngineWidgets import QWebEngineView
+from PyQt6.QtWidgets import (
+    QDialog, QVBoxLayout, QDialogButtonBox, QGridLayout, QWidget, QCheckBox, QComboBox, QLabel
+)
+from backend import Process
+from backend.db.models import Equipment
+from backend.validators.pydant import PydProcedure, PydEquipmentRole, PydTips, PydEquipment
+from tools import get_application_from_parent, render_details_template
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
 class EquipmentUsage(QDialog):
 
-    def __init__(self, parent, procedure: Procedure):
+    def __init__(self, parent, procedure: PydProcedure):
         super().__init__(parent)
         self.procedure = procedure
         self.setWindowTitle(f"Equipment Checklist - {procedure.name}")
         self.used_equipment = self.procedure.equipment
-        # self.kit = self.procedure.kittype
+        self.kit = self.procedure.kittype
         self.opt_equipment = procedure.proceduretype.get_equipment()
         self.layout = QVBoxLayout()
+        self.app = get_application_from_parent(parent)
+        self.webview = QWebEngineView(parent=self)
+        self.webview.setContextMenuPolicy(Qt.ContextMenuPolicy.NoContextMenu)
+        self.webview.setMinimumSize(1200, 800)
+        self.webview.setMaximumWidth(1200)
+        # NOTE: Decide if exporting should be allowed.
+        self.layout = QGridLayout()
+        # NOTE: button to export a pdf version
+        self.layout.addWidget(self.webview, 1, 0, 10, 10)
         self.setLayout(self.layout)
-        self.populate_form()
+        self.setFixedWidth(self.webview.width() + 20)
-
+        # NOTE: setup channel
-    def populate_form(self):
+        self.channel = QWebChannel()
-        """
+        self.channel.registerObject('backend', self)
-        Create form widgets
+        html = self.construct_html(procedure=procedure)
-        """
+        self.webview.setHtml(html)
+        self.webview.page().setWebChannel(self.channel)
         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
-        label = self.LabelRow(parent=self)
+        self.layout.addWidget(self.buttonBox, 11, 1, 1, 1)
-        self.layout.addWidget(label)
-        for equipment in self.opt_equipment:
-            widg = equipment.to_form(parent=self, used=self.used_equipment)
-            self.layout.addWidget(widg)
-            widg.update_processes()
-        self.layout.addWidget(self.buttonBox)
 
-    def parse_form(self) -> Generator[PydEquipment, None, None]:
+    @classmethod
-        """
+    def construct_html(cls, procedure: PydProcedure, child: bool = False):
-        Pull info from all RoleComboBox widgets
+        proceduretype = procedure.proceduretype
+        proceduretype_dict = proceduretype.details_dict()
+        run = procedure.run
+        html = render_details_template(
+            template_name="support/equipment_usage",
+            css_in=[],
+            js_in=[],
+            proceduretype=proceduretype_dict,
+            run=run.details_dict(),
+            procedure=procedure.__dict__,
+            child=child
+        )
+        return html
 
-        Returns:
+    @pyqtSlot(str, str, str, str)
-            Generator[PydEquipment, None, None]: All equipment pulled from widgets
+    def update_equipment(self, equipmentrole: str, equipment: str, process: str, tips: str):
-        """
+        try:
-        for widget in self.findChildren(QWidget):
+            equipment_of_interest = next(
-            match widget:
+                (item for item in self.procedure.equipment if item.equipmentrole == equipmentrole))
-                case RoleComboBox():
+        except StopIteration:
-                    if widget.check.isChecked():
+            equipment_of_interest = None
-                        item = widget.parse_form()
+        equipment = Equipment.query(name=equipment)
-                        if item:
+        if equipment_of_interest:
-                            yield item
+            eoi = self.procedure.equipment.pop(self.procedure.equipment.index(equipment_of_interest))
-                        else:
+        else:
-                            continue
+            eoi = equipment.to_pydantic(proceduretype=self.procedure.proceduretype)
-                    else:
+        eoi.name = equipment.name
-                        continue
+        eoi.asset_number = equipment.asset_number
-                case _:
+        eoi.nickname = equipment.nickname
-                    continue
+        process = next((prcss for prcss in equipment.process if prcss.name == process))
+        eoi.process = process.to_pydantic()
+        tips = next((tps for tps in equipment.tips if tps.name == tips))
+        eoi.tips = tips.to_pydantic()
+        self.procedure.equipment.append(eoi)
+        logger.debug(f"Updated equipment: {self.procedure.equipment}")
 
-    class LabelRow(QWidget):
+    def save_procedure(self):
-        """Provides column headers"""
+        sql, _ = self.procedure.to_sql()
-
+        sql.save()
-        def __init__(self, parent) -> None:
-            super().__init__(parent)
-            self.layout = QGridLayout()
-            self.check = QCheckBox()
-            self.layout.addWidget(self.check, 0, 0)
-            self.check.stateChanged.connect(self.check_all)
-            for iii, item in enumerate(["Role", "Equipment", "Process", "Tips"], start=1):
-                label = QLabel(item)
-                label.setMaximumWidth(200)
-                label.setMinimumWidth(200)
-                self.layout.addWidget(label, 0, iii, alignment=Qt.AlignmentFlag.AlignRight)
-            self.setLayout(self.layout)
-
-        def check_all(self):
-            """
-            Toggles all checkboxes in the form
-            """
-            for object in self.parent().findChildren(QCheckBox):
-                object.setChecked(self.check.isChecked())
 
 
 class RoleComboBox(QWidget):
@@ -124,7 +130,6 @@ class RoleComboBox(QWidget):
         """
         equip = self.box.currentText()
         equip2 = next((item for item in self.role.equipment if item.name == equip), self.role.equipment[0])
-        logger.debug(f"Equip2: {equip2}")
         with QSignalBlocker(self.process) as blocker:
             self.process.clear()
         self.process.addItems([item for item in equip2.process if item in self.role.process])
@@ -180,7 +185,7 @@ class RoleComboBox(QWidget):
     def toggle_checked(self):
         """
         If this equipment is disabled, the input fields will be disabled.
-        """        
+        """
         for widget in self.findChildren(QWidget):
             match widget:
                 case QCheckBox():

src/submissions/frontend/widgets/equipment_usage_2.py

@@ -1,131 +0,0 @@
-'''
-Creates forms that the user can enter equipment info into.
-'''
-import sys
-from pprint import pformat
-from PyQt6.QtCore import Qt, QSignalBlocker, pyqtSlot
-from PyQt6.QtWebChannel import QWebChannel
-from PyQt6.QtWebEngineWidgets import QWebEngineView
-from PyQt6.QtWidgets import (
-    QDialog, QComboBox, QCheckBox, QLabel, QWidget, QVBoxLayout, QDialogButtonBox, QGridLayout
-)
-from backend.db.models import Equipment, Run, Process, Procedure, Tips
-from backend.validators.pydant import PydEquipment, PydEquipmentRole, PydTips, PydProcedure
-import logging
-from typing import Generator
-
-from tools import get_application_from_parent, render_details_template, flatten_list
-
-logger = logging.getLogger(f"submissions.{__name__}")
-
-
-class EquipmentUsage(QDialog):
-
-    def __init__(self, parent, procedure: PydProcedure):
-        super().__init__(parent)
-        self.procedure = procedure
-        self.setWindowTitle(f"Equipment Checklist - {procedure.name}")
-        self.used_equipment = self.procedure.equipment
-        self.kit = self.procedure.kittype
-        self.opt_equipment = procedure.proceduretype.get_equipment()
-        self.layout = QVBoxLayout()
-        self.app = get_application_from_parent(parent)
-        self.webview = QWebEngineView(parent=self)
-        self.webview.setContextMenuPolicy(Qt.ContextMenuPolicy.NoContextMenu)
-        self.webview.setMinimumSize(1200, 800)
-        self.webview.setMaximumWidth(1200)
-        # NOTE: Decide if exporting should be allowed.
-        # self.webview.loadFinished.connect(self.activate_export)
-        self.layout = QGridLayout()
-        # NOTE: button to export a pdf version
-        self.layout.addWidget(self.webview, 1, 0, 10, 10)
-        self.setLayout(self.layout)
-        self.setFixedWidth(self.webview.width() + 20)
-        # NOTE: setup channel
-        self.channel = QWebChannel()
-        self.channel.registerObject('backend', self)
-        html = self.construct_html(procedure=procedure)
-        self.webview.setHtml(html)
-        self.webview.page().setWebChannel(self.channel)
-        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, 1, 1, 1)
-
-    @classmethod
-    def construct_html(cls, procedure: PydProcedure, child: bool = False):
-        proceduretype = procedure.proceduretype
-        proceduretype_dict = proceduretype.details_dict()
-        run = procedure.run
-        # proceduretype_dict['equipment_json'] = flatten_list([item['equipment_json'] for item in proceduretype_dict['equipment']])
-        # proceduretype_dict['equipment_json'] = [
-        #     {'name': 'Liquid Handler', 'equipment': [
-        #         {'name': 'Other', 'asset_number': 'XXX', 'processes': [
-        #             {'name': 'Trust Me', 'tips': ['Blah']},
-        #             {'name': 'No Me', 'tips': ['Blah', 'Crane']}
-        #         ]
-        #          },
-        #         {'name': 'Biomek', 'asset_number': '5015530', 'processes': [
-        #             {'name': 'Sample Addition', 'tips': ['Axygen 20uL']
-        #              }
-        #         ]
-        #          }
-        #     ]
-        #      }
-        # ]
-        # if procedure.equipment:
-        #     for equipmentrole in proceduretype_dict['equipment']:
-        #         # NOTE: Check if procedure equipment is present and move to head of the list if so.
-        #         try:
-        #             relevant_procedure_item = next((equipment for equipment in procedure.equipment if
-        #                                             equipment.equipmentrole == equipmentrole['name']))
-        #         except StopIteration:
-        #             continue
-        #         item_in_er_list = next((equipment for equipment in equipmentrole['equipment'] if
-        #                                 equipment['name'] == relevant_procedure_item.name))
-        #         equipmentrole['equipment'].insert(0, equipmentrole['equipment'].pop(
-        #             equipmentrole['equipment'].index(item_in_er_list)))
-        html = render_details_template(
-            template_name="support/equipment_usage",
-            css_in=[],
-            js_in=[],
-            proceduretype=proceduretype_dict,
-            run=run.details_dict(),
-            procedure=procedure.__dict__,
-            child=child
-        )
-        return html
-
-    @pyqtSlot(str, str, str, str)
-    def update_equipment(self, equipmentrole: str, equipment: str, process: str, tips: str):
-
-        try:
-            equipment_of_interest = next(
-                (item for item in self.procedure.equipment if item.equipmentrole == equipmentrole))
-        except StopIteration:
-            equipment_of_interest = None
-        equipment = Equipment.query(name=equipment)
-        if equipment_of_interest:
-            eoi = self.procedure.equipment.pop(self.procedure.equipment.index(equipment_of_interest))
-        else:
-            eoi = equipment.to_pydantic(proceduretype=self.procedure.proceduretype)
-        eoi.name = equipment.name
-        eoi.asset_number = equipment.asset_number
-        eoi.nickname = equipment.nickname
-        process = next((prcss for prcss in equipment.process if prcss.name == process))
-        eoi.process = process.to_pydantic()
-        tips = next((tps for tps in equipment.tips if tps.name == tips))
-        eoi.tips = tips.to_pydantic()
-        self.procedure.equipment.append(eoi)
-        logger.debug(f"Updated equipment: {self.procedure.equipment}")
-
-    def save_procedure(self):
-        sql, _ = self.procedure.to_sql()
-        logger.debug(pformat(sql.__dict__))
-        # import pickle
-        # with open("sql.pickle", "wb") as f:
-        #     pickle.dump(sql, f)
-        # with open("pyd.pickle", "wb") as f:
-        #     pickle.dump(self.procedure, f)
-        sql.save()

src/submissions/frontend/widgets/functions.py

@@ -39,7 +39,7 @@ def select_open_file(obj: QMainWindow, file_extension: str | None = None) -> Pat
             logger.warning(f"No file selected, cancelling.")
             return
     obj.last_dir = fname.parent
-    logger.debug(f"File selected: {fname}")
+    logger.info(f"File selected: {fname}")
     return fname
 
 

src/submissions/frontend/widgets/gel_checker.py

@@ -5,10 +5,9 @@ from operator import itemgetter
 from PyQt6.QtWidgets import (
     QWidget, QDialog, QGridLayout, QLabel, QLineEdit, QDialogButtonBox, QTextEdit, QComboBox
 )
-import pyqtgraph as pg
 from PyQt6.QtGui import QIcon
 from PIL import Image
-import logging, numpy as np
+import logging, numpy as np, pyqtgraph as pg
 from pprint import pformat
 from typing import Tuple, List
 from pathlib import Path

src/submissions/frontend/widgets/info_tab.py

@@ -34,7 +34,6 @@ class InfoPane(QWidget):
         report = Report()
         self.start_date = self.datepicker.start_date.date().toPyDate()
         self.end_date = self.datepicker.end_date.date().toPyDate()
-        # logger.debug(f"Start date: {self.start_date}, End date: {self.end_date}")
         if self.datepicker.start_date.date() > self.datepicker.end_date.date():
             lastmonth = self.datepicker.end_date.date().addDays(-31)
             msg = f"Start date after end date is not allowed! Setting to {lastmonth.toString()}."

src/submissions/frontend/widgets/misc.py

@@ -1,7 +1,7 @@
 """
 Contains miscellaneous widgets for frontend functions
 """
-import math
+import math, logging
 from PyQt6.QtGui import QStandardItem, QIcon
 from PyQt6.QtWidgets import (
     QLabel, QLineEdit, QComboBox, QDateEdit, QPushButton, QWidget,
@@ -10,7 +10,6 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtCore import Qt, QDate, QSize
 from tools import jinja_template_loading
 from backend.db.models import *
-import logging
 
 logger = logging.getLogger(f"submissions.{__name__}")
 

src/submissions/frontend/widgets/omni_add_edit.py

@@ -3,7 +3,7 @@ A widget to handle adding/updating any database object.
 """
 from datetime import date
 from pprint import pformat
-from typing import Any, Tuple
+from typing import Any, Tuple, List
 from pydantic import BaseModel
 from PyQt6.QtWidgets import (
     QLabel, QDialog, QWidget, QLineEdit, QGridLayout, QComboBox, QDialogButtonBox, QDateEdit, QSpinBox, QDoubleSpinBox,
@@ -13,6 +13,8 @@ from sqlalchemy import String, TIMESTAMP, INTEGER, FLOAT, JSON, BLOB
 from sqlalchemy.orm import ColumnProperty
 import logging
 from sqlalchemy.orm.relationships import _RelationshipDeclared
+from backend.db.models import BaseClass
+from backend.validators.pydant import PydBaseClass
 from tools import Report, report_result
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -20,19 +22,17 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 class AddEdit(QDialog):
 
-    def __init__(self, parent, instance: Any | None = None, managers: set = set()):
+    def __init__(self, parent, instance: Any | None = None, managers: set = set(), disabled: List[str] = []):
         super().__init__(parent)
-        # logger.debug(f"Managers: {managers}")
+        logger.debug(f"Disable = {disabled}")
         self.instance = instance
         self.object_type = instance.__class__
         self.managers = managers
-        # logger.debug(f"Managers: {managers}")
         self.layout = QGridLayout(self)
         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
-        # logger.debug(f"Fields: {pformat(self.instance.omnigui_instance_dict)}")
         fields = {k: v for k, v in self.instance.omnigui_instance_dict.items() if "id" not in k}
         # NOTE: Move 'name' to the front
         try:
@@ -41,13 +41,13 @@ class AddEdit(QDialog):
             pass
         height_counter = 0
         for key, field in fields.items():
+            disable = key in disabled
             try:
                 value = getattr(self.instance, key)
             except AttributeError:
                 value = None
             try:
-                logger.debug(f"{key} property: {type(field['class_attr'].property)}")
+                widget = EditProperty(self, key=key, column_type=field, value=value, disable=disable)
-                widget = EditProperty(self, key=key, column_type=field, value=value)
             except AttributeError as e:
                 logger.error(f"Problem setting widget {key}: {e}")
                 continue
@@ -55,7 +55,7 @@ class AddEdit(QDialog):
                 self.layout.addWidget(widget, self.layout.rowCount(), 0)
                 height_counter += 1
         self.layout.addWidget(self.buttonBox)
-        self.setWindowTitle(f"Add/Edit {self.object_type.__name__} - Manager: {self.managers}")
+        self.setWindowTitle(f"Add/Edit {self.object_type.__name__}")# - Manager: {self.managers}")
         self.setMinimumSize(600, 50 * height_counter)
         self.setLayout(self.layout)
 
@@ -64,11 +64,8 @@ class AddEdit(QDialog):
         report = Report()
         parsed = {result[0].strip(":"): result[1] for result in
                   [item.parse_form() for item in self.findChildren(EditProperty)] if result[0]}
-        # logger.debug(f"Parsed form: {parsed}")
         model = self.object_type.pydantic_model
-        # logger.debug(f"Model type: {model.__name__}")
         if model.__name__ == "PydElastic":
-            # logger.debug(f"We have an elastic model.")
             parsed['instance'] = self.instance
         # NOTE: Hand-off to pydantic model for validation.
         # NOTE: Also, why am I not just using the toSQL method here. I could write one for contact.
@@ -78,8 +75,9 @@ class AddEdit(QDialog):
 
 class EditProperty(QWidget):
 
-    def __init__(self, parent: AddEdit, key: str, column_type: Any, value):
+    def __init__(self, parent: AddEdit, key: str, column_type: Any, value, disable: bool):
         super().__init__(parent)
+        logger.debug(f"Widget column type for {key}: {column_type}")
         self.name = key
         self.label = QLabel(key.title().replace("_", " "))
         self.layout = QGridLayout()
@@ -88,6 +86,7 @@ class EditProperty(QWidget):
             self.property_class = column_type['class_attr'].property.entity.class_
         except AttributeError:
             self.property_class = None
+        logger.debug(f"Property class: {self.property_class}")
         try:
             self.is_list = column_type['class_attr'].property.uselist
         except AttributeError:
@@ -96,23 +95,26 @@ class EditProperty(QWidget):
             case ColumnProperty():
                 self.column_property_set(column_type, value=value)
             case _RelationshipDeclared():
-                if not self.property_class.skip_on_edit:
+                try:
+                    check = self.property_class.skip_on_edit
+                except AttributeError:
+                    check = False
+                if not check:
                     self.relationship_property_set(column_type, value=value)
                 else:
                     return
             case _:
                 logger.error(f"{column_type} not a supported type.")
                 return
+        self.widget.setDisabled(disable)
         self.layout.addWidget(self.label, 0, 0, 1, 1)
         self.layout.addWidget(self.widget, 0, 1, 1, 3)
         self.setLayout(self.layout)
 
     def relationship_property_set(self, relationship, value=None):
         self.widget = QComboBox()
-        # logger.debug(self.parent().managers)
         for manager in self.parent().managers:
             if self.name in manager.aliases:
-                # logger.debug(f"Name: {self.name} is in aliases: {manager.aliases}")
                 choices = [manager.name]
                 self.widget.setEnabled(False)
                 break
@@ -127,11 +129,17 @@ class EditProperty(QWidget):
         if isinstance(instance_value, list):
             instance_value = next((item.name for item in instance_value), None)
         if instance_value:
+            match instance_value:
+                case x if issubclass(instance_value.__class__, BaseClass):
+                    instance_value = instance_value.name
+                case x if issubclass(instance_value.__class__, PydBaseClass):
+                    instance_value = instance_value.name
+                case _:
+                    pass
             choices.insert(0, choices.pop(choices.index(instance_value)))
         self.widget.addItems(choices)
 
     def column_property_set(self, column_property, value=None):
-        # logger.debug(f"Column Property: {column_property['class_attr'].expression} {column_property}, Value: {value}")
         match column_property['class_attr'].expression.type:
             case String():
                 if value is None:
@@ -176,7 +184,6 @@ class EditProperty(QWidget):
             check = self.widget
         except AttributeError:
             return None, None
-        # match self.widget
         match check:
             case QLineEdit():
                 value = self.widget.text()

src/submissions/frontend/widgets/omni_search.py

@@ -1,7 +1,6 @@
 """
 Search box that performs fuzzy search for various object types
 """
-from copy import deepcopy
 from pprint import pformat
 from typing import Tuple, Any, List, Generator
 from pandas import DataFrame
@@ -10,8 +9,8 @@ from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout, QDialog,
     QTableView, QWidget, QLineEdit, QGridLayout, QComboBox, QDialogButtonBox
 )
-from .submission_table import pandasModel
+from . import pandasModel
-import logging
+import logging, sys
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -72,18 +71,14 @@ class SearchBox(QDialog):
                 self.object_type = self.original_type
             else:
                 self.object_type = self.original_type.find_regular_subclass(self.sub_class.currentText())
-        # logger.debug(f"Object type: {self.object_type} - {self.object_type.searchables}")
+        for item in self.object_type.get_searchables():
-        # logger.debug(f"Original type: {self.original_type} - {self.original_type.searchables}")
+            if item in [thing for thing in search_fields]:
-        for item in self.object_type.searchables:
-            if item['field'] in [item['field'] for item in search_fields]:
-                logger.debug(f"Already have {item['field']}")
                 continue
             else:
                 search_fields.append(item)
-        logger.debug(f"Search fields: {search_fields}")
         for iii, searchable in enumerate(search_fields):
-            widget = FieldSearch(parent=self, label=searchable['label'], field_name=searchable['field'])
+            widget = FieldSearch(parent=self, label=searchable, field_name=searchable)
-            widget.setObjectName(searchable['field'])
+            widget.setObjectName(searchable)
             self.layout.addWidget(widget, 1 + iii, 0)
             widget.search_widget.textChanged.connect(self.update_data)
         self.update_data()
@@ -168,11 +163,10 @@ class SearchResults(QTableView):
         self.context = kwargs
         self.parent = parent
         self.object_type = object_type
-        try:
+        # try:
-            self.extras = extras + [item for item in deepcopy(self.object_type.searchables)]
+        #     self.extras = extras + [item for item in deepcopy(self.object_type.searchables)]
-        except AttributeError:
+        # except AttributeError:
-            self.extras = extras
+        #     self.extras = extras
-        # logger.debug(f"Extras: {self.extras}")
 
     def setData(self, df: DataFrame) -> None:
         """
@@ -181,10 +175,11 @@ class SearchResults(QTableView):
 
         self.data = df
         try:
-            self.columns_of_interest = [dict(name=item['field'], column=self.data.columns.get_loc(item['field'])) for
+            self.columns_of_interest = [dict(name=item, column=self.data.columns.get_loc(item)) for
-                                        item in self.extras]
+                                        item in self.object_type.get_searchables()]
         except KeyError:
             self.columns_of_interest = []
+        logger.debug(f"Columns of Interest: {pformat(self.columns_of_interest)}")
         try:
             self.data['id'] = self.data['id'].apply(str)
             self.data['id'] = self.data['id'].str.zfill(3)
@@ -209,10 +204,13 @@ class SearchResults(QTableView):
             None
         """
         context = {item['name']: x.sibling(x.row(), item['column']).data() for item in self.columns_of_interest}
+        logger.debug(f"Context: {pformat(context)}")
         try:
             object = self.object_type.query(**context)
-        except KeyError:
+        except KeyError as e:
+            logger.error(e)
             object = None
+        logger.debug(f"Object: {object}")
         try:
             object.edit_from_search(obj=self.parent, **context)
         except AttributeError as e:

src/submissions/frontend/widgets/procedure_creation.py

@@ -1,18 +1,15 @@
 """
-
+Main module to construct the procedure form
 """
 from __future__ import annotations
-import sys, logging, os, re, datetime
+import sys, logging, re, datetime
-from pathlib import Path
 from pprint import pformat
 from PyQt6.QtCore import pyqtSlot, Qt
-from PyQt6.QtGui import QContextMenuEvent, QAction
 from PyQt6.QtWebChannel import QWebChannel
 from PyQt6.QtWebEngineWidgets import QWebEngineView
-from PyQt6.QtWidgets import QDialog, QGridLayout, QMenu, QDialogButtonBox
+from PyQt6.QtWidgets import QDialog, QGridLayout, QDialogButtonBox
-from typing import TYPE_CHECKING, Any, List
+from typing import TYPE_CHECKING, List
 if TYPE_CHECKING:
-    from backend.db.models import Run, Procedure
     from backend.validators import PydProcedure, PydEquipment
 from tools import get_application_from_parent, render_details_template, sanitize_object_for_json
 
@@ -26,7 +23,6 @@ class ProcedureCreation(QDialog):
         self.edit = edit
         self.run = procedure.run
         self.procedure = procedure
-        # logger.debug(f"procedure: {pformat(self.procedure.__dict__)}")
         self.proceduretype = procedure.proceduretype
         self.setWindowTitle(f"New {self.proceduretype.name} for {self.run.rsl_plate_number}")
         self.plate_map = self.proceduretype.construct_plate_map(sample_dicts=self.procedure.sample)
@@ -56,7 +52,7 @@ class ProcedureCreation(QDialog):
 
 
     def set_html(self):
-        from .equipment_usage_2 import EquipmentUsage
+        from .equipment_usage import EquipmentUsage
         proceduretype_dict = self.proceduretype.details_dict()
         # NOTE: Add --New-- as an option for reagents.
         for key, value in self.procedure.reagentrole.items():
@@ -73,19 +69,15 @@ class ProcedureCreation(QDialog):
                                         equipment['name'] == relevant_procedure_item.name))
                 equipmentrole['equipment'].insert(0, equipmentrole['equipment'].pop(
                     equipmentrole['equipment'].index(item_in_er_list)))
-        proceduretype_dict['equipment_section'] = EquipmentUsage.construct_html(procedure=self.procedure, child=True)
         proceduretype_dict['equipment'] = [sanitize_object_for_json(object) for object in proceduretype_dict['equipment']]
-        logger.debug(proceduretype_dict['equipment'])
-        self.update_equipment = EquipmentUsage.update_equipment
         regex = re.compile(r".*R\d$")
         proceduretype_dict['previous'] = [""] + [item.name for item in self.run.procedure if item.proceduretype == self.proceduretype and not bool(regex.match(item.name))]
+        # sys.exit(f"ProcedureDict:\n{pformat(proceduretype_dict)}")
         html = render_details_template(
             template_name="procedure_creation",
-            # css_in=['new_context_menu'],
             js_in=["procedure_form", "grid_drag", "context_menu"],
             proceduretype=proceduretype_dict,
             run=self.run.details_dict(),
-            # procedure=self.procedure.__dict__,
             procedure=self.procedure,
             plate_map=self.plate_map,
             edit=self.edit
@@ -93,9 +85,9 @@ class ProcedureCreation(QDialog):
         self.webview.setHtml(html)
 
     @pyqtSlot(str, str, str, str)
-    def update_equipment(self, equipmentrole: str, equipment: str, process: str, tips: str):
+    def update_equipment(self, equipmentrole: str, equipment: str, processversion: str, tips: str):
-        from backend.db.models import Equipment
+        from backend.db.models import Equipment, ProcessVersion, TipsLot
-        # logger.debug("Updating equipment")
+        logger.debug(f"\n\nEquipmentRole: {equipmentrole}, Equipment: {equipment}, Process: {processversion}, Tips: {tips}\n\n")
         try:
             equipment_of_interest = next(
                 (item for item in self.procedure.equipment if item.equipmentrole == equipmentrole))
@@ -109,17 +101,26 @@ class ProcedureCreation(QDialog):
         eoi.name = equipment.name
         eoi.asset_number = equipment.asset_number
         eoi.nickname = equipment.nickname
-        # logger.warning("Setting processes.")
+        process_name, version = processversion.split("-v")
-        eoi.process = [process for process in equipment.get_processes(equipmentrole=equipmentrole)]
+        processversion = ProcessVersion.query(name=process_name, version=version, limit=1)
+        eoi.processversion = processversion.to_pydantic()
+        try:
+            tips_manufacturer, tipsref, lot = [item if item != "" else None for item in tips.split("-")]
+            tips = TipsLot.query(manufacturer=tips_manufacturer, ref=tipsref, lot=lot)
+            eoi.tips = tips
+        except ValueError:
+            logger.warning(f"No tips info to unpack")
         self.procedure.equipment.append(eoi)
-        # logger.debug(f"Updated equipment: {pformat(self.procedure.equipment)}")
 
     @pyqtSlot(str, str)
     def text_changed(self, key: str, new_value: str):
-        logger.debug(f"New value for {key}: {new_value}")
         match key:
             case "rsl_plate_num":
                 setattr(self.procedure.run, key, new_value)
+            case "repeat_of":
+                from backend.db.models import Procedure
+                parent = Procedure.query(name=new_value, limit=1)
+                self.procedure.repeat_of = parent
             case _:
                 attribute = getattr(self.procedure, key)
                 match attribute:
@@ -127,19 +128,14 @@ class ProcedureCreation(QDialog):
                         attribute['value'] = new_value.strip('\"')
                     case _:
                         setattr(self.procedure, key, new_value.strip('\"'))
-        logger.debug(f"Set value for {key}: {getattr(self.procedure, key)}")
-
-
 
     @pyqtSlot(str, bool)
     def check_toggle(self, key: str, ischecked: bool):
-        logger.debug(f"{key} is checked: {ischecked}")
         setattr(self.procedure, key, ischecked)
 
     @pyqtSlot(str)
     def update_kit(self, kittype):
         self.procedure.update_kittype_reagentroles(kittype=kittype)
-        logger.debug({k: v for k, v in self.procedure.__dict__.items() if k != "plate_map"})
         self.set_html()
 
     @pyqtSlot(list)
@@ -155,33 +151,17 @@ class ProcedureCreation(QDialog):
         from backend.validators.pydant import PydReagent
         expiry = datetime.datetime.strptime(expiry, "%Y-%m-%d")
         pyd = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
-        logger.debug(pyd)
         self.procedure.reagentrole[reagentrole].insert(0, pyd)
-        logger.debug(pformat(self.procedure.__dict__))
         self.set_html()
 
     @pyqtSlot(str, str)
     def update_reagent(self, reagentrole: str, name_lot_expiry: str):
-        logger.debug(f"{reagentrole}: {name_lot_expiry}")
         try:
             name, lot, expiry = name_lot_expiry.split(" - ")
         except ValueError as e:
-            logger.debug(f"Couldn't perform split due to {e}")
             return
         self.procedure.update_reagents(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
 
     def return_sql(self, new: bool = False):
-        return self.procedure.to_sql(new=new)
+        output = self.procedure.to_sql(new=new)
-
+        return output
-# class ProcedureWebViewer(QWebEngineView):
-#
-#     def __init__(self, *args, **kwargs):
-#         super().__init__(*args, **kwargs)
-#
-#     def contextMenuEvent(self, event: QContextMenuEvent):
-# self.menu = self.page().createStandardContextMenu()
-# self.menu = self.createStandardContextMenu()
-# add_sample = QAction("Add Sample")
-# self.menu = QMenu()
-# self.menu.addAction(add_sample)
-# self.menu.popup(event.globalPos())

src/submissions/frontend/widgets/sample_checker.py

@@ -1,5 +1,7 @@
+"""
+
+"""
 import logging
-from pathlib import Path
 from typing import List
 from PyQt6.QtCore import Qt, pyqtSlot
 from PyQt6.QtWebChannel import QWebChannel
@@ -22,7 +24,6 @@ class SampleChecker(QDialog):
             self.rsl_plate_number = RSLNamer.construct_new_plate_name(clientsubmission.to_dict())
         else:
             self.rsl_plate_number = clientsubmission
-        logger.debug(f"RSL Plate number: {self.rsl_plate_number}")
         self.samples = samples
         self.setWindowTitle(title)
         self.app = get_application_from_parent(parent)
@@ -35,16 +36,11 @@ class SampleChecker(QDialog):
         self.channel = QWebChannel()
         self.channel.registerObject('backend', self)
         # NOTE: Used to maintain javascript functions.
-        # 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()]
         try:
             samples = self.formatted_list
         except AttributeError as e:
             logger.error(f"Problem getting sample list: {e}")
             samples = []
-        # html = template.render(samples=samples, css=css, rsl_plate_number=self.rsl_plate_number)
         html = render_details_template(template_name="sample_checker", samples=samples, rsl_plate_number=self.rsl_plate_number)
         self.webview.setHtml(html)
         self.webview.page().setWebChannel(self.channel)
@@ -55,13 +51,8 @@ class SampleChecker(QDialog):
         self.layout.addWidget(self.buttonBox, 11, 9, 1, 1, alignment=Qt.AlignmentFlag.AlignRight)
         self.setLayout(self.layout)
 
-        # with open("sample_checker_rendered.html", "w") as f:
-        #     f.write(html)
-        logger.debug(f"HTML sample checker written!")
-
     @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}")
         try:
             item = next((sample for sample in self.samples if int(submission_rank) == sample.submission_rank))
         except StopIteration:
@@ -71,7 +62,6 @@ class SampleChecker(QDialog):
 
     @pyqtSlot(int, bool)
     def enable_sample(self, submission_rank: int, enabled: bool):
-        logger.debug(f"Name: {submission_rank}, Enabled: {enabled}")
         try:
             item = next((sample for sample in self.samples if int(submission_rank) == sample.submission_rank))
         except StopIteration:
@@ -81,14 +71,12 @@ class SampleChecker(QDialog):
 
     @pyqtSlot(str)
     def set_rsl_plate_number(self, rsl_plate_number: str):
-        logger.debug(f"RSL plate num: {rsl_plate_number}")
         self.rsl_plate_number = rsl_plate_number
 
     @property
     def formatted_list(self) -> List[dict]:
         output = []
         for sample in self.samples:
-            # logger.debug(sample)
             s = sample.improved_dict(dictionaries=False)
             if s['sample_id'] in [item['sample_id'] for item in output]:
                 s['color'] = "red"

src/submissions/frontend/widgets/submission_details.py

@@ -62,14 +62,9 @@ class SubmissionDetails(QDialog):
             css = f.read()
         key = object.__class__.__name__.lower()
         d = {key: details}
-        logger.debug(f"Using details: {pformat(d['procedure']['equipment'])}")
         html = template.render(**d, css=[css])
         self.webview.setHtml(html)
         self.setWindowTitle(f"{object.__class__.__name__} Details - {object.name}")
-        # with open(f"{object.__class__.__name__}_details_rendered.html", "w") as f:
-            # f.write(html)
-            # pass
-
 
     def activate_export(self) -> None:
         """
@@ -96,10 +91,10 @@ class SubmissionDetails(QDialog):
 
     @pyqtSlot(str)
     def equipment_details(self, equipment: str | Equipment):
-        logger.debug(f"Equipment details")
         if isinstance(equipment, str):
             equipment = Equipment.query(name=equipment)
-        base_dict = equipment.to_sub_dict(full_data=True)
+        # base_dict = equipment.to_sub_dict(full_data=True)
+        base_dict = equipment.details_dict()
         template = equipment.details_template
         template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
@@ -110,10 +105,10 @@ class SubmissionDetails(QDialog):
 
     @pyqtSlot(str)
     def process_details(self, process: str | Process):
-        logger.debug(f"Process details")
         if isinstance(process, str):
             process = Process.query(name=process)
-        base_dict = process.to_sub_dict(full_data=True)
+        # base_dict = process.to_sub_dict(full_data=True)
+        base_dict = process.details_dict()
         template = process.details_template
         template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
@@ -124,10 +119,10 @@ class SubmissionDetails(QDialog):
 
     @pyqtSlot(str)
     def tips_details(self, tips: str | Tips):
-        logger.debug(f"Equipment details: {tips}")
         if isinstance(tips, str):
             tips = Tips.query(lot=tips)
-        base_dict = tips.to_sub_dict(full_data=True)
+        # base_dict = tips.to_sub_dict(full_data=True)
+        base_dict = tips.details_dict()
         template = tips.details_template
         template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
@@ -144,10 +139,10 @@ class SubmissionDetails(QDialog):
         Args:
             sample (str): Submitter Id of the sample.
         """
-        logger.debug(f"Sample details.")
         if isinstance(sample, str):
             sample = Sample.query(sample_id=sample)
-        base_dict = sample.to_sub_dict(full_data=True)
+        # base_dict = sample.to_sub_dict(full_data=True)
+        base_dict = sample.details_dict()
         exclude = ['procedure', 'excluded', 'colour', 'tooltip']
         base_dict['excluded'] = exclude
         template = sample.details_template
@@ -155,8 +150,6 @@ class SubmissionDetails(QDialog):
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
             css = f.read()
         html = template.render(sample=base_dict, css=css)
-        # with open(f"{sample.sample_id}.html", 'w') as f:
-        #     f.write(html)
         self.webview.setHtml(html)
         self.setWindowTitle(f"Sample Details - {sample.sample_id}")
 
@@ -169,13 +162,13 @@ class SubmissionDetails(QDialog):
             kit (str | KitType): Name of kittype.
             reagent (str | Reagent): Lot number of the reagent
         """
-        logger.debug(f"Reagent details.")
         if isinstance(reagent, str):
             reagent = Reagent.query(lot=reagent)
         if isinstance(proceduretype, str):
             self.proceduretype = ProcedureType.query(name=proceduretype)
-        base_dict = reagent.to_sub_dict(proceduretype=self.proceduretype, full_data=True)
+        # base_dict = reagent.to_sub_dict(proceduretype=self.proceduretype, full_data=True)
         # base_dict = reagent.details_dict(proceduretype=self.proceduretype, full_data=True)
+        base_dict = reagent.details_dict()
         env = jinja_template_loading()
         temp_name = "reagent_details.html"
         try:
@@ -221,7 +214,6 @@ class SubmissionDetails(QDialog):
         Args:
             run (str | BasicRun): Submission of interest.
         """
-        logger.debug(f"Run details.")
         if isinstance(run, str):
             run = Run.query(name=run)
         self.rsl_plate_number = run.rsl_plate_number
@@ -234,7 +226,6 @@ class SubmissionDetails(QDialog):
         template_path = Path(self.template.environment.loader.__getattribute__("searchpath")[0])
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
             css = f.read()
-        # logger.debug(f"Base dictionary of procedure {self.name}: {pformat(self.base_dict)}")
         self.html = self.template.render(sub=self.base_dict, permission=is_power_user(), css=css)
         self.webview.setHtml(self.html)
 
@@ -273,7 +264,6 @@ class SubmissionComment(QDialog):
     """
 
     def __init__(self, parent, submission: Run) -> None:
-        logger.debug(parent)
         super().__init__(parent)
         self.app = get_application_from_parent(parent)
         self.submission = submission
@@ -293,7 +283,7 @@ class SubmissionComment(QDialog):
         self.layout.addWidget(self.buttonBox, alignment=Qt.AlignmentFlag.AlignBottom)
         self.setLayout(self.layout)
 
-    def parse_form(self) -> List[dict]:
+    def parse_form(self) -> dict:
         """
         Adds comment to procedure object.
         """

src/submissions/frontend/widgets/submission_table.py

@@ -1,260 +1,18 @@
 """
 Contains widgets specific to the procedure summary and procedure details.
 """
-
+import sys, logging
-import sys, logging, re
 from pprint import pformat
-
+from PyQt6.QtWidgets import QMenu, QTreeView, QAbstractItemView
-from PyQt6.QtWidgets import QTableView, QMenu, QTreeView, QStyledItemDelegate, QStyle, QStyleOptionViewItem, \
+from PyQt6.QtCore import QModelIndex
-    QHeaderView, QAbstractItemView, QWidget, QTreeWidgetItemIterator
+from PyQt6.QtGui import QAction, QCursor, QStandardItemModel, QStandardItem, QContextMenuEvent
-from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel, pyqtSlot, QModelIndex
+from typing import List
-from PyQt6.QtGui import QAction, QCursor, QStandardItemModel, QStandardItem, QIcon, QColor, QContextMenuEvent
+from backend.db.models import Run, ClientSubmission, Procedure
-from typing import Dict, List
+from tools import get_application_from_parent
-
-# from backend import Procedure
-from backend.db.models.submissions import Run, ClientSubmission
-from backend.db.models.procedures import  Procedure
-from tools import Report, Result, report_result, get_application_from_parent
-from .functions import select_open_file
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
-class pandasModel(QAbstractTableModel):
-    """
-    pandas model for inserting summary sheet into gui
-    NOTE: Copied from Stack Overflow. I have no idea how it actually works.
-    """
-
-    def __init__(self, data) -> None:
-        QAbstractTableModel.__init__(self)
-        self._data = data
-
-    def rowCount(self, parent=None) -> int:
-        """
-        does what it says
-
-        Args:
-            parent (_type_, optional): _description_. Defaults to None.
-
-        Returns:
-            int: number of rows in data
-        """
-        return self._data.shape[0]
-
-    def columnCount(self, parent=None) -> int:
-        """
-        does what it says
-
-        Args:
-            parent (_type_, optional): _description_. Defaults to None.
-
-        Returns:
-            int: number of columns in data
-        """
-        return self._data.shape[1]
-
-    def data(self, index, role=Qt.ItemDataRole.DisplayRole) -> str | None:
-        if index.isValid():
-            if role == Qt.ItemDataRole.DisplayRole:
-                return str(self._data.iloc[index.row(), index.column()])
-        return None
-
-    def headerData(self, col, orientation, role):
-        if orientation == Qt.Orientation.Horizontal and role == Qt.ItemDataRole.DisplayRole:
-            return self._data.columns[col]
-        return None
-
-
-class SubmissionsSheet(QTableView):
-    """
-    presents procedure summary to user in tab1
-    """
-
-    def __init__(self, parent) -> None:
-        super().__init__(parent)
-        self.app = self.parent()
-        self.report = Report()
-        try:
-            page_size = self.app.page_size
-        except AttributeError:
-            page_size = 250
-        self.set_data(page=1, page_size=page_size)
-        self.resizeColumnsToContents()
-        self.resizeRowsToContents()
-        self.setSortingEnabled(True)
-        self.doubleClicked.connect(lambda x: Run.query(id=x.sibling(x.row(), 0).data()).show_details(self))
-        # NOTE: Have to procedure native query here because mine just returns results?
-        self.total_count = Run.__database_session__.query(Run).count()
-
-    def set_data(self, page: int = 1, page_size: int = 250) -> None:
-        """
-        sets data in model
-        """
-        # self.data = ClientSubmission.submissions_to_df(page=page, page_size=page_size)
-        self.data = Run.submissions_to_df(page=page, page_size=page_size)
-        try:
-            self.data['Id'] = self.data['Id'].apply(str)
-            self.data['Id'] = self.data['Id'].str.zfill(4)
-        except KeyError as e:
-            logger.error(f"Could not alter id to string due to {e}")
-        proxyModel = QSortFilterProxyModel()
-        proxyModel.setSourceModel(pandasModel(self.data))
-        self.setModel(proxyModel)
-
-    def contextMenuEvent(self, event):
-        """
-        Creates actions for right click menu events.
-
-        Args:
-            event (_type_): the item of interest
-        """
-        # NOTE: Get current row index
-        id = self.selectionModel().currentIndex()
-        # NOTE: Convert to data in id column (i.e. column 0)
-        id = id.sibling(id.row(), 0).data()
-        submission = Run.query(id=id)
-        self.menu = QMenu(self)
-        self.con_actions = submission.custom_context_events()
-        for k in self.con_actions.keys():
-            action = QAction(k, self)
-            action.triggered.connect(lambda _, action_name=k: self.triggered_action(action_name=action_name))
-            self.menu.addAction(action)
-        # NOTE: add other required actions
-        self.menu.popup(QCursor.pos())
-
-    def triggered_action(self, action_name: str):
-        """
-        Calls the triggered action from the context menu
-
-        Args:
-            action_name (str): name of the action from the menu
-        """
-        func = self.con_actions[action_name]
-        func(obj=self)
-
-    @report_result
-    def link_extractions(self):
-        """
-        Pull extraction logs into the db
-        """
-        report = Report()
-        result = self.link_extractions_function()
-        report.add_result(result)
-        return report
-
-    def link_extractions_function(self):
-        """
-        Link extractions from runlogs to imported procedure
-
-        Args:
-            obj (QMainWindow): original app window
-
-        Returns:
-            Tuple[QMainWindow, dict]: Collection of new main app window and result dict
-        """
-        report = Report()
-        fname = select_open_file(self, file_extension="csv")
-        with open(fname.__str__(), 'r') as f:
-            # NOTE: split csv on commas
-            runs = [col.strip().split(",") for col in f.readlines()]
-        count = 0
-        for run in runs:
-            new_run = dict(
-                start_time=run[0].strip(),
-                rsl_plate_number=run[1].strip(),
-                sample_count=run[2].strip(),
-                status=run[3].strip(),
-                experiment_name=run[4].strip(),
-                end_time=run[5].strip()
-            )
-            # NOTE: elution columns are item 6 in the comma split list to the end
-            for ii in range(6, len(run)):
-                new_run[f"column{str(ii - 5)}_vol"] = run[ii]
-            # NOTE: Lookup imported procedure
-            sub = Run.query(name=new_run['name'])
-            # NOTE: If no such procedure exists, move onto the next procedure
-            if sub is None:
-                continue
-            try:
-                count += 1
-            except AttributeError:
-                continue
-            sub.set_attribute('extraction_info', new_run)
-            sub.save()
-        report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
-        return report
-
-    @report_result
-    def link_pcr(self):
-        """
-        Pull pcr logs into the db
-        """
-        report = Report()
-        result = self.link_pcr_function()
-        report.add_result(result)
-        return report
-
-    def link_pcr_function(self):
-        """
-        Link PCR data from procedure logs to an imported procedure
-
-        Args:
-            obj (QMainWindow): original app window
-
-        Returns:
-            Tuple[QMainWindow, dict]: Collection of new main app window and result dict
-        """
-        report = Report()
-        fname = select_open_file(self, file_extension="csv")
-        with open(fname.__str__(), 'r') as f:
-            # NOTE: split csv rows on comma
-            runs = [col.strip().split(",") for col in f.readlines()]
-        count = 0
-        for run in runs:
-            new_run = dict(
-                start_time=run[0].strip(),
-                rsl_plate_number=run[1].strip(),
-                biomek_status=run[2].strip(),
-                quant_status=run[3].strip(),
-                experiment_name=run[4].strip(),
-                end_time=run[5].strip()
-            )
-            # NOTE: lookup imported procedure
-            sub = Run.query(rsl_number=new_run['name'])
-            # NOTE: if imported procedure doesn't exist move on to next procedure
-            if sub is None:
-                continue
-            sub.set_attribute('pcr_info', new_run)
-            # NOTE: check if pcr_info already exists
-            sub.save()
-        report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
-        return report
-
-
-# class ClientSubmissionDelegate(QStyledItemDelegate):
-#
-#     def __init__(self, parent=None):
-#         super(ClientSubmissionDelegate, self).__init__(parent)
-#         pixmapi = QStyle.StandardPixmap.SP_ToolBarHorizontalExtensionButton
-#         icon1 = QWidget().style().standardIcon(pixmapi)
-#         pixmapi = QStyle.StandardPixmap.SP_ToolBarVerticalExtensionButton
-#         icon2 = QWidget().style().standardIcon(pixmapi)
-#         self._plus_icon = icon1
-#         self._minus_icon = icon2
-#
-#     def initStyleOption(self, option, index):
-#         super(ClientSubmissionDelegate, self).initStyleOption(option, index)
-#         if not index.parent().isValid():
-#             is_open = bool(option.state & QStyle.StateFlag.State_Open)
-#             option.features |= QStyleOptionViewItem.ViewItemFeature.HasDecoration
-#             option.icon = self._minus_icon if is_open else self._plus_icon
-
-
-# class RunDelegate(ClientSubmissionDelegate):
-#     pass
-
-
 class SubmissionsTree(QTreeView):
     """
     https://stackoverflow.com/questions/54385437/how-can-i-make-a-table-that-can-collapse-its-rows-into-categories-in-qt
@@ -264,20 +22,12 @@ class SubmissionsTree(QTreeView):
         super(SubmissionsTree, self).__init__(parent)
         self.app = get_application_from_parent(parent)
         self.total_count = ClientSubmission.__database_session__.query(ClientSubmission).count()
-        # self.setIndentation(0)
         self.setExpandsOnDoubleClick(False)
-        # self.clicked.connect(self.on_clicked)
-        # delegate1 = ClientSubmissionDelegate(self)
-        # self.setItemDelegateForColumn(0, delegate1)
         self.model = model
         self.setModel(self.model)
-        # self.header().setSectionResizeMode(0, QHeaderView.sectionResizeMode(self,0).ResizeToContents)
         self.setSelectionBehavior(QAbstractItemView.selectionBehavior(self).SelectRows)
-        # self.setStyleSheet("background-color: #0D1225;")
         self.set_data()
         self.doubleClicked.connect(self.show_details)
-        # self.setContextMenuPolicy(Qt.ContextMenuPolicy.CustomContextMenu)
-        # self.customContextMenuRequested.connect(self.open_menu)
         self.setStyleSheet("""
             QTreeView {
                 background-color: #f5f5f5;
@@ -294,20 +44,13 @@ class SubmissionsTree(QTreeView):
             }
         """)
 
-        # Enable alternating row colors
+        # Note: Enable alternating row colors
         self.setAlternatingRowColors(True)
         self.setIndentation(20)
         self.setItemsExpandable(True)
-        # self.expanded.connect(self.expand_item)
-
         for ii in range(2):
             self.resizeColumnToContents(ii)
 
-    # @pyqtSlot(QModelIndex)
-    # def on_clicked(self, index):
-    #     if not index.parent().isValid() and index.column() == 0:
-    #         self.setExpanded(index, not self.isExpanded(index))
-
     def expand_item(self, event: QModelIndex):
         logger.debug(f"Data: {event.data()}")
         logger.debug(f"Parent {event.parent().data()}")
@@ -327,18 +70,11 @@ class SubmissionsTree(QTreeView):
         """
         indexes = self.selectedIndexes()
         dicto = next((item.data(1) for item in indexes if item.data(1)))
-        logger.debug(f"Dicto: {pformat(dicto)}")
         query_obj = dicto['item_type'].query(name=dicto['query_str'], limit=1)
-        logger.debug(f"Querying: {query_obj}")
         # NOTE: Convert to data in id column (i.e. column 0)
-        # id = id.sibling(id.row(), 0).data()
-        # logger.debug(id.model().query_group_object(id.row()))
-        # clientsubmission = id.model().query_group_object(id.row())
         self.menu = QMenu(self)
         self.con_actions = query_obj.custom_context_events
-        logger.debug(f"Context menu actions: {self.con_actions}")
         for key in self.con_actions.keys():
-            logger.debug(key)
             match key.lower():
                 case "add procedure":
                     action = QMenu(self.menu)
@@ -362,7 +98,7 @@ class SubmissionsTree(QTreeView):
                     action = QAction(key, self)
                     action.triggered.connect(lambda _, action_name=key: self.con_actions[action_name](obj=self))
                     self.menu.addAction(action)
-        # # NOTE: add other required actions
+        # NOTE: add other required actions
         self.menu.popup(QCursor.pos())
 
     def set_data(self, page: int = 1, page_size: int = 250) -> None:
@@ -372,8 +108,6 @@ class SubmissionsTree(QTreeView):
         self.clear()
         self.data = [item.to_dict(full_data=True) for item in
                      ClientSubmission.query(chronologic=True, page=page, page_size=page_size)]
-        logger.debug(f"setting data:\n {pformat(self.data)}")
-        # sys.exit()
         root = self.model.invisibleRootItem()
         for submission in self.data:
             group_str = f"{submission['submissiontype']}-{submission['submitter_plate_id']}-{submission['submitted_date']}"
@@ -382,26 +116,21 @@ class SubmissionsTree(QTreeView):
                 query_str=submission['submitter_plate_id'],
                 item_type=ClientSubmission
             ))
-            # logger.debug(f"Added {submission_item}")
             for run in submission['run']:
-                # self.model.append_element_to_group(group_item=group_item, element=run)
                 run_item = self.model.add_child(parent=submission_item, child=dict(
                     name=run['plate_number'],
                     query_str=run['plate_number'],
                     item_type=Run
                 ))
-                # logger.debug(f"Added {run_item}")
                 for procedure in run['procedures']:
                     procedure_item = self.model.add_child(parent=run_item, child=dict(
                         name=procedure['name'],
                         query_str=procedure['name'],
                         item_type=Procedure
                     ))
-                    # logger.debug(f"Added {procedure_item}")
 
     def _populateTree(self, children, parent):
         for child in children:
-            logger.debug(child)
             child_item = QStandardItem(child['name'])
             parent.appendRow(child_item)
             if isinstance(children, List):
@@ -409,22 +138,13 @@ class SubmissionsTree(QTreeView):
 
     def clear(self):
         if self.model != None:
-            # self.model.clear()       # works
             self.model.setRowCount(0)  # works
 
     def show_details(self, sel: QModelIndex):
-        # id = self.selectionModel().currentIndex()
         # NOTE: Convert to data in id column (i.e. column 0)
-        # id = id.sibling(id.row(), 1)
         indexes = self.selectedIndexes()
         dicto = next((item.data(1) for item in indexes if item.data(1)))
-        # try:
-        #     id = int(id.data())
-        # except ValueError:
-        #     return
-        # Run.query(id=id).show_details(self)
         obj = dicto['item_type'].query(name=dicto['query_str'], limit=1)
-        logger.debug(obj)
         obj.show_details(self)
 
     def link_extractions(self):
@@ -436,15 +156,6 @@ class SubmissionsTree(QTreeView):
 
 class ClientSubmissionRunModel(QStandardItemModel):
 
-
-    def __init__(self, parent=None):
-        super(ClientSubmissionRunModel, self).__init__(parent)
-        # headers = ["", "id", "Plate Number", "Started Date", "Completed Date", "Signed By"]
-        # self.setColumnCount(len(headers))
-        # self.setHorizontalHeaderLabels(headers)
-
-
-
     def add_child(self, parent: QStandardItem, child:dict):
         item = QStandardItem(child['name'])
         item.setData(dict(item_type=child['item_type'], query_str=child['query_str']), 1)
@@ -453,4 +164,4 @@ class ClientSubmissionRunModel(QStandardItemModel):
         return item
 
     def edit_item(self):
-        pass
+        pass

src/submissions/frontend/widgets/submission_widget.py

@@ -1,24 +1,22 @@
 """
 Contains all procedure related frontend functions
 """
-import sys
+import sys, logging
-
 from PyQt6.QtWidgets import (
     QWidget, QPushButton, QVBoxLayout,
     QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QHBoxLayout, QGridLayout
 )
 from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
 from .functions import select_open_file, select_save_file
-import logging
 from pathlib import Path
 from tools import Report, Result, check_not_nan, main_form_style, report_result, get_application_from_parent
 from backend.validators import PydReagent, PydClientSubmission, PydSample
-from backend.db import (
+from backend.db.models import (
-    ClientLab, SubmissionType, Reagent,
+    ClientLab, SubmissionType, Reagent, ReagentLot,
     ReagentRole, ProcedureTypeReagentRoleAssociation, Run, ClientSubmission
 )
 from pprint import pformat
-from .pop_ups import QuestionAsker, AlertPop
+from .pop_ups import QuestionAsker
 from .omni_add_edit import AddEdit
 from typing import List, Tuple
 from datetime import date
@@ -121,37 +119,16 @@ class SubmissionFormContainer(QWidget):
             report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
             return report
         # NOTE: create sheetparser using excel sheet and context from gui
-        # try:
-        #     self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
-        # except PermissionError:
-        #     logger.error(f"Couldn't get permission to access file: {fname}")
-        #     return
-        # except AttributeError:
-        #     self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
-        # try:
-        #     # self.prsr = SheetParser(filepath=fname)
-        #     self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
-        # except PermissionError:
-        #     logger.error(f"Couldn't get permission to access file: {fname}")
-        #     return
-        # except AttributeError:
-        #     self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
-
-        # self.pydclientsubmission = self.clientsubmissionparser.to_pydantic()
-        # self.pydsamples = self.sampleparser.to_pydantic()
-        # logger.debug(f"Samples: {pformat(self.pydclientsubmission.sample)}")
         self.clientsubmission_manager = DefaultClientSubmissionManager(parent=self, input_object=fname)
         self.pydclientsubmission = self.clientsubmission_manager.to_pydantic()
         checker = SampleChecker(self, "Sample Checker", self.pydclientsubmission.sample)
         if checker.exec():
-            # logger.debug(pformat(self.pydclientsubmission.sample))
             try:
                 assert isinstance(self.pydclientsubmission, PydClientSubmission)
             except AssertionError as e:
                 logger.error(f"Got wrong type for {self.pydclientsubmission}: {type(self.pydclientsubmission)}")
                 raise e
             self.form = self.pydclientsubmission.to_form(parent=self)
-            # self.form.samples = self.pydsamples
             self.layout().addWidget(self.form)
         else:
             message = "Submission cancelled."
@@ -160,7 +137,7 @@ class SubmissionFormContainer(QWidget):
         return report
 
     @report_result
-    def add_reagent(self, instance: Reagent | None = None):
+    def add_reagent(self, instance: ReagentLot | None = None):
         """
         Action to create new reagent in DB.
 
@@ -172,7 +149,7 @@ class SubmissionFormContainer(QWidget):
         """
         report = Report()
         if not instance:
-            instance = Reagent()
+            instance = ReagentLot()
         dlg = AddEdit(parent=self, instance=instance)
         if dlg.exec():
             reagent = dlg.parse_form()
@@ -195,14 +172,11 @@ class SubmissionFormWidget(QWidget):
         self.pyd = pyd
         self.missing_info = []
         self.submissiontype = SubmissionType.query(name=self.pyd.submissiontype['value'])
-        # basic_submission_class = self.submission_type.submission_class
-        # logger.debug(f"Basic procedure class: {basic_submission_class}")
         defaults = Run.get_default_info("form_recover", "form_ignore", submissiontype=self.pyd.submissiontype['value'])
         self.recover = defaults['form_recover']
         self.ignore = defaults['form_ignore']
         self.layout = QVBoxLayout()
         for k in list(self.pyd.model_fields.keys()):# + list(self.pyd.model_extra.keys()):
-            logger.debug(f"Pydantic field: {k}")
             if k in self.ignore:
                 logger.warning(f"{k} in form_ignore {self.ignore}, not creating widget")
                 continue
@@ -218,7 +192,6 @@ class SubmissionFormWidget(QWidget):
                     value = self.pyd.model_extra[k]
                 except KeyError:
                     value = dict(value=None, missing=True)
-            logger.debug(f"Pydantic value: {value}")
             add_widget = self.create_widget(key=k, value=value, submission_type=self.submissiontype,
                                             run_object=Run(), disable=check)
             if add_widget is not None:
@@ -230,7 +203,6 @@ class SubmissionFormWidget(QWidget):
                 self.layout.addWidget(self.disabler)
                 self.disabler.checkbox.checkStateChanged.connect(self.disable_reagents)
         self.setStyleSheet(main_form_style)
-        # self.scrape_reagents(self.kittype)
         self.setLayout(self.layout)
 
     def disable_reagents(self):
@@ -298,7 +270,6 @@ class SubmissionFormWidget(QWidget):
             if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
                 reagent.setParent(None)
         reagents, integrity_report, missing_reagents = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit)
-        # logger.debug(f"Reagents: {reagents}")
         expiry_report = self.pyd.check_reagent_expiries(exempt=missing_reagents)
         for reagent in reagents:
             add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.extraction_kit)
@@ -364,34 +335,6 @@ class SubmissionFormWidget(QWidget):
             return report
         base_submission = self.pyd.to_sql()
         # NOTE: check output message for issues
-        # try:
-        #     trigger = result.results[-1]
-        #     code = trigger.code
-        # except IndexError as e:
-        #     logger.error(result.results)
-        #     logger.error(f"Problem getting error code: {e}")
-        #     code = 0
-        # match code:
-        #     # NOTE: code 0: everything is fine.
-        #     case 0:
-        #         pass
-        #     # NOTE: code 1: ask for overwrite
-        #     case 1:
-        #         dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_number}?", message=trigger.msg)
-        #         if dlg.exec():
-        #             # NOTE: Do not add duplicate reagents.
-        #             pass
-        #         else:
-        #             self.app.ctx.database_session.rollback()
-        #             report.add_result(Result(msg="Overwrite cancelled", status="Information"))
-        #             return report
-        #     # NOTE: code 2: No RSL plate number given
-        #     case 2:
-        #         report.add_result(result)
-        #         return report
-        #     case _:
-        #         pass
-        # NOTE: add reagents to procedure object
         if base_submission is None:
             return
         for reagent in base_submission.reagents:
@@ -450,7 +393,6 @@ class SubmissionFormWidget(QWidget):
                     if field is not None:
                         info[field] = value
         self.pyd.reagents = reagents
-        # logger.debug(f"Reagents from form: {reagents}")
         for item in self.recover:
             if hasattr(self, item):
                 value = getattr(self, item)
@@ -558,29 +500,29 @@ class SubmissionFormWidget(QWidget):
                     # NOTE: set combobox values to lookedup values
                     add_widget.addItems(labs)
                     add_widget.setToolTip("Select submitting lab.")
-                case 'kittype':
+                # case 'kittype':
-                    # NOTE: if extraction kittype not available, all other values fail
+                #     # NOTE: if extraction kittype not available, all other values fail
-                    if not check_not_nan(value):
+                #     if not check_not_nan(value):
-                        msg = AlertPop(message="Make sure to check your extraction kittype in the excel sheet!",
+                #         msg = AlertPop(message="Make sure to check your extraction kittype in the excel sheet!",
-                                       status="warning")
+                #                        status="warning")
-                        msg.exec()
+                #         msg.exec()
-                    # NOTE: create combobox to hold looked up kits
+                #     # NOTE: create combobox to hold looked up kits
-                    add_widget = MyQComboBox(scrollWidget=parent)
+                #     add_widget = MyQComboBox(scrollWidget=parent)
-                    # NOTE: lookup existing kits by 'proceduretype' decided on by sheetparser
+                #     # NOTE: lookup existing kits by 'proceduretype' decided on by sheetparser
-                    uses = [item.name for item in submission_type.kit_types]
+                #     uses = [item.name for item in submission_type.kit_types]
-                    obj.uses = uses
+                #     obj.uses = uses
-                    if check_not_nan(value):
+                #     if check_not_nan(value):
-                        try:
+                #         try:
-                            uses.insert(0, uses.pop(uses.index(value)))
+                #             uses.insert(0, uses.pop(uses.index(value)))
-                        except ValueError:
+                #         except ValueError:
-                            logger.warning(f"Couldn't find kittype in list, skipping move to top of list.")
+                #             logger.warning(f"Couldn't find kittype in list, skipping move to top of list.")
-                        obj.ext_kit = value
+                #         obj.ext_kit = value
-                    else:
+                #     else:
-                        logger.error(f"Couldn't find {obj.prsr.sub['kittype']}")
+                #         logger.error(f"Couldn't find {obj.prsr.sub['kittype']}")
-                        obj.ext_kit = uses[0]
+                #         obj.ext_kit = uses[0]
-                    add_widget.addItems(uses)
+                #     add_widget.addItems(uses)
-                    add_widget.setToolTip("Select extraction kittype.")
+                #     add_widget.setToolTip("Select extraction kittype.")
-                    parent.extraction_kit = add_widget.currentText()
+                #     parent.extraction_kit = add_widget.currentText()
                 case 'submission_category':
                     add_widget = MyQComboBox(scrollWidget=parent)
                     categories = ['Diagnostic', "Surveillance", "Research"]
@@ -813,11 +755,8 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
             self.disabler.setHidden(True)
         except AttributeError:
             pass
-        # save_btn = QPushButton("Save")
         self.sample = samples
-        logger.debug(f"Samples: {self.sample}")
         start_run_btn = QPushButton("Save")
-        # self.layout.addWidget(save_btn)
         self.layout.addWidget(start_run_btn)
         start_run_btn.clicked.connect(self.create_new_submission)
 
@@ -846,7 +785,6 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
                     field, value = widget.parse_form()
                     if field is not None:
                         info[field] = value
-        # logger.debug(f"Reagents from form: {reagents}")
         for item in self.recover:
             if hasattr(self, item):
                 value = getattr(self, item)
@@ -865,7 +803,6 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
     @report_result
     def create_new_submission(self, *args) -> Report:
         pyd = self.to_pydantic()
-        logger.debug(f"Pydantic: {pyd}")
         sql = pyd.to_sql()
         for sample in pyd.sample:
             if isinstance(sample, PydSample):
@@ -874,9 +811,7 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
             if sample.sample_id.lower() in ["", "blank"]:
                 continue
             sample.save()
-            # if sample not in sql.sample:
             sql.add_sample(sample=sample)
-        logger.debug(pformat(sql.__dict__))
         try:
             del sql._misc_info['sample']
         except KeyError:

src/submissions/frontend/widgets/summary.py

@@ -3,7 +3,7 @@ Pane to hold information e.g. cost summary.
 """
 from .info_tab import InfoPane
 from PyQt6.QtWidgets import QWidget, QLabel, QPushButton
-from backend.db import ClientLab
+from backend.db.models import ClientLab
 from backend.excel.reports import ReportMaker
 from .misc import CheckableComboBox
 import logging

src/submissions/frontend/widgets/turnaround.py

@@ -4,7 +4,7 @@ Pane showing turnaround time summary.
 from PyQt6.QtWidgets import QWidget, QPushButton, QComboBox, QLabel
 from .info_tab import InfoPane
 from backend.excel.reports import TurnaroundMaker
-from backend.db import SubmissionType
+from backend.db.models import SubmissionType
 from frontend.visualizations.turnaround_chart import TurnaroundChart
 import logging
 

src/submissions/templates/procedure_details.html

@@ -56,10 +56,15 @@
     {% endif %}
     {% if procedure['sample'] %}
     <button type="button"><h3><u>Procedure Samples:</u></h3></button>
+    {% if procedure['platemap']|length > 5 %}
+    <br>
+    {{ procedure['platemap'] }}
+    {% else %}
     <p>{% for sample in procedure['sample'] %}
-        &nbsp;&nbsp;&nbsp;&nbsp;<a class="{% if sample['active'] %}data-link {% else %}unused {% endif %}sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
+        <a class="{% if sample['active'] %}data-link {% else %}unused {% endif %}sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
     {% endfor %}</p>
     {% endif %}
+    {% endif %}
     {% endblock %}
 {% if not child %}
 </body>

src/submissions/templates/support/plate_map.html

@@ -1,7 +1,11 @@
         <div class="plate" id="plate-container" style="grid-template-columns: repeat({{ plate_columns }}, {{ vw }}vw);grid-template-rows: repeat({{ plate_rows }}, {{ vw }}vw);">
             {% for sample in samples %}
-                <div class="well" draggable="true" id="{{ sample['well_id'] }}" style="background-color: {{ sample['background_color'] }};">
+                <div class="well" draggable="true" id="{{ sample['sample_id'] }}" style="background-color: {{ sample['background_color'] }};">
-                  <p style="font-size: 0.7em; text-align: center; word-wrap: break-word;">{{ sample['sample_id'] }}</p>
+                  {% if creation %}
+                    <p style="font-size: 0.7em; text-align: center; word-wrap: break-word;">{{ sample['sample_id'] }}</p>
+                  {% else %}
+                    <a class="data-link sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
+                  {% endif %}
                 </div>
             {% endfor %}
         </div>

src/submissions/tools/__init__.py

@@ -1,18 +1,17 @@
-'''
+"""
 Contains miscellaenous functions used by both frontend and backend.
-'''
+"""
 from __future__ import annotations
-import builtins, importlib, time, logging, re, yaml, sys, os, stat, platform, getpass, json, numpy as np, pandas as pd
+import builtins, importlib, time, logging, re, yaml, sys, os, stat, platform, getpass, json, numpy as np, pandas as pd, \
-import itertools
+    itertools, openpyxl
+from copy import copy
 from collections import OrderedDict
 from datetime import date, datetime, timedelta
 from json import JSONDecodeError
+from pprint import pformat
 from threading import Thread
 from inspect import getmembers, isfunction, stack
-from types import NoneType
-
 from dateutil.easter import easter
-from dateutil.parser import parse
 from jinja2 import Environment, FileSystemLoader
 from logging import handlers, Logger
 from pathlib import Path
@@ -60,7 +59,6 @@ main_form_style = '''
 
 page_size = 250
 
-# micro_char = uni_char = "\u03BC"
 
 def divide_chunks(input_list: list, chunk_count: int) -> Generator[Any, Any, None]:
     """
@@ -447,16 +445,18 @@ def jinja_template_loading() -> Environment:
     return env
 
 
-def render_details_template(template_name:str, css_in:List[str]|str=[], js_in:List[str]|str=[], **kwargs) -> str:
+def render_details_template(template_name: str, css_in: List[str] | str = [], js_in: List[str] | str = [],
+                            **kwargs) -> str:
     if isinstance(css_in, str):
         css_in = [css_in]
+    env = jinja_template_loading()
+    html_folder = Path(env.loader.__getattribute__("searchpath")[0])
     css_in = ["styles"] + css_in
-    css_in = [project_path.joinpath("src", "submissions", "templates", "css", f"{c}.css") for c in css_in]
+    css_in = [html_folder.joinpath("css", f"{c}.css") for c in css_in]
     if isinstance(js_in, str):
         js_in = [js_in]
     js_in = ["details"] + js_in
-    js_in = [project_path.joinpath("src", "submissions", "templates", "js", f"{j}.js") for j in js_in]
+    js_in = [html_folder.joinpath("js", f"{j}.js") for j in js_in]
-    env = jinja_template_loading()
     template = env.get_template(f"{template_name}.html")
     # template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
     css_out = []
@@ -467,7 +467,6 @@ def render_details_template(template_name:str, css_in:List[str]|str=[], js_in:Li
     for js in js_in:
         with open(js, "r") as f:
             js_out.append(f.read())
-    # logger.debug(f"Kwargs: {kwargs}")
     return template.render(css=css_out, js=js_out, **kwargs)
 
 
@@ -489,10 +488,10 @@ def convert_well_to_row_column(input_str: str) -> Tuple[int, int]:
         return None, None
     return row, column
 
+
 # Copy a sheet with style, format, layout, ect. from one Excel file to another Excel file
 # Please add the ..path\\+\\file..  and  ..sheet_name.. according to your desire.
-import openpyxl
+
-from copy import copy
 
 
 def copy_xl_sheet(source_sheet, target_sheet):
@@ -509,8 +508,8 @@ def copy_sheet_attributes(source_sheet, target_sheet):
     target_sheet.page_margins = copy(source_sheet.page_margins)
     target_sheet.freeze_panes = copy(source_sheet.freeze_panes)
 
-    # set row dimensions
+    # NOTE: set row dimensions
-    # So you cannot copy the row_dimensions attribute. Does not work (because of meta data in the attribute I think). So we copy every row's row_dimensions. That seems to work.
+    # NOTE: So you cannot copy the row_dimensions attribute. Does not work (because of meta data in the attribute I think). So we copy every row's row_dimensions. That seems to work.
     for rn in range(len(source_sheet.row_dimensions)):
         target_sheet.row_dimensions[rn] = copy(source_sheet.row_dimensions[rn])
 
@@ -519,12 +518,15 @@ def copy_sheet_attributes(source_sheet, target_sheet):
     else:
         target_sheet.sheet_format.defaultColWidth = copy(source_sheet.sheet_format.defaultColWidth)
 
-    # set specific column width and hidden property
+    # NOTE: set specific column width and hidden property
-    # we cannot copy the entire column_dimensions attribute so we copy selected attributes
+    # NOTE: we cannot copy the entire column_dimensions attribute so we copy selected attributes
     for key, value in source_sheet.column_dimensions.items():
-        target_sheet.column_dimensions[key].min = copy(source_sheet.column_dimensions[key].min)   # Excel actually groups multiple columns under 1 key. Use the min max attribute to also group the columns in the targetSheet
+        target_sheet.column_dimensions[key].min = copy(source_sheet.column_dimensions[
-        target_sheet.column_dimensions[key].max = copy(source_sheet.column_dimensions[key].max)  # https://stackoverflow.com/questions/36417278/openpyxl-can-not-read-consecutive-hidden-columns discussed the issue. Note that this is also the case for the width, not onl;y the hidden property
+                                                           key].min)  # Excel actually groups multiple columns under 1 key. Use the min max attribute to also group the columns in the targetSheet
-        target_sheet.column_dimensions[key].width = copy(source_sheet.column_dimensions[key].width) # set width for every column
+        target_sheet.column_dimensions[key].max = copy(source_sheet.column_dimensions[
+                                                           key].max)  # https://stackoverflow.com/questions/36417278/openpyxl-can-not-read-consecutive-hidden-columns discussed the issue. Note that this is also the case for the width, not onl;y the hidden property
+        target_sheet.column_dimensions[key].width = copy(
+            source_sheet.column_dimensions[key].width)  # set width for every column
         target_sheet.column_dimensions[key].hidden = copy(source_sheet.column_dimensions[key].hidden)
 
 
@@ -534,11 +536,9 @@ def copy_cells(source_sheet, target_sheet):
             source_cell = cell
             if isinstance(source_cell, openpyxl.cell.read_only.EmptyCell):
                 continue
-            target_cell = target_sheet.cell(column=c+1, row=r+1)
+            target_cell = target_sheet.cell(column=c + 1, row=r + 1)
-
             target_cell._value = source_cell._value
             target_cell.data_type = source_cell.data_type
-
             if source_cell.has_style:
                 target_cell.font = copy(source_cell.font)
                 target_cell.border = copy(source_cell.border)
@@ -546,15 +546,13 @@ def copy_cells(source_sheet, target_sheet):
                 target_cell.number_format = copy(source_cell.number_format)
                 target_cell.protection = copy(source_cell.protection)
                 target_cell.alignment = copy(source_cell.alignment)
-
             if not isinstance(source_cell, openpyxl.cell.ReadOnlyCell) and source_cell.hyperlink:
                 target_cell._hyperlink = copy(source_cell.hyperlink)
-
             if not isinstance(source_cell, openpyxl.cell.ReadOnlyCell) and source_cell.comment:
                 target_cell.comment = copy(source_cell.comment)
 
 
-def list_str_comparator(input_str:str, listy: List[str], mode: Literal["starts_with", "contains"]) -> bool:
+def list_str_comparator(input_str: str, listy: List[str], mode: Literal["starts_with", "contains"]) -> bool:
     match mode:
         case "starts_with":
             if any([input_str.startswith(item) for item in listy]):
@@ -567,6 +565,7 @@ def list_str_comparator(input_str:str, listy: List[str], mode: Literal["starts_w
             else:
                 return False
 
+
 def sort_dict_by_list(dictionary: dict, order_list: list) -> dict:
     output = OrderedDict()
     for item in order_list:
@@ -602,14 +601,12 @@ def setup_lookup(func):
             elif v is not None:
                 sanitized_kwargs[k] = v
         return func(*args, **sanitized_kwargs)
-
     return wrapper
 
 
 def check_object_in_manager(manager: list, object_name: object) -> Tuple[Any, bool]:
     if manager is None:
         return None, False
-    # logger.debug(f"Manager: {manager}, aliases: {manager.aliases}, Key: {object_name}")
     if object_name in manager.aliases:
         return manager, True
     relationships = [getattr(manager.__class__, item) for item in dir(manager.__class__)
@@ -617,21 +614,17 @@ def check_object_in_manager(manager: list, object_name: object) -> Tuple[Any, bo
     relationships = [item for item in relationships if isinstance(item.property, _RelationshipDeclared)]
     for relationship in relationships:
         if relationship.key == object_name and "association" not in relationship.key:
-            logger.debug(f"Checking {relationship.key}")
             try:
                 rel_obj = getattr(manager, relationship.key)
                 if rel_obj is not None:
-                    logger.debug(f"Returning {rel_obj}")
                     return rel_obj, False
             except AttributeError:
                 pass
         if "association" in relationship.key:
             try:
-                logger.debug(f"Checking association {relationship.key}")
                 rel_obj = next((getattr(item, object_name) for item in getattr(manager, relationship.key)
                                 if getattr(item, object_name) is not None), None)
                 if rel_obj is not None:
-                    logger.debug(f"Returning {rel_obj}")
                     return rel_obj, False
             except AttributeError:
                 pass
@@ -862,7 +855,6 @@ def check_authorization(func):
             report.add_result(
                 Result(owner=func.__str__(), code=1, msg=error_msg, status="warning"))
             return report, kwargs
-
     return wrapper
 
 
@@ -888,7 +880,6 @@ def under_development(func):
                 Result(owner=func.__str__(), code=1, msg=error_msg,
                        status="warning"))
             return report
-
     return wrapper
 
 
@@ -906,7 +897,6 @@ def report_result(func):
 
     @wraps(func)
     def wrapper(*args, **kwargs):
-        # logger.info(f"Report result being called by {func.__name__}")
         output = func(*args, **kwargs)
         match output:
             case Report():
@@ -931,6 +921,7 @@ def report_result(func):
                 logger.error(f"Problem reporting due to {e}")
                 logger.error(result.msg)
         if output:
+            logger.info(f"Report result being called by {func.__name__}")
             if is_list_etc(output):
                 true_output = tuple(item for item in output if not isinstance(item, Report))
                 if len(true_output) == 1:
@@ -943,7 +934,6 @@ def report_result(func):
         else:
             true_output = None
         return true_output
-
     return wrapper
 
 
@@ -962,11 +952,32 @@ def is_list_etc(object):
 
 
 def create_holidays_for_year(year: int | None = None) -> List[date]:
-    def find_nth_monday(year, month, occurence: int | None = None, day: int | None = None):
+    """
-        if not occurence:
+    Gives stat holidays for the input year.
-            occurence = 1
+
+    Args:
+        year (int | None, optional): The input year as an integer. Defaults to None.
+
+    Returns:
+        List[date]
+    """
+    def find_nth_monday(year, month, occurrence: int | None = None, day: int | None = None) -> date:
+        """
+        Gets the nth (eg 2nd) monday of the given month.
+
+        Args:
+            year (int): The year the month occurs in.
+            month (int): The month of interest.
+            occurrence (int): The n in nth.
+            day (int): The day of the month to start after.
+
+        Returns:
+            date
+        """
+        if not occurrence:
+            occurrence = 1
         if not day:
-            day = occurence * 7
+            day = occurrence * 7
         max_days = (date(2012, month + 1, 1) - date(2012, month, 1)).days
         if day > max_days:
             day = max_days
@@ -977,17 +988,16 @@ def create_holidays_for_year(year: int | None = None) -> List[date]:
         offset = -d.weekday()  # weekday == 0 means Monday
         output = d + timedelta(offset)
         return output.date()
-
     if not year:
         year = date.today().year
-    # NOTE: Includes New Year's day for next year.
+    # NOTE: Static holidays. Includes New Year's day for next year.
     holidays = [date(year, 1, 1), date(year, 7, 1), date(year, 9, 30),
                 date(year, 11, 11), date(year, 12, 25), date(year, 12, 26),
                 date(year + 1, 1, 1)]
     # NOTE: Labour Day
     holidays.append(find_nth_monday(year, 9))
     # NOTE: Thanksgiving
-    holidays.append(find_nth_monday(year, 10, occurence=2))
+    holidays.append(find_nth_monday(year, 10, occurrence=2))
     # NOTE: Victoria Day
     holidays.append(find_nth_monday(year, 5, day=25))
     # NOTE: Easter, etc
@@ -1007,7 +1017,6 @@ def check_dictionary_inclusion_equality(listo: List[dict] | dict, dicto: dict) -
     Returns:
         bool: True if dicto is equal to any dictionary in the list.
     """
-    # logger.debug(f"Comparing: {listo} and {dicto}")
     if isinstance(dicto, list) and isinstance(listo, list):
         return listo == dicto
     elif isinstance(dicto, dict) and isinstance(listo, dict):
@@ -1018,22 +1027,43 @@ def check_dictionary_inclusion_equality(listo: List[dict] | dict, dicto: dict) -
         raise TypeError(f"Unsupported variable: {type(listo)}")
 
 
-def flatten_list(input_list: list):
+def flatten_list(input_list: list) -> list:
+    """
+    Takes nested lists and returns a single flat list.
+
+    Args:
+        input_list (list): input nested list.
+
+    Returns:
+        list:
+    """
     return list(itertools.chain.from_iterable(input_list))
 
 
-def sanitize_object_for_json(input_dict: dict) -> dict:
+def sanitize_object_for_json(input_dict: dict) -> dict | str:
+    """
+    Takes an object and makes sure its components can be converted to JSON
+
+    Args:
+        input_dict (dict): Dictionary of interest
+
+    Returns:
+        dict:
+    """
     if not isinstance(input_dict, dict):
         match input_dict:
             case int() | float() | bool():
                 pass
             case _:
                 try:
-                    js = json.dumps(input_dict)
+                    input_dict = json.dumps(input_dict)
                 except TypeError:
-                    input_dict = str(input_dict)
+                    match input_dict:
-        return input_dict
+                        case str():
-        # return input_dict
+                            pass
+                        case _:
+                            input_dict = str(input_dict)
+        return input_dict.strip('\"')
     output = {}
     for key, value in input_dict.items():
         match value:
@@ -1041,22 +1071,43 @@ def sanitize_object_for_json(input_dict: dict) -> dict:
                 value = [sanitize_object_for_json(object) for object in value]
             case dict():
                 value = sanitize_object_for_json(value)
-
             case _:
                 try:
-                    js = json.dumps(value)
+                    value = json.dumps(value)
                 except TypeError:
-                    value = str(value)
+                    match value:
+                        case str():
+                            pass
+                        case _:
+                            value = str(value)
+        if isinstance(value, str):
+            value = value.strip('\"')
         output[key] = value
     return output
 
 
-def create_plate_grid(rows: int, columns: int):
+def create_plate_grid(rows: int, columns: int) -> dict:
-    matrix = np.array([[0 for yyy in range(1, columns + 1)] for xxx in range(1, rows + 1)])
+    """
-    return {iii: (item[0][1]+1, item[0][0]+1) for iii, item in enumerate(np.ndenumerate(matrix), start=1)}
+    Makes an x by y array to represent a plate.
+
+    Args:
+        rows (int): Number of rows.
+        columns (int): Number of columns
+
+    Returns:
+        dict: cell number : (row, column)
+    """
+    # NOTE: columns/rows
+    # matrix = np.array([[0 for yyy in range(1, columns + 1)] for xxx in range(1, rows + 1)])
+    # NOTE: rows/columns
+    matrix = np.array([[0 for xxx in range(1, rows + 1)] for yyy in range(1, columns + 1)])
+    return {iii: (item[0][1] + 1, item[0][0] + 1) for iii, item in enumerate(np.ndenumerate(matrix), start=1)}
 
 
 class classproperty(property):
+    """
+    Allows for properties on classes as well as objects.
+    """
     def __get__(self, owner_self, owner_cls):
         return self.fget(owner_cls)
 
@@ -1396,6 +1447,16 @@ class Settings(BaseSettings, extra="allow"):
 
     @classmethod
     def get_alembic_db_path(cls, alembic_path, mode=Literal['path', 'schema', 'user', 'pass']) -> Path | str:
+        """
+        Retrieves database variables from alembic.ini file.
+
+        Args:
+            alembic_path (Any): Path of the alembic.ini file.
+            mode (Literal['path', 'schema', 'user', 'pass']): Variable of interest.
+
+        Returns:
+            Path | str
+        """
         c = ConfigParser()
         c.read(alembic_path)
         url = c['alembic']['sqlalchemy.url']

submissions.spec

@@ -32,8 +32,10 @@ a = Analysis(
     binaries=[],
     datas=[
             ("src\\config.yml", "files"),
-            ("src\\submissions\\templates\\*", "files\\templates"),
+            ("src\\submissions\\templates\\*.html", "files\\templates"),
-            ("src\\submissions\\templates\\css\\*", "files\\templates\\css"),
+            ("src\\submissions\\templates\\css\\*.css", "files\\templates\\css"),
+            ("src\\submissions\\templates\\js\\*.js", "files\\templates\\js"),
+            ("src\\submissions\\templates\\support\\*", "files\\templates\\support"),
             ("docs\\build", "files\\docs"),
             ("src\\submissions\\resources\\*", "files\\resources"),
             ("alembic.ini", "files"),
@@ -51,12 +53,32 @@ a = Analysis(
 )
 pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher)
 
+#exe = EXE(
+#    pyz,
+#    a.scripts,
+#    a.binaries,
+#    a.datas,
+#    [],
+#    name=f"{__project__}_{__version__}",
+#    debug=True,
+#    bootloader_ignore_signals=False,
+#    strip=False,
+#    upx=True,
+#    upx_exclude=[],
+#    runtime_tmpdir=None,
+#    console=True,
+#    disable_windowed_traceback=False,
+#    argv_emulation=False,
+#    target_arch=None,
+#    codesign_identity=None,
+#    entitlements_file=None,
+#)
 exe = EXE(
     pyz,
     a.scripts,
     [],
     exclude_binaries=True,
-    name=f"{__project__}_{__version__}",
+    name=f"{__project__}_{__version__}_2",
     debug=True,
     bootloader_ignore_signals=False,
     strip=False,