Pre code cleanup and documentation.

src/submissions/backend/db/__init__.py

@@ -69,6 +69,6 @@ def update_log(mapper, connection, target):
     else:
         logger.info(f"No changes detected, not updating logs.")
 
-
+if ctx.database_schema == "sqlite":
-# event.listen(LogMixin, 'after_update', update_log, propagate=True)
+    event.listen(LogMixin, 'after_update', update_log, propagate=True)
-# event.listen(LogMixin, 'after_insert', update_log, propagate=True)
+    event.listen(LogMixin, 'after_insert', update_log, propagate=True)

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

@@ -4,8 +4,8 @@ Contains all models for sqlalchemy
 from __future__ import annotations
 import sys, logging
 
-import pandas as pd
+from pandas import DataFrame
-from sqlalchemy import Column, INTEGER, String, JSON, inspect
+from sqlalchemy import Column, INTEGER, String, JSON
 from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
 from sqlalchemy.ext.declarative import declared_attr
 from sqlalchemy.exc import ArgumentError
@@ -100,11 +100,21 @@ class BaseClass(Base):
         Returns:
             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=singles)
 
     @classmethod
-    def find_regular_subclass(cls, name: str | None = None):
+    def find_regular_subclass(cls, name: str | None = None) -> Any:
+        """
+
+        Args:
+            name (str): name of subclass of interest.
+
+        Returns:
+            Any: Subclass of this object
+
+        """
         if not name:
             return cls
         if " " in name:
@@ -140,7 +150,7 @@ class BaseClass(Base):
         return query.limit(50).all()
 
     @classmethod
-    def results_to_df(cls, objects: list, **kwargs) -> pd.DataFrame:
+    def results_to_df(cls, objects: list, **kwargs) -> DataFrame:
         """
 
         Args:
@@ -148,15 +158,15 @@ class BaseClass(Base):
             **kwargs (): Arguments necessary for the to_sub_dict method. eg extraction_kit=X
 
         Returns:
-            pd.Dataframe
+            Dataframe
         """
         records = [obj.to_sub_dict(**kwargs) for obj in objects]
-        return pd.DataFrame.from_records(records)
+        return DataFrame.from_records(records)
 
     @classmethod
     def query(cls, **kwargs) -> Any | List[Any]:
         """
-        Default query function for models. Overridden in most models.
+        Default query function for models. Overridden in most models with additional filters.
 
         Returns:
             Any | List[Any]: Result of query execution.
@@ -209,11 +219,9 @@ class BaseClass(Base):
         """
         # logger.debug(f"Saving object: {pformat(self.__dict__)}")
         report = Report()
-        state = inspect(self)
         try:
             self.__database_session__.add(self)
             self.__database_session__.commit()
-            return state
         except Exception as e:
             logger.critical(f"Problem saving object: {e}")
             logger.error(f"Error message: {type(e)}")

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

@@ -1,3 +1,8 @@
+"""
+Contains the audit log class and functions.
+"""
+from typing import List
+
 from dateutil.parser import parse
 from sqlalchemy.orm import declarative_base, DeclarativeMeta, Query
 from . import BaseClass
@@ -13,7 +18,7 @@ class AuditLog(Base):
 
     __tablename__ = "_auditlog"
 
-    id = Column(INTEGER, primary_key=True)  #: primary key
+    id = Column(INTEGER, primary_key=True, autoincrement=True)  #: primary key
     user = Column(String(64))
     time = Column(TIMESTAMP)
     object = Column(String(64))
@@ -23,7 +28,17 @@ class AuditLog(Base):
         return f"<{self.user} @ {self.time}>"
 
     @classmethod
-    def query(cls, start_date: date | str | int | None = None, end_date: date | str | int | None = None, ):
+    def query(cls, start_date: date | str | int | None = None, end_date: date | str | int | None = None) -> List["AuditLog"]:
+        """
+        Searches for database transactions by date.
+
+        Args:
+            start_date (date | str | int | None, Optional): Earliest date sought. Defaults to None
+            end_date (date | str | int | None, Optional): Latest date sought. Defaults to None
+
+        Returns:
+            List[AuditLog]: List of transactions made to the database.
+        """
         session = BaseClass.__database_session__
         query: Query = session.query(cls)
         if start_date is not None and end_date is None:

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

@@ -401,7 +401,7 @@ class ReagentRole(BaseClass):
         super().save()
 
 
-class Reagent(BaseClass):
+class Reagent(BaseClass, LogMixin):
     """
     Concrete reagent instance
     """

src/submissions/tools/__init__.py

@@ -955,10 +955,6 @@ def report_result(func):
         match output:
             case Report():
                 report = output
-            # case InstanceState():
-            #     for attr in output.attrs:
-            #         print(f"{attr}: {attr.load_history()}")
-            #     return
             case tuple():
                 try:
                     report = [item for item in output if isinstance(item, Report)][0]