Mid-progress adding controls to pydantic creation.

src/submissions/backend/db/__init__.py

@@ -1,8 +1,10 @@
 """
 All database related operations.
 """
-from sqlalchemy import event
+import sqlalchemy.orm
+from sqlalchemy import event, inspect
 from sqlalchemy.engine import Engine
+
 from tools import ctx
 
 
@@ -16,7 +18,7 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
     Args:
         dbapi_connection (_type_): _description_
         connection_record (_type_): _description_
-    """    
+    """
     cursor = dbapi_connection.cursor()
     # print(ctx.database_schema)
     if ctx.database_schema == "sqlite":
@@ -34,3 +36,39 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
 
 
 from .models import *
+
+
+def update_log(mapper, connection, target):
+    logger.debug("\n\nBefore update\n\n")
+    state = inspect(target)
+    logger.debug(state)
+    update = dict(user=getuser(), time=datetime.now(), object=str(state.object), changes=[])
+    logger.debug(update)
+    for attr in state.attrs:
+        hist = attr.load_history()
+        if not hist.has_changes():
+            continue
+        added = [str(item) for item in hist.added]
+        deleted = [str(item) for item in hist.deleted]
+        change = dict(field=attr.key, added=added, deleted=deleted)
+        logger.debug(f"Adding: {pformat(change)}")
+        try:
+            update['changes'].append(change)
+        except Exception as e:
+            logger.error(f"Something went horribly wrong adding attr: {attr.key}: {e}")
+            continue
+
+    logger.debug(f"Adding to audit logs: {pformat(update)}")
+    if update['changes']:
+        # Note: must use execute as the session will be busy at this point.
+        # https://medium.com/@singh.surbhicse/creating-audit-table-to-log-insert-update-and-delete-changes-in-flask-sqlalchemy-f2ca53f7b02f
+        table = AuditLog.__table__
+        logger.debug(f"Adding to {table}")
+        connection.execute(table.insert().values(**update))
+        # logger.debug("Here is where I would insert values, if I was able.")
+    else:
+        logger.info(f"No changes detected, not updating logs.")
+
+
+# event.listen(LogMixin, 'after_update', update_log, propagate=True)
+# event.listen(LogMixin, 'after_insert', update_log, propagate=True)

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

@@ -5,7 +5,7 @@ from __future__ import annotations
 import sys, logging
 
 import pandas as pd
-from sqlalchemy import Column, INTEGER, String, JSON
+from sqlalchemy import Column, INTEGER, String, JSON, event, inspect
 from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
 from sqlalchemy.ext.declarative import declared_attr
 from sqlalchemy.exc import ArgumentError
@@ -22,6 +22,12 @@ Base: DeclarativeMeta = declarative_base()
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
+class LogMixin(Base):
+
+    __abstract__ = True
+
+
+
 class BaseClass(Base):
     """
     Abstract class to pass ctx values to all SQLAlchemy objects.
@@ -99,6 +105,15 @@ class BaseClass(Base):
         singles = list(set(cls.singles + BaseClass.singles))
         return dict(singles=singles)
 
+    @classmethod
+    def find_regular_subclass(cls, name: str | None = None):
+        if not name:
+            return cls
+        if " " in name:
+            search = name.title().replace(" ", "")
+        logger.debug(f"Searching for subclass: {search}")
+        return next((item for item in cls.__subclasses__() if item.__name__ == search), cls)
+
     @classmethod
     def fuzzy_search(cls, **kwargs):
         query: Query = cls.__database_session__.query(cls)
@@ -175,9 +190,11 @@ 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)}")
@@ -186,6 +203,8 @@ class BaseClass(Base):
             return report
 
 
+
+
 class ConfigItem(BaseClass):
     """
     Key:JSON objects to store config settings in database. 
@@ -222,6 +241,7 @@ from .controls import *
 from .organizations import *
 from .kits import *
 from .submissions import *
+from .audit import AuditLog
 
 # NOTE: Add a creator to the submission 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/controls.py

@@ -16,6 +16,7 @@ from typing import List, Literal, Tuple, Generator
 from dateutil.parser import parse
 from re import Pattern
 
+
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
@@ -429,6 +430,10 @@ class PCRControl(Control):
         fig = PCRFigure(df=df, modes=[])
         return report, fig
 
+    def to_pydantic(self):
+        from backend.validators import PydPCRControl
+        return PydPCRControl(**self.to_sub_dict())
+
 
 class IridaControl(Control):
 
@@ -878,3 +883,7 @@ class IridaControl(Control):
             exclude = [re.sub(rerun_regex, "", sample) for sample in sample_names if rerun_regex.search(sample)]
             df = df[df.name not in exclude]
         return df
+
+    def to_pydantic(self):
+        from backend.validators import PydIridaControl
+        return PydIridaControl(**self.__dict__)

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

@@ -567,7 +567,7 @@ class Reagent(BaseClass):
         return cls.execute_query(query=query, limit=limit)
 
     @check_authorization
-    def edit_from_search(self, **kwargs):
+    def edit_from_search(self, obj, **kwargs):
         from frontend.widgets.misc import AddReagentForm
         role = ReagentRole.query(kwargs['role'])
         if role:
@@ -1279,7 +1279,10 @@ class SubmissionReagentAssociation(BaseClass):
         Returns:
             str: Representation of this SubmissionReagentAssociation
         """
-        return f"<{self.submission.rsl_plate_num} & {self.reagent.lot}>"
+        try:
+            return f"<{self.submission.rsl_plate_num} & {self.reagent.lot}>"
+        except AttributeError:
+            return f"<Unknown Submission & {self.reagent.lot}"
 
     def __init__(self, reagent=None, submission=None):
         if isinstance(reagent, list):

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

@@ -12,8 +12,8 @@ from zipfile import ZipFile
 from tempfile import TemporaryDirectory, TemporaryFile
 from operator import itemgetter
 from pprint import pformat
-from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact
-from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
+from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, event, inspect
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.orm.attributes import flag_modified
 from sqlalchemy.ext.associationproxy import association_proxy
@@ -36,7 +36,7 @@ from PIL import Image
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
-class BasicSubmission(BaseClass):
+class BasicSubmission(BaseClass, LogMixin):
     """
     Concrete of basic submission which polymorphs into BacterialCulture and Wastewater
     """
@@ -544,7 +544,7 @@ class BasicSubmission(BaseClass):
                     field_value = len(self.samples)
                 else:
                     field_value = value
-            case "ctx" | "csv" | "filepath" | "equipment":
+            case "ctx" | "csv" | "filepath" | "equipment" | "controls":
                 return
             case item if item in self.jsons():
                 match key:
@@ -577,10 +577,13 @@ class BasicSubmission(BaseClass):
                 except AttributeError:
                     field_value = value
         # NOTE: insert into field
-        try:
-            self.__setattr__(key, field_value)
-        except AttributeError as e:
-            logger.error(f"Could not set {self} attribute {key} to {value} due to \n{e}")
+        current = self.__getattribute__(key)
+        if field_value and current != field_value:
+            logger.debug(f"Updated value: {key}: {current} to {field_value}")
+            try:
+                self.__setattr__(key, field_value)
+            except AttributeError as e:
+                logger.error(f"Could not set {self} attribute {key} to {value} due to \n{e}")
 
     def update_subsampassoc(self, sample: BasicSample, input_dict: dict):
         """
@@ -1339,7 +1342,7 @@ class BasicSubmission(BaseClass):
 
 # Below are the custom submission types
 
-class BacterialCulture(BasicSubmission):
+class BacterialCulture(BasicSubmission, LogMixin):
     """
     derivative submission type from BasicSubmission
     """
@@ -1426,7 +1429,7 @@ class BacterialCulture(BasicSubmission):
         return input_dict
 
 
-class Wastewater(BasicSubmission):
+class Wastewater(BasicSubmission, LogMixin):
     """
     derivative submission type from BasicSubmission
     """
@@ -2189,6 +2192,8 @@ class BasicSample(BaseClass):
     Base of basic sample which polymorphs into BCSample and WWSample
     """
 
+    searchables = ['submitter_id']
+
     id = Column(INTEGER, primary_key=True)  #: primary key
     submitter_id = Column(String(64), nullable=False, unique=True)  #: identification from submitter
     sample_type = Column(String(32))  #: mode_sub_type of sample
@@ -2509,6 +2514,9 @@ class BasicSample(BaseClass):
         if dlg.exec():
             pass
 
+    def edit_from_search(self, obj, **kwargs):
+        self.show_details(obj)
+
 
 # Below are the custom sample types
 
@@ -2516,6 +2524,9 @@ class WastewaterSample(BasicSample):
     """
     Derivative wastewater sample
     """
+
+    searchables = BasicSample.searchables + ['ww_processing_num', 'ww_full_sample_id', 'rsl_number']
+
     id = Column(INTEGER, ForeignKey('_basicsample.id'), primary_key=True)
     ww_processing_num = Column(String(64))  #: wastewater processing number
     ww_full_sample_id = Column(String(64))  #: full id given by entrics