Sanity checking.

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

@@ -3,6 +3,8 @@ Contains all models for sqlalchemy
 '''
 from __future__ import annotations
 import sys, logging
+
+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
@@ -11,8 +13,6 @@ from pathlib import Path
 
 # Load testing environment
 if 'pytest' in sys.modules:
-    from pathlib import Path
-
     sys.path.append(Path(__file__).parents[4].absolute().joinpath("tests").__str__())
 
 Base: DeclarativeMeta = declarative_base()
@@ -46,7 +46,7 @@ class BaseClass(Base):
         Returns:
             Session: DB session from ctx settings.
         """
-        if not 'pytest' in sys.modules:
+        if 'pytest' not in sys.modules:
             from tools import ctx
         else:
             from test_settings import ctx
@@ -60,7 +60,7 @@ class BaseClass(Base):
         Returns:
             Path: Location of the Submissions directory in Settings object
         """
-        if not 'pytest' in sys.modules:
+        if 'pytest' not in sys.modules:
             from tools import ctx
         else:
             from test_settings import ctx
@@ -74,7 +74,7 @@ class BaseClass(Base):
         Returns:
             Path: Location of the Submissions backup directory in Settings object
         """
-        if not 'pytest' in sys.modules:
+        if 'pytest' not in sys.modules:
             from tools import ctx
         else:
             from test_settings import ctx
@@ -104,8 +104,9 @@ class BaseClass(Base):
         Execute sqlalchemy query.
 
         Args:
-            query (Query): input query object
-            limit (int): Maximum number of results. (0 = all)
+            model (Any, optional): model to be queried. Defaults to None
+            query (Query, optional): input query object. Defaults to None
+            limit (int): Maximum number of results. (0 = all). Defaults to 0
 
         Returns:
             Any | List[Any]: Single result if limit = 1 or List if other.
@@ -153,6 +154,19 @@ class BaseClass(Base):
             self.__database_session__.rollback()
 
 
+class ConfigItem(BaseClass):
+    id = Column(INTEGER, primary_key=True)
+    key = Column(String(32))
+    value = Column(JSON)
+
+    def __repr__(self):
+        return f"ConfigItem({self.key} : {self.value})"
+
+    @classmethod
+    def get_config_items(cls):
+        return cls.__database_session__.query(cls).all()
+
+
 from .controls import *
 # import order must go: orgs, kit, subs due to circular import issues
 from .organizations import *

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

@@ -43,7 +43,7 @@ class ControlType(BaseClass):
 
         Returns:
             ControlType | List[ControlType]: Single result if the limit = 1, else a list.
-        """        
+        """
         query = cls.__database_session__.query(cls)
         match name:
             case str():
@@ -83,7 +83,7 @@ class ControlType(BaseClass):
 
         Returns:
             List[ControlType]: Control types that have targets
-        """        
+        """
         return [item for item in cls.query() if item.targets != []]
 
     @classmethod
@@ -93,7 +93,7 @@ class ControlType(BaseClass):
 
         Returns:
             Pattern: Constructed pattern
-        """        
+        """
         strings = list(set([item.name.split("-")[0] for item in cls.get_positive_control_types()]))
         return re.compile(rf"(^{'|^'.join(strings)})-.*", flags=re.IGNORECASE)
 
@@ -175,19 +175,19 @@ class Control(BaseClass):
         output = []
         # logger.debug("load json string for mode (i.e. contains, matches, kraken2)")
         try:
-            # data = json.loads(getattr(self, mode))
             data = self.__getattribute__(mode)
         except TypeError:
             data = {}
         logger.debug(f"Length of data: {len(data)}")
         # logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'")
         for genus in data:
-            _dict = {}
-            _dict['name'] = self.name
-            _dict['submitted_date'] = self.submitted_date
-            _dict['genus'] = genus
+            _dict = dict(
+                name=self.name,
+                submitted_date=self.submitted_date,
+                genus=genus,
+                target='Target' if genus.strip("*") in self.controltype.targets else "Off-target"
+            )
             # logger.debug("get Target or Off-target of genus")
-            _dict['target'] = 'Target' if genus.strip("*") in self.controltype.targets else "Off-target"
             # logger.debug("set 'contains_hashes', etc for genus")
             for key in data[genus]:
                 _dict[key] = data[genus][key]
@@ -247,13 +247,13 @@ class Control(BaseClass):
             case _:
                 pass
         # by date range
-        if start_date != None and end_date == None:
+        if start_date is not None and end_date is None:
             logger.warning(f"Start date with no end date, using today.")
             end_date = date.today()
-        if end_date != None and start_date == None:
+        if end_date is not None and start_date is None:
             logger.warning(f"End date with no start date, using Jan 1, 2023")
             start_date = date(2023, 1, 1)
-        if start_date != None:
+        if start_date is not None:
             match start_date:
                 case date():
                     # logger.debug(f"Lookup control by start date({start_date})")