mid refactor for improved rebustness and readability

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

@@ -21,7 +21,7 @@ class KitType(Base):
     name = Column(String(64), unique=True) #: name of kit
     submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
     used_for = Column(JSON) #: list of names of sample types this kit can process
-    cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit
+    cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit NOTE: depreciated, use the constant and mutable costs instead
     mutable_cost = Column(FLOAT(2)) #: dollar amount that can change with number of columns (reagents, tips, etc)
     constant_cost = Column(FLOAT(2)) #: dollar amount that will remain constant (plates, man hours, etc)
     reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
@@ -81,9 +81,7 @@ class Reagent(Base):
         Returns:
             str: string representing this object's type and lot number
         """    
-        lot = str(self.lot)
-        r_type = str(self.type)    
-        return f"{r_type} - {lot}"
+        return str(self.lot)
 
     def to_sub_dict(self) -> dict:
         """

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

@@ -16,6 +16,9 @@ class WWSample(Base):
     rsl_plate = relationship("Wastewater", back_populates="samples") #: relationship to parent plate
     rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_submission_id"))
     collection_date = Column(TIMESTAMP) #: Date submission received
+    well_number = Column(String(8)) #: location on plate
+    # The following are fields from the sample tracking excel sheet Ruth put together.
+    # I have no idea when they will be implemented or how.
     testing_type = Column(String(64)) 
     site_status = Column(String(64))
     notes = Column(String(2000))
@@ -24,7 +27,7 @@ class WWSample(Base):
     seq_submitted = Column(BOOLEAN())
     ww_seq_run_id = Column(String(64))
     sample_type = Column(String(8))
-    well_number = Column(String(8)) #: location on plate
+    
 
     def to_string(self) -> str:
         """

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

@@ -35,6 +35,7 @@ class BasicSubmission(Base):
     run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from kit costs at time of creation.
     uploaded_by = Column(String(32)) #: user name of person who submitted the submission to the database.
 
+    # Allows for subclassing into ex. BacterialCulture, Wastewater, etc.
     __mapper_args__ = {
         "polymorphic_identity": "basic_submission",
         "polymorphic_on": submission_type,
@@ -148,23 +149,25 @@ class BasicSubmission(Base):
         }
         return output
 
-# Below are the custom submission 
+# Below are the custom submission types
 
 class  BacterialCulture(BasicSubmission):
     """
     derivative submission type from BasicSubmission
     """    
-    # control_id = Column(INTEGER, ForeignKey("_control_samples.id", ondelete="SET NULL", name="fk_BC_control_id"))
     controls = relationship("Control", back_populates="submission", uselist=True) #: A control sample added to submission
     samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
-    # bc_sample_id = Column(INTEGER, ForeignKey("_bc_samples.id", ondelete="SET NULL", name="fk_BC_sample_id"))
     __mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"}
 
-
     def to_dict(self) -> dict:
+        """
+        Extends parent class method to add controls to dict
+
+        Returns:
+            dict: dictionary used in submissions summary
+        """        
         output = super().to_dict()
         output['controls'] = [item.to_sub_dict() for item in self.controls]
-        # logger.debug(f"{self.rsl_plate_num} technician: {output}")
         return output