documentation and converted to username based exclusion of adding new kits

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

@@ -3,26 +3,29 @@ from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table
 from sqlalchemy.orm import relationship
 from datetime import datetime as dt
 
+# table containing reagents/submission relationships
 reagents_submissions = Table("_reagents_submissions", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("submission_id", INTEGER, ForeignKey("_submissions.id")))
 
 class BasicSubmission(Base):
-
+    """
+    Base of basic submission which polymorphs into BacterialCulture and Wastewater
+    """
     __tablename__ = "_submissions"
 
     id = Column(INTEGER, primary_key=True) #: primary key   
     rsl_plate_num = Column(String(32), unique=True) #: RSL name (e.g. RSL-22-0012)
     submitter_plate_num = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
     submitted_date = Column(TIMESTAMP) #: Date submission received
-    submitting_lab = relationship("Organization", back_populates="submissions") #: client
+    submitting_lab = relationship("Organization", back_populates="submissions") #: client org
     submitting_lab_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_BS_sublab_id"))
     sample_count = Column(INTEGER) #: Number of samples in the submission
     extraction_kit = relationship("KitType", back_populates="submissions") #: The extraction kit used
     extraction_kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", name="fk_BS_extkit_id"))
-    submission_type = Column(String(32))
-    technician = Column(String(64))
+    submission_type = Column(String(32)) #: submission type (should be string in D3 of excel sheet)
+    technician = Column(String(64)) #: initials of processing tech
     # Move this into custom types?
-    reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions)
-    reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id"))
+    reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions) #: relationship to reagents
+    reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
 
     __mapper_args__ = {
         "polymorphic_identity": "basic_submission",
@@ -30,10 +33,23 @@ class BasicSubmission(Base):
         "with_polymorphic": "*",
     }
 
-    def to_string(self):
+    def to_string(self) -> str:
+        """
+        string presenting basic submission
+
+        Returns:
+            str: string representing rsl plate number and submitter plate number
+        """        
         return f"{self.rsl_plate_num} - {self.submitter_plate_num}"
 
-    def to_dict(self):
+    def to_dict(self) -> dict:
+        """
+        dictionary used in submissions summary
+
+        Returns:
+            dict: dictionary used in submissions summary
+        """        
+        # get lab from nested organization object
         try:
             sub_lab = self.submitting_lab.name
         except AttributeError:
@@ -42,6 +58,7 @@ class BasicSubmission(Base):
             sub_lab = sub_lab.replace("_", " ").title()
         except AttributeError:
             pass
+        # get extraction kit name from nested kit object
         try:
             ext_kit = self.extraction_kit.name
         except AttributeError:
@@ -60,7 +77,14 @@ class BasicSubmission(Base):
         return output
 
 
-    def report_dict(self):
+    def report_dict(self) -> dict:
+        """
+        dictionary used in creating reports
+
+        Returns:
+            dict: dictionary used in creating reports
+        """        
+        # get lab name from nested organization object 
         try:
             sub_lab = self.submitting_lab.name
         except AttributeError:
@@ -69,10 +93,12 @@ class BasicSubmission(Base):
             sub_lab = sub_lab.replace("_", " ").title()
         except AttributeError:
             pass
+        # get extraction kit name from nested kittype object
         try:
             ext_kit = self.extraction_kit.name
         except AttributeError:
             ext_kit = None
+        # get extraction kit cost from nested kittype object
         try:
             cost = self.extraction_kit.cost_per_run
         except AttributeError:
@@ -93,6 +119,9 @@ class BasicSubmission(Base):
 # Below are the custom submission 
 
 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)
@@ -101,6 +130,9 @@ class  BacterialCulture(BasicSubmission):
     
 
 class Wastewater(BasicSubmission):
+    """
+    derivative submission type from BasicSubmission
+    """    
     samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
     # ww_sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
     __mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}