Renaming ReagentType to ReagentRole

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

@@ -13,24 +13,27 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 # table containing organization/contact relationship
 orgs_contacts = Table(
-                        "_orgs_contacts", 
-                        Base.metadata, 
-                        Column("org_id", INTEGER, ForeignKey("_organization.id")), 
-                        Column("contact_id", INTEGER, ForeignKey("_contact.id")), 
-                        # __table_args__ = {'extend_existing': True} 
-                        extend_existing = True
-                    )
+    "_orgs_contacts",
+    Base.metadata,
+    Column("org_id", INTEGER, ForeignKey("_organization.id")),
+    Column("contact_id", INTEGER, ForeignKey("_contact.id")),
+    # __table_args__ = {'extend_existing': True}
+    extend_existing=True
+)
+
 
 class Organization(BaseClass):
     """
     Base of organization
     """
-    
-    id = Column(INTEGER, primary_key=True) #: primary key  
-    name = Column(String(64)) #: organization name
-    submissions = relationship("BasicSubmission", back_populates="submitting_lab") #: submissions this organization has submitted
-    cost_centre = Column(String()) #: cost centre used by org for payment
-    contacts = relationship("Contact", back_populates="organization", secondary=orgs_contacts) #: contacts involved with this org
+
+    id = Column(INTEGER, primary_key=True)  #: primary key
+    name = Column(String(64))  #: organization name
+    submissions = relationship("BasicSubmission",
+                               back_populates="submitting_lab")  #: submissions this organization has submitted
+    cost_centre = Column(String())  #: cost centre used by org for payment
+    contacts = relationship("Contact", back_populates="organization",
+                            secondary=orgs_contacts)  #: contacts involved with this org
 
     def __repr__(self) -> str:
         return f"<Organization({self.name})>"
@@ -38,10 +41,10 @@ class Organization(BaseClass):
     @classmethod
     @setup_lookup
     def query(cls,
-                id:int|None=None, 
-                name:str|None=None,
-                limit:int=0,
-                ) -> Organization|List[Organization]:
+              id: int | None = None,
+              name: str | None = None,
+              limit: int = 0,
+              ) -> Organization | List[Organization]:
         """
         Lookup organizations in the database by a number of parameters.
 
@@ -51,11 +54,11 @@ class Organization(BaseClass):
 
         Returns:
             Organization|List[Organization]: 
-        """    
+        """
         query: Query = cls.__database_session__.query(cls)
         match id:
             case int():
-                query = query.filter(cls.id==id)
+                query = query.filter(cls.id == id)
                 limit = 1
             case _:
                 pass
@@ -73,33 +76,35 @@ class Organization(BaseClass):
     def save(self):
         super().save()
 
+
 class Contact(BaseClass):
     """
     Base of Contact
     """
-    
-    id = Column(INTEGER, primary_key=True) #: primary key  
-    name = Column(String(64)) #: contact name
-    email = Column(String(64)) #: contact email
-    phone = Column(String(32)) #: contact phone number
-    organization = relationship("Organization", back_populates="contacts", uselist=True, secondary=orgs_contacts) #: relationship to joined organization
-    submissions = relationship("BasicSubmission", back_populates="contact") #: submissions this contact has submitted
+
+    id = Column(INTEGER, primary_key=True)  #: primary key
+    name = Column(String(64))  #: contact name
+    email = Column(String(64))  #: contact email
+    phone = Column(String(32))  #: contact phone number
+    organization = relationship("Organization", back_populates="contacts", uselist=True,
+                                secondary=orgs_contacts)  #: relationship to joined organization
+    submissions = relationship("BasicSubmission", back_populates="contact")  #: submissions this contact has submitted
 
     def __repr__(self) -> str:
         """
         Returns:
             str: Representation of this Contact
-        """        
+        """
         return f"<Contact({self.name})>"
 
     @classmethod
     @setup_lookup
-    def query(cls, 
-                name:str|None=None,
-                email:str|None=None,
-                phone:str|None=None,
-                limit:int=0,
-                ) -> Contact|List[Contact]:
+    def query(cls,
+              name: str | None = None,
+              email: str | None = None,
+              phone: str | None = None,
+              limit: int = 0,
+              ) -> Contact | List[Contact]:
         """
         Lookup contacts in the database by a number of parameters.
 
@@ -111,29 +116,28 @@ class Contact(BaseClass):
 
         Returns:
             Contact|List[Contact]: Contact(s) of interest.
-        """            
+        """
         # super().query(session)
         query: Query = cls.__database_session__.query(cls)
         match name:
             case str():
                 # logger.debug(f"Looking up contact with name: {name}")
-                query = query.filter(cls.name==name)
+                query = query.filter(cls.name == name)
                 limit = 1
             case _:
                 pass
         match email:
             case str():
                 # logger.debug(f"Looking up contact with email: {name}")
-                query = query.filter(cls.email==email)
+                query = query.filter(cls.email == email)
                 limit = 1
             case _:
                 pass
         match phone:
             case str():
                 # logger.debug(f"Looking up contact with phone: {name}")
-                query = query.filter(cls.phone==phone)
+                query = query.filter(cls.phone == phone)
                 limit = 1
             case _:
                 pass
         return cls.execute_query(query=query, limit=limit)
-