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)
-    

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

@@ -248,6 +248,7 @@ class BasicSubmission(BaseClass):
             ext_info = self.extraction_info
         except TypeError:
             ext_info = None
+
         output = {
             "id": self.id,
             "plate_number": self.rsl_plate_num,
@@ -257,8 +258,7 @@ class BasicSubmission(BaseClass):
             "submitting_lab": sub_lab,
             "sample_count": self.sample_count,
             "extraction_kit": ext_kit,
-            "cost": self.run_cost,
-
+            "cost": self.run_cost
         }
         if report:
             return output
@@ -299,6 +299,15 @@ class BasicSubmission(BaseClass):
         except Exception as e:
             logger.error(f"Error setting comment: {self.comment}, {e}")
             comments = None
+        try:
+            contact = self.contact.name
+        except AttributeError as e:
+            logger.error(f"Problem setting contact: {e}")
+            contact = "NA"
+        try:
+            contact_phone = self.contact.phone
+        except AttributeError:
+            contact_phone = "NA"
         output["submission_category"] = self.submission_category
         output["technician"] = self.technician
         output["reagents"] = reagents
@@ -308,9 +317,9 @@ class BasicSubmission(BaseClass):
         output["equipment"] = equipment
         output["cost_centre"] = cost_centre
         output["signed_by"] = self.signed_by
-        output["contact"] = self.contact.name
-        output["contact_phone"] = self.contact.phone
-
+        # logger.debug(f"Setting contact to: {contact} of type: {type(contact)}")
+        output["contact"] = contact
+        output["contact_phone"] = contact_phone
         return output
 
     def calculate_column_count(self) -> int:
@@ -431,7 +440,7 @@ class BasicSubmission(BaseClass):
         excluded = ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
                     'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
                     'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
-                    'signed_by']
+                    'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact']
         for item in excluded:
             try:
                 df = df.drop(item, axis=1)
@@ -544,7 +553,6 @@ class BasicSubmission(BaseClass):
         # logger.debug("To dict complete")
         new_dict = {}
         for key, value in dicto.items():
-            # start = time()
             # logger.debug(f"Checking {key}")
             missing = value is None or value in ['', 'None']
             match key:
@@ -1403,6 +1411,10 @@ class WastewaterArtic(BasicSubmission):
     gel_info = Column(JSON)  #: unstructured data from gel.
     gel_controls = Column(JSON)  #: locations of controls on the gel
     source_plates = Column(JSON)  #: wastewater plates that samples come from
+    artic_date = Column(TIMESTAMP)  #: Date Artic Performed
+    ngs_date = Column(TIMESTAMP)  #: Date submission received
+    gel_date = Column(TIMESTAMP)  #: Date submission received
+    gel_barcode = Column(String(16))
 
     __mapper_args__ = dict(polymorphic_identity="Wastewater Artic",
                            polymorphic_load="inline",
@@ -1418,12 +1430,18 @@ class WastewaterArtic(BasicSubmission):
         output = super().to_dict(full_data=full_data, backup=backup, report=report)
         if self.artic_technician in [None, "None"]:
             output['artic_technician'] = self.technician
+        else:
+            output['artic_technician'] = self.artic_technician
         if report:
             return output
         output['gel_info'] = self.gel_info
         output['gel_image'] = self.gel_image
         output['dna_core_submission_number'] = self.dna_core_submission_number
         output['source_plates'] = self.source_plates
+        output['artic_date'] = self.artic_date or self.submitted_date
+        output['ngs_date'] = self.ngs_date or self.submitted_date
+        output['gel_date'] = self.gel_date or self.submitted_date
+        output['gel_barcode'] = self.gel_barcode
         return output
 
     @classmethod
@@ -1756,19 +1774,22 @@ class WastewaterArtic(BasicSubmission):
                 output.append(dicto)
                 continue
             for item in self.source_plates:
-                old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
+                if assoc.sample.id is None:
+                    old_plate = None
+                else:
+                    old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
                 if old_plate is not None:
                     set_plate = old_plate.submission.rsl_plate_num
-                    logger.debug(dicto['WW Processing Num'])
-                    if dicto['WW Processing Num'].startswith("NTC"):
-                        dicto['Well'] = dicto['WW Processing Num']
+                    # logger.debug(f"Dictionary: {pformat(dicto)}")
+                    if dicto['ww_processing_num'].startswith("NTC"):
+                        dicto['well'] = dicto['ww_processing_num']
                     else:
-                        dicto['Well'] = f"{row_map[old_plate.row]}{old_plate.column}"
+                        dicto['well'] = f"{row_map[old_plate.row]}{old_plate.column}"
                     break
-                elif dicto['WW Processing Num'].startswith("NTC"):
-                    dicto['Well'] = dicto['WW Processing Num']
+                elif dicto['ww_processing_num'].startswith("NTC"):
+                    dicto['well'] = dicto['ww_processing_num']
             dicto['plate_name'] = set_plate
-            logger.debug(f"Here is our raw sample: {pformat(dicto)}")
+            # logger.debug(f"Here is our raw sample: {pformat(dicto)}")
             output.append(dicto)
         return output
 
@@ -1801,7 +1822,7 @@ class WastewaterArtic(BasicSubmission):
         fname = select_open_file(obj=obj, file_extension="jpg")
         dlg = GelBox(parent=obj, img_path=fname, submission=self)
         if dlg.exec():
-            self.dna_core_submission_number, img_path, output, comment = dlg.parse_form()
+            self.dna_core_submission_number, self.gel_barcode, img_path, output, comment = dlg.parse_form()
             self.gel_image = img_path.name
             self.gel_info = output
             dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
@@ -2135,7 +2156,7 @@ class BasicSample(BaseClass):
         if dlg.exec():
             pass
 
-#Below are the custom sample types
+# Below are the custom sample types
 
 class WastewaterSample(BasicSample):
     """
@@ -2235,6 +2256,7 @@ class WastewaterSample(BasicSample):
             searchables.append(dict(label=label, field=item))
         return searchables
 
+
 class BacterialCultureSample(BasicSample):
     """
     base of bacterial culture sample