Renaming ReagentType to ReagentRole

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

@@ -83,6 +83,7 @@ class Contact(BaseClass):
     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:
         """

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

@@ -10,7 +10,7 @@ from zipfile import ZipFile
 from tempfile import TemporaryDirectory
 from operator import attrgetter, itemgetter
 from pprint import pformat
-from . import BaseClass, Reagent, SubmissionType, KitType, Organization
+from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.orm.attributes import flag_modified
@@ -65,6 +65,9 @@ class BasicSubmission(BaseClass):
         String(64))  #: ["Research", "Diagnostic", "Surveillance", "Validation"], else defaults to submission_type_name
     cost_centre = Column(
         String(64))  #: Permanent storage of used cost centre in case organization field changed in the future.
+    contact = relationship("Contact", back_populates="submissions")  #: client org
+    contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
+                                                   name="fk_BS_contact_id"))  #: client lab id from _organizations
 
     submission_sample_associations = relationship(
         "SubmissionSampleAssociation",
@@ -255,6 +258,7 @@ class BasicSubmission(BaseClass):
             "sample_count": self.sample_count,
             "extraction_kit": ext_kit,
             "cost": self.run_cost,
+
         }
         if report:
             return output
@@ -304,6 +308,9 @@ 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
+
         return output
 
     def calculate_column_count(self) -> int:
@@ -453,6 +460,8 @@ class BasicSubmission(BaseClass):
                 # logger.debug(f"Looking up organization: {value}")
                 field_value = Organization.query(name=value)
                 # logger.debug(f"Got {field_value} for organization {value}")
+            case "contact":
+                field_value = Contact.query(name=value)
             case "samples":
                 for sample in value:
                     # logger.debug(f"Parsing {sample} to sql.")
@@ -1196,7 +1205,7 @@ class BacterialCulture(BasicSubmission):
                 new_lot = matched.group()
                 try:
                     pos_control_reg = \
-                    [reg for reg in input_dict['reagents'] if reg['type'] == "Bacterial-Positive Control"][0]
+                    [reg for reg in input_dict['reagents'] if reg['role'] == "Bacterial-Positive Control"][0]
                 except IndexError:
                     logger.error(f"No positive control reagent listed")
                     return input_dict

src/submissions/backend/excel/writer.py

@@ -148,7 +148,7 @@ class ReagentWriter(object):
         output = []
         for reagent in reagent_list:
             try:
-                mp_info = map[reagent['type']]
+                mp_info = map[reagent['role']]
             except KeyError:
                 continue
             placeholder = copy(reagent)

src/submissions/backend/validators/pydant.py

@@ -104,7 +104,7 @@ class PydReagent(BaseModel):
         if value != None:
             return convert_nans_to_nones(str(value))
         else:
-            return values.data['type']
+            return values.data['role']
 
     def improved_dict(self) -> dict:
         try:
@@ -123,7 +123,7 @@ class PydReagent(BaseModel):
         #     output[k] = value
         return {k: getattr(self, k) for k in fields}
 
-    def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, SubmissionReagentAssociation]:
+    def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, SubmissionReagentAssociation, Report]:
         """
         Converts this instance into a backend.db.models.kit.Reagent instance
 
@@ -168,6 +168,7 @@ class PydReagent(BaseModel):
                     # reagent.reagent_submission_associations.append(assoc)
                 else:
                     assoc = None
+            report.add_result(Result(owner = __name__, code=0, msg="New reagent created.", status="Information"))
         else:
             if submission is not None and reagent not in submission.reagents:
                 assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
@@ -177,7 +178,8 @@ class PydReagent(BaseModel):
                 assoc = None
                 # add end-of-life extension from reagent type to expiry date
                 # NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
-        return reagent, assoc
+
+        return reagent, assoc, report
 
 
 class PydSample(BaseModel, extra='allow'):
@@ -353,6 +355,7 @@ class PydSubmission(BaseModel, extra='allow'):
     samples: List[PydSample]
     equipment: List[PydEquipment] | None = []
     cost_centre: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
+    contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
 
     @field_validator('equipment', mode='before')
     @classmethod
@@ -567,6 +570,17 @@ class PydSubmission(BaseModel, extra='allow'):
             case _:
                 return value
 
+    @field_validator("contact")
+    @classmethod
+    def get_contact_from_org(cls, value, values):
+        check = Contact.query(name=value['value'])
+        if check is None:
+            org = Organization.query(name=values.data['submitting_lab']['value'])
+            contact = org.contacts[0].name
+            return dict(value=contact, missing=True)
+        else:
+            return value
+
     def __init__(self, **data):
         super().__init__(**data)
         # this could also be done with default_factory
@@ -664,7 +678,7 @@ class PydSubmission(BaseModel, extra='allow'):
                         instance.submission_reagent_associations = []
                     # logger.debug(f"Looking through {self.reagents}")
                     for reagent in self.reagents:
-                        reagent, assoc = reagent.toSQL(submission=instance)
+                        reagent, assoc, _ = reagent.toSQL(submission=instance)
                         # logger.debug(f"Association: {assoc}")
                         if assoc is not None:# and assoc not in instance.submission_reagent_associations:
                             instance.submission_reagent_associations.append(assoc)