Adding sample associations to basicsubmission

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

@@ -336,15 +336,15 @@ class BasicSubmission(BaseClass, LogMixin):
     kittypes = relationship("KitType", back_populates="submissions",
                                secondary=kittypes_submissions)  #: submissions this kit was used for
 
-    # submission_sample_associations = relationship(
-    #     "SubmissionSampleAssociation",
-    #     back_populates="submission",
-    #     cascade="all, delete-orphan",
-    # )  #: Relation to SubmissionSampleAssociation
-    #
-    # samples = association_proxy("submission_sample_associations",
-    #                             "sample", creator=lambda sample: SubmissionSampleAssociation(
-    #         sample=sample))  #: Association proxy to SubmissionSampleAssociation.samples
+    submission_sample_associations = relationship(
+        "SubmissionSampleAssociation",
+        back_populates="submission",
+        cascade="all, delete-orphan",
+    )  #: Relation to SubmissionSampleAssociation
+
+    samples = association_proxy("submission_sample_associations",
+                                "sample", creator=lambda sample: SubmissionSampleAssociation(
+            sample=sample))  #: Association proxy to SubmissionSampleAssociation.samples
 
     submission_reagent_associations = relationship(
         "SubmissionReagentAssociation",
@@ -600,20 +600,20 @@ class BasicSubmission(BaseClass, LogMixin):
             except Exception as e:
                 logger.error(f"We got an error retrieving reagents: {e}")
                 reagents = []
-            finally:
-                dicto, _ = self.extraction_kit.construct_xl_map_for_use(self.submission_type)
-                for k, v in dicto.items():
-                    if k == 'info':
-                        continue
-                    if not any([item['role'] == k for item in reagents]):
-                        expiry = "NA"
-                        reagents.append(
-                            dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
-                                 missing=True))
+            # finally:
+            #     dicto, _ = self.extraction_kit.construct_xl_map_for_use(self.submission_type)
+            #     for k, v in dicto.items():
+            #         if k == 'info':
+            #             continue
+            #         if not any([item['role'] == k for item in reagents]):
+            #             expiry = "NA"
+            #             reagents.append(
+            #                 dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
+            #                      missing=True))
             samples = self.generate_associations(name="submission_sample_associations")
             equipment = self.generate_associations(name="submission_equipment_associations")
             tips = self.generate_associations(name="submission_tips_associations")
-            cost_centre = self.cost_centre
+            # cost_centre = self.cost_centre
             custom = self.custom
             controls = [item.to_sub_dict() for item in self.controls]
         else:
@@ -648,7 +648,7 @@ class BasicSubmission(BaseClass, LogMixin):
         output["comment"] = comments
         output["equipment"] = equipment
         output["tips"] = tips
-        output["cost_centre"] = cost_centre
+        # output["cost_centre"] = cost_centre
         output["signed_by"] = self.signed_by
         output["contact"] = contact
         output["contact_phone"] = contact_phone

src/submissions/backend/validators/pydant.py

@@ -1343,7 +1343,7 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
     comment: dict | None = Field(default=dict(value="", missing=True), validate_default=True)
     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)
-    submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
+    submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
 
     @field_validator("sample_count")
     @classmethod
@@ -1354,7 +1354,7 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
             raise f"sample count value must be an integer"
         return value
 
-    @field_validator("submitter_plate_num")
+    @field_validator("submitter_plate_id")
     @classmethod
     def create_submitter_plate_num(cls, value, values):
         if value['value'] in [None, "None"]:
@@ -1373,6 +1373,13 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
             check = True
         if check:
             return dict(value=date.today(), missing=True)
+        else:
+            match value['value']:
+                case str():
+                    value['value'] = datetime.strptime(value['value'], "%Y-%m-%d")
+                    value['value'] = datetime.combine(value['value'], datetime.now().time())
+                case _:
+                    pass
         return value
 
     def filter_field(self, key: str) -> Any:
@@ -1437,11 +1444,5 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
         for key, value in self.improved_dict().items():
             if isinstance(value, dict):
                 value = value['value']
-            # if hasattr(sql, key):
-            #     try:
             sql.set_attribute(key, value)
-            #     except AttributeError:
-            #         continue
-            # else:
-            #     sql.misc_info[key] = value
-        print(sql.__dict__)
+        return sql