placeholder

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

@@ -389,13 +389,13 @@ class BaseClass(Base):
         except AttributeError:
             return super().__setattr__(key, value)
         if isinstance(field_type, InstrumentedAttribute):
-            # logger.debug(f"{key} is an InstrumentedAttribute.")
+            logger.debug(f"{key} is an InstrumentedAttribute.")
             match field_type.property:
                 case ColumnProperty():
-                    # logger.debug(f"Setting ColumnProperty to {value}")
+                    logger.debug(f"Setting ColumnProperty to {value}")
                     return super().__setattr__(key, value)
                 case _RelationshipDeclared():
-                    # logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
+                    logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
                     if field_type.property.uselist:
                         logger.debug(f"Setting with uselist")
                         existing = self.__getattribute__(key)
@@ -409,7 +409,8 @@ class BaseClass(Base):
                                 value = existing + [value]
                         else:
                             if isinstance(value, list):
-                                value = value
+                                # value = value
+                                pass
                             else:
                                 value = [value]
                         value = list(set(value))
@@ -421,7 +422,13 @@ class BaseClass(Base):
                                 value = value[0]
                             else:
                                 raise ValueError("Object is too long to parse a single value.")
-                        return super().__setattr__(key, value)
+                        try:
+                            return super().__setattr__(key, value)
+                        except AttributeError:
+                            logger.debug(f"Possible attempt to set relationship to simple var type.")
+                            relationship_class = field_type.property.entity.entity
+                            value = relationship_class.query(name=value)
+                            return super().__setattr__(key, value)
                 case _:
                     return super().__setattr__(key, value)
         else:

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

@@ -46,7 +46,7 @@ class ClientSubmission(BaseClass, LogMixin):
     """
 
     id = Column(INTEGER, primary_key=True)  #: primary key
-    submitter_plate_num = Column(String(127), unique=True)  #: The number given to the submission by the submitting lab
+    submitter_plate_id = 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 org
     submitting_lab_id = Column(INTEGER, ForeignKey("_organization.id", ondelete="SET NULL",
@@ -56,7 +56,7 @@ class ClientSubmission(BaseClass, LogMixin):
     sample_count = Column(INTEGER)  #: Number of samples in the submission
     comment = Column(JSON)
     runs = relationship("BasicSubmission", back_populates="client_submission")  #: many-to-one relationship
-
+    misc_info = Column(JSON)
     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
@@ -92,6 +92,16 @@ class ClientSubmission(BaseClass, LogMixin):
             except AttributeError:
                 self._submission_category = "NA"
 
+    def __init__(self):
+        super().__init__()
+        self.misc_info = {}
+
+    def set_attribute(self, key, value):
+        if hasattr(self, key):
+            super().__setattr__(key, value)
+        else:
+            self.misc_info[key] = value
+
     @classmethod
     def recruit_parser(cls):
         pass
@@ -237,7 +247,7 @@ class ClientSubmission(BaseClass, LogMixin):
         output = {
             "id": self.id,
             "submission_type": self.submission_type_name,
-            "submitter_plate_number": self.submitter_plate_num,
+            "submitter_plate_number": self.submitter_plate_id,
             "submitted_date": self.submitted_date.strftime("%Y-%m-%d"),
             "submitting_lab": sub_lab,
             "sample_count": self.sample_count,
@@ -279,11 +289,14 @@ class ClientSubmission(BaseClass, LogMixin):
         output["runs"] = runs
         return output
 
+
 class BasicSubmission(BaseClass, LogMixin):
     """
     Object for an entire submission run. Links to client submissions, reagents, equipment, processes
     """
 
+
+
     id = Column(INTEGER, primary_key=True)  #: primary key
     rsl_plate_num = Column(String(32), unique=True, nullable=False)  #: RSL name (e.g. RSL-22-0012)
     client_submission_id = Column(INTEGER, ForeignKey("_clientsubmission.id", ondelete="SET NULL",
@@ -384,6 +397,10 @@ class BasicSubmission(BaseClass, LogMixin):
     def organization(self):
         return self.submitting_lab
 
+    @hybrid_property
+    def name(self):
+        return self.rsl_plate_num
+
     @classproperty
     def jsons(cls) -> List[str]:
         """
@@ -567,8 +584,8 @@ class BasicSubmission(BaseClass, LogMixin):
             "id": self.id,
             "plate_number": self.rsl_plate_num,
             "submission_type": self.client_submission.submission_type_name,
-            "submitter_plate_number": self.client_submission.submitter_plate_num,
-            "submitted_date": self.client_submission.submitted_date.strftime("%Y-%m-%d"),
+            "submitter_plate_number": self.client_submission.submitter_plate_id,
+            "started_date": self.client_submission.submitted_date.strftime("%Y-%m-%d"),
             "submitting_lab": sub_lab,
             "sample_count": self.client_submission.sample_count,
             "extraction_kit": "Change submissions.py line 388",