Writer improvements.

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

@@ -644,7 +644,7 @@ class BaseClass(Base):
         return output
 
     @classmethod
-    def clean_details_dict(cls, dictionary):
+    def clean_details_for_render(cls, dictionary):
         output = {}
         for k, value in dictionary.items():
             match value:
@@ -668,7 +668,6 @@ class BaseClass(Base):
                 case _:
                     pass
             output[k] = value
-
         return output
 
 

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

@@ -1572,7 +1572,7 @@ class Procedure(BaseClass):
         for reagent in output.reagent:
             match reagent:
                 case dict():
-                    reagent['reagentrole'] = next((reagentrole.name for reagentrole in self.kittype.reagentrole if reagentrole == reagent['reagentrole']), None)
+                    # reagent['reagentrole'] = next((reagentrole.name for reagentrole in self.kittype.reagentrole if reagentrole == reagent['reagentrole']), None)
                     reagents.append(PydReagent(**reagent))
                 case PydReagent():
                     reagents.append(reagent)
@@ -2067,10 +2067,12 @@ class ProcedureReagentAssociation(BaseClass):
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['reagent']}
         output = output['reagent'].details_dict()
+
         misc = output['misc_info']
         output.update(relevant)
+        output['reagentrole'] = self.reagentrole
         output['misc_info'] = misc
-        # output['results'] = [result.details_dict() for result in output['results']]
+        logger.debug(f"Output: {pformat(output)}")
         return output
 
     def delete(self, **kwargs):

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

@@ -438,7 +438,10 @@ class Run(BaseClass, LogMixin):
         if self._started_date:
             return self._started_date
         else:
-            value = min([proc.started_date for proc in self.procedure])
+            try:
+                value = min([proc.started_date for proc in self.procedure])
+            except ValueError:
+                value = datetime.now()
             return value
 
     @started_date.setter
@@ -2191,6 +2194,7 @@ class ProcedureSampleAssociation(BaseClass):
     sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True)  #: id of associated equipment
     row = Column(INTEGER)
     column = Column(INTEGER)
+    plate_rank = Column(INTEGER)
 
     procedure = relationship(Procedure,
                              back_populates="proceduresampleassociation")  #: associated procedure