Checking kit integrity on import.

src/submissions/backend/db/__init__.py

@@ -576,17 +576,23 @@ def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None,
         list: Control instances.
     """
     
-    # logger.debug(f"Using dates: {start_date} to {end_date}")
-    query = ctx['database_session'].query(models.ControlType).filter_by(name=con_type)
-    try:
-        output = query.first().instances
-    except AttributeError:
-        output = None
-    # Hacky solution to my not being able to get the sql query to work.
+    logger.debug(f"Using dates: {start_date} to {end_date}")
     if start_date != None and end_date != None:
-        output = [item for item in output if item.submitted_date.date() > start_date and item.submitted_date.date() < end_date]
-    # logger.debug(f"Type {con_type}: {query.first()}")
+        output = ctx['database_session'].query(models.Control).join(models.ControlType).filter_by(name=con_type).filter(models.Control.submitted_date.between(start_date.strftime("%Y-%m-%d"), end_date.strftime("%Y-%m-%d"))).all()
+    else:
+        output = ctx['database_session'].query(models.Control).join(models.ControlType).filter_by(name=con_type).all()
+    logger.debug(f"Returned controls between dates: {output}")
     return output
+    # query = ctx['database_session'].query(models.ControlType).filter_by(name=con_type)
+    # try:
+    #     output = query.first().instances
+    # except AttributeError:
+    #     output = None
+    # # Hacky solution to my not being able to get the sql query to work.
+    # if start_date != None and end_date != None:
+    #     output = [item for item in output if item.submitted_date.date() > start_date and item.submitted_date.date() < end_date]
+    # # logger.debug(f"Type {con_type}: {query.first()}")
+    # return output
 
 
 def get_control_subtypes(ctx:dict, type:str, mode:str) -> list[str]:

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

@@ -39,9 +39,18 @@ class Control(Base):
     # UniqueConstraint('name', name='uq_control_name')
     submission_id = Column(INTEGER, ForeignKey("_submissions.id")) #: parent submission id
     submission = relationship("BacterialCulture", back_populates="controls", foreign_keys=[submission_id]) #: parent submission
+    refseq_version = Column(String(16))
+    kraken2_version = Column(String(16))
+    kraken2_db_version = Column(String(32))
 
 
-    def to_sub_dict(self):
+    def to_sub_dict(self) -> dict:
+        """
+        Converts object into convenient dictionary for use in submission summary
+
+        Returns:
+            dict: output dictionary containing: Name, Type, Targets, Top Kraken results
+        """        
         kraken = json.loads(self.kraken)
         kraken_cnt_total = sum([kraken[item]['kraken_count'] for item in kraken])
         new_kraken = []
@@ -61,3 +70,46 @@ class Control(Base):
         }
         return output
 
+    def convert_by_mode(self, mode:str) -> list[dict]:
+        """
+        split control object into analysis types
+
+        Args:
+            control (models.Control): control to be parsed into list
+            mode (str): analysis type
+
+        Returns:
+            list[dict]: list of records
+        """    
+        output = []
+        data = json.loads(getattr(self, mode))
+        # if len(data) == 0:
+        #     data = self.create_dummy_data(mode)
+        logger.debug(f"Length of data: {len(data)}")
+        for genus in data:
+            _dict = {}
+            _dict['name'] = self.name
+            _dict['submitted_date'] = self.submitted_date
+            _dict['genus'] = genus
+            _dict['target'] = 'Target' if genus.strip("*") in self.controltype.targets else "Off-target"
+            
+            for key in data[genus]:
+                _dict[key] = data[genus][key]
+                if _dict[key] == {}:
+                    print(self.name, mode)
+            output.append(_dict)
+        # logger.debug(output)
+        return output
+    
+    def create_dummy_data(self, mode):
+        match mode:
+            case "contains":
+                data = {"Nothing": {"contains_hashes":"0/400", "contains_ratio":0.0}}
+            case "matches":
+                data = {"Nothing": {"matches_hashes":"0/400", "matches_ratio":0.0}}
+            case "kraken":
+                data = {"Nothing": {"kraken_percent":0.0, "kraken_count":0}}
+            case _:
+                data = {}
+        return data
+

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

@@ -4,6 +4,7 @@ from sqlalchemy.orm import relationship
 from datetime import datetime as dt
 import logging
 import json
+from json.decoder import JSONDecodeError
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -74,6 +75,9 @@ class BasicSubmission(Base):
             ext_info = json.loads(self.extraction_info)
         except TypeError:
             ext_info = None
+        except JSONDecodeError as e:
+            ext_info = None
+            logger.debug(f"Json error in {self.rsl_plate_num}: {e}")
         try:
             reagents = [item.to_sub_dict() for item in self.reagents]
         except: