Added importing of PCR results.

src/submissions/backend/db/functions.py

@@ -5,6 +5,7 @@ Convenience functions for interacting with the database.
 from . import models
 from .models.kits import reagenttypes_kittypes
 from .models.submissions import reagents_submissions
+from .models.samples import WWSample
 import pandas as pd
 import sqlalchemy.exc
 import sqlite3
@@ -392,7 +393,11 @@ def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
     try:
         df = df.drop("ext_info", axis=1)
     except:
-        logger.warning(f"Couldn't drop 'controls' column from submissionsheet df.")
+        logger.warning(f"Couldn't drop 'ext_info' column from submissionsheet df.")
+    try:
+        df = df.drop("pcr_info", axis=1)
+    except:
+        logger.warning(f"Couldn't drop 'pcr_info' column from submissionsheet df.")
     return df
      
     
@@ -676,4 +681,39 @@ def delete_submission_by_id(ctx:dict, id:int) -> None:
     for sample in sub.samples:
         ctx['database_session'].delete(sample)
     ctx["database_session"].delete(sub)
+    ctx["database_session"].commit()
+
+
+def lookup_ww_sample_by_rsl_sample_number(ctx:dict, rsl_number:str) -> models.WWSample:
+    """
+    Retrieves wastewater sampel from database by rsl sample number
+
+    Args:
+        ctx (dict): settings passed dwon from gui
+        rsl_number (str): sample number assigned by robotics lab
+
+    Returns:
+        models.WWSample: instance of wastewater sample
+    """    
+    return ctx['database_session'].query(models.WWSample).filter(models.WWSample.rsl_number==rsl_number).first()
+
+
+def update_ww_sample(ctx:dict, sample_obj:dict):
+    """
+    Retrieves wastewater sample by rsl number (sample_obj['sample']) and updates values from constructed dictionary
+
+    Args:
+        ctx (dict): settings passed down from gui
+        sample_obj (dict): dictionary representing new values for database object
+    """    
+    ww_samp = lookup_ww_sample_by_rsl_sample_number(ctx=ctx, rsl_number=sample_obj['sample'])
+    if ww_samp != None:
+        for key, value in sample_obj.items():
+            logger.debug(f"Setting {key} to {value}")
+            # set attribute 'key' to 'value'
+            setattr(ww_samp, key, value)
+    else:
+        logger.error(f"Unable to find sample {sample_obj['sample']}")
+        return
+    ctx['database_session'].add(ww_samp)
     ctx["database_session"].commit()

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

@@ -2,7 +2,7 @@
 All models for individual samples.
 '''
 from . import Base
-from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, FLOAT, BOOLEAN
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, FLOAT, BOOLEAN, JSON
 from sqlalchemy.orm import relationship
 
 
@@ -25,11 +25,12 @@ class WWSample(Base):
     testing_type = Column(String(64)) 
     site_status = Column(String(64))
     notes = Column(String(2000))
-    ct_n1 = Column(FLOAT(2))
-    ct_n2 = Column(FLOAT(2))
+    ct_n1 = Column(FLOAT(2)) #: AKA ct for N1
+    ct_n2 = Column(FLOAT(2)) #: AKA ct for N2
     seq_submitted = Column(BOOLEAN())
     ww_seq_run_id = Column(String(64))
     sample_type = Column(String(8))
+    pcr_results = Column(JSON)
     
 
     def to_string(self) -> str:
@@ -48,9 +49,13 @@ class WWSample(Base):
         Returns:
             dict: well location and id NOTE: keys must sync with BCSample to_sub_dict below
         """
+        if self.ct_n1 != None and self.ct_n2 != None:
+            name = f"{self.ww_sample_full_id}\n\t- ct N1: {'{:.2f}'.format(self.ct_n1)}, ct N2: {'{:.2f}'.format(self.ct_n1)}"
+        else:
+            name = self.ww_sample_full_id
         return {
             "well": self.well_number,
-            "name": self.ww_sample_full_id,
+            "name": name,
         }
 
 

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

@@ -179,5 +179,20 @@ class Wastewater(BasicSubmission):
     derivative submission type from BasicSubmission
     """    
     samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
+    pcr_info = Column(JSON)
     # ww_sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
-    __mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}
+    __mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}
+
+    def to_dict(self) -> dict:
+        """
+        Extends parent class method to add controls to dict
+
+        Returns:
+            dict: dictionary used in submissions summary
+        """        
+        output = super().to_dict()
+        try:
+            output['pcr_info'] = json.loads(self.pcr_info)
+        except TypeError as e:
+            pass
+        return output