added kraken data to details.

src/submissions/backend/db/__init__.py

@@ -341,6 +341,12 @@ def submissions_to_df(ctx:dict, type:str|None=None) -> pd.DataFrame:
     # pass to lookup function
     subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, type=type)]
     df = pd.DataFrame.from_records(subs)
+    # logger.debug(f"Pre: {df['Technician']}")
+    try:
+        df = df.drop("controls", axis=1)
+    except:
+        logger.warning(f"Couldn't drop 'controls' column from submissionsheet df.")
+    # logger.debug(f"Post: {df['Technician']}")
     return df
      
     

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

@@ -1,6 +1,11 @@
 from . import Base
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey
 from sqlalchemy.orm import relationship
+import logging
+from operator import itemgetter
+import json
+
+logger = logging.getLogger(f"submissions.{__name__}")
 
 class ControlType(Base):
     """
@@ -35,3 +40,24 @@ class Control(Base):
     submission_id = Column(INTEGER, ForeignKey("_submissions.id")) #: parent submission id
     submission = relationship("BacterialCulture", back_populates="controls", foreign_keys=[submission_id]) #: parent submission
 
+
+    def to_sub_dict(self):
+        kraken = json.loads(self.kraken)
+        kraken_cnt_total = sum([kraken[item]['kraken_count'] for item in kraken])
+        new_kraken = []
+        for item in kraken:
+            kraken_percent = kraken[item]['kraken_count'] / kraken_cnt_total
+            new_kraken.append({'name': item, 'kraken_count':kraken[item]['kraken_count'], 'kraken_percent':"{0:.0%}".format(kraken_percent)})
+        new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)
+        if self.controltype.targets == []:
+            targets = ["None"]
+        else:
+            targets = self.controltype.targets
+        output = {
+            "name" : self.name,
+            "type" : self.controltype.name,
+            "targets" : " ,".join(targets),
+            "kraken" : new_kraken[0:5]
+        }
+        return output
+

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

@@ -2,6 +2,9 @@ from . import Base
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT
 from sqlalchemy.orm import relationship
 from datetime import datetime as dt
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
 
 # table containing reagents/submission relationships
 reagents_submissions = Table("_reagents_submissions", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("submission_id", INTEGER, ForeignKey("_submissions.id")))
@@ -28,6 +31,7 @@ class BasicSubmission(Base):
     reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
     extraction_info = Column(JSON) #: unstructured output from the extraction table logger.
     run_cost = Column(FLOAT(2))
+    uploaded_by = Column(String(32))
 
     __mapper_args__ = {
         "polymorphic_identity": "basic_submission",
@@ -77,6 +81,7 @@ class BasicSubmission(Base):
             "Technician": self.technician,
             "Cost": self.run_cost,
         }
+        logger.debug(f"{self.rsl_plate_num} technician: {output['Technician']}")
         return output
 
 
@@ -107,6 +112,7 @@ class BasicSubmission(Base):
         #     cost = self.extraction_kit.cost_per_run
         # except AttributeError:
         #     cost = None
+        
         output = {
             "id": self.id,
             "Plate Number": self.rsl_plate_num,
@@ -131,6 +137,13 @@ class  BacterialCulture(BasicSubmission):
     samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
     # bc_sample_id = Column(INTEGER, ForeignKey("_bc_samples.id", ondelete="SET NULL", name="fk_BC_sample_id"))
     __mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"}
+
+
+    def to_dict(self) -> dict:
+        output = super().to_dict()
+        output['controls'] = [item.to_sub_dict() for item in self.controls]
+        # logger.debug(f"{self.rsl_plate_num} technician: {output}")
+        return output
     
 
 class Wastewater(BasicSubmission):

src/submissions/backend/excel/reports.py

@@ -165,7 +165,7 @@ def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -
     """    
     df = DataFrame.from_records(input)
     safe = ['name', 'submitted_date', 'genus', 'target']
-    logger.debug(df)
+    # logger.debug(df)
     for column in df.columns:
         if "percent" in column:
             count_col = [item for item in df.columns if "count" in item][0]