Updated parsers and chart constructors.

src/submissions/backend/db/functions.py

@@ -20,6 +20,7 @@ from getpass import getuser
 import numpy as np
 import yaml
 from pathlib import Path
+from math import ceil
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -161,9 +162,13 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
     # calculate cost of the run: immutable cost + mutable times number of columns
     # This is now attached to submission upon creation to preserve at-run costs incase of cost increase in the future.
     try:
-        instance.run_cost = instance.extraction_kit.immutable_cost + (instance.extraction_kit.mutable_cost * ((instance.sample_count / 8)/12))
-    except (TypeError, AttributeError):
-        logger.debug(f"Looks like that kit doesn't have cost breakdown yet, using full plate cost.")
+        # ceil(instance.sample_count / 8) will get number of columns
+        # the cost of a full run multiplied by (that number / 12) is x twelfths the cost of a full run
+        logger.debug(f"Instance extraction kit details: {instance.extraction_kit.__dict__}")
+        cols_count = ceil(int(instance.sample_count) / 8)
+        instance.run_cost = instance.extraction_kit.constant_cost + (instance.extraction_kit.mutable_cost * (cols_count / 12))
+    except (TypeError, AttributeError) as e:
+        logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using full plate cost.")
         instance.run_cost = instance.extraction_kit.cost_per_run
     # We need to make sure there's a proper rsl plate number
     try:

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

@@ -105,6 +105,9 @@ class Control(Base):
             for key in data[genus]:
                 _dict[key] = data[genus][key]
             output.append(_dict)
+        # Have to triage kraken data to keep program from getting overwhelmed
+        if "kraken" in mode:
+            output = sorted(output, key=lambda d: d[f"{mode}_count"], reverse=True)[:49]
         return output
     
     def create_dummy_data(self, mode:str) -> dict:

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

@@ -25,8 +25,8 @@ class KitType(Base):
     submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
     used_for = Column(JSON) #: list of names of sample types this kit can process
     cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit NOTE: depreciated, use the constant and mutable costs instead
-    mutable_cost = Column(FLOAT(2)) #: dollar amount that can change with number of columns (reagents, tips, etc)
-    constant_cost = Column(FLOAT(2)) #: dollar amount that will remain constant (plates, man hours, etc)
+    mutable_cost = Column(FLOAT(2)) #: dollar amount per plate that can change with number of columns (reagents, tips, etc)
+    constant_cost = Column(FLOAT(2)) #: dollar amount per plate that will remain constant (plates, man hours, etc)
     reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
     reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
     
@@ -110,4 +110,16 @@ class Reagent(Base):
             "type": type,
             "lot": self.lot,
             "expiry": place_holder.strftime("%Y-%m-%d")
-        }
+        }
+    
+
+# class Discounts(Base):
+#     """
+#     Relationship table for client labs for certain kits.
+#     """
+#     __tablename__ = "_discounts"
+
+#     id = Column(INTEGER, primary_key=True) #: primary key
+#     kit = relationship("KitType") #: joined parent reagent type
+#     kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete='SET NULL', name="fk_kit_type_id"))
+#     client = relationship("Organization")

src/submissions/backend/excel/parser.py

@@ -107,8 +107,8 @@ class SheetParser(object):
             """            
             for ii, row in df.iterrows():
                 # skip positive control
-                if ii == 11:
-                    continue
+                # if ii == 12:
+                #     continue
                 logger.debug(f"Running reagent parse for {row[1]} with type {type(row[1])} and value: {row[2]} with type {type(row[2])}")
                 if not isinstance(row[2], float) and check_not_nan(row[1]):
                     # must be prefixed with 'lot_' to be recognized by gui
@@ -117,7 +117,10 @@ class SheetParser(object):
                     except AttributeError:
                         pass
                     if reagent_type == "//":
-                        reagent_type = row[0].replace(' ', '_').lower().strip()
+                        if check_not_nan(row[2]):
+                            reagent_type = row[0].replace(' ', '_').lower().strip()
+                        else:
+                            continue
                     try:
                         output_var = row[2].upper()
                     except AttributeError:
@@ -142,10 +145,11 @@ class SheetParser(object):
         # reagents
         # must be prefixed with 'lot_' to be recognized by gui
         # Todo: find a more adaptable way to read reagents.
-        reagent_range = submission_info.iloc[1:13, 4:8]
+        reagent_range = submission_info.iloc[1:14, 4:8]
+        logger.debug(reagent_range)
         parse_reagents(reagent_range)
         # get individual sample info
-        sample_parser = SampleParser(submission_info.iloc[15:111])
+        sample_parser = SampleParser(submission_info.iloc[16:112])
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
         logger.debug(f"Parser result: {self.sub}")
         self.sub['samples'] = sample_parse()

src/submissions/backend/excel/reports.py

@@ -9,6 +9,7 @@ import sys
 from pathlib import Path
 import re
 from tools import check_if_app
+import asyncio
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -109,9 +110,10 @@ def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -
         if column not in safe:
             if subtype != None and column != subtype:
                 del df[column]
+    # logger.debug(df)
     # move date of sample submitted on same date as previous ahead one.
     df = displace_date(df)
-    df.sort_values('submitted_date').to_excel("controls.xlsx", engine="openpyxl")
+    # df.sort_values('submitted_date').to_excel("controls.xlsx", engine="openpyxl")
     # ad hoc method to make data labels more accurate.
     df = df_column_renamer(df=df)
     return df
@@ -131,8 +133,8 @@ def df_column_renamer(df:DataFrame) -> DataFrame:
     return df.rename(columns = {
         "contains_ratio":"contains_shared_hashes_ratio",
         "matches_ratio":"matches_shared_hashes_ratio",
-        "kraken_count":"kraken2_read_count",
-        "kraken_percent":"kraken2_read_percent"
+        "kraken_count":"kraken2_read_count_(top_20)",
+        "kraken_percent":"kraken2_read_percent_(top_20)"
     })