Upgrades to cost calculation methods

CHANGELOG.md

@@ -1,5 +1,10 @@
+## 202305.01
+
+- Improved kit cost calculation.
+
 ## 202304.04
 
+- Added in discounts for kits based on kit used and submitting client.
 - Kraken controls graph now only pulls top 20 results to prevent crashing.
 - Improved cost calculations per column in a 96 well plate.
 

TODO.md

@@ -1 +1 @@
-- [ ] Move bulk of functions from frontend.__init__ to frontend.functions as __init__ is getting bloated.
+- [x] Move bulk of functions from frontend.__init__ to frontend.functions as __init__ is getting bloated.

alembic.ini

@@ -56,7 +56,7 @@ version_path_separator = os  # Use os.pathsep. Default configuration used for ne
 # output_encoding = utf-8
 
 ; sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
-sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230302.db
+sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230427.db
 ; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\tests\test_assets\submissions_test.db
 
 

alembic/versions/83b06f3f4869_updated_discount_table.py

@@ -0,0 +1,30 @@
+"""updated discount table
+
+Revision ID: 83b06f3f4869
+Revises: cc9672a505f5
+Create Date: 2023-04-27 13:04:35.886294
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import sqlite
+
+# revision identifiers, used by Alembic.
+revision = '83b06f3f4869'
+down_revision = 'cc9672a505f5'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_discounts', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('name', sa.String(length=128), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_discounts', schema=None) as batch_op:
+        batch_op.drop_column('name')
+    # ### end Alembic commands ###

alembic/versions/cc9672a505f5_added_discount_table.py

@@ -0,0 +1,37 @@
+"""added discount table
+
+Revision ID: cc9672a505f5
+Revises: 00de69ad6eab
+Create Date: 2023-04-27 12:58:41.331563
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'cc9672a505f5'
+down_revision = '00de69ad6eab'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('_discounts',
+    sa.Column('id', sa.INTEGER(), nullable=False),
+    sa.Column('kit_id', sa.INTEGER(), nullable=True),
+    sa.Column('client_id', sa.INTEGER(), nullable=True),
+    sa.Column('amount', sa.FLOAT(precision=2), nullable=True),
+    sa.ForeignKeyConstraint(['client_id'], ['_organizations.id'], name='fk_org_id', ondelete='SET NULL'),
+    sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_kit_type_id', ondelete='SET NULL'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('_discounts')
+    # ### end Alembic commands ###

alembic/versions/dc780c868efd_split_mutable_costs_into_96_and_24.py

@@ -0,0 +1,51 @@
+"""split mutable costs into 96 and 24
+
+Revision ID: dc780c868efd
+Revises: 83b06f3f4869
+Create Date: 2023-05-01 14:05:47.762441
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import sqlite
+
+# revision identifiers, used by Alembic.
+revision = 'dc780c868efd'
+down_revision = '83b06f3f4869'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('_alembic_tmp__kits')
+    with op.batch_alter_table('_kits', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('mutable_cost_96', sa.FLOAT(precision=2), nullable=True))
+        batch_op.add_column(sa.Column('mutable_cost_24', sa.FLOAT(precision=2), nullable=True))
+        batch_op.drop_column('mutable_cost')
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    
+    with op.batch_alter_table('_kits', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('mutable_cost', sa.FLOAT(), nullable=True))
+        batch_op.drop_column('mutable_cost_24')
+        batch_op.drop_column('mutable_cost_96')
+
+    op.create_table('_alembic_tmp__kits',
+    sa.Column('id', sa.INTEGER(), nullable=False),
+    sa.Column('name', sa.VARCHAR(length=64), nullable=True),
+    sa.Column('used_for', sqlite.JSON(), nullable=True),
+    sa.Column('cost_per_run', sa.FLOAT(), nullable=True),
+    sa.Column('reagent_types_id', sa.INTEGER(), nullable=True),
+    sa.Column('constant_cost', sa.FLOAT(), nullable=True),
+    sa.Column('mutable_cost_96', sa.FLOAT(), nullable=True),
+    sa.Column('mutable_cost_24', sa.FLOAT(), nullable=True),
+    sa.ForeignKeyConstraint(['reagent_types_id'], ['_reagent_types.id'], ondelete='SET NULL'),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('name')
+    )
+    # ### end Alembic commands ###

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202304.4b"
+__version__ = "202305.1b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
 

src/submissions/backend/db/functions.py

@@ -164,13 +164,24 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
     try:
         # 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__}")
+        logger.debug(f"Calculating costs for procedure...")
-        cols_count = ceil(int(instance.sample_count) / 8)
+        # cols_count = ceil(int(instance.sample_count) / 8)
-        instance.run_cost = instance.extraction_kit.constant_cost + (instance.extraction_kit.mutable_cost * (cols_count / 12))
+        # instance.run_cost = instance.extraction_kit.constant_cost + (instance.extraction_kit.mutable_cost * (cols_count / 12))
+        instance.calculate_base_cost()
     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
+    logger.debug(f"Calculated base run cost of: {instance.run_cost}")
+    try:
+        logger.debug("Checking and applying discounts...")
+        discounts = [item.amount for item in lookup_discounts_by_org_and_kit(ctx=ctx, kit_id=instance.extraction_kit.id, lab_id=instance.submitting_lab.id)]
+        logger.debug(f"We got discounts: {discounts}")
+        discounts = sum(discounts)
+        instance.run_cost = instance.run_cost - discounts
+    except Exception as e:
+        logger.error(f"An unknown exception occurred: {e}")
     # We need to make sure there's a proper rsl plate number
+    logger.debug(f"We've got a total cost of {instance.run_cost}")
     try:
         logger.debug(f"Constructed instance: {instance.to_string()}")
     except AttributeError as e:
@@ -466,7 +477,7 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
             continue
         # A submission type may use multiple kits.
         for kt in exp[type]['kits']:
-            kit = models.KitType(name=kt, used_for=[type.replace("_", " ").title()], constant_cost=exp[type]["kits"][kt]["constant_cost"], mutable_cost=exp[type]["kits"][kt]["mutable_cost"])
+            kit = models.KitType(name=kt, used_for=[type.replace("_", " ").title()], constant_cost=exp[type]["kits"][kt]["constant_cost"], mutable_cost_column=exp[type]["kits"][kt]["mutable_cost_column"])
             # A kit contains multiple reagent types.
             for r in exp[type]['kits'][kt]['reagenttypes']:
                 # check if reagent type already exists.
@@ -737,3 +748,9 @@ def update_ww_sample(ctx:dict, sample_obj:dict):
         return
     ctx['database_session'].add(ww_samp)
     ctx["database_session"].commit()
+
+def lookup_discounts_by_org_and_kit(ctx:dict, kit_id:int, lab_id:int):
+    return ctx['database_session'].query(models.Discount).join(models.KitType).join(models.Organization).filter(and_(
+        models.KitType.id==kit_id, 
+        models.Organization.id==lab_id
+        )).all()

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

@@ -7,7 +7,7 @@ Base = declarative_base()
 metadata = Base.metadata
 
 from .controls import Control, ControlType
-from .kits import KitType, ReagentType, Reagent
+from .kits import KitType, ReagentType, Reagent, Discount
 from .organizations import Organization, Contact
 from .samples import WWSample, BCSample
 from .submissions import BasicSubmission, BacterialCulture, Wastewater

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

@@ -25,7 +25,9 @@ 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 per plate that can change with number of columns (reagents, tips, etc)
+    # TODO: Change below to 'mutable_cost_column' and 'mutable_cost_sample' before moving to production.
+    mutable_cost_column = Column(FLOAT(2)) #: dollar amount per 96 well plate that can change with number of columns (reagents, tips, etc)
+    mutable_cost_sample = Column(FLOAT(2)) #: dollar amount that can change with number of samples (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
@@ -113,13 +115,16 @@ class Reagent(Base):
         }
     
 
-# class Discounts(Base):
+class Discount(Base):
-#     """
+    """
-#     Relationship table for client labs for certain kits.
+    Relationship table for client labs for certain kits.
-#     """
+    """
-#     __tablename__ = "_discounts"
+    __tablename__ = "_discounts"
 
-#     id = Column(INTEGER, primary_key=True) #: primary key
+    id = Column(INTEGER, primary_key=True) #: primary key
-#     kit = relationship("KitType") #: joined parent reagent type
+    kit = relationship("KitType") #: joined parent reagent type
-#     kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete='SET NULL', name="fk_kit_type_id"))
+    kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete='SET NULL', name="fk_kit_type_id"))
-#     client = relationship("Organization")
+    client = relationship("Organization") #: joined client lab
+    client_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete='SET NULL', name="fk_org_id"))
+    name = Column(String(128))
+    amount = Column(FLOAT(2))

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

@@ -8,6 +8,7 @@ from datetime import datetime as dt
 import logging
 import json
 from json.decoder import JSONDecodeError
+from math import ceil
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -152,6 +153,8 @@ class BasicSubmission(Base):
         }
         return output
     
+    
+
 # Below are the custom submission types
 
 class  BacterialCulture(BasicSubmission):
@@ -174,6 +177,18 @@ class  BacterialCulture(BasicSubmission):
         return output
     
 
+    def calculate_base_cost(self):
+        try:
+            cols_count_96 = ceil(int(self.sample_count) / 8)
+        except Exception as e:
+            logger.error(f"Column count error: {e}")
+        # cols_count_24 = ceil(int(self.sample_count) / 3)
+        try:
+            self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
+        except Exception as e:
+            logger.error(f"Calculation error: {e}")
+    
+
 class Wastewater(BasicSubmission):
     """
     derivative submission type from BasicSubmission
@@ -196,3 +211,15 @@ class Wastewater(BasicSubmission):
         except TypeError as e:
             pass
         return output
+    
+    def calculate_base_cost(self):
+        try:
+            cols_count_96 = ceil(int(self.sample_count) / 8) + 1 #: Adding in one column to account for 24 samples + ext negatives
+        except Exception as e:
+            logger.error(f"Column count error: {e}")
+        # cols_count_24 = ceil(int(self.sample_count) / 3)
+        try:
+            self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
+        except Exception as e:
+            logger.error(f"Calculation error: {e}")
+    

src/submissions/backend/excel/parser.py

@@ -11,7 +11,7 @@ import logging
 from collections import OrderedDict
 import re
 import numpy as np
-from datetime import date
+from datetime import date, datetime
 import uuid
 from tools import check_not_nan, RSLNamer
 
@@ -129,8 +129,12 @@ class SheetParser(object):
                     logger.debug(f"Output variable is {output_var}")
                     logger.debug(f"Expiry date for imported reagent: {row[3]}")
                     if check_not_nan(row[3]):
+                        try:
                             expiry = row[3].date()
+                        except AttributeError as e:
+                            expiry = datetime.strptime(row[3], "%Y-%m-%d")
                     else:
+                        logger.debug(f"Date: {row[3]}")
                         expiry = date.today()
                     self.sub[f"lot_{reagent_type}"] = {'lot':output_var, 'exp':expiry}
         submission_info = self.parse_generic("Sample List")
@@ -265,8 +269,8 @@ class SampleParser(object):
         new_list = []
         for sample in self.samples:
             new = WWSample()
-            if check_not_nan(sample["Unnamed: 9"]):
+            if check_not_nan(sample["Unnamed: 7"]):
-                new.rsl_number = sample['Unnamed: 9']
+                new.rsl_number = sample['Unnamed: 7'] # previously Unnamed: 9
             else:
                 logger.error(f"No RSL sample number found for this sample.")
                 continue
@@ -282,9 +286,9 @@ class SampleParser(object):
                 new.collection_date = sample['Unnamed: 5']
             else:
                 new.collection_date = date.today()
-            new.testing_type = sample['Unnamed: 6']
+            # new.testing_type = sample['Unnamed: 6']
-            new.site_status = sample['Unnamed: 7']
+            # new.site_status = sample['Unnamed: 7']
-            new.notes = str(sample['Unnamed: 8'])
+            new.notes = str(sample['Unnamed: 6']) # previously Unnamed: 8
             new.well_number = sample['Unnamed: 1']
             new_list.append(new)
         return new_list