Improved reporting, price tracking

src/submissions/backend/db/__init__.py

@@ -5,7 +5,7 @@ import sqlite3
 # from sqlalchemy.exc import IntegrityError, OperationalError
 # from sqlite3 import IntegrityError, OperationalError
 import logging
-from datetime import date, datetime
+from datetime import date, datetime, timedelta
 from sqlalchemy import and_
 import uuid
 import base64
@@ -132,6 +132,12 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
         except AttributeError:
             logger.debug(f"Could not set attribute: {item} to {info_dict[item]}")
             continue
+        # calculate cost of the run: immutable cost + mutable times number of columns
+        try:
+            instance.run_cost = instance.extraction_kit.immutable_cost + (instance.extraction_kit.mutable_cost * ((instance.sample_count / 8)/12))
+        except TypeError:
+            logger.debug(f"Looks like that kit doesn't have cost breakdown yet, using full plate cost.")
+            instance.run_cost = instance.extraction_kit.cost_per_run
     logger.debug(f"Constructed instance: {instance.to_string()}")
     logger.debug(msg)
     return instance, {'message':msg}
@@ -395,12 +401,13 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
         exp (dict): Experiment dictionary created from yaml file
     """
     try:
-        super_users = ctx['super_users']
+        power_users = ctx['power_users']
     except KeyError:
         logger.debug("This user does not have permission to add kits.")
         return {'code':1,'message':"This user does not have permission to add kits."}
-    if getuser not in super_users:
-        logger.debug("This user does not have permission to add kits.")
+    logger.debug(f"Adding kit for user: {getuser()}")
+    if getuser() not in power_users:
+        logger.debug(f"{getuser()} does not have permission to add kits.")
         return {'code':1, 'message':"This user does not have permission to add kits."}
     for type in exp:
         if type == "password":
@@ -410,7 +417,7 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
             for r in exp[type]['kits'][kt]['reagenttypes']:
                 look_up = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==r).first()
                 if look_up == None:
-                    rt = models.ReagentType(name=r.replace(" ", "_").lower(), eol_ext=datetime.timedelta(30*exp[type]['kits'][kt]['reagenttypes'][r]['eol_ext']), kits=[kit])
+                    rt = models.ReagentType(name=r.replace(" ", "_").lower(), eol_ext=timedelta(30*exp[type]['kits'][kt]['reagenttypes'][r]['eol_ext']), kits=[kit])
                 else:
                     rt = look_up
                     rt.kits.append(kit)

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

@@ -18,6 +18,8 @@ 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
+    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)
     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
     

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

@@ -1,5 +1,5 @@
 from . import Base
-from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT
 from sqlalchemy.orm import relationship
 from datetime import datetime as dt
 
@@ -26,6 +26,8 @@ class BasicSubmission(Base):
     # Move this into custom types?
     reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions) #: relationship to reagents
     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))
 
     __mapper_args__ = {
         "polymorphic_identity": "basic_submission",
@@ -73,6 +75,7 @@ class BasicSubmission(Base):
             "Sample Count": self.sample_count,
             "Extraction Kit": ext_kit,
             "Technician": self.technician,
+            "Cost": self.run_cost,
         }
         return output
 
@@ -99,10 +102,11 @@ class BasicSubmission(Base):
         except AttributeError:
             ext_kit = None
         # get extraction kit cost from nested kittype object
-        try:
-            cost = self.extraction_kit.cost_per_run
-        except AttributeError:
-            cost = None
+        # depreciated as it will change kit cost overtime
+        # try:
+        #     cost = self.extraction_kit.cost_per_run
+        # except AttributeError:
+        #     cost = None
         output = {
             "id": self.id,
             "Plate Number": self.rsl_plate_num,
@@ -112,7 +116,7 @@ class BasicSubmission(Base):
             "Submitting Lab": sub_lab,
             "Sample Count": self.sample_count,
             "Extraction Kit": ext_kit,
-            "Cost": cost
+            "Cost": self.run_cost
         }
         return output