Addition of autofilling excel forms. Improved pydantic validation.

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

@@ -55,11 +55,8 @@ class ReagentType(Base):
     instances = relationship("Reagent", back_populates="type") #: concrete instances of this reagent type
     eol_ext = Column(Interval()) #: extension of life interval
     required = Column(INTEGER, server_default="1") #: sqlite boolean to determine if reagent type is essential for the kit
-    # __table_args__ = (
-    #     CheckConstraint(required >= 0, name='check_required_positive'),
-    #     CheckConstraint(required < 2, name='check_required_less_2'),
-    #     {})
-    
+    last_used = Column(String(32)) #: last used lot number of this type of reagent
+
     @validates('required')
     def validate_age(self, key, value):
         if not 0 <= value < 2:
@@ -125,6 +122,13 @@ class Reagent(Base):
             "expiry": place_holder.strftime("%Y-%m-%d")
         }
     
+    def to_reagent_dict(self) -> dict:
+        return {
+            "type": self.type.name,
+            "lot": self.lot,
+            "expiry": self.expiry.strftime("%Y-%m-%d")
+        }
+    
 
 class Discount(Base):
     """

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

@@ -6,6 +6,7 @@ from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, FLOAT, BO
 from sqlalchemy.orm import relationship
 import logging
 
+
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
@@ -22,7 +23,7 @@ class WWSample(Base):
     rsl_plate = relationship("Wastewater", back_populates="samples") #: relationship to parent plate
     rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_submission_id"))
     collection_date = Column(TIMESTAMP) #: Date submission received
-    well_number = Column(String(8)) #: location on 24 well plate
+    well_number = Column(String(8)) #: location on 96 well plate
     # The following are fields from the sample tracking excel sheet Ruth put together.
     # I have no idea when they will be implemented or how.
     testing_type = Column(String(64)) 
@@ -36,7 +37,7 @@ class WWSample(Base):
     ww_seq_run_id = Column(String(64))
     sample_type = Column(String(8))
     pcr_results = Column(JSON)
-    elution_well = Column(String(8)) #: location on 96 well plate
+    well_24 = Column(String(8)) #: location on 24 well plate
     artic_rsl_plate = relationship("WastewaterArtic", back_populates="samples")
     artic_well_number = Column(String(8))
     
@@ -57,10 +58,6 @@ class WWSample(Base):
         Returns:
             dict: well location and id NOTE: keys must sync with BCSample to_sub_dict below
         """
-        # well_col = self.well_number[1:]
-        # well_row = self.well_number[0]
-        # if well_col > 4:
-        #     well
         if self.ct_n1 != None and self.ct_n2 != None:
             # logger.debug(f"Using well info in name.")
             name = f"{self.ww_sample_full_id}\n\t- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})\n\t- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
@@ -87,8 +84,8 @@ class WWSample(Base):
         except TypeError as e:
             logger.error(f"Couldn't check positives for {self.rsl_number}. Looks like there isn't PCR data.")
             return None
-        well_row = row_dict[self.elution_well[0]]
-        well_col = self.elution_well[1:]
+        well_row = row_dict[self.well_number[0]]
+        well_col = self.well_number[1:]
         # if positive:
         #     try:
         #         # The first character of the elution well is the row

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

@@ -5,7 +5,6 @@ import math
 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
 import json
 from json.decoder import JSONDecodeError
@@ -164,7 +163,8 @@ class BasicSubmission(Base):
     
     def calculate_base_cost(self):
         try:
-            cols_count_96 = ceil(int(self.sample_count) / 8)
+            # cols_count_96 = ceil(int(self.sample_count) / 8)
+            cols_count_96 = self.calculate_column_count()
         except Exception as e:
             logger.error(f"Column count error: {e}")
         # cols_count_24 = ceil(int(self.sample_count) / 3)
@@ -173,6 +173,11 @@ class BasicSubmission(Base):
         except Exception as e:
             logger.error(f"Calculation error: {e}")
 
+    def calculate_column_count(self):
+            columns = [int(sample.well_number[-2:]) for sample in self.samples]
+            logger.debug(f"Here are the columns for {self.rsl_plate_num}: {columns}")
+            return max(columns)
+
 # Below are the custom submission types
 
 class  BacterialCulture(BasicSubmission):