Missing sample message after Artic parsing.

src/submissions/backend/db/functions.py

@@ -31,6 +31,7 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
     cursor.execute("PRAGMA foreign_keys=ON")
     cursor.close()
 
+
 def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None|dict:
     """
     Upserts submissions into database
@@ -799,9 +800,21 @@ def lookup_discounts_by_org_and_kit(ctx:dict, kit_id:int, lab_id:int):
         )).all()
 
 def hitpick_plate(submission:models.BasicSubmission, plate_number:int=0) -> list:
+    """
+    Creates a list of sample positions and statuses to be used by plate mapping and csv output to biomek software.
+
+    Args:
+        submission (models.BasicSubmission): Input submission
+        plate_number (int, optional): plate position in the series of selected plates. Defaults to 0.
+
+    Returns:
+        list: list of sample dictionaries.
+    """    
     plate_dicto = []
     for sample in submission.samples:
         # have sample report back its info if it's positive, otherwise, None
+        method_list = [func for func in dir(sample) if callable(getattr(sample, func))]
+        logger.debug(f"Method list of sample: {method_list}")
         samp = sample.to_hitpick()
         if samp == None:
             continue
@@ -811,6 +824,43 @@ def hitpick_plate(submission:models.BasicSubmission, plate_number:int=0) -> list
             # if len(dicto) < 88:
             this_sample = dict(
                 plate_number = plate_number,
+                sample_name = samp['name'],
+                column = samp['col'],
+                row = samp['row'],
+                positive = samp['positive'],
+                plate_name = submission.rsl_plate_num
+            )
+            # append to plate samples
+            plate_dicto.append(this_sample)
+            # append to all samples
+    # image = make_plate_map(plate_dicto)
+    return plate_dicto
+
+def platemap_plate(submission:models.BasicSubmission) -> list:
+    """
+    Depreciated. Replaced by new functionality in hitpick_plate
+
+    Args:
+        submission (models.BasicSubmission): Input submission
+
+    Returns:
+        list: list of sample dictionaries
+    """    
+    plate_dicto = []
+    for sample in submission.samples:
+        # have sample report back its info if it's positive, otherwise, None
+        
+        try:
+            samp = sample.to_platemap()
+        except AttributeError:
+            continue
+        if samp == None:
+            continue
+        else:
+            logger.debug(f"Item name: {samp['name']}")
+            # plate can handle 88 samples to leave column for controls
+            # if len(dicto) < 88:
+            this_sample = dict(
                 sample_name = samp['name'],
                 column = samp['col'],
                 row = samp['row'],

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

@@ -62,8 +62,10 @@ class WWSample(Base):
         # 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})"
         else:
+            # logger.debug(f"NOT using well info in name for: {self.ww_sample_full_id}")
             name = self.ww_sample_full_id
         return {
             "well": self.well_number,
@@ -85,18 +87,23 @@ 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
-        if positive:
-            try:
-                # The first character of the elution well is the row
-                well_row = row_dict[self.elution_well[0]]
-                # The remaining charagers are the columns
-                well_col = self.elution_well[1:]
-            except TypeError as e:
-                logger.error(f"This sample doesn't have elution plate info.")
-                return None
-            return dict(name=self.ww_sample_full_id, row=well_row, col=well_col)
-        else:
-            return None
+        well_row = row_dict[self.elution_well[0]]
+        well_col = self.elution_well[1:]
+        # if positive:
+        #     try:
+        #         # The first character of the elution well is the row
+        #         well_row = row_dict[self.elution_well[0]]
+        #         # The remaining charagers are the columns
+        #         well_col = self.elution_well[1:]
+        #     except TypeError as e:
+        #         logger.error(f"This sample doesn't have elution plate info.")
+        #         return None
+        return dict(name=self.ww_sample_full_id, 
+                    row=well_row, 
+                    col=well_col, 
+                    positive=positive)
+        # else:
+        #     return None
 
 
 class BCSample(Base):
@@ -134,7 +141,24 @@ class BCSample(Base):
             "name": f"{self.sample_id} - ({self.organism})",
         }
 
+    def to_hitpick(self) -> dict|None:
+        """
+        Outputs a dictionary of locations
 
+        Returns:
+            dict: dictionary of sample id, row and column in elution plate
+        """        
+        # dictionary to translate row letters into numbers
+        row_dict = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
+        # if either n1 or n2 is positive, include this sample
+        well_row = row_dict[self.well_number[0]]
+        # The remaining charagers are the columns
+        well_col = self.well_number[1:]
+        return dict(name=self.sample_id, 
+                    row=well_row, 
+                    col=well_col, 
+                    positive=False)
+        
 # class ArticSample(Base):
 #     """
 #     base of artic sample

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

@@ -1,6 +1,7 @@
 '''
 Models for the main submission types.
 '''
+import math
 from . import Base
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT
 from sqlalchemy.orm import relationship
@@ -246,5 +247,24 @@ class WastewaterArtic(BasicSubmission):
     derivative submission type for artic wastewater
     """    
     samples = relationship("WWSample", back_populates="artic_rsl_plate", uselist=True)
-    # Can in use the pcr_info from the wastewater? Cause I can't define pcr_info here due to conflicts with that
-    __mapper_args__ = {"polymorphic_identity": "wastewater_artic", "polymorphic_load": "inline"}
+    # Can it use the pcr_info from the wastewater? Cause I can't define pcr_info here due to conflicts with that
+    # Not necessary because we don't get any results for this procedure.
+    __mapper_args__ = {"polymorphic_identity": "wastewater_artic", "polymorphic_load": "inline"}
+
+    def calculate_base_cost(self):
+        """
+        This method overrides parent method due to multiple output plates from a single submission
+        """        
+        logger.debug(f"Hello from calculate base cost in WWArtic")
+        try:
+            cols_count_96 = ceil(int(self.sample_count) / 8)
+        except Exception as e:
+            logger.error(f"Column count error: {e}")
+        # Since we have multiple output plates per submission form, the constant cost will have to reflect this.
+        output_plate_count = math.ceil(int(self.sample_count) / 16)
+        logger.debug(f"Looks like we have {output_plate_count} output plates.")
+        const_cost = self.extraction_kit.constant_cost * output_plate_count
+        try:
+            self.run_cost = const_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}")