Added importing of PCR results.

src/submissions/backend/db/functions.py

@@ -5,6 +5,7 @@ Convenience functions for interacting with the database.
 from . import models
 from .models.kits import reagenttypes_kittypes
 from .models.submissions import reagents_submissions
+from .models.samples import WWSample
 import pandas as pd
 import sqlalchemy.exc
 import sqlite3
@@ -392,7 +393,11 @@ def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
     try:
         df = df.drop("ext_info", axis=1)
     except:
-        logger.warning(f"Couldn't drop 'controls' column from submissionsheet df.")
+        logger.warning(f"Couldn't drop 'ext_info' column from submissionsheet df.")
+    try:
+        df = df.drop("pcr_info", axis=1)
+    except:
+        logger.warning(f"Couldn't drop 'pcr_info' column from submissionsheet df.")
     return df
      
     
@@ -676,4 +681,39 @@ def delete_submission_by_id(ctx:dict, id:int) -> None:
     for sample in sub.samples:
         ctx['database_session'].delete(sample)
     ctx["database_session"].delete(sub)
+    ctx["database_session"].commit()
+
+
+def lookup_ww_sample_by_rsl_sample_number(ctx:dict, rsl_number:str) -> models.WWSample:
+    """
+    Retrieves wastewater sampel from database by rsl sample number
+
+    Args:
+        ctx (dict): settings passed dwon from gui
+        rsl_number (str): sample number assigned by robotics lab
+
+    Returns:
+        models.WWSample: instance of wastewater sample
+    """    
+    return ctx['database_session'].query(models.WWSample).filter(models.WWSample.rsl_number==rsl_number).first()
+
+
+def update_ww_sample(ctx:dict, sample_obj:dict):
+    """
+    Retrieves wastewater sample by rsl number (sample_obj['sample']) and updates values from constructed dictionary
+
+    Args:
+        ctx (dict): settings passed down from gui
+        sample_obj (dict): dictionary representing new values for database object
+    """    
+    ww_samp = lookup_ww_sample_by_rsl_sample_number(ctx=ctx, rsl_number=sample_obj['sample'])
+    if ww_samp != None:
+        for key, value in sample_obj.items():
+            logger.debug(f"Setting {key} to {value}")
+            # set attribute 'key' to 'value'
+            setattr(ww_samp, key, value)
+    else:
+        logger.error(f"Unable to find sample {sample_obj['sample']}")
+        return
+    ctx['database_session'].add(ww_samp)
     ctx["database_session"].commit()

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

@@ -2,7 +2,7 @@
 All models for individual samples.
 '''
 from . import Base
-from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, FLOAT, BOOLEAN
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, FLOAT, BOOLEAN, JSON
 from sqlalchemy.orm import relationship
 
 
@@ -25,11 +25,12 @@ class WWSample(Base):
     testing_type = Column(String(64)) 
     site_status = Column(String(64))
     notes = Column(String(2000))
-    ct_n1 = Column(FLOAT(2))
-    ct_n2 = Column(FLOAT(2))
+    ct_n1 = Column(FLOAT(2)) #: AKA ct for N1
+    ct_n2 = Column(FLOAT(2)) #: AKA ct for N2
     seq_submitted = Column(BOOLEAN())
     ww_seq_run_id = Column(String(64))
     sample_type = Column(String(8))
+    pcr_results = Column(JSON)
     
 
     def to_string(self) -> str:
@@ -48,9 +49,13 @@ class WWSample(Base):
         Returns:
             dict: well location and id NOTE: keys must sync with BCSample to_sub_dict below
         """
+        if self.ct_n1 != None and self.ct_n2 != None:
+            name = f"{self.ww_sample_full_id}\n\t- ct N1: {'{:.2f}'.format(self.ct_n1)}, ct N2: {'{:.2f}'.format(self.ct_n1)}"
+        else:
+            name = self.ww_sample_full_id
         return {
             "well": self.well_number,
-            "name": self.ww_sample_full_id,
+            "name": name,
         }
 
 

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

@@ -179,5 +179,20 @@ class Wastewater(BasicSubmission):
     derivative submission type from BasicSubmission
     """    
     samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
+    pcr_info = Column(JSON)
     # ww_sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
-    __mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}
+    __mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}
+
+    def to_dict(self) -> dict:
+        """
+        Extends parent class method to add controls to dict
+
+        Returns:
+            dict: dictionary used in submissions summary
+        """        
+        output = super().to_dict()
+        try:
+            output['pcr_info'] = json.loads(self.pcr_info)
+        except TypeError as e:
+            pass
+        return output

src/submissions/backend/excel/parser.py

@@ -1,16 +1,18 @@
 '''
 contains parser object for pulling values from client generated submission sheets.
 '''
+from getpass import getuser
 import pandas as pd
 from pathlib import Path
 from backend.db.models import WWSample, BCSample
+from backend.db import lookup_ww_sample_by_rsl_sample_number
 import logging
 from collections import OrderedDict
 import re
 import numpy as np
 from datetime import date
 import uuid
-from tools import check_not_nan
+from tools import check_not_nan, retrieve_rsl_number
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -203,6 +205,7 @@ class SheetParser(object):
         sample_parser = SampleParser(submission_info.iloc[16:40])
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
         self.sub['samples'] = sample_parse()
+        self.sub['csv'] = self.xl.parse("Copy to import file", dtype=object)
 
 
 class SampleParser(object):
@@ -284,3 +287,112 @@ class SampleParser(object):
             new.well_number = sample['Unnamed: 1']
             new_list.append(new)
         return new_list
+
+
+class PCRParser(object):
+    """
+    Object to pull data from Design and Analysis PCR export file.
+    """    
+    def __init__(self, ctx:dict, filepath:Path|None = None) -> None:
+        """
+        Initializes object.
+
+        Args:
+            ctx (dict): settings passed down from gui.
+            filepath (Path | None, optional): file to parse. Defaults to None.
+        """        
+        self.ctx = ctx
+        logger.debug(f"Parsing {filepath.__str__()}")        
+        if filepath == None:
+            logger.error(f"No filepath given.")
+            self.xl = None
+        else:
+            try:
+                self.xl = pd.ExcelFile(filepath.__str__())
+            except ValueError as e:
+                logger.error(f"Incorrect value: {e}")
+                self.xl = None
+            except PermissionError:
+                logger.error(f"Couldn't get permissions for {filepath.__str__()}. Operation might have been cancelled.")
+                return
+        # self.pcr = OrderedDict()
+        self.pcr = {}
+        self.plate_num, self.submission_type = retrieve_rsl_number(filepath.__str__())
+        logger.debug(f"Set plate number to {self.plate_num} and type to {self.submission_type}")
+        self.samples = []
+        parser = getattr(self, f"parse_{self.submission_type}")
+        parser()
+        
+
+    def parse_general(self, sheet_name:str):
+        """
+        Parse general info rows for all types of PCR results
+
+        Args:
+            sheet_name (str): Name of sheet in excel workbook that holds info.
+        """        
+        df = self.xl.parse(sheet_name=sheet_name, dtype=object).fillna("")
+        # self.pcr['file'] = df.iloc[1][1]
+        self.pcr['comment'] = df.iloc[0][1]
+        self.pcr['operator'] = df.iloc[1][1]
+        self.pcr['barcode'] = df.iloc[2][1]
+        self.pcr['instrument'] = df.iloc[3][1]
+        self.pcr['block_type'] = df.iloc[4][1]
+        self.pcr['instrument_name'] = df.iloc[5][1]
+        self.pcr['instrument_serial'] = df.iloc[6][1]
+        self.pcr['heated_cover_serial'] = df.iloc[7][1]
+        self.pcr['block_serial'] = df.iloc[8][1]
+        self.pcr['run-start'] = df.iloc[9][1]
+        self.pcr['run_end'] = df.iloc[10][1]
+        self.pcr['run_duration'] = df.iloc[11][1]
+        self.pcr['sample_volume'] = df.iloc[12][1]
+        self.pcr['cover_temp'] = df.iloc[13][1]
+        self.pcr['passive_ref'] = df.iloc[14][1]
+        self.pcr['pcr_step'] = df.iloc[15][1]
+        self.pcr['quant_cycle_method'] = df.iloc[16][1]
+        self.pcr['analysis_time'] = df.iloc[17][1]
+        self.pcr['software'] = df.iloc[18][1]
+        self.pcr['plugin'] = df.iloc[19][1]
+        self.pcr['exported_on'] = df.iloc[20][1]
+        self.pcr['imported_by'] = getuser()
+        return df
+
+    def parse_wastewater(self):
+        """
+        Parse specific to wastewater samples.
+        """        
+        df = self.parse_general(sheet_name="Results")
+        self.samples_df = df.iloc[23:][0:]
+        # iloc is [row][column]
+        for ii, row in self.samples_df.iterrows():
+            try:
+                sample_obj = [sample for sample in self.samples if sample['sample'] == row[3]][0]    
+            except IndexError:
+                sample_obj = dict(
+                    sample = row[3],
+                )
+            logger.debug(f"Got sample obj: {sample_obj}") 
+            # logger.debug(f"row: {row}")
+            # rsl_num = row[3]
+            # # logger.debug(f"Looking up: {rsl_num}")
+            # ww_samp = lookup_ww_sample_by_rsl_sample_number(ctx=self.ctx, rsl_number=rsl_num)
+            # logger.debug(f"Got: {ww_samp}")
+            match row[4]:
+                case "N1":
+                    if isinstance(row[12], float):
+                        sample_obj['ct_n1'] = row[12]
+                    else:
+                        sample_obj['ct_n1'] = 0.0
+                case "N2":
+                    if isinstance(row[12], float):
+                        sample_obj['ct_n2'] = row[12]
+                    else:
+                        sample_obj['ct_n2'] = 0.0
+                case _:
+                    logger.warning(f"Unexpected input for row[4]: {row[4]}")
+            self.samples.append(sample_obj)
+                
+
+
+            
+