Added importing of PCR results.

src/submissions/__init__.py

@@ -1,6 +1,22 @@
 # __init__.py
 
+from pathlib import Path
+
 # Version of the realpython-reader package
-__version__ = "202303.3b"
+__project__ = "submissions"
+__version__ = "202303.4b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
+
+project_path = Path(__file__).parents[2].absolute()
+
+class bcolors:
+    HEADER = '\033[95m'
+    OKBLUE = '\033[94m'
+    OKCYAN = '\033[96m'
+    OKGREEN = '\033[92m'
+    WARNING = '\033[93m'
+    FAIL = '\033[91m'
+    ENDC = '\033[0m'
+    BOLD = '\033[1m'
+    UNDERLINE = '\033[4m'

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)
+                
+
+
+            
+            

src/submissions/frontend/__init__.py

@@ -1,6 +1,7 @@
 '''
 Operations for all user interactions.
 '''
+import inspect
 import json
 import re
 import sys
@@ -23,15 +24,15 @@ from xhtml2pdf import pisa
 # import plotly.express as px
 import yaml
 import pprint
-from backend.excel import convert_data_list_to_df, make_report_xlsx, make_report_html, SheetParser
+from backend.excel import convert_data_list_to_df, make_report_xlsx, make_report_html, SheetParser, PCRParser
 from backend.db import (construct_submission_info, lookup_reagent, 
     construct_reagent, store_submission, lookup_kittype_by_use,
     lookup_regent_by_type_name, lookup_all_orgs, lookup_submissions_by_date_range,
     get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
     get_control_subtypes, lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num,
-    create_org_from_yaml, store_reagent
+    create_org_from_yaml, store_reagent, lookup_ww_sample_by_rsl_sample_number, lookup_kittype_by_name,
+    update_ww_sample
 )
-from backend.db import lookup_kittype_by_name
 from .functions import extract_form_info
 from tools import check_not_nan, check_kit_integrity, check_if_app
 # from backend.excel.reports import 
@@ -89,9 +90,11 @@ class App(QMainWindow):
         helpMenu.addAction(self.helpAction)
         helpMenu.addAction(self.docsAction)
         fileMenu.addAction(self.importAction)
+        fileMenu.addAction(self.importPCRAction)
         reportMenu.addAction(self.generateReportAction)
         maintenanceMenu.addAction(self.joinControlsAction)
         maintenanceMenu.addAction(self.joinExtractionAction)
+        maintenanceMenu.addAction(self.joinPCRAction)
         
     def _createToolBar(self):
         """
@@ -107,13 +110,15 @@ class App(QMainWindow):
         """
         creates actions
         """        
-        self.importAction = QAction("&Import", self)
+        self.importAction = QAction("&Import Submission", self)
+        self.importPCRAction = QAction("&Import PCR Results", self)
         self.addReagentAction = QAction("Add Reagent", self)
         self.generateReportAction = QAction("Make Report", self)
         self.addKitAction = QAction("Import Kit", self)
         self.addOrgAction = QAction("Import Org", self)
         self.joinControlsAction = QAction("Link Controls")
-        self.joinExtractionAction = QAction("Link Ext Logs")
+        self.joinExtractionAction = QAction("Link Extraction Logs")
+        self.joinPCRAction = QAction("Link PCR Logs")
         self.helpAction = QAction("&About", self)
         self.docsAction = QAction("&Docs", self)
 
@@ -123,6 +128,7 @@ class App(QMainWindow):
         connect menu and tool bar item to functions
         """
         self.importAction.triggered.connect(self.importSubmission)
+        self.importPCRAction.triggered.connect(self.importPCRResults)
         self.addReagentAction.triggered.connect(self.add_reagent)
         self.generateReportAction.triggered.connect(self.generateReport)
         self.addKitAction.triggered.connect(self.add_kit)
@@ -133,6 +139,7 @@ class App(QMainWindow):
         self.table_widget.datepicker.end_date.dateChanged.connect(self._controls_getter)
         self.joinControlsAction.triggered.connect(self.linkControls)
         self.joinExtractionAction.triggered.connect(self.linkExtractions)
+        self.joinPCRAction.triggered.connect(self.linkPCR)
         self.helpAction.triggered.connect(self.showAbout)
         self.docsAction.triggered.connect(self.openDocs)
 
@@ -180,7 +187,8 @@ class App(QMainWindow):
             (?P<submitted_date>^submitted_date$) |
             (?P<submitting_lab>)^submitting_lab$ |
             (?P<samples>)^samples$ |
-            (?P<reagent>^lot_.*$)
+            (?P<reagent>^lot_.*$) |
+            (?P<csv>^csv$)
         """, re.VERBOSE)
         for item in prsr.sub:
             logger.debug(f"Item: {item}")
@@ -213,14 +221,19 @@ class App(QMainWindow):
                         msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
                         msg.exec()
                     # create combobox to hold looked up kits
+                    # add_widget = KitSelector(ctx=self.ctx, submission_type=prsr.sub['submission_type'], parent=self)
                     add_widget = QComboBox()
+                    # add_widget.currentTextChanged.connect(self.kit_reload)
                     # lookup existing kits by 'submission_type' decided on by sheetparser
                     uses = [item.__str__() for item in lookup_kittype_by_use(ctx=self.ctx, used_by=prsr.sub['submission_type'])]
                     # if len(uses) > 0:
                     add_widget.addItems(uses)
                     # else:
                         # add_widget.addItems(['bacterial_culture'])
-                    self.ext_kit = prsr.sub[item]
+                    if check_not_nan(prsr.sub[item]):
+                        self.ext_kit = prsr.sub[item]
+                    else:
+                        self.ext_kit = add_widget.currentText()
                 case 'submitted_date':
                     # create label
                     self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
@@ -234,7 +247,9 @@ class App(QMainWindow):
                         add_widget.setDate(date.today())
                 case 'reagent':
                     # create label
-                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
+                    reg_label = QLabel(item.replace("_", " ").title())
+                    reg_label.setObjectName(f"lot_{item}_label")
+                    self.table_widget.formlayout.addWidget(reg_label)
                     # create reagent choice widget
                     add_widget = ImportReagent(ctx=self.ctx, item=item, prsr=prsr)
                     self.reagents[item] = prsr.sub[item]
@@ -243,10 +258,13 @@ class App(QMainWindow):
                     logger.debug(f"{item}: {prsr.sub[item]}")
                     self.samples = prsr.sub[item]
                     add_widget = None
+                case 'csv':
+                    self.csv = prsr.sub[item]
                 case _:
                     # anything else gets added in as a line edit
                     self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                     add_widget = QLineEdit()
+                    logger.debug(f"Setting widget text to {str(prsr.sub[item]).replace('_', ' ')}")
                     add_widget.setText(str(prsr.sub[item]).replace("_", " "))
             try:
                 add_widget.setObjectName(item)
@@ -256,21 +274,59 @@ class App(QMainWindow):
                 logger.error(e)
         # compare self.reagents with expected reagents in kit
         if hasattr(self, 'ext_kit'):
-            kit = lookup_kittype_by_name(ctx=self.ctx, name=self.ext_kit)
-            kit_integrity = check_kit_integrity(kit, [item.replace("lot_", "") for item in self.reagents])
-            if kit_integrity != None:
-                msg = AlertPop(message=kit_integrity['message'], status="critical")
-                msg.exec()
-                for item in kit_integrity['missing']:
-                    self.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
-                    add_widget = ImportReagent(ctx=self.ctx, item=item)
-                    self.table_widget.formlayout.addWidget(add_widget)
+            self.kit_integrity_completion()
         # create submission button
+        # submit_btn = QPushButton("Submit")
+        # submit_btn.setObjectName("submit_btn")
+        # self.table_widget.formlayout.addWidget(submit_btn)
+        # submit_btn.clicked.connect(self.submit_new_sample)
+        logger.debug(f"Imported reagents: {self.reagents}")
+
+
+    def kit_reload(self):
+        """
+        Removes all reagents from form before running kit integrity completion.
+        """        
+        for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
+            # item.setParent(None)
+            if isinstance(item, QLabel):
+                if item.text().startswith("Lot"):
+                    item.setParent(None)
+            else:
+                logger.debug(f"Type of {item.objectName()} is {type(item)}")
+                if item.objectName().startswith("lot_"):
+                    item.setParent(None)
+        self.kit_integrity_completion()
+    
+
+    def kit_integrity_completion(self):
+        """
+        Performs check of imported reagents
+        NOTE: this will not change self.reagents which should be fine
+        since it's only used when looking up 
+        """        
+        logger.debug(inspect.currentframe().f_back.f_code.co_name)
+        kit_widget = self.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
+        logger.debug(f"Kit selector: {kit_widget}")
+        self.ext_kit = kit_widget.currentText()
+        logger.debug(f"Checking integrity of {self.ext_kit}")
+        kit = lookup_kittype_by_name(ctx=self.ctx, name=self.ext_kit)
+        reagents_to_lookup = [item.replace("lot_", "") for item in self.reagents]
+        logger.debug(f"Reagents for lookup for {kit.name}: {reagents_to_lookup}")
+        kit_integrity = check_kit_integrity(kit, reagents_to_lookup)
+        if kit_integrity != None:
+            msg = AlertPop(message=kit_integrity['message'], status="critical")
+            msg.exec()
+            for item in kit_integrity['missing']:
+                self.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
+                add_widget = ImportReagent(ctx=self.ctx, item=item)
+                self.table_widget.formlayout.addWidget(add_widget)
         submit_btn = QPushButton("Submit")
+        submit_btn.setObjectName("lot_submit_btn")
         self.table_widget.formlayout.addWidget(submit_btn)
         submit_btn.clicked.connect(self.submit_new_sample)
-        logger.debug(f"Imported reagents: {self.reagents}")
         
+
     def submit_new_sample(self):
         """
         Attempt to add sample to database when 'submit' button clicked
@@ -341,6 +397,15 @@ class App(QMainWindow):
         # reset form
         for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
             item.setParent(None)
+        if hasattr(self, 'csv'):
+            dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
+            if dlg.exec():
+                home_dir = Path(self.ctx["directory_path"]).joinpath(f"{base_submission.rsl_plate_num}.csv").resolve().__str__()
+                fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".csv")[0])
+                try:
+                    self.csv.to_csv(fname.__str__(), index=False)
+                except PermissionError:
+                    logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
 
 
     def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None):
@@ -468,8 +533,6 @@ class App(QMainWindow):
         msg.exec()
 
 
-
-
     def _controls_getter(self):
         """
         Lookup controls from database and send to chartmaker
@@ -550,6 +613,9 @@ class App(QMainWindow):
 
 
     def linkControls(self):
+        """
+        Adds controls pulled from irida to relevant submissions
+        """        
         all_bcs = lookup_all_submissions_by_type(self.ctx, "Bacterial Culture")
         logger.debug(all_bcs)
         all_controls = get_all_controls(self.ctx)
@@ -598,6 +664,9 @@ class App(QMainWindow):
 
 
     def linkExtractions(self):
+        """
+        Links extraction logs from .csv files to relevant submissions.
+        """        
         home_dir = str(Path(self.ctx["directory_path"]))
         fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "csv(*.csv)")[0])
         with open(fname.__str__(), 'r') as f:
@@ -648,6 +717,107 @@ class App(QMainWindow):
         dlg.exec()
 
 
+    def linkPCR(self):
+        """
+        Links PCR logs from .csv files to relevant submissions.
+        """        
+        home_dir = str(Path(self.ctx["directory_path"]))
+        fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "csv(*.csv)")[0])
+        with open(fname.__str__(), 'r') as f:
+            runs = [col.strip().split(",") for col in f.readlines()]
+        count = 0
+        for run in runs:
+            obj = dict(
+                    start_time=run[0].strip(), 
+                    rsl_plate_num=run[1].strip(), 
+                    biomek_status=run[2].strip(), 
+                    quant_status=run[3].strip(),
+                    experiment_name=run[4].strip(),
+                    end_time=run[5].strip()
+                )
+            # for ii in range(6, len(run)):
+            #     obj[f"column{str(ii-5)}_vol"] = run[ii]
+            sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=obj['rsl_plate_num'])
+            try:
+                logger.debug(f"Found submission: {sub.rsl_plate_num}")
+            except AttributeError:
+                continue
+            if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
+                existing = json.loads(sub.pcr_info)
+            else:
+                existing = None
+            try:
+                if json.dumps(obj) in sub.pcr_info:
+                    logger.debug(f"Looks like we already have that info.")
+                    continue
+                else:
+                    count += 1
+            except TypeError:
+                logger.error(f"No json to dump")
+            if existing != None:
+                try:
+                    logger.debug(f"Updating {type(existing)}: {existing} with {type(obj)}: {obj}")
+                    existing.append(obj)
+                    logger.debug(f"Setting: {existing}")
+                    sub.pcr_info = json.dumps(existing)
+                except TypeError:
+                    logger.error(f"Error updating!")
+                    sub.pcr_info = json.dumps([obj])
+                logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
+            else:
+                sub.pcr_info = json.dumps([obj])        
+            self.ctx['database_session'].add(sub)
+            self.ctx["database_session"].commit()
+        dlg = AlertPop(message=f"We added {count} logs to the database.", status='information')
+        dlg.exec()
+
+
+    def importPCRResults(self):
+        """
+        Imports results exported from Design and Analysis .eds files
+        """        
+        home_dir = str(Path(self.ctx["directory_path"]))
+        fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "xlsx(*.xlsx)")[0])
+        parser = PCRParser(ctx=self.ctx, filepath=fname)
+        logger.debug(f"Attempting lookup for {parser.plate_num}")
+        sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=parser.plate_num)
+        try:
+            logger.debug(f"Found submission: {sub.rsl_plate_num}")
+        except AttributeError:
+            logger.error(f"Submission of number {parser.plate_num} not found.")
+            return
+        # jout = json.dumps(parser.pcr)
+        count = 0
+        if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
+            existing = json.loads(sub.pcr_info)
+        else:
+            # jout = None
+            existing = None
+        if existing != None:
+            try:
+                logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
+                if json.dumps(parser.pcr) not in sub.pcr_info:
+                    existing.append(parser.pcr)
+                logger.debug(f"Setting: {existing}")
+                sub.pcr_info = json.dumps(existing)
+            except TypeError:
+                logger.error(f"Error updating!")
+                sub.pcr_info = json.dumps([parser.pcr])
+            logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
+        else:
+            sub.pcr_info = json.dumps([parser.pcr])
+        self.ctx['database_session'].add(sub)
+        logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
+        logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
+        self.ctx["database_session"].commit()
+        logger.debug(f"Got {len(parser.samples)} to update!")
+        for sample in parser.samples:
+            logger.debug(f"Running update on: {sample['sample']}")
+            update_ww_sample(ctx=self.ctx, sample_obj=sample)
+        dlg = AlertPop(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
+        dlg.exec()
+
+
 class AddSubForm(QWidget):
     
     def __init__(self, parent):

src/submissions/frontend/custom_widgets/misc.py

@@ -2,6 +2,7 @@
 Contains miscellaneous widgets for frontend functions
 '''
 from datetime import date
+import typing
 from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout,
     QLineEdit, QComboBox, QDialog, 
@@ -10,10 +11,11 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
 )
 from PyQt6.QtCore import Qt, QDate, QSize
+# from submissions.backend.db.functions import lookup_kittype_by_use
 # from submissions.backend.db import lookup_regent_by_type_name_and_kit_name
 from tools import check_not_nan
 from ..functions import extract_form_info
-from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name#, lookup_regent_by_type_name_and_kit_name
+from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name, lookup_kittype_by_use#, lookup_regent_by_type_name_and_kit_name
 from backend.excel.parser import SheetParser
 from jinja2 import Environment, FileSystemLoader
 import sys
@@ -329,9 +331,13 @@ class ImportReagent(QComboBox):
             else:
                 if len(relevant_reagents) > 1:
                     logger.debug(f"Found {prsr.sub[item]['lot']} in relevant reagents: {relevant_reagents}. Moving to front of list.")
-                    relevant_reagents.insert(0, relevant_reagents.pop(relevant_reagents.index(prsr.sub[item]['lot'])))
+                    idx = relevant_reagents.index(str(prsr.sub[item]['lot']))
+                    logger.debug(f"The index we got for {prsr.sub[item]['lot']} in {relevant_reagents} was {idx}")
+                    moved_reag = relevant_reagents.pop(idx)
+                    relevant_reagents.insert(0, moved_reag)
                 else:
                     logger.debug(f"Found {prsr.sub[item]['lot']} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
         logger.debug(f"New relevant reagents: {relevant_reagents}")
+        self.setObjectName(f"lot_{item}")
         self.addItems(relevant_reagents)
-        
+        

src/submissions/templates/submission_details.html

@@ -3,9 +3,10 @@
     <head>
         <title>Submission Details for {{ sub['Plate Number'] }}</title>
     </head>
+    {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info'] %}
     <body>
         <h2><u>Submission Details for {{ sub['Plate Number'] }}</u></h2>
-        <p>{% for key, value in sub.items() if key != 'reagents' and key != 'samples' and key != 'controls' and key != 'ext_info' %}
+        <p>{% for key, value in sub.items() if key not in excluded %}
             {% if loop.index == 1 %}
                 &nbsp;&nbsp;&nbsp;{% if key=='Cost' %}{{ key }}: {{ "${:,.2f}".format(value) }}{% else %}{{ key }}: {{ value }}{% endif %}<br>
             {% else %}
@@ -62,5 +63,25 @@
         {% endfor %}</p>
         {% endfor %}
         {% endif %}
+        {% if sub['pcr_info'] %}
+        {% for entry in sub['pcr_info'] %}
+        {% if 'comment' not in entry.keys() %}
+            <h3><u>qPCR Momentum Status:</u></h3>
+        {% else %}
+            <h3><u>qPCR Status:</u></h3>
+        {% endif %}
+        <p>{% for key, value in entry.items() if key != 'imported_by'%}
+            {% if loop.index == 1%}
+                &nbsp;&nbsp;&nbsp;{{ key|replace('_', ' ')|title() }}: {{ value }}<br>
+            {% else %}
+                {% if "column" in key %}
+                    &nbsp;&nbsp;&nbsp;&nbsp;{{ key|replace('_', ' ')|title() }}: {{ value }}uL<br>
+                {% else %}
+                    &nbsp;&nbsp;&nbsp;&nbsp;{{ key|replace('_', ' ')|title() }}: {{ value }}<br>
+                {% endif %}
+            {% endif %}
+        {% endfor %}</p>
+        {% endfor %}
+        {% endif %}
     </body>
 </html>

src/submissions/templates/submission_details.txt

@@ -1,6 +1,7 @@
 {# template for constructing submission details #}
-
-{% for key, value in sub.items() if key != 'reagents' and key != 'samples' and key != 'controls' and key != 'ext_info' %}
+{% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info'] %}
+{# for key, value in sub.items() if key != 'reagents' and key != 'samples' and key != 'controls' and key != 'ext_info' #}
+{% for key, value in sub.items() if key not in excluded %}
 {% if key=='Cost' %} {{ key }}: {{ "${:,.2f}".format(value) }} {% else %} {{ key }}: {{ value }} {% endif %}
 {% endfor %}
 Reagents:
@@ -9,7 +10,7 @@ Reagents:
 {% if sub['samples']%}
 Samples:
 {% for item in sub['samples'] %}
-    {{ item['well'] }}: {{ item['name'] }}{% endfor %}{% endif %}
+    {{ item['well'] }}: {{ item['name'] }}{% endfor %}{% endif %} 
 {% if sub['controls'] %}
 Attached Controls:
 {% for item in sub['controls'] %}
@@ -22,6 +23,10 @@ Attached Controls:
 {% if sub['ext_info'] %}{% for entry in sub['ext_info'] %}
 Extraction Status:
 {% for key, value in entry.items() %}
-    {{ key|replace('_', ' ')|title() }}: {{ value }}{% endfor %}
-{% endfor %}
-{% endif %}
+    {{ key|replace('_', ' ')|title() }}: {{ value }}{% endfor %}{% endfor %}{% endif %}
+{% if sub['pcr_info'] %}{% for entry in sub['pcr_info'] %}
+{% if 'comment' not in entry.keys() %}qPCR Momentum Status:{% else %}
+qPCR Status{% endif %}
+{% for key, value in entry.items() if key != 'imported_by' %}
+    {{ key|replace('_', ' ')|title() }}: {{ value }}{% endfor %}{% endfor %}
+{% endif %}

src/submissions/tools/__init__.py

@@ -1,11 +1,13 @@
 '''
 Contains miscellaenous functions used by both frontend and backend.
 '''
+import re
 import sys
 import numpy as np
 import logging
 import getpass
 from backend.db.models import BasicSubmission, KitType
+from typing import Tuple
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -115,4 +117,15 @@ def check_if_app(ctx:dict=None) -> bool:
     if getattr(sys, 'frozen', False):
         return True
     else:
-        return False
+        return False
+    
+
+def retrieve_rsl_number(in_str:str) -> Tuple[str, str]:
+    in_str = in_str.split("\\")[-1]
+    logger.debug(f"Attempting match of {in_str}")
+    regex = re.compile(r"""
+        (?P<wastewater>RSL-WW-20\d{6})|(?P<bacterial_culture>RSL-\d{2}-\d{4})
+        """, re.VERBOSE)
+    m = regex.search(in_str)
+    return (m.group(), m.lastgroup)
+