moved frontend function check_not_nan to tools

alembic.ini

@@ -55,8 +55,8 @@ version_path_separator = os  # Use os.pathsep. Default configuration used for ne
 # are written from script.py.mako
 # output_encoding = utf-8
 
-sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
+; sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
-; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230130.db
+sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230213.db
 
 
 [post_write_hooks]

alembic/env.py

@@ -7,6 +7,7 @@ from alembic import context
 import sys
 from pathlib import Path
 sys.path.append(Path(__file__).parents[1].joinpath("src").resolve().__str__())
+sys.path.append(Path(__file__).parents[1].joinpath("src", "submissions").resolve().__str__())
 print(sys.path)
 
 # this is the Alembic Config object, which provides

src/submissions/__init__.py

@@ -1,4 +1,4 @@
 # __init__.py
 
 # Version of the realpython-reader package
-__version__ = "1.2.3"
+__version__ = "1.3.0"

src/submissions/backend/db/__init__.py

@@ -15,6 +15,7 @@ import json
 # from dateutil.relativedelta import relativedelta
 from getpass import getuser
 import numpy as np
+from tools import check_not_nan
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -101,8 +102,13 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
     # convert submission type into model name
     query = info_dict['submission_type'].replace(" ", "")
     # check database for existing object
+    if info_dict["rsl_plate_num"] == 'nan' or info_dict["rsl_plate_num"] == None or not check_not_nan(info_dict["rsl_plate_num"]):
+        code = 2
+        instance = None
+        msg = "A proper RSL plate number is required."
+        return instance, {'code': 2, 'message': "A proper RSL plate number is required."}
     instance = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
-    msg = "This submission already exists.\nWould you like to overwrite?"
+    
     # get model based on submission type converted above
     logger.debug(f"Looking at models for submission type: {query}")
     model = getattr(models, query)
@@ -113,6 +119,10 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
         instance = model()
         logger.debug(f"Submission doesn't exist yet, creating new instance: {instance}")
         msg = None
+        code =0
+    else:
+        code = 1
+        msg = "This submission already exists.\nWould you like to overwrite?"
     for item in info_dict:
         logger.debug(f"Setting {item} to {info_dict[item]}")
         # set fields based on keys in dictionary
@@ -151,9 +161,14 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
     except (TypeError, AttributeError):
         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
+    # We need to make sure there's a proper rsl plate number
+    
+    try:
         logger.debug(f"Constructed instance: {instance.to_string()}")
+    except AttributeError as e:
+        logger.debug(f"Something went wrong constructing instance {info_dict['rsl_plate_num']}: {e}")
     logger.debug(msg)
-    return instance, {'message':msg}
+    return instance, {'code':code, 'message':msg}
     
 
 def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
@@ -244,7 +259,7 @@ def lookup_kittype_by_use(ctx:dict, used_by:str) -> list[models.KitType]:
     Returns:
         list[models.KitType]: list of kittypes that have that sample type in their uses
     """    
-    return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by))
+    return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by)).all()
 
 def lookup_kittype_by_name(ctx:dict, name:str) -> models.KitType:
     """
@@ -278,7 +293,7 @@ def lookup_regent_by_type_name(ctx:dict, type_name:str) -> list[models.Reagent]:
 
 def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:str) -> list[models.Reagent]:
     """
-    Lookup reagents by their type name and kits they belong to (Broken)
+    Lookup reagents by their type name and kits they belong to (Broken... maybe cursed, I'm not sure.)
 
     Args:
         ctx (dict): settings pass by gui
@@ -292,10 +307,6 @@ def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:st
     # Hang on, this is going to be a long one.
     # by_type = ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name.endswith(type_name)).all()
     rt_types = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name.endswith(type_name))
-    
-    
-    
-
     # add filter for kit name... which I can not get to work.
     # add_in = by_type.join(models.ReagentType.kits).filter(models.KitType.name==kit_name)
     try:
@@ -315,7 +326,7 @@ def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:st
     return output
 
 
-def lookup_all_submissions_by_type(ctx:dict, type:str|None=None) -> list[models.BasicSubmission]:
+def lookup_all_submissions_by_type(ctx:dict, sub_type:str|None=None) -> list[models.BasicSubmission]:
     """
     Get all submissions, filtering by type if given
 
@@ -326,10 +337,10 @@ def lookup_all_submissions_by_type(ctx:dict, type:str|None=None) -> list[models.
     Returns:
         _type_: list of retrieved submissions
     """
-    if type == None:
+    if sub_type == None:
         subs = ctx['database_session'].query(models.BasicSubmission).all()
     else:
-        subs = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==type.lower().replace(" ", "_")).all()
+        subs = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==sub_type.lower().replace(" ", "_")).all()
     return subs
 
 def lookup_all_orgs(ctx:dict) -> list[models.Organization]:
@@ -358,7 +369,7 @@ def lookup_org_by_name(ctx:dict, name:str|None) -> models.Organization:
     logger.debug(f"Querying organization: {name}")
     return ctx['database_session'].query(models.Organization).filter(models.Organization.name==name).first()
 
-def submissions_to_df(ctx:dict, type:str|None=None) -> pd.DataFrame:
+def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
     """
     Convert submissions looked up by type to dataframe
 
@@ -369,9 +380,9 @@ def submissions_to_df(ctx:dict, type:str|None=None) -> pd.DataFrame:
     Returns:
         pd.DataFrame: dataframe constructed from retrieved submissions
     """    
-    logger.debug(f"Type: {type}")
+    logger.debug(f"Type: {sub_type}")
     # pass to lookup function
-    subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, type=type)]
+    subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, sub_type=sub_type)]
     df = pd.DataFrame.from_records(subs)
     # logger.debug(f"Pre: {df['Technician']}")
     try:
@@ -435,13 +446,16 @@ def get_all_Control_Types_names(ctx:dict) -> list[models.ControlType]:
     return conTypes
 
 
-def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
+def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
     """
     Create and store a new kit in the database based on a .yml file
 
     Args:
         ctx (dict): Context dictionary passed down from frontend
         exp (dict): Experiment dictionary created from yaml file
+
+    Returns:
+        dict: a dictionary containing results of db addition
     """    
     try:
         power_users = ctx['power_users']
@@ -474,6 +488,44 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
     ctx['database_session'].commit()
     return {'code':0, 'message':'Kit has been added'}
 
+def create_org_from_yaml(ctx:dict, org:dict) -> dict:
+    """
+    Create and store a new organization based on a .yml file
+
+    Args:
+        ctx (dict): Context dictionary passed down from frontend
+        org (dict): Dictionary containing organization info.
+
+    Returns:
+        dict: dictionary containing results of db addition
+    """    
+    try:
+        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 organizations."}
+    logger.debug(f"Adding organization 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 organizations."}
+    for client in org:
+        cli_org = models.Organization(name=client.replace(" ", "_").lower(), cost_centre=org[client]['cost centre'])
+        for contact in org[client]['contacts']:
+            cont_name = list(contact.keys())[0]
+            look_up = ctx['database_session'].query(models.Contact).filter(models.Contact.name==cont_name).first()
+            if look_up == None:
+                cli_cont = models.Contact(name=cont_name, phone=contact[cont_name]['phone'], email=contact[cont_name]['email'], organization=[cli_org])
+            else:
+                cli_cont = look_up
+                cli_cont.organization.append(cli_org)
+                # cli_org.contacts.append(cli_cont)
+            # cli_org.contact_ids.append_foreign_key(cli_cont.id)
+            ctx['database_session'].add(cli_cont)
+            logger.debug(cli_cont.__dict__)
+        ctx['database_session'].add(cli_org)
+    ctx["database_session"].commit()
+    return {"code":0, "message":"Organization has been added."}
+
 
 def lookup_all_sample_types(ctx:dict) -> list[str]:
     """
@@ -511,7 +563,7 @@ def get_all_available_modes(ctx:dict) -> list[str]:
 
 
 
-def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None, end_date:date|None=None) -> list:
+def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None, end_date:date|None=None) -> list[models.Control]:
     """
     Returns a list of control objects that are instances of the input controltype.
 
@@ -571,4 +623,4 @@ def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str):
 
 
 def lookup_submissions_using_reagent(ctx:dict, reagent:models.Reagent) -> list[models.BasicSubmission]:
-    return ctx['database_session'].query(models.BasicSubmission).join(reagents_submissions).filter(reagents_submissions.c.reagent_id==reagent.id)
+    return ctx['database_session'].query(models.BasicSubmission).join(reagents_submissions).filter(reagents_submissions.c.reagent_id==reagent.id).all()

src/submissions/backend/db/functions/__init__.py

@@ -1,21 +1,21 @@
-from ..models import *
+# from ..models import *
-import logging
+# import logging
 
-logger = logging.getLogger(f"submissions.{__name__}")
+# logger = logging.getLogger(f"submissions.{__name__}")
 
-def check_kit_integrity(sub:BasicSubmission):
+# def check_kit_integrity(sub:BasicSubmission):
-    ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
+#     ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
-    logger.debug(f"Kit reagents: {ext_kit_rtypes}")
+#     logger.debug(f"Kit reagents: {ext_kit_rtypes}")
-    reagenttypes = [reagent.type.name for reagent in sub.reagents]
+#     reagenttypes = [reagent.type.name for reagent in sub.reagents]
-    logger.debug(f"Submission reagents: {reagenttypes}")
+#     logger.debug(f"Submission reagents: {reagenttypes}")
-    check = set(ext_kit_rtypes) == set(reagenttypes)
+#     check = set(ext_kit_rtypes) == set(reagenttypes)
-    logger.debug(f"Checking if reagents match kit contents: {check}")
+#     logger.debug(f"Checking if reagents match kit contents: {check}")
-    common = list(set(ext_kit_rtypes).intersection(reagenttypes))
+#     common = list(set(ext_kit_rtypes).intersection(reagenttypes))
-    logger.debug(f"common reagents types: {common}")
+#     logger.debug(f"common reagents types: {common}")
-    if check:
+#     if check:
-        result = None
+#         result = None
-    else:
+#     else:
-        result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[x.upper for x in ext_kit_rtypes if x not in common]}\n\nAlternatively, you may have set the wrong extraction kit."}
+#         result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[x.upper for x in ext_kit_rtypes if x not in common]}\n\nAlternatively, you may have set the wrong extraction kit."}
-    return result
+#     return result
     
     

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

@@ -36,7 +36,7 @@ class Contact(Base):
     """
     __tablename__ = "_contacts"
 
-    id = id = Column(INTEGER, primary_key=True) #: primary key  
+    id = Column(INTEGER, primary_key=True) #: primary key  
     name = Column(String(64)) #: contact name
     email = Column(String(64)) #: contact email
     phone = Column(String(32)) #: contact phone number

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

@@ -1,5 +1,5 @@
 from . import Base
-from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, FLOAT, BOOLEAN
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, FLOAT, BOOLEAN
 from sqlalchemy.orm import relationship
 
 

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

@@ -17,7 +17,7 @@ class BasicSubmission(Base):
     __tablename__ = "_submissions"
 
     id = Column(INTEGER, primary_key=True) #: primary key   
-    rsl_plate_num = Column(String(32), unique=True) #: RSL name (e.g. RSL-22-0012)
+    rsl_plate_num = Column(String(32), unique=True, nullable=False) #: RSL name (e.g. RSL-22-0012)
     submitter_plate_num = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
     submitted_date = Column(TIMESTAMP) #: Date submission received
     submitting_lab = relationship("Organization", back_populates="submissions") #: client org

src/submissions/backend/excel/parser.py

@@ -1,13 +1,13 @@
 import pandas as pd
 from pathlib import Path
-from backend.db.models.samples import WWSample, BCSample
+from backend.db.models import WWSample, BCSample
 import logging
 from collections import OrderedDict
 import re
 import numpy as np
 from datetime import date
 import uuid
-from frontend.functions import check_not_nan
+from tools import check_not_nan
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -15,7 +15,7 @@ class SheetParser(object):
     """
     object to pull and contain data from excel file
     """
-    def __init__(self, filepath:Path|None = None, **kwargs) -> None:
+    def __init__(self, filepath:Path|None = None, **kwargs):
         """
         Args:
             filepath (Path | None, optional): file path to excel sheet. Defaults to None.
@@ -77,12 +77,12 @@ class SheetParser(object):
         """        
         submission_info = self.xl.parse(sheet_name=sheet_name, dtype=object)
         
-        self.sub['submitter_plate_num'] = submission_info.iloc[0][1] #if pd.isnull(submission_info.iloc[0][1]) else string_formatter(submission_info.iloc[0][1])
+        self.sub['submitter_plate_num'] = submission_info.iloc[0][1]
-        self.sub['rsl_plate_num'] =  submission_info.iloc[10][1] #if pd.isnull(submission_info.iloc[10][1]) else string_formatter(submission_info.iloc[10][1])
+        self.sub['rsl_plate_num'] =  submission_info.iloc[10][1]
-        self.sub['submitted_date'] = submission_info.iloc[1][1] #if pd.isnull(submission_info.iloc[1][1]) else submission_info.iloc[1][1].date()#.strftime("%Y-%m-%d")
+        self.sub['submitted_date'] = submission_info.iloc[1][1]
-        self.sub['submitting_lab'] = submission_info.iloc[0][3] #if pd.isnull(submission_info.iloc[0][3]) else string_formatter(submission_info.iloc[0][3]) 
+        self.sub['submitting_lab'] = submission_info.iloc[0][3]
-        self.sub['sample_count'] = submission_info.iloc[2][3] #if pd.isnull(submission_info.iloc[2][3]) else string_formatter(submission_info.iloc[2][3])
+        self.sub['sample_count'] = submission_info.iloc[2][3]
-        self.sub['extraction_kit'] = submission_info.iloc[3][3] #if #pd.isnull(submission_info.iloc[3][3]) else string_formatter(submission_info.iloc[3][3])
+        self.sub['extraction_kit'] = submission_info.iloc[3][3]
         
         return submission_info
 
@@ -93,6 +93,12 @@ class SheetParser(object):
         """
 
         def _parse_reagents(df:pd.DataFrame) -> None:
+            """
+            Pulls reagents from the bacterial sub-dataframe
+
+            Args:
+                df (pd.DataFrame): input sub dataframe
+            """            
             for ii, row in df.iterrows():
                 # skip positive control
                 if ii == 11:
@@ -119,16 +125,15 @@ class SheetParser(object):
                     # self.sub[f"lot_{reagent_type}"] = output_var
                     # update 2023-02-10 to above allowing generation of expiry date in adding reagent to db.
                     logger.debug(f"Expiry date for imported reagent: {row[3]}")
-                    try:
+                    # try:
-                        check = not np.isnan(row[3])
+                    #     check = not np.isnan(row[3])
-                    except TypeError:
+                    # except TypeError:
-                        check = True
+                    #     check = True
-                    if check:
+                    if check_not_nan(row[3]):
                         expiry = row[3].date()
                     else:
                         expiry = date.today()
                     self.sub[f"lot_{reagent_type}"] = {'lot':output_var, 'exp':expiry}
-
         submission_info = self._parse_generic("Sample List")
         # iloc is [row][column] and the first row is set as header row so -2
         tech = str(submission_info.iloc[11][1])
@@ -161,32 +166,38 @@ class SheetParser(object):
         self.sub['samples'] = sample_parse()
 
 
-
-
-
     def _parse_wastewater(self) -> None:
         """
         pulls info specific to wastewater sample type
         """        
 
         def _parse_reagents(df:pd.DataFrame) -> None:
-            logger.debug(df)
+            """
+            Pulls reagents from the bacterial sub-dataframe
+
+            Args:
+                df (pd.DataFrame): input sub dataframe
+            """
+            # logger.debug(df)
             for ii, row in df.iterrows():
-                try:
+                # try:
-                    check = not np.isnan(row[5])
+                #     check = not np.isnan(row[5])
-                except TypeError:
+                # except TypeError:
-                    check = True
+                #     check = True
-                if not isinstance(row[5], float) and check:
+                if not isinstance(row[5], float) and check_not_nan(row[5]):
                     # must be prefixed with 'lot_' to be recognized by gui
+                    # regex below will remove 80% from 80% ethanol in the Wastewater kit.
                     output_key = re.sub(r"\d{1,3}%", "", row[0].lower().strip().replace(' ', '_'))
                     try:
                         output_var = row[5].upper()
                     except AttributeError:
-                        logger.debug(f"Couldn't upperize {row[2]}, must be a number")
+                        logger.debug(f"Couldn't upperize {row[5]}, must be a number")
                         output_var = row[5]
-                    self.sub[f"lot_{output_key}"] = output_var
+                    if check_not_nan(row[7]):
-
+                        expiry = row[7].date()
-        # submission_info = self.xl.parse("WW Submissions (ENTER HERE)")
+                    else:
+                        expiry = date.today()
+                    self.sub[f"lot_{output_key}"] = {'lot':output_var, 'exp':expiry}
         submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
         enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
         enr_reagent_range = enrichment_info.iloc[0:4, 9:20]
@@ -214,18 +225,12 @@ class SheetParser(object):
         # self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14] #if pd.isnull(qprc_info.iloc[2][14]) else string_formatter(qprc_info.iloc[2][14])
         # self.sub['lot_positive_control'] = qprc_info.iloc[3][14] #if pd.isnull(qprc_info.iloc[3][14]) else string_formatter(qprc_info.iloc[3][14])
         # self.sub['lot_ddh2o'] = qprc_info.iloc[4][14] #if pd.isnull(qprc_info.iloc[4][14]) else string_formatter(qprc_info.iloc[4][14])
-        # gt individual sample info
+        # get individual sample info
         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()
 
 
-
-
-
-    
-
-
 class SampleParser(object):
     """
     object to pull data for samples in excel sheet and construct individual sample objects
@@ -242,6 +247,7 @@ class SampleParser(object):
         Returns:
             list[BCSample]: list of sample objects
         """       
+        # logger.debug(f"Samples: {self.samples}") 
         new_list = []
         for sample in self.samples:
             new = BCSample()
@@ -297,13 +303,3 @@ class SampleParser(object):
             new.well_number = sample['Unnamed: 1']
             new_list.append(new)
         return new_list
-    
-
-# def string_formatter(input):
-#     logger.debug(f"{input} : {type(input)}")
-#     match input:
-#         case int() | float() | np.float64:
-#             return "{:0.0f}".format(input)
-#         case _:
-#             return input
-        

src/submissions/backend/excel/reports.py

@@ -10,6 +10,7 @@ from pathlib import Path
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
+# set path of templates depending on pyinstaller/raw python
 if getattr(sys, 'frozen', False):
     loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
 else:

src/submissions/frontend/__init__.py

@@ -19,21 +19,23 @@ from xhtml2pdf import pisa
 # import plotly.express as px
 import yaml
 import pprint
-import numpy as np
 from backend.excel.parser import SheetParser
 from backend.excel.reports import convert_control_by_mode, convert_data_list_to_df
 from backend.db import (construct_submission_info, lookup_reagent, 
     construct_reagent, store_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
+    get_control_subtypes, lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num,
+    create_org_from_yaml
 )
-from .functions import check_kit_integrity, check_not_nan
+
+from .functions import check_kit_integrity
+from tools import check_not_nan
 from backend.excel.reports import make_report_xlsx, make_report_html
 
 import numpy
 from frontend.custom_widgets.sub_details import SubmissionsSheet
-from frontend.custom_widgets.pop_ups import AddReagentQuestion, OverwriteSubQuestion, AlertPop
+from frontend.custom_widgets.pop_ups import AlertPop, QuestionAsker
 from frontend.custom_widgets import AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker
 import logging
 import difflib
@@ -96,6 +98,7 @@ class App(QMainWindow):
         self.addToolBar(toolbar)
         toolbar.addAction(self.addReagentAction)
         toolbar.addAction(self.addKitAction)
+        toolbar.addAction(self.addOrgAction)
 
     def _createActions(self):
         """
@@ -105,6 +108,7 @@ class App(QMainWindow):
         self.addReagentAction = QAction("Add Reagent", self)
         self.generateReportAction = QAction("Make Report", self)
         self.addKitAction = QAction("Add Kit", self)
+        self.addOrgAction = QAction("Add Org", self)
         self.joinControlsAction = QAction("Link Controls")
         self.joinExtractionAction = QAction("Link Ext Logs")
 
@@ -117,6 +121,7 @@ class App(QMainWindow):
         self.addReagentAction.triggered.connect(self.add_reagent)
         self.generateReportAction.triggered.connect(self.generateReport)
         self.addKitAction.triggered.connect(self.add_kit)
+        self.addOrgAction.triggered.connect(self.add_org)
         self.table_widget.control_typer.currentIndexChanged.connect(self._controls_getter)
         self.table_widget.mode_typer.currentIndexChanged.connect(self._controls_getter)
         self.table_widget.datepicker.start_date.dateChanged.connect(self._controls_getter)
@@ -183,7 +188,7 @@ class App(QMainWindow):
                     # create label
                     self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                     # if extraction kit not available, all other values fail
-                    if np.isnan(prsr.sub[item]):
+                    if not check_not_nan(prsr.sub[item]):
                         msg = AlertPop(message="Make sure to check your extraction kit!", status="warning")
                         msg.exec()
                     # create combobox to hold looked up kits
@@ -231,7 +236,7 @@ class App(QMainWindow):
                         elif isinstance(reagent, str):
                             output_reg.append(reagent)
                     relevant_reagents = output_reg
-                    logger.debug(f"Relevant reagents: {relevant_reagents}")
+                    logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
                     # if reagent in sheet is not found insert it into items
                     if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
                         if check_not_nan(prsr.sub[item]['lot']):
@@ -272,11 +277,13 @@ class App(QMainWindow):
             logger.debug(f"Looked up reagent: {wanted_reagent}")
             # if reagent not found offer to add to database
             if wanted_reagent == None:
-                dlg = AddReagentQuestion(reagent_type=reagent, reagent_lot=reagents[reagent])
+                # dlg = AddReagentQuestion(reagent_type=reagent, reagent_lot=reagents[reagent])
+                r_lot = reagents[reagent]
+                dlg = QuestionAsker(title=f"Add {r_lot}?", message=f"Couldn't find reagent type {reagent.replace('_', ' ').title().strip('Lot')}: {r_lot} in the database.\n\nWould you like to add it?")
                 if dlg.exec():
                     logger.debug(f"checking reagent: {reagent} in self.reagents. Result: {self.reagents[reagent]}")
                     expiry_date = self.reagents[reagent]['exp']
-                    wanted_reagent = self.add_reagent(reagent_lot=reagents[reagent], reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
+                    wanted_reagent = self.add_reagent(reagent_lot=r_lot, reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
                 else:
                     logger.debug("Will not add reagent.")
             if wanted_reagent != None:
@@ -287,14 +294,23 @@ class App(QMainWindow):
         info['uploaded_by'] = getuser()
         # construct submission object
         logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
-        base_submission, output = construct_submission_info(ctx=self.ctx, info_dict=info)
+        base_submission, result = construct_submission_info(ctx=self.ctx, info_dict=info)
         # check output message for issues
-        if output['message'] != None:
+        match result['code']:
-            dlg = OverwriteSubQuestion(output['message'], base_submission.rsl_plate_num)
+            case 1:
+        # if output['code'] > 0:
+            # dlg = OverwriteSubQuestion(output['message'], base_submission.rsl_plate_num)
+                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
                 if dlg.exec():
                     base_submission.reagents = []
                 else:
                     return
+            case 2:
+                dlg = AlertPop(message=result['message'], status='critical')
+                dlg.exec()
+                return
+            case _:
+                pass
         # add reagents to submission object
         for reagent in parsed_reagents:
             base_submission.reagents.append(reagent)
@@ -447,20 +463,59 @@ class App(QMainWindow):
             return
         # send to kit creator function
         result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
-        msg = QMessageBox()
+        # msg = QMessageBox()
         # msg.setIcon(QMessageBox.critical)
         match result['code']:
             case 0:
-                msg.setText("Kit added")
+                msg = AlertPop(message=result['message'], status='info')
-                msg.setInformativeText(result['message'])
+                # msg.setText("Kit added")
-                msg.setWindowTitle("Kit added")
+                # msg.setInformativeText(result['message'])
+                # msg.setWindowTitle("Kit added")
             case 1:
-                msg.setText("Permission Error")
+                msg = AlertPop(message=result['message'], status='critical')
-                msg.setInformativeText(result['message'])
+                # msg.setText("Permission Error")
-                msg.setWindowTitle("Permission Error")
+                # msg.setInformativeText(result['message'])
+                # msg.setWindowTitle("Permission Error")
         msg.exec()
 
 
+    def add_org(self):
+        """
+        Constructs new kit from yaml and adds to DB.
+        """
+        # setup file dialog to find yaml flie
+        home_dir = str(Path(self.ctx["directory_path"]))
+        fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "yml(*.yml)")[0])
+        assert fname.exists()
+        # read yaml file
+        try:
+            with open(fname.__str__(), "r") as stream:
+                try:
+                    org = yaml.load(stream, Loader=yaml.Loader)
+                except yaml.YAMLError as exc:
+                    logger.error(f'Error reading yaml file {fname}: {exc}')
+                    return {}
+        except PermissionError:
+            return
+        # send to kit creator function
+        result = create_org_from_yaml(ctx=self.ctx, org=org)
+        # msg = QMessageBox()
+        # msg.setIcon(QMessageBox.critical)
+        match result['code']:
+            case 0:
+                msg = AlertPop(message=result['message'], status='information')
+                # msg.setText("Organization added")
+                # msg.setInformativeText(result['message'])
+                # msg.setWindowTitle("Kit added")
+            case 1:
+                msg = AlertPop(message=result['message'], status='critical')
+                # msg.setText("Permission Error")
+                # msg.setInformativeText(result['message'])
+                # msg.setWindowTitle("Permission Error")
+        msg.exec()
+
+
+
 
     def _controls_getter(self):
         """

src/submissions/frontend/custom_widgets/pop_ups.py

@@ -22,50 +22,67 @@ loader = FileSystemLoader(loader_path)
 env = Environment(loader=loader)
 
 
-class AddReagentQuestion(QDialog):
+# class AddReagentQuestion(QDialog):
+#     """
+#     dialog to ask about adding a new reagne to db
+#     """    
+#     def __init__(self, reagent_type:str, reagent_lot:str) -> QDialog:
+#         super().__init__()
+
+#         self.setWindowTitle(f"Add {reagent_lot}?")
+
+#         QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
+
+#         self.buttonBox = QDialogButtonBox(QBtn)
+#         self.buttonBox.accepted.connect(self.accept)
+#         self.buttonBox.rejected.connect(self.reject)
+
+#         self.layout = QVBoxLayout()
+#         message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title().strip('Lot')}: {reagent_lot} in the database.\n\nWould you like to add it?")
+#         self.layout.addWidget(message)
+#         self.layout.addWidget(self.buttonBox)
+#         self.setLayout(self.layout)
+
+
+# class OverwriteSubQuestion(QDialog):
+#     """
+#     dialog to ask about overwriting existing submission
+#     """    
+#     def __init__(self, message:str, rsl_plate_num:str) -> QDialog:
+#         super().__init__()
+
+#         self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
+
+#         QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
+
+#         self.buttonBox = QDialogButtonBox(QBtn)
+#         self.buttonBox.accepted.connect(self.accept)
+#         self.buttonBox.rejected.connect(self.reject)
+
+#         self.layout = QVBoxLayout()
+#         message = QLabel(message)
+#         self.layout.addWidget(message)
+#         self.layout.addWidget(self.buttonBox)
+#         self.setLayout(self.layout)
+
+
+class QuestionAsker(QDialog):
     """
-    dialog to ask about adding a new reagne to db
+    dialog to ask yes/no questions
     """    
-    def __init__(self, reagent_type:str, reagent_lot:str) -> QDialog:
+    def __init__(self, title:str, message:str) -> QDialog:
         super().__init__()
-
+        self.setWindowTitle(title)
-        self.setWindowTitle(f"Add {reagent_lot}?")
-
         QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
-
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
-
-        self.layout = QVBoxLayout()
-        message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title().strip('Lot')}: {reagent_lot} in the database.\n\nWould you like to add it?")
-        self.layout.addWidget(message)
-        self.layout.addWidget(self.buttonBox)
-        self.setLayout(self.layout)
-
-
-class OverwriteSubQuestion(QDialog):
-    """
-    dialog to ask about overwriting existing submission
-    """    
-    def __init__(self, message:str, rsl_plate_num:str) -> QDialog:
-        super().__init__()
-
-        self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
-
-        QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
-
-        self.buttonBox = QDialogButtonBox(QBtn)
-        self.buttonBox.accepted.connect(self.accept)
-        self.buttonBox.rejected.connect(self.reject)
-
         self.layout = QVBoxLayout()
         message = QLabel(message)
         self.layout.addWidget(message)
         self.layout.addWidget(self.buttonBox)
         self.setLayout(self.layout)
 
-
 class AlertPop(QMessageBox):
 
     def __init__(self, message:str, status:str) -> QMessageBox:

src/submissions/frontend/functions.py

@@ -21,11 +21,3 @@ def check_kit_integrity(sub:BasicSubmission):
     return result
     
 
-def check_not_nan(cell_contents) -> bool:
-    try:
-        return not np.isnan(cell_contents)
-    except ValueError:
-        return True
-    except Exception as e:
-        logger.debug(f"Check encounteded unknown error: {e}")
-        return False

src/submissions/tools/__init__.py

@@ -0,0 +1,13 @@
+import numpy as np
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+def check_not_nan(cell_contents) -> bool:
+    try:
+        return not np.isnan(cell_contents)
+    except TypeError:
+        return True
+    except Exception as e:
+        logger.debug(f"Check encounteded unknown error: {type(e).__name__} - {e}")
+        return False

tests/test_database_functions.py

@@ -1,8 +0,0 @@
-from sqlalchemy import create_engine   
-from sqlalchemy.orm import Session
-from src.submissions.backend.db.models import *
-from src.submissions.backend.db import get_kits_by_use
- 
-engine = create_engine("sqlite+pysqlite:///:memory:", echo=True, future=True)
-session = Session(engine)
-metadata.create_all(engine)