qubit-tools/qubittool/tool.py

import sys, os
import pandas as pd
import csv
import openpyxl
from openpyxl import Workbook, load_workbook
from openpyxl.worksheet.table import Table, TableStyleInfo
from openpyxl.worksheet.dimensions import ColumnDimension
from openpyxl.worksheet.worksheet import Worksheet
from openpyxl.utils import cell
from openpyxl.styles import PatternFill, Border, Side, Alignment

from rowmodel import RowModel

def read_qubit_doc_by_accession(keys:dict, path:str):
    # collect values_by_sample_names string ids #
    with open(path, 'r', newline='', encoding='utf-8') as csvfile:
        reader = csv.DictReader(csvfile)        
        for row in reader:
            try:
                if keys[ row["Test Name"] ]: 
                    rmv:RowModel = keys[ row["Test Name"] ]
                    rmv.set_testdate(row["Test Date"])
                    #rmv.set_qubitrunid(row["Run ID"])
                    rmv.set_runvalngml(row["Green RFU"])
                    rmv.set_sampleconc(row["Original sample conc."])
                    rmv.set_tubeconc(row["Qubit tube conc."])
                    print("{}:{}".format(rmv.get_qubitrunid(), rmv.get_Id()))
            except KeyError:
                pass
    return

def read_qubit_doc_by_order(keys:dict, path:str):
    # collect values_by_sample_names string ids #
    with open(path, 'r', newline='', encoding='utf-8') as csvfile:
        reader = csv.DictReader(csvfile)        
        rowlist:list = list()
        for row in reader:
            rowlist.append(row)
        if len( rowlist ) < 1:
            return
        indx:int = len( rowlist ) - 1
        for key in keys:
            try:
                row = rowlist[indx]
                if row is None:
                    return
                indx = indx - 1
                if row["Test Name"]: 
                    rmv:RowModel = keys[key]
                    rmv.set_testdate(row["Test Date"])
                    #rmv.set_qubitrunid(row["Run ID"])
                    rmv.set_runvalngml(row["Green RFU"])
                    rmv.set_sampleconc(row["Original sample conc."])
                    rmv.set_tubeconc(row["Qubit tube conc."])
                    print("{}:{}".format(rmv.get_qubitrunid(), rmv.get_Id()))
            except KeyError:
                pass
            except IndexError:
                return
    return

def write_run_doc(dm:dict, path:str):
    # write excel run_doc section with values_from_qubit by string ids #
    sheetdata:list = []
    wb = openpyxl.load_workbook(path, read_only=False)
    sheets = wb.sheetnames
    ws:Worksheet = None
    for sheetname in sheets:
        if sheetname == "Output":
            ws = wb.get_sheet_by_name(sheetname)
            break
    if ws == None: 
        ws = wb.create_sheet(title="Output")
        ws.title = "Output"
        wb.worksheets.append(ws)
    
    ws.append( ["No.", "SampleID", "Sysmex Inostics ID (Accession ID)","Secondary ID (Customer ID)","Plasma Vol. [mL]","Qubit run ID","ng/µL","GE/µL"] )
    ws.column_dimensions["C"].width = 19.23
    ws.column_dimensions["D"].width = 18.23
    ws.column_dimensions["E"].width = 15.23
    ws.column_dimensions["F"].width = 14.23
    ws.column_dimensions["G"].width = 18.23
    ix:int = 0
    for r in dm:
        model:RowModel = dm[r]
        ix=ix+1
        ws.append([ix, "", model.get_Id(), model.get_customerid(), model.get_plasmavolml(), model.get_qubitrunid(), 
        model.get_sampleconc(), convert_to_GE(model.get_sampleconc())])

    grayFill = PatternFill(start_color='D0CECE', end_color='D0CECE',
                       fill_type='solid')

    for columns in ws.iter_cols(min_col=1, max_col=2, min_row=None, max_row=None):
        for cell in columns:
            cell.fill = grayFill

    wb.save(path)
    wb.close()
    return

def convert_to_numeric(vlu, stndv:float=0.0):
    try:
        return float(vlu)
    except Exception as e:
        return decimal.Decimal(stndv)

def convert_to_GE(vlu, stndfv:float=0.0033):
    try:
        return float(vlu) / stndfv
    except Exception as e:
        return "undefined"

def read_collect_run_doc_name_strids(min_col:int=1, path:str=None):
    wb = openpyxl.load_workbook(path, read_only=True)
    ws = wb.active
    if ws.title != "Documentation":
       raise Exception("Run Doc not found, set Active worksheet")

    ProtocolRunID = ws.cell(3,3).value
    InosticsID = None
    CustomerID = None
    PlasmaID = None
    InosticsIDKeys = {}
    for row in ws.iter_rows(max_row=30, min_col=min_col):
        for cell in row:
            if InosticsID == None and cell.value and isinstance(cell.value, str) and "Inostics ID" in cell.value:
                InosticsID = cell.column
                continue
            
            if CustomerID == None and cell.value and isinstance(cell.value, str) and "Relevant Customer ID" in cell.value:
                CustomerID = cell.column
                continue

            if PlasmaID == None and cell.value and isinstance(cell.value, str) and "Plasma Vol" in cell.value:
                PlasmaID = cell.column
                continue
            
            if cell.value and InosticsID == cell.column:
                InosticsIDKeys[cell.value] = RowModel(cell.coordinate, cell.value)
                rmv:RowModel = InosticsIDKeys[cell.value]
                if ProtocolRunID != None :
                    rmv.set_qubitrunid(ProtocolRunID)
                continue

            if cell.value and CustomerID == cell.column:
                print(F"{cell.coordinate}:{cell.row}x{cell.column}={cell.value}") 
                try:
                    if InosticsIDKeys[row[InosticsID-1].value] != None: 
                        rmv:RowModel = InosticsIDKeys[row[InosticsID-1].value]
                        rmv.set_customerid( cell.value )
                except:
                    pass

            if cell.value and PlasmaID == cell.column:
                print(F"{cell.coordinate}:{cell.row}x{cell.column}={cell.value}") 
                try:
                    if InosticsIDKeys[row[InosticsID-1].value] != None: 
                        rmv:RowModel = InosticsIDKeys[row[InosticsID-1].value]
                        rmv.set_plasmavolml( convert_to_numeric(cell.value) )
                except:
                    pass
    wb.close()
    return InosticsIDKeys