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

<<<<<<< HEAD
codex:dict = {"cfDNA from Plasma":None}
codex.update ( {"gDNA from cells":"BM"} )
codex.update({"gDNA from Buffy Coat":"BC"})

=======
>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
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
        fmtId = formatInosticsId( model.get_Id(), model.get_materialid() )
        ws.append([ix, "", fmtId, 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

<<<<<<< HEAD
def formatInosticsId(id:str=None, matrl:str=None):
    iid = id.split("-", 1)[0]
    ncd:str = ""
    try:
        if codex[matrl] is None: 
            ncd =  "" 
        else: 
            ncd = codex[matrl]  
        if iid:
            return iid + ncd 
    except Exception as e:
        pass
    return iid

=======
>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
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
<<<<<<< HEAD
    MaterialID = None
=======
>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
    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
            
<<<<<<< HEAD
            if MaterialID==None and cell.value and isinstance(cell.value, str) and "Sample Material" in cell.value:
                MaterialID = cell.column
                continue

=======
>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
            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
<<<<<<< HEAD

            if cell.value and MaterialID == 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_materialid( cell.value )
                except:
                    pass
=======
>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
    wb.close()
    return InosticsIDKeys