#!/usr/bin/env python
import wx
import os
import sys
import db_obj
import wx.grid as gridlib
db_path = ''
class bac_form(wx.App):
'''main class for the GUI application '''
def __init__(self, redirect=False, filename=None):
wx.App.__init__(self, redirect, filename)
class bac_grid(gridlib.Grid):
def __init__(self, parent):
'''grid class that shows all the bacs in a table'''
#initialize the grid
gridlib.Grid.__init__(self, parent, -1)
#get the data
bac_data = db_test.get_data()
#creates the grid using the amount of data to set number
#of rows and columns
if not len(bac_data) == 0:
self.CreateGrid(len(bac_data), len(bac_data[0]))
#name each column
self.SetColLabelValue(0, 'Bac ID')
self.SetColLabelValue(1, 'Clone')
self.SetColLabelValue(2, 'Date')
self.SetColLabelValue(3, 'Source')
self.SetColLabelValue(4, 'Gene')
self.SetColLabelValue(5, 'Chromosome')
self.SetColLabelValue(6, 'Start')
self.SetColLabelValue(7, 'End')
self.SetColLabelValue(8, 'Antibiotic')
self.SetColLabelValue(9, 'Location')
self.SetColLabelValue(10, 'Temper.')
self.SetColLabelValue(11, '# of tubes')
self.SetColLabelValue(12, 'Box #')
self.SetColLabelValue(13, 'Cell #')
self.SetColLabelValue(14, 'Dna extr')
self.SetColLabelValue(15, 'FISH')
self.SetColLabelValue(16, 'PCR')
self.SetColLabelValue(17, 'Projects')
self.SetColLabelValue(18, 'Comments')
self.SetColLabelValue(19, 'Link')
self.SetColLabelValue(20, 'References')
#put the data in the grid, we're done
for i, j in enumerate(bac_data):
for m, n in enumerate(j):
self.SetCellValue(i, m, str(n))
self.SetReadOnly(i, m, True)
else:
wx.MessageBox("There is nothing in the database.\nTry adding something first")
class view_bacs(wx.Frame):
'''frame class tha contains the grid'''
def __init__(self, parent, id, title, pos = wx.DefaultPosition, size = wx.DefaultSize, style = wx.DEFAULT_FRAME_STYLE):
wx.Frame.__init__(self, parent, id, title, pos, size, style)
self.__do_layout()
self.__do_binding()
self.grid_row = 0
def __do_layout(self):
'''creates the layout'''
self.bac_list = bac_grid(self)
def __do_binding(self):
self.Bind(gridlib.EVT_GRID_CELL_RIGHT_CLICK, self.on_rightclick)
def on_rightclick(self, event):
self.grid_row = event.GetRow()
self.popup_id1 = wx.NewId()
self.popup_id2 = wx.NewId()
self.Bind(wx.EVT_MENU, self.on_edit, id=self.popup_id1)
self.Bind(wx.EVT_MENU, self.on_delete, id=self.popup_id2)
menu = wx.Menu()
item = wx.MenuItem(menu, self.popup_id1, 'Edit')
item2 = wx.MenuItem(menu, self.popup_id2, 'Delete')
menu.AppendItem(item)
menu.AppendItem(item2)
self.PopupMenu(menu)
menu.Destroy()
def on_edit(self, event):
for i in range(1, self.bac_list.GetNumberCols()):
self.bac_list.SetReadOnly(self.grid_row, i, False)
menu = wx.Menu()
self.save_edit = menu.Append(-1, 'Save changes', '')
self.menubar = wx.MenuBar()
self.menubar.Append(menu, 'Save')
self.SetMenuBar(self.menubar)
self.Bind(wx.EVT_MENU, self.edit_values, self.save_edit)
def edit_values(self, event):
values_list = {}
values_list['idbac'] = self.bac_list.GetCellValue(self.grid_row, 0)
values_list['clone'] = self.bac_list.GetCellValue(self.grid_row, 1)
values_list['sdate'] = self.bac_list.GetCellValue(self.grid_row, 2)
values_list['source'] = self.bac_list.GetCellValue(self.grid_row, 3)
values_list['gene'] = self.bac_list.GetCellValue(self.grid_row, 4)
values_list['chromosome'] = self.bac_list.GetCellValue(self.grid_row, 5)
values_list['startpos'] = int(self.bac_list.GetCellValue(self.grid_row, 6))
values_list['endpos'] = int(self.bac_list.GetCellValue(self.grid_row, 7))
values_list['antibiotic'] = self.bac_list.GetCellValue(self.grid_row, 8)
values_list['location1'] = self.bac_list.GetCellValue(self.grid_row, 9)
try:
values_list['temperature'] = int(self.bac_list.GetCellValue(self.grid_row, 10))
except:
values_list['temperature'] = 'None'
values_list['tubes'] = int(self.bac_list.GetCellValue(self.grid_row, 11))
values_list['box'] = int(self.bac_list.GetCellValue(self.grid_row, 12))
values_list['cell'] = self.bac_list.GetCellValue(self.grid_row, 13)
values_list['dnaex'] = self.bac_list.GetCellValue(self.grid_row, 14)
values_list['validation'] = self.bac_list.GetCellValue(self.grid_row, 15)
values_list['pcr'] = self.bac_list.GetCellValue(self.grid_row, 16)
values_list['projects'] = self.bac_list.GetCellValue(self.grid_row, 17)
values_list['comments'] = self.bac_list.GetCellValue(self.grid_row, 18)
values_list['genelink'] = self.bac_list.GetCellValue(self.grid_row, 19)
values_list['refs'] = self.bac_list.GetCellValue(self.grid_row, 20)
for i in range(1, self.bac_list.GetNumberCols()):
self.bac_list.SetReadOnly(self.grid_row, i, True)
db_test.edit_data(values_list)
def on_delete(self, event):
idbac = self.bac_list.GetCellValue(self.grid_row, 0)
db_test.delete_entry(idbac)
wx.MessageBox("Bac with id " + idbac + " was deleted")
self.bac_list.DeleteRows(self.grid_row)
class bacs(wx.Frame):
'''main application frame'''
def __init__(self, parent, id):
wx.Frame.__init__(self, parent, id, 'BACs', size = (600, 400), style = wx.DEFAULT_FRAME_STYLE)
self.__do_layout()
self.__do_binding()
def __do_layout(self):
'''creates the layout'''
#use a gridbagsizer in order to make conf easier
my_sizer = self.my_sizer = wx.GridBagSizer(20, 20)
panel = wx.Panel(self, -1, style = wx.TAB_TRAVERSAL | wx.CLIP_CHILDREN | wx.FULL_REPAINT_ON_RESIZE)
bac_date = self.bac_date = wx.DatePickerCtrl(panel, size=(120,-1), style=wx.DP_DROPDOWN | wx.DP_SHOWCENTURY)
#setup of window elements
clone = self.clone = wx.TextCtrl(panel, -1, '', size = (100, -1))
source = self.source = wx.TextCtrl(panel, -1, '', size = (100, -1))
projects = self.projects = wx.TextCtrl(panel, -1, '', size = (100, -1))
chromosome = self.chromo = wx.TextCtrl(panel, -1, '', size = (100, -1))
start = self.start = wx.TextCtrl(panel, -1, '', size = (100, -1))
end = self.end = wx.TextCtrl(panel, -1, '', size = (100, -1))
gene = self.gene = wx.TextCtrl(panel, -1, '', size = (100, -1))
dna = self.dna = wx.CheckBox(panel, -1, " DNA extraction")
validation = self.validation = wx.CheckBox(panel, -1, " FISH")
pcr = self.pcr = wx.CheckBox(panel, -1, " PCR")
#drop-down lists
temper_list = ['-80', '-20']
location_list = ['Richardson', 'Botterel']
antibiotic_list = ['chloramphenicol', 'kanamycin']
comments = self.comments = wx.TextCtrl(panel, -1, '', size = (250, 54), style=wx.TE_MULTILINE)
temperature = self.temperature = wx.ComboBox(panel, -1, '', wx.DefaultPosition, (100, -1), temper_list, wx.CB_DROPDOWN)
location1 = self.location = wx.ComboBox(panel, -1, '', wx.DefaultPosition, (100, -1), location_list, wx.CB_DROPDOWN)
antibiotic = self.anti = wx.ComboBox(panel, -1, '', wx.DefaultPosition, (100, -1), antibiotic_list, wx.CB_DROPDOWN)
box = self.box = wx.TextCtrl(panel, -1, '', size = (100, 18))
tubes = self.tubes = wx.TextCtrl(panel, -1, '', size = (100, 18))
add_button = self.add_button = wx.Button(panel, -1, "Add", size = (120, 30))
cancel_button = self.cancel_button = wx.Button(panel, -1, "Cancel", size = (120, 30))
grid_button = self.grid = wx.Button(panel, -1, 'Show BAC list', size = (120, 30))
#postioning elements on the grid layout
my_sizer.Add(wx.StaticText(panel, label = 'Date'), (0, 1))
my_sizer.Add(bac_date, (0, 2))
my_sizer.Add(wx.StaticText(panel, label = 'Clone'), (1, 1))
my_sizer.Add(clone, (1, 2))
my_sizer.Add(wx.StaticText(panel, label = 'Source'), (1, 3))
my_sizer.Add(source, (1, 4))
my_sizer.Add(wx.StaticText(panel, label = 'Projects'), (2, 1))
my_sizer.Add(projects, (2, 2))
my_sizer.Add(wx.StaticText(panel, label = 'Chromosome'), (2, 3))
my_sizer.Add(chromosome, (2, 4))
my_sizer.Add(wx.StaticText(panel, label = 'Start position'), (3, 1))
my_sizer.Add(start, (3, 2))
my_sizer.Add(wx.StaticText(panel, label = 'End position'), (3, 3))
my_sizer.Add(end, (3, 4))
my_sizer.Add(wx.StaticText(panel, label = 'Gene'), (4, 1))
my_sizer.Add(gene, (4, 2))
my_sizer.Add(wx.StaticText(panel, label = 'Antibiotic'), (4, 3))
my_sizer.Add(antibiotic, (4, 4))
my_sizer.Add(wx.StaticText(panel, label = 'Glycerol stock'), (5, 2))
my_sizer.Add(wx.StaticText(panel, label = 'Location'), (6, 1))
my_sizer.Add(location1, (6, 2))
my_sizer.Add(wx.StaticText(panel, label = 'Temperature'), (6, 3))
my_sizer.Add(temperature, (6, 4))
my_sizer.Add(wx.StaticText(panel, -1, label = 'Number of tubes'), (7, 1))
my_sizer.Add(tubes, (7, 2))
my_sizer.Add(wx.StaticText(panel, -1, label = 'Box and Cell #'), (7, 3))
my_sizer.Add(box, (7, 4))
my_sizer.Add(wx.StaticText(panel, -1, label = 'Comments'), (8, 1))
my_sizer.Add(comments, (8, 2), (2, 4))
my_sizer.Add(dna, (10, 1))
my_sizer.Add(validation, (10, 2))
my_sizer.Add(pcr, (10, 3))
my_sizer.Add(add_button, (11, 1))
my_sizer.Add(cancel_button, (11, 2))
my_sizer.Add(grid_button, (12, 1))
my_sizer.Add((11, 10), (9, 1))
my_sizer.Add((11, 10), (1,5))
box = wx.BoxSizer()
box.Add(my_sizer, 0, wx.ALL, 10)
panel.SetSizerAndFit(box)
self.SetClientSize(panel.GetSize())
def __do_binding(self):
'''does the binding'''
self.Bind(wx.EVT_BUTTON, self.add_values, self.add_button)
self.Bind(wx.EVT_BUTTON, self.show_grid, self.grid)
self.Bind(wx.EVT_BUTTON, self.on_cancel, self.cancel_button)
def load_data_box(self):
'''deprecated'''
for i in self.bac_data:
yield i
def on_load_data(self, event):
'''deprecated'''
db_test.load_data()
self.bac_data = db_test.get_data()
self.forward.Enable(True)
self.a = self.load_data_box()
b = self.a.next()
def add_values(self, event):
'''insert a value in the database'''
not_exec = False
values_list = {}
values_list['projects'] = str(self.projects.GetValue())
values_list['comments'] = str(self.comments.GetValue())
try:
values_list['temperature'] = int(self.temperature.GetValue())
except:
wx.MessageBox('Please select a temperature to continue')
not_exec = True
box_cell = self.box.GetValue().split(' ')
try:
values_list['box'] = int(box_cell[0])
values_list['cell'] = str(box_cell[1])
except:
wx.MessageBox('Enter box number and cell number separated by a space')
not_exec = True
values_list['tubes'] = int(self.tubes.GetValue())
values_list['chromosome'] = str(self.chromo.GetValue())
values_list['antibiotic'] = str(self.anti.GetValue())
values_list['sdate'] = str(self.bac_date.GetValue())
values_list['clone'] = str(self.clone.GetValue())
values_list['source'] = str(self.source.GetValue())
try:
values_list['location1'] = str(self.location.GetValue())
except:
wx.MessageBox('Please select a location')
not_exec = True
try:
values_list['startpos'] = int(self.start.GetValue())
except:
values_list.append(0)
try:
values_list['endpos'] = int(self.end.GetValue())
except:
values_list.append(0)
values_list['gene'] = str(self.gene.GetValue())
values_list['genelink'] = ''
values_list['dnaex'] = self.dna.GetValue()
values_list['validation'] = self.validation.GetValue()
values_list['pcr'] = self.pcr.GetValue()
values_list['refs'] = ''
if not_exec == False:
db_test.add_data(values_list)
self.on_cancel(wx.EVT_BUTTON)
def on_cancel(self, event):
self.clone.SetValue('')
self.source.SetValue('')
self.projects.SetValue('')
self.chromo.SetValue('')
self.start.SetValue('')
self.end.SetValue('')
self.gene.SetValue('')
self.dna.SetValue(False)
self.validation.SetValue(False)
self.pcr.SetValue(False)
self.comments.SetValue('')
self.temperature.SetValue('')
self.location.SetValue('')
self.anti.SetValue('')
self.box.SetValue('')
self.tubes.SetValue('')
def show_grid(self, event):
'''calls the grid frame to show contents'''
my_bacs = view_bacs(self, -1, 'BAC list', size = (600, 400), style = wx.DEFAULT_FRAME_STYLE)
my_bacs.Show()
if __name__ == '__main__':
if sys.platform == 'darwin':
db_path = open('db.txt').readlines()[0].strip()
db_test = db_obj.Bac('bac', db_path)
else:
db_test = db_obj.Bac('bac')
app = bac_form(redirect = False)
frame = bacs(parent=None, id = -1)
frame.CentreOnScreen()
frame.Show()
app.MainLoop()
