# encoding=utf8

'''

Created on Jul 9, 2013

@author: james

'''

from Tkinter import *

import Tkinter, os, codecs

import time, re, tkMessageBox

from tkFileDialog import askopenfilename

import sys

reload(sys)

sys.setdefaultencoding('utf8')

if __name__ == '__main__':

# data containers

root = Tk()

root.title('Relation Annotation Tool V1.0 ')

currentProtein = ''

UniprotID = ''

tagLists = {}

tagIndex = 0

cancel = False

idPrefix = 'PROT'

targetFilePath = ''

# get order list

def readOrder(path, orderList):

for line in open(path):

if line == '':

continue

line = line[:-1]

splits = line.split('\t')

orderList.append((u'task\\' + splits[0], int(splits[1])))

return orderList

# read tasks and orders

def readOrders():

try:

orderList = []

for path in os.listdir('orders'):

orderList += (readOrder('orders/' + path, orderList))

orderList = sorted(orderList, key=lambda tup:tup[1], reverse=True)

return [tup[0] for tup in orderList]

except:

return

# Open next file that need to be annnotated in 'task' folder

def autoNext():

global targetFilePath

saveFile()

clearData()

txtFileSet = readAlltxtFilenames()

taggedFileSet = readAlltaggedFilenames()

flag = False

for path in orderList:

if path in txtFileSet and path not in taggedFileSet:

targetFilePath = path

root.title('Relation Annotation Tool ' + targetFilePath)

readFile = open(path, 'r')

allLines = ''.join(readFile.readlines())

readFile.close()

text.insert(1.0, allLines)

flag = True

break

if not flag:

tkMessageBox.showinfo("Congratulations!", "No task file in 'task' folder. To annotate a file, choose 'file->open'")

def openBySelf():

global targetFilePath

selectedFile = askopenfilename(initialdir='task', filetypes=[("txt files", "*.txt")])

print selectedFile

if selectedFile == '':

return

else:

saveFile()

txtFileSet = readAlltxtFilenames()

taggedFileSet = readAlltaggedFilenames()

print 'aa'

try:

readFile = open(selectedFile, 'r')

allLines = ''.join(readFile.readlines())

readFile.close()

targetFilePath = selectedFile

clearData()

text.insert(1.0, allLines)

root.title('Relation Annotation Tool ' + targetFilePath)

except:

pass

def readAlltxtFilenames(path=u'task'):

try:

txtFileSet = set()

for f in os.listdir(path):

filePath = os.path.join(path, f)

if os.path.isdir(filePath):

txtFileSet = txtFileSet.union(readAlltxtFilenames(path=filePath))

elif filePath.endswith('.txt'):

txtFileSet.add(filePath)

return txtFileSet

except:

return

def readAlltaggedFilenames(path=u'task'):

try:

taggedFileSet = set()

for f in os.listdir(path):

filePath = os.path.join(path, f)

if os.path.isdir(filePath):

taggedFileSet = taggedFileSet.union(readAlltaggedFilenames(path=filePath))

elif filePath.endswith('.tagged'):

taggedFileSet.add(filePath[:-1 * len('.tagged')])

return taggedFileSet

except:

return

# convert taglist into strings£¬for saving

def taglistEncode():

strTags = ''

tags = []

for tagName in text.tag_names():

if tagName.startswith(idPrefix):

tags.append('\t'.join(tagLists[tagName]))

return '\n'.join(tags)

# delete all tags of a text

def clearTags(textWidget):

for tagName in textWidget.tag_names():

textWidget.tag_delete(tagName)

# clear data

def clearData():

global currentProtein

global UniprotID

global tagLists

global tagIndex

global cancel

entryP1.delete(0, END)

entryP2.delete(0, END)

entryKW.delete(0, END)

text.delete(1.0, END)

textEntities.delete(1.0, END)

textrelation.delete(1.0, END)

clearTags(text)

clearTags(textEntities)

clearTags(textrelation)

currentProtein = ''

UniprotID = ''

tagLists = {}

tagIndex = 0

cancel = False

idPrefix = 'PROT'

def saveFile():

saveFilePath = targetFilePath + '.tagged'

saveFile1(saveFilePath)

# save file

def saveFile1(path):

sourceText = text.get(1.0, END)

sourceEntities = textEntities.get(1.0, END)

relationl = []

for line in textrelation.get(1.0, END).split('\n'):

if line != '':

relationl.append(line)

trelations = '\n'.join(relationl)

savefile = open(path, 'w')

savefile.write('###Source text###\n')

savefile.write(sourceText)

savefile.write('\n\n###Entities###\n')

savefile.write(sourceEntities)

savefile.write('\n\n###Relations###\n')

savefile.write(trelations)

savefile.close()

# form a relation

def relationrecordEncode(p1, p2, keywords):

return '<([' + p1 + '])> ' + keywords + ' <([' + p2 + '])>'

# decode a relation record into a tuple

def relationRecordDecode(str):

splits = re.split('<([|])>', str)

dc = {}

dc['p1'] = len(splits) == 5 and splits[1] or ''

dc['p2'] = len(splits) == 5 and splits[3] or ''

dc['kw'] = len(splits) == 5 and splits[2] or ''

return dc

# right click selected text, to add the selected text into keyword text field

def fillKeyWord(str):

if entryKW.get() != '':

entryKW.insert(END, ',')

entryKW.insert(END, str)

# center the window

def center(win):

win.update_idletasks()

width = win.winfo_width()

height = win.winfo_height()

x = (win.winfo_screenwidth() / 2) - (width / 2)

y = (win.winfo_screenheight() / 2) - (height / 2)

win.geometry('{0}x{1}+{2}+{3}'.format(width, height, x, y))

# right click an entity record in textEntities text area£¬to put the entities into entity text field

def fillEntityFromEntities(index):

strindex = str(index)

prefix = strindex[0:strindex.find('.') + 1]

start = float(prefix + '0')

line = textEntities.get(start, textEntities.index(prefix + 'end'))

if entryP1.get() == '':

entryP1.insert(END, line)

elif entryP2.get() == '':

entryP2.insert(END, line)

# left click a highlighted entity, to put it into the entity text field

def fillEntityFromText(event, tagName):

line = '\t'.join(tagLists[tagName])

if entryP1.get() == '':

entryP1.insert(END, line)

elif entryP2.get() == '':

entryP2.insert(END, line)

def updateTag(textId, tagName, buttonStr, func):

textId.tag_delete(tagName)

textId.tag_add(tagName, 1.0, textrelation.index('end'))

textId.tag_bind(tagName, buttonStr, func)

# insert relation

def insertRelation():

p1 = entryP1.get()

p2 = entryP2.get()

keywords = entryKW.get()

if p1 != '' and p2 != '' and keywords != '':

str = relationrecordEncode(p1, p2, keywords) + '\n'

textrelation.insert(END, str)

updateTag(textrelation, 'tag_relation', '<Button-3>', lambda x: deleterelation(textrelation.index(CURRENT)))

entryP1.delete(0, END)

entryP2.delete(0, END)

# delete a relation by right click

def deleterelation(index):

strindex = str(index)

prefix = strindex[0:strindex.find('.') + 1]

start = float(prefix + '0')

textrelation.delete(start, textrelation.index(prefix + 'end'))

updateTag(textrelation, 'tag_relation', '<Button-3>', lambda x: deleterelation(textrelation.index(CURRENT)))

def handlerAdaptor(fun, **kwds):

return lambda event, fun = fun, kwds = kwds: fun(event, **kwds)

# add an entity

def insertEntity(str):

textEntities.insert(END, str)

textEntities.tag_delete('tag_entities')

textEntities.tag_add('tag_entities', 1.0, textEntities.index('end'))

textEntities.tag_bind('tag_entities', '<Button-1>', lambda x: fillEntityFromEntities(textEntities.index(CURRENT)))

def getEntity(UniprotID , currentProtein, first, last):

return (UniprotID , currentProtein, first, last)

def entityEncode(tup):

return '\t'.join(tup)

def entityDecoder(str):

return str.split('\t')

# annotate an entity

def annoteEntity():

global tagIndex

global currentProtein

global UniprotID

global cancel

currentProtein = text.selection_get()

first = text.index('sel.first')

last = text.index('sel.last')

msg_box(currentProtein);

if not cancel and UniprotID != '':

tagName = idPrefix + str(tagIndex)

tagIndex += 1

text.tag_add(tagName, first , last)

text.tag_config(tagName, background='black', foreground='yellow')

text.tag_bind(tagName, '<Button-3>', handlerAdaptor(cancelTag, tagName=tagName))

text.tag_bind(tagName, '<Button-1>', handlerAdaptor(fillEntityFromText, tagName=tagName))

tagLists[tagName] = getEntity(UniprotID , currentProtein, first, last);

insertEntity(entityEncode(tagLists[tagName]) + '\n')

UniprotID = ''

currentProtein = ''

cancel = False

# delete highlighted entity

def cancelTag(event, tagName):

text.tag_delete(tagName)

item = entityEncode(tagLists[tagName])

if tagName in tagLists:

del tagLists[tagName]

updateEntities()

if entryP1.get() == item:

entryP1.delete(0, END)

if entryP2.get() == item:

entryP2.delete(0, END)

i = 0

for line in textrelation.get(1.0, END).split('\n'):

i += 1

if item in line:

deleterelation(float(str(i) + '.0'))

# refresh entities

def updateEntities():

textEntities.delete(1.0, textEntities.index('end'))

for i in range(0, tagIndex):

tagName = idPrefix + str(i)

if tagName in tagLists:

textEntities.insert(textEntities.index('end'), '\t'.join(tagLists[tagName]) + '\n')

# clear text widged

def delete(textWidget, str):

content = textWidget.get(1.0, END)

i = 0

for line in content.split('\n'):

i += 1

if str in line:

textWidget.delete(float(str(i) + '.0'), textWidget.index(str(i) + '.end'))

#

def help_box():

top = Toplevel(root)

top.title('README.md')

top.transient(root)

top.grab_set()

lf = LabelFrame(top, borderwidth=0)

text = Text(lf)

scroll = Scrollbar(lf, command=text.yview)

text.configure(yscrollcommand=scroll.set)

text.pack(side=LEFT)

scroll.pack(side=RIGHT, fill=Y)

lf.pack(side = TOP)

lines = ''.join(file('readme.txt', 'r').readlines())

text.insert(1.0, lines)

cbutton = Button(top, text='confirm', command=top.destroy)

cbutton.pack(side=BOTTOM)

center(top)

top.wait_window()

def msg_box(proteinName, title='Annotate entity ID', msg='Annotate entity ID'):

top = Toplevel(root)

top.title(title)

top.transient(root)

top.grab_set()

# label0 = Label(top, text=msg)

# label0.pack()

lfContent = LabelFrame(top, borderwidth=0)

lfContent.pack(side=TOP)

lfEntry = LabelFrame(lfContent, borderwidth=0)

lfLabel = LabelFrame(lfContent, borderwidth=0)

lfEntry.pack(side=RIGHT)

lfLabel.pack(side=LEFT)

Label(lfLabel, text='Entity name: ').pack(side=TOP)

Label(lfLabel, text='Entity ID :').pack(side=BOTTOM)

entryProt = Entry(lfEntry, width=40)

entryProt.insert(0, proteinName)

entryProt.pack(side=TOP)

entryId = Entry(lfEntry, width=40)

entryId.pack(side=BOTTOM)

entryId.focus()

lfButtons = LabelFrame(top, borderwidth=0)

lfButtons.pack(side=BOTTOM)

button2 = Button(lfButtons, text='confirm', command=lambda: submit_name(entryId, top))

button2.pack(side=LEFT)

button3 = Button(lfButtons, text='cancel',

command=lambda: cancelIDAnno(top))

button3.pack(side=RIGHT)

center(top)

top.wait_window()

def cancelIDAnno(top):

global cancel

top.destroy()

cancel = True

def submit_name(entry0, top):

global UniprotID

UniprotID = entry0.get()

top.destroy()

def empty(event):

return 'break'

# read file

orderList = readOrders()

txtFileSet = readAlltxtFilenames()

taggedFileSet = readAlltaggedFilenames()

# GUI drawing

menubar = Menu(root)

# Entity Frame

labelframeNER = LabelFrame(root, text='Text')

labelframeNER.pack(fill='both', expand='yes', side=LEFT)

lfNER = LabelFrame(labelframeNER, borderwidth=0)

lfNER.pack(side=BOTTOM)

Button(labelframeNER, text='Annotate Entity', fg='blue', bd=2, width=28, command=annoteEntity).pack(side=BOTTOM)

text = Text(lfNER, height=26, width=80)

text.tag_bind('sel', '<Button-1>', lambda x: fillKeyWord(text.selection_get()))

scroll = Scrollbar(lfNER, command=text.yview)

text.configure(yscrollcommand=scroll.set)

text.pack(side=LEFT)

scroll.pack(side=LEFT, fill=Y)

flag = False

if orderList != None:

for path in orderList:

if path in txtFileSet and path not in taggedFileSet:

targetFilePath = path

root.title('Relation Annotation Tool ' + targetFilePath)

readFile = open(path, 'r')

allLines = ''.join(readFile.readlines())

readFile.close()

text.insert(1.0, allLines)

flag = True

break

if not flag:

tkMessageBox.showinfo("Congratulations!", "No task file in 'task' folder. To annotate a file, choose 'file->open'")

text.bind('<Key>', empty)

text.bind("<Control-s>", lambda x:saveFile())

# Engity List Frame

labelframeEntities = LabelFrame(root, text='Entities')

labelframeEntities.pack(fill='both', expand='yes', side=LEFT)

lfEntities = LabelFrame(labelframeEntities, borderwidth=0)

lfEntities.pack(side=BOTTOM)

textEntities = Text(lfEntities, height=26, width=40)

textEntities.bind('<Key>', empty)

textEntities.bind("<Control-s>", lambda x:saveFile())

scrollEntities = Scrollbar(lfEntities, command=text.yview)

textEntities.configure(yscrollcommand=scrollEntities.set)

textEntities.pack(side=LEFT)

scrollEntities.pack(side=LEFT, fill=Y)

textEntities.tag_add('tag_entities', 1.0, textEntities.index('end'));

textEntities.tag_bind('tag_entities', '<Button-1>', lambda x: fillEntityFromEntities(textEntities.index(CURRENT)))

titleFrame = LabelFrame(labelframeEntities, border=0)

label = Label(titleFrame, text='Entity ID\t\tEntity Name\tStart\tEnd')

label.pack(side=BOTTOM)

titleFrame.pack(side=BOTTOM)

# Relation Frame

labelframerelation = LabelFrame(root, text='Relations')

labelframerelation.pack(fill='both', expand='yes', side=LEFT)

labelframeP1 = LabelFrame(labelframerelation, borderwidth=0)

entryP1 = Entry(labelframeP1)

labelframeP2 = LabelFrame(labelframerelation, borderwidth=0)

entryP2 = Entry(labelframeP2)

labelframeKW = LabelFrame(labelframerelation, borderwidth=0)

entryKW = Entry(labelframeKW)

Label(labelframeP1, text='Entity 1 :').pack(side=LEFT)

Label(labelframeP2, text='Entity 2 :').pack(side=LEFT)

Label(labelframeKW, text='Relation Keyword:').pack(side=LEFT)

entryP1.pack(side=LEFT)

entryP2.pack(side=LEFT)

entryKW.pack(side=LEFT)

Button(labelframeP1, text='Clear', command=lambda: entryP1.delete(0, END)).pack(side=LEFT)

Button(labelframeP2, text='Clear', command=lambda: entryP2.delete(0, END)).pack(side=LEFT)

Button(labelframeKW, text='Clear', command=lambda: entryKW.delete(0, END)).pack(side=LEFT)

labelframeP1.pack(side=TOP)

labelframeP2.pack(side=TOP)

labelframeKW.pack(side=TOP)

Button(labelframerelation, text='Annotate a relation', fg='blue', bd=2, width=28, command=insertRelation).pack(side=TOP)

lfrelation = LabelFrame(labelframerelation, borderwidth=0)

lfrelation.pack(side=BOTTOM)

textrelation = Text(lfrelation, height=26, width=70)

scrollrelation = Scrollbar(lfrelation, command=text.yview)

textrelation.tag_add('tag_relation', 1.0, textrelation.index('end'))

textrelation.configure(yscrollcommand=scrollrelation.set)

textrelation.pack(side=LEFT)

scrollrelation.pack(side=LEFT, fill=Y)

# Create Menus

filemenu = Menu(menubar, tearoff=0)

filemenu.add_command(label='Next file', command=autoNext)

filemenu.add_command(label='Open', command=openBySelf)

filemenu.add_separator()

filemenu.add_command(label='Save', command=saveFile, accelerator="Ctrl+S")

filemenu.add_separator()

filemenu.add_command(label='Quit', command=root.quit)

menubar.add_cascade(label='File', menu=filemenu)

helpmenu = Menu(menubar, tearoff=0)

helpmenu.add_command(label='How to', command=help_box)

menubar.add_cascade(label='Help', menu=helpmenu)

# display menu

root.config(menu=menubar)

root.bind_all("<Control-s>", lambda x:saveFile())

# centerwindow

center(root)

mainloop()