def SaveWhiteListSemanticEdit(listWL, listBL, typeVar, wl_look_head,
wl_look_stub, wl_look_super, wl_look_data,
bl_look_head, bl_look_stub, bl_look_super,
bl_look_data, WhiteListWindow, project_name,
rule_name, vClsIn):
global currentWhiteList
global currentBlackList
global semanticTypes
selected = []
for item in semanticTypes:
if (listWL.getstatus(item) == "on"):
selected.append(item.split(".")[-1])
currentWhiteList = selected
currentBlackList = []
currentBlackList = listBL.split('\n')
rule_path = "Projects/" + project_name + "/" + vClsIn.get(
) + "/" + rule_name
FileManipulationHelper.CreateFoderIfNotExist(rule_path)
semType = True
FileManipulationHelper.SaveCueListSem(rule_path, rule_name,
currentWhiteList, currentBlackList,
typeVar, wl_look_head, wl_look_stub,
wl_look_super, wl_look_data,
bl_look_head, bl_look_stub,
bl_look_super, bl_look_data)
#FileManipulationHelper.MakeRuleCFGFile(rule_path, look_head, look_stub, look_super, look_data, look_all,vClsIn,vDefUnit,vPosUnit,pragVar)
WhiteListWindow.withdraw()
def SaveSintacticRules(rules, window, project_name, rule_name, variable_name):
global lab2
window.withdraw()
#top = Toplevel()
get_rules = FileManipulationHelper.loadRules(project_name, variable_name)
rule_path = 'Projects/' + variable_name + '/' + project_name + '/' + rule_name
FileManipulationHelper.SaveSyntacticRules(rules, project_name, rule_name,
variable_name)
def FinishFirstScreen(variab, E2, Lb3, s):
if (variab.get() == "NP"):
project_name = E2.get()
else:
pos = Lb3.curselection()[0]
project_name = Lb3.get(pos)
#tkMessageBox.showinfo("Project selected", project_name)
s.withdraw()
FileManipulationHelper.CreateFoderIfNotExist("Projects/" + project_name)
FileManipulationHelper.CreateProjectCfgFileIfNotExist("Projects/" +
project_name)
LoadFirstCfGScreen(project_name)
def ClearDBTables(project_name):
dbSettings = FileManipulationHelper.LoadDBConfigFile(project_name)
query = QueryDBClass.QueryDBCalss(dbSettings['Host'], dbSettings['User'],
dbSettings['Pass'],
dbSettings['Database'])
query.ClearCreatedTables()
query.CreateAdditionalTables()
def MakeChangesToSyntacticRules(project_name, rule_name, variable_name):
top = Toplevel()
#top.protocol("WM_DELETE_WINDOW", on_closing)
top.title("Modify selected rules")
top.geometry('{}x{}'.format(400, 300))
topframe = Frame(top, height=10)
topframe.pack()
frame = Frame(top)
frame.pack()
topframe2 = Frame(top, height=10)
topframe2.pack()
rules = StringVar()
rulelist = Text(frame, height=15, width=40)
rulelist.grid(row=1, sticky='w')
fpaths = []
rules = []
path = 'Projects/' + project_name + '/' + variable_name + '/' + rule_name + '/' + 'SyntacticRules.sin'
rules = FileManipulationHelper.LoadRules(path)
i = 1
for w in rules:
rulelist.insert(str(i) + '.0', w)
i = i + 1
skip_val = IntVar()
skip_val.set(0)
saveButton = Button(
frame,
text="Next",
bg="green",
fg="black",
command=lambda: SaveSintacticRules(rulelist.get(
"1.0", END), top, project_name, rule_name, variable_name)).grid(
row=2, sticky='w')
pass
def SaveRuleEdit(project_name, rule_name, add, vClsIn, vDefUnit, vPosUnit,
pragVar, ruleType, ruleMech, wl_look_head, wl_look_stub,
wl_look_super, wl_look_data):
global currentWhiteList
global currentBlackList
rule_path = "Projects/" + project_name + "/" + vClsIn.get().replace(
'\n', '') + "/" + rule_name
FileManipulationHelper.CreateFoderIfNotExist(rule_path)
vRuleType = StringVar()
vLexSemRule = StringVar()
vRuleType.set(ruleType)
vLexSemRule.set(ruleMech)
FileManipulationHelper.MakeRuleCFGFile(rule_path, vClsIn, vDefUnit,
vPosUnit, pragVar, vRuleType,
vLexSemRule, wl_look_head,
wl_look_stub, wl_look_super,
wl_look_data)
add.withdraw()
def AddEditVariable(project_name, vRuleName, vRuleType, RuleNameView,
RulesListBox):
RuleNameView.withdraw()
rule_path = "Projects/" + project_name + "/" + vRuleName.get().replace(
'\n', '')
FileManipulationHelper.CreateFoderIfNotExist(rule_path)
f = open(rule_path + '/var_config.cfg', 'w')
f.write("VariableName:" + str(vRuleName.get().replace('\n', '')) + '\n')
f.write("VariableType:" + str(vRuleType.get().replace('\n', '')) + '\n')
f.close()
RulesListBox.insert('', 'end', vRuleName.get(), text=vRuleName.get())
def SaveRule(project_name, rule_name, add, vClsIn, vDefUnit, vPosUnit, pragVar,
RulesListBox, vRuleType, vLexSemRule, wl_look_head, wl_look_stub,
wl_look_super, wl_look_data):
global currentWhiteList
global currentBlackList
rule_path = "Projects/" + project_name + "/" + vClsIn.get(
) + "/" + rule_name
FileManipulationHelper.CreateFoderIfNotExist(rule_path)
#FileManipulationHelper.SaveWhiteList(rule_path, currentWhiteList)
#FileManipulationHelper.SaveBlackList(rule_path, currentBlackList)
FileManipulationHelper.MakeRuleCFGFile(rule_path, vClsIn, vDefUnit,
vPosUnit, pragVar, vRuleType,
vLexSemRule, wl_look_head,
wl_look_stub, wl_look_super,
wl_look_data)
RulesListBox.insert(vClsIn.get(), 'end', text=rule_name)
add.withdraw()
if (vLexSemRule.get() == "Lexical"):
WhiteListWindow(project_name, rule_name, vClsIn)
if (vLexSemRule.get() == "Semantic"):
SemanticListWindow(project_name, rule_name, vClsIn)
def SaveDBSettings(HostName, PortName, UserName, PassName, DatabaseName,
DataConfig, project_name):
hostname = HostName.get()
portname = PortName.get()
username = UserName.get()
passname = PassName.get()
database = DatabaseName.get()
DataConfig.withdraw()
FileManipulationHelper.SaveToConfigFile(project_name, hostname, portname,
username, passname, database)
pass
def SaveSintacticRules(rules, window,project_name,rule_name,variable_name):
global lab2
window.withdraw()
#top = Toplevel()
get_rules = FileManipulationHelper.loadRules(project_name,variable_name)
rule_path = 'Projects/'+variable_name+'/'+project_name+'/'+rule_name
FileManipulationHelper.SaveSyntacticRules(rules,project_name,rule_name,variable_name)
#processing_rules = RuleClasses_LoadRulesForProcessingClass.LoadRulesForProcessing(project_name)
#top.protocol("WM_DELETE_WINDOW", on_closing)
def LoadConfigScreen():
s = Tix.Toplevel()
s.protocol("WM_DELETE_WINDOW", on_closing)
s.title("Table InfExtractor")
s.geometry('{}x{}'.format(500, 500))
topframe = Tix.Frame(s, height=10)
topframe.pack()
frame = Tix.Frame(s)
frame.pack()
newproject = Tix.Radiobutton(frame,
text="Create New Project",
variable=variab,
value="NP",
command=lambda: EnableLEntity(E2, Lb3))
newproject.pack()
newprojectFrame = Tix.Frame(frame, height=100)
names = Tix.StringVar()
label_projectName = Tix.Label(newprojectFrame, textvariable=names)
names.set("Project Name")
label_projectName.pack(side=Tix.LEFT)
E2 = Tix.Entry(newprojectFrame, bd=5)
E2.pack(side=Tix.LEFT)
newprojectFrame.pack()
loadproject = Tix.Radiobutton(frame,
text="Load Project",
variable=variab,
value="LP",
command=lambda: EnableLB(Lb3, E2))
loadproject.pack()
loadprojectFrame = Tix.Frame(frame, height=100)
loadprojectFrame.pack()
Lb3 = Tix.Listbox(loadprojectFrame, width=80, height=20)
projects = FileManipulationHelper.readProjects()
i = 1
for p in projects:
Lb3.insert(i, p)
i = i + 1
Lb3.pack()
Lb3.configure(exportselection=False)
Lb3.configure(state=Tix.DISABLED)
variab.set("NP")
newproject.select()
BottomFrame = Tix.Frame(s, height=10)
BottomFrame.pack()
NextButtonFrame = Tix.Frame(s)
NextButtonFrame.pack()
NextButton = Tix.Button(
NextButtonFrame,
text="Next",
fg="black",
command=lambda: FinishFirstScreen(variab, E2, Lb3, s))
NextButton.pack()
def SaveWhiteListEdit(listWL, listBL, typeVar, wl_look_head, wl_look_stub,
wl_look_super, wl_look_data, bl_look_head, bl_look_stub,
bl_look_super, bl_look_data, WhiteListWindow,
project_name, rule_name, vClsIn):
global currentWhiteList
global currentBlackList
listWL
currentWhiteList = []
currentBlackList = []
currentWhiteList = listWL.split('\n')
currentBlackList = listBL.split('\n')
rule_path = "Projects/" + project_name + "/" + vClsIn.get(
) + "/" + rule_name
FileManipulationHelper.CreateFoderIfNotExist(rule_path)
FileManipulationHelper.SaveCueList(rule_path, rule_name, currentWhiteList,
currentBlackList, typeVar, wl_look_head,
wl_look_stub, wl_look_super,
wl_look_data, bl_look_head,
bl_look_stub, bl_look_super,
bl_look_data)
#FileManipulationHelper.MakeRuleCFGFile(rule_path, look_head, look_stub, look_super, look_data, look_all,vClsIn,vDefUnit,vPosUnit,pragVar)
WhiteListWindow.withdraw()
def EditSintacticRules(project_name, rule_name, ChoseSintRulesWindow, fname,
variable_name):
ChoseSintRulesWindow.withdraw()
top = Toplevel()
#top.protocol("WM_DELETE_WINDOW", on_closing)
top.title("Modify selected rules")
top.geometry('{}x{}'.format(400, 300))
topframe = Frame(top, height=10)
topframe.pack()
frame = Frame(top)
frame.pack()
topframe2 = Frame(top, height=10)
topframe2.pack()
rules = StringVar()
rulelist = Text(frame, height=15, width=40)
rulelist.grid(row=1, sticky='w')
fpaths = []
if fname.get() == '':
SaveSintacticRules(rulelist.get("1.0", END), top, project_name,
variable_name)
return
else:
fpaths.append(fname.get())
rules = []
for path in fpaths:
rules = rules + FileManipulationHelper.LoadRules(path)
i = 1
for w in rules:
rulelist.insert(str(i) + '.0', w)
i = i + 1
saveButton = Button(
frame,
text="Next",
bg="green",
fg="black",
command=lambda: SaveSintacticRules(rulelist.get(
"1.0", END), top, project_name, rule_name, variable_name)).grid(
row=2, sticky='w')
pass
Lb1.pack()
size = Lb1.size()
refreshButton = Tix.Button(
top,
text="Refresh",
fg="black",
command=lambda: RefreshDatabaseData(Lb1, project_name))
refreshButton.pack()
processing_rules = LoadRulesForProcessing(project_name)
thread = Thread(target=ProcessDataV,
args=(project_name, processing_rules, top, extracted))
thread.start()
print "thread finished...exiting"
pass
def on_closing():
global main
main.destroy()
##################################################################
lab2 = None
main = Tix.Tk()
variab = Tix.StringVar()
FileManipulationHelper.CreateFolderStructure()
main.withdraw()
LoadConfigScreen()
main.protocol("WM_DELETE_WINDOW", on_closing)
main.mainloop()
def WhiteListWindowEdit(project_name, rule_name, variable):
typeVar = Tix.StringVar()
WhiteListWindow = Tix.Toplevel()
WhiteListWindow.title("Edit White Cue List")
WhiteListWindow.geometry('{}x{}'.format(550, 550))
itemsFrame = Tix.Frame(WhiteListWindow)
itemsFrame.pack(side=Tix.LEFT)
choiseFrame = Tix.Frame(WhiteListWindow, width=130)
choiseFrame.pack(side=Tix.RIGHT)
wl_where_to_look = Tix.Label(choiseFrame,
text="Where to look in whitelist?").grid(
row=2, column=0, sticky='w')
wl_look_head = Tix.IntVar()
wl_HeaderCB = Tix.Checkbutton(choiseFrame,
text="Header",
variable=wl_look_head).grid(row=3,
column=0,
sticky='w')
wl_look_stub = Tix.IntVar()
wl_StubCB = Tix.Checkbutton(choiseFrame,
text="Stub",
variable=wl_look_stub).grid(row=4,
column=0,
sticky='w')
wl_look_super = Tix.IntVar()
wl_SuperRowCB = Tix.Checkbutton(choiseFrame,
text="Super-row",
variable=wl_look_super).grid(row=5,
column=0,
sticky='w')
wl_look_data = Tix.IntVar()
wl_DataCB = Tix.Checkbutton(choiseFrame,
text="Data",
variable=wl_look_data).grid(row=6,
column=0,
sticky='w')
bl_where_to_look = Tix.Label(choiseFrame,
text="Where to look in blacklist?").grid(
row=7, column=0, sticky='w')
bl_look_head = Tix.IntVar()
bl_HeaderCB = Tix.Checkbutton(choiseFrame,
text="Header",
variable=bl_look_head).grid(row=8,
column=0,
sticky='w')
bl_look_stub = Tix.IntVar()
bl_StubCB = Tix.Checkbutton(choiseFrame,
text="Stub",
variable=bl_look_stub).grid(row=9,
column=0,
sticky='w')
bl_look_super = Tix.IntVar()
bl_SuperRowCB = Tix.Checkbutton(choiseFrame,
text="Super-row",
variable=bl_look_super).grid(row=10,
column=0,
sticky='w')
bl_look_data = Tix.IntVar()
bl_DataCB = Tix.Checkbutton(choiseFrame,
text="Data",
variable=bl_look_data).grid(row=11,
column=0,
sticky='w')
#look_all = Tix.IntVar()
#EverywhereCB = Tix.Checkbutton(choiseFrame,text="Everywhere",variable=look_all).grid(row=7,column=0,sticky='w')
namerule_label2 = Tix.Label(
itemsFrame,
text=
"To look for annotations ids (such as CUI from UMLS)\nwrite [annID]: (eg. '[annID]:C1696465'). To look\nfor annotation types (such as Semantic Type\nin UMLS) write [annType]: in front of cue (e.g.\n'[annType]:Biomedical or Dental Materia' or\n'[annType]:(bodm)'). To write just lexical cue,\njust write word, without prefixes, or [word]:\n(e.g. 'age' or '[word]:age')",
justify=Tix.LEFT).grid(row=0, sticky='w')
namerule_label = Tix.Label(
itemsFrame, text="List of terms in whitelsit").grid(row=1, sticky='w')
WhiteListText = Tix.Text(itemsFrame, height=10, width=50)
WhiteListText.grid(row=2, sticky='w')
whitelist = FileManipulationHelper.loadWhiteList(project_name, rule_name,
variable)
namerule_label2 = Tix.Label(
itemsFrame, text="List of terms in blacklsit").grid(row=3, sticky='w')
BlackListText = Tix.Text(itemsFrame, height=10, width=50)
BlackListText.grid(row=4, sticky='w')
blacklist = FileManipulationHelper.loadBlackList(project_name, rule_name,
variable)
i = 1
afterWordList = False
for w in whitelist:
w = w.replace('\n', '')
splitted = w.split(':')
#if splitted[0]=='Type':
# if splitted[1]=='WhiteList':
# typeVar.set(type[0])
# else:
# typeVar.set(type[1])
if splitted[0] == 'Header':
wl_look_head.set(int(splitted[1]))
if splitted[0] == 'Stub':
wl_look_stub.set(int(splitted[1]))
if splitted[0] == 'Super-row':
wl_look_super.set(int(splitted[1]))
if splitted[0] == 'Data':
wl_look_data.set(int(splitted[1]))
#if splitted[0]=='All':
# look_all.set(int(splitted[1]))
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
WhiteListText.insert(str(i) + '.0', w + '\n')
i = i + 1
afterWordList = False
for w in blacklist:
w = w.replace('\n', '')
splitted = w.split(':')
#if splitted[0]=='Type':
# if splitted[1]=='WhiteList':
# typeVar.set(type[0])
# else:
# typeVar.set(type[1])
if splitted[0] == 'Header':
bl_look_head.set(int(splitted[1]))
if splitted[0] == 'Stub':
bl_look_stub.set(int(splitted[1]))
if splitted[0] == 'Super-row':
bl_look_super.set(int(splitted[1]))
if splitted[0] == 'Data':
bl_look_data.set(int(splitted[1]))
#if splitted[0]=='All':
# look_all.set(int(splitted[1]))
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
BlackListText.insert(str(i) + '.0', w + '\n')
i = i + 1
ClsVar = Tix.StringVar()
ClsVar.set(variable)
saveButton = Tix.Button(
itemsFrame,
text="Save",
fg="black",
command=lambda: SaveWhiteListEdit(
WhiteListText.get("1.0", Tix.END), BlackListText.get(
"1.0", Tix.END), typeVar, wl_look_head, wl_look_stub,
wl_look_super, wl_look_data, bl_look_head, bl_look_stub,
bl_look_super, bl_look_data, WhiteListWindow, project_name,
rule_name, ClsVar)).grid(row=12, column=0, sticky='w')
def WhiteListWindowEdit(project_name,rule_name,variable):
typeVar =Tix.StringVar()
WhiteListWindow =Tix.Toplevel()
WhiteListWindow.title("Edit White Cue List")
WhiteListWindow.geometry('{}x{}'.format(550, 550))
itemsFrame = Tix.Frame(WhiteListWindow)
itemsFrame.pack(side=Tix.LEFT)
choiseFrame = Tix.Frame(WhiteListWindow,width=130)
choiseFrame.pack(side=Tix.RIGHT)
wl_where_to_look = Tix.Label(choiseFrame,text="Where to look in whitelist?").grid(row=2,column=0,sticky='w')
wl_look_head = Tix.IntVar()
wl_HeaderCB = Tix.Checkbutton(choiseFrame,text="Header",variable = wl_look_head).grid(row=3,column=0,sticky='w')
wl_look_stub = Tix.IntVar()
wl_StubCB = Tix.Checkbutton(choiseFrame,text="Stub",variable = wl_look_stub).grid(row=4,column=0,sticky='w')
wl_look_super = Tix.IntVar()
wl_SuperRowCB = Tix.Checkbutton(choiseFrame,text="Super-row",variable = wl_look_super).grid(row=5,column=0,sticky='w')
wl_look_data = Tix.IntVar()
wl_DataCB = Tix.Checkbutton(choiseFrame,text="Data",variable = wl_look_data).grid(row=6,column=0,sticky='w')
bl_where_to_look = Tix.Label(choiseFrame,text="Where to look in blacklist?").grid(row=7,column=0,sticky='w')
bl_look_head = Tix.IntVar()
bl_HeaderCB = Tix.Checkbutton(choiseFrame,text="Header",variable = bl_look_head).grid(row=8,column=0,sticky='w')
bl_look_stub = Tix.IntVar()
bl_StubCB = Tix.Checkbutton(choiseFrame,text="Stub",variable = bl_look_stub).grid(row=9,column=0,sticky='w')
bl_look_super = Tix.IntVar()
bl_SuperRowCB = Tix.Checkbutton(choiseFrame,text="Super-row",variable = bl_look_super).grid(row=10,column=0,sticky='w')
bl_look_data = Tix.IntVar()
bl_DataCB = Tix.Checkbutton(choiseFrame,text="Data",variable = bl_look_data).grid(row=11,column=0,sticky='w')
#look_all = Tix.IntVar()
#EverywhereCB = Tix.Checkbutton(choiseFrame,text="Everywhere",variable=look_all).grid(row=7,column=0,sticky='w')
namerule_label2 = Tix.Label(itemsFrame,text="To look for annotations ids (such as CUI from UMLS)\nwrite [annID]: (eg. '[annID]:C1696465'). To look\nfor annotation types (such as Semantic Type\nin UMLS) write [annType]: in front of cue (e.g.\n'[annType]:Biomedical or Dental Materia' or\n'[annType]:(bodm)'). To write just lexical cue,\njust write word, without prefixes, or [word]:\n(e.g. 'age' or '[word]:age')", justify=Tix.LEFT).grid(row=0,sticky='w')
namerule_label = Tix.Label(itemsFrame,text="List of terms in whitelsit").grid(row=1,sticky='w')
WhiteListText = Tix.Text(itemsFrame,height=10,width=50)
WhiteListText.grid(row=2,sticky='w')
whitelist = FileManipulationHelper.loadWhiteList(project_name, rule_name,variable)
namerule_label2 = Tix.Label(itemsFrame,text="List of terms in blacklsit").grid(row=3,sticky='w')
BlackListText = Tix.Text(itemsFrame,height=10,width=50)
BlackListText.grid(row=4,sticky='w')
blacklist = FileManipulationHelper.loadBlackList(project_name, rule_name,variable)
i = 1
afterWordList = False
for w in whitelist:
w = w.replace('\n','')
splitted = w.split(':')
#if splitted[0]=='Type':
# if splitted[1]=='WhiteList':
# typeVar.set(type[0])
# else:
# typeVar.set(type[1])
if splitted[0]=='Header':
wl_look_head.set(int(splitted[1]))
if splitted[0]=='Stub':
wl_look_stub.set(int(splitted[1]))
if splitted[0]=='Super-row':
wl_look_super.set(int(splitted[1]))
if splitted[0]=='Data':
wl_look_data.set(int(splitted[1]))
#if splitted[0]=='All':
# look_all.set(int(splitted[1]))
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
WhiteListText.insert(str(i)+'.0',w+'\n')
i=i+1
afterWordList = False
for w in blacklist:
w = w.replace('\n','')
splitted = w.split(':')
#if splitted[0]=='Type':
# if splitted[1]=='WhiteList':
# typeVar.set(type[0])
# else:
# typeVar.set(type[1])
if splitted[0]=='Header':
bl_look_head.set(int(splitted[1]))
if splitted[0]=='Stub':
bl_look_stub.set(int(splitted[1]))
if splitted[0]=='Super-row':
bl_look_super.set(int(splitted[1]))
if splitted[0]=='Data':
bl_look_data.set(int(splitted[1]))
#if splitted[0]=='All':
# look_all.set(int(splitted[1]))
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
BlackListText.insert(str(i)+'.0',w+'\n')
i=i+1
ClsVar = Tix.StringVar()
ClsVar.set(variable)
saveButton = Tix.Button(itemsFrame,text="Save",fg="black",command=lambda:SaveWhiteListEdit(WhiteListText.get("1.0",Tix.END),BlackListText.get("1.0",Tix.END),typeVar,wl_look_head,wl_look_stub,wl_look_super,wl_look_data,bl_look_head,bl_look_stub,bl_look_super,bl_look_data,WhiteListWindow,project_name,rule_name,ClsVar)).grid(row=12,column=0,sticky='w')
def SemanticListWindowEdit(project_name,rule_name,variable_name):#
WhiteListWindow =Tix.Toplevel()
WhiteListWindow.title("Edit Cue List")
WhiteListWindow.geometry('{}x{}'.format(550, 400))
itemsFrame = Tix.Frame(WhiteListWindow)
itemsFrame.pack(side=Tix.LEFT)
choiseFrame = Tix.Frame(WhiteListWindow,width=130)
choiseFrame.pack(side=Tix.RIGHT)
#type = ['WhiteList','BlackList']
typeVar = Tix.StringVar()
#typeVar.set(type[0])
#TypeLabel = Label(choiseFrame,text="ListType").grid(row=0,column=0,sticky='w')
#drop = OptionMenu(choiseFrame,typeVar,*type)
#drop.grid(row=1,column=0,sticky='w')
where_to_look = Tix.Label(choiseFrame,text="Where to look for white list variables?").grid(row=2,column=0,sticky='w')
wl_look_head = Tix.IntVar()
WLHeaderCB = Tix.Checkbutton(choiseFrame,text="Header",variable = wl_look_head).grid(row=3,column=0,sticky='w')
wl_look_stub = Tix.IntVar()
WLStubCB = Tix.Checkbutton(choiseFrame,text="Stub",variable = wl_look_stub).grid(row=4,column=0,sticky='w')
wl_look_super = Tix.IntVar()
WLSuperRowCB = Tix.Checkbutton(choiseFrame,text="Super-row",variable = wl_look_super).grid(row=5,column=0,sticky='w')
wl_look_data = Tix.IntVar()
WLDataCB = Tix.Checkbutton(choiseFrame,text="Data",variable = wl_look_data).grid(row=6,column=0,sticky='w')
where_to_look2 = Tix.Label(choiseFrame,text="Where to look for black list variables?").grid(row=7,column=0,sticky='w')
bl_look_head = Tix.IntVar()
BLHeaderCB = Tix.Checkbutton(choiseFrame,text="Header",variable = bl_look_head).grid(row=8,column=0,sticky='w')
bl_look_stub = Tix.IntVar()
BLStubCB = Tix.Checkbutton(choiseFrame,text="Stub",variable = bl_look_stub).grid(row=9,column=0,sticky='w')
bl_look_super = Tix.IntVar()
BLSuperRowCB = Tix.Checkbutton(choiseFrame,text="Super-row",variable = bl_look_super).grid(row=10,column=0,sticky='w')
bl_look_data = Tix.IntVar()
BLDataCB = Tix.Checkbutton(choiseFrame,text="Data",variable = bl_look_data).grid(row=11,column=0,sticky='w')
namerule_label = Tix.Label(itemsFrame,text="List of terms in whitelsit").grid(row=0,sticky='w')
whitelist = Tix.CheckList(itemsFrame,width=350)
whitelist.grid(row=1,sticky='w')
createSemanticWhiteList(whitelist)
whitelist.autosetmode()
namerule_label2 = Tix.Label(itemsFrame,text="List of terms in blacklist").grid(row=2,sticky='w')
blacklist = Tix.Text(itemsFrame,height=5,width=50)
blacklist.grid(row=3,sticky='w')
whitelist_list = FileManipulationHelper.loadWhiteList(project_name, rule_name,variable_name)
blacklist_list = FileManipulationHelper.loadBlackList(project_name, rule_name,variable_name)
i = 1
afterWordList = False
for w in whitelist_list:
w = w.replace('\n','')
splitted = w.split(':')
#if splitted[0]=='Type':
# if splitted[1]=='WhiteList':
# typeVar.set(type[0])
# else:
# typeVar.set(type[1])
if splitted[0]=='Header':
wl_look_head.set(int(splitted[1]))
if splitted[0]=='Stub':
wl_look_stub.set(int(splitted[1]))
if splitted[0]=='Super-row':
wl_look_super.set(int(splitted[1]))
if splitted[0]=='Data':
wl_look_data.set(int(splitted[1]))
#if splitted[0]=='All':
# look_all.set(int(splitted[1]))
if w == "SemanticTypes:":
afterWordList = True
continue
if afterWordList == True:
cur = 0
for item in semanticTypes:
if(w == item.split('.')[-1]):
whitelist.setstatus(item,"on")
cur = cur + 1
i=i+1
afterWordList = False
for w in blacklist_list:
w = w.replace('\n','')
splitted = w.split(':')
#if splitted[0]=='Type':
# if splitted[1]=='WhiteList':
# typeVar.set(type[0])
# else:
# typeVar.set(type[1])
if splitted[0]=='Header':
bl_look_head.set(int(splitted[1]))
if splitted[0]=='Stub':
bl_look_stub.set(int(splitted[1]))
if splitted[0]=='Super-row':
bl_look_super.set(int(splitted[1]))
if splitted[0]=='Data':
bl_look_data.set(int(splitted[1]))
#if splitted[0]=='All':
# look_all.set(int(splitted[1]))
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
blacklist.insert(str(i)+'.0',w+'\n')
i=i+1
saveButton = Tix.Button(itemsFrame,text="Save",fg="black",command=lambda:SaveWhiteListSemanticEdit(whitelist,blacklist.get("1.0",Tix.END),typeVar,wl_look_head,wl_look_stub,wl_look_super,wl_look_data,bl_look_head,bl_look_stub,bl_look_super,bl_look_data,WhiteListWindow,project_name,rule_name)).grid(row=4,sticky='w')
pass
def EditRule(project_name, Lb1):
global currentWhiteList
global currentBlackList
currentWhiteList = []
currentBlackList = []
add = Toplevel()
add.title("Edit Rule")
add.geometry('{}x{}'.format(400, 300))
itemsFrame = Frame(add, height=130)
itemsFrame.pack()
vRuleName = StringVar()
# Obtain rule/vaiable properly. The following won't work
pos = Lb1.selection()[0]
vRuleName.set(Lb1.item(pos)['text'])
vClsIn = StringVar()
vClsIn.set(Lb1.parent(pos).replace('\n', ''))
namerule_label = Label(itemsFrame,
text="Name of the rule").grid(row=0,
column=0,
sticky='w')
rulename_entry = Entry(itemsFrame, textvariable=vRuleName,
state=DISABLED).grid(row=0, column=1, sticky='w')
rule_name = vRuleName.get()
cfg = FileManipulationHelper.loadRuleConfig(project_name, rule_name,
vClsIn.get())
ruleType = cfg['RuleType'].replace('\n', '')
ClassLabel = Label(itemsFrame, text="Class name of result",
state=DISABLED).grid(row=2, column=0, sticky='w')
ClassInput = Entry(itemsFrame, textvariable=vClsIn)
ClassInput.grid(row=3, sticky='w')
vDefUnit = StringVar()
vPosUnit = StringVar()
if ruleType == 'Numeric' or ruleType == "Categorical":
DefUnitLabel = Label(itemsFrame, text="Default unit")
DefUnitLabel.grid(row=4, column=0, sticky='w')
vDefUnit = StringVar()
DefUnInput = Entry(itemsFrame, textvariable=vDefUnit)
DefUnInput.grid(row=5, sticky='w')
PosUnitLabel = Label(itemsFrame,
text="Possible units (comma separated)")
PosUnitLabel.grid(row=6, column=0, sticky='w')
PosUnInput = Entry(itemsFrame, textvariable=vPosUnit)
PosUnInput.grid(row=7, sticky='w')
ruleMech = cfg['RuleCreationMech'].replace('\n', '')
where_to_look = Label(itemsFrame,
text="Where to look for data?").grid(row=2,
column=1,
sticky='w')
wl_look_head = IntVar()
if ('DataInHeader' in cfg.keys() and cfg['DataInHeader'] != None
and cfg['DataInHeader'] == '1'):
wl_look_head.set(1)
else:
wl_look_head.set(0)
WLHeaderCB = Checkbutton(itemsFrame, text="Header",
variable=wl_look_head).grid(row=3,
column=1,
sticky='w')
wl_look_stub = IntVar()
if ('DataInStub' in cfg.keys() and cfg['DataInStub'] != None
and cfg['DataInStub'] == '1'):
wl_look_stub.set(1)
else:
wl_look_stub.set(0)
WLStubCB = Checkbutton(itemsFrame, text="Stub",
variable=wl_look_stub).grid(row=4,
column=1,
sticky='w')
wl_look_super = IntVar()
if ('DataInSuperRow' in cfg.keys() and cfg['DataInSuperRow'] != None
and cfg['DataInSuperRow'] == '1'):
wl_look_super.set(1)
else:
wl_look_super.set(0)
WLSuperRowCB = Checkbutton(itemsFrame,
text="Super-row",
variable=wl_look_super).grid(row=5,
column=1,
sticky='w')
wl_look_data = IntVar()
if ('DataInData' in cfg.keys() and cfg['DataInData'] != None
and cfg['DataInData'] == '1'):
wl_look_data.set(1)
else:
wl_look_data.set(0)
WLDataCB = Checkbutton(itemsFrame, text="Data",
variable=wl_look_data).grid(row=6,
column=1,
sticky='w')
if ruleMech == 'Lexical':
editWhiteList = Button(itemsFrame,
text="Edit Sem/Lexical Cue List",
command=lambda: WhiteListWindowEdit(
project_name, rule_name,
vClsIn.get().replace('\n', ''))).grid(
row=8, column=0, sticky='w')
else:
editWhiteList = Button(itemsFrame,
text="Edit Semantic Cue List",
command=lambda: SemanticListWindowEdit(
project_name, rule_name,
vClsIn.get().replace('\n', ''))).grid(
row=8, column=0, sticky='w')
if ruleType != "String":
SyntacticRules = Button(itemsFrame,
text="Edit Syntactic rules",
command=lambda: MakeChangesToSyntacticRules(
project_name, rule_name,
vClsIn.get().replace('\n', ''))).grid(
row=9, column=0, sticky='w')
#editBlackList = Button(itemsFrame,text="Edit Black Cue List",command=lambda:BlackListWindowEdit(project_name,rule_name)).grid(row=2,column=0,sticky='w')
text_of_where_to_look = StringVar()
DBSettings = FileManipulationHelper.LoadDBConfigFile(project_name)
db = QueryDBClass.QueryDBCalss(DBSettings['Host'], DBSettings['User'],
DBSettings['Pass'], DBSettings['Database'])
prags = db.GetPragmaticClasses()
prags.insert(0, "Any")
pragVar = StringVar()
pragVar.set(cfg['PragClass'])
if ruleType == 'Numeric' or ruleType == 'Categorical':
vDefUnit.set(cfg['DefUnit'])
vPosUnit.set(cfg['PosUnit'])
vClsIn.set(cfg['Class'].replace('\n', ''))
PragLabel = Label(itemsFrame,
text="Table type (pragmatics)").grid(row=7,
column=1,
sticky='w')
drop = OptionMenu(itemsFrame, pragVar, *prags)
drop.grid(row=8, column=1, sticky='w')
save = Button(itemsFrame,
text="Save",
fg="black",
command=lambda: SaveRuleEdit(
project_name, rule_name, add, vClsIn, vDefUnit, vPosUnit,
pragVar, ruleType, ruleMech, wl_look_head, wl_look_stub,
wl_look_super, wl_look_data)).grid(row=9,
column=1,
sticky='w')
def SemanticListWindowEdit(project_name, rule_name, variable_name): #
WhiteListWindow = Tix.Toplevel()
WhiteListWindow.title("Edit Cue List")
WhiteListWindow.geometry('{}x{}'.format(550, 400))
itemsFrame = Tix.Frame(WhiteListWindow)
itemsFrame.pack(side=Tix.LEFT)
choiseFrame = Tix.Frame(WhiteListWindow, width=130)
choiseFrame.pack(side=Tix.RIGHT)
#type = ['WhiteList','BlackList']
typeVar = Tix.StringVar()
#typeVar.set(type[0])
#TypeLabel = Label(choiseFrame,text="ListType").grid(row=0,column=0,sticky='w')
#drop = OptionMenu(choiseFrame,typeVar,*type)
#drop.grid(row=1,column=0,sticky='w')
where_to_look = Tix.Label(
choiseFrame,
text="Where to look for white list variables?").grid(row=2,
column=0,
sticky='w')
wl_look_head = Tix.IntVar()
WLHeaderCB = Tix.Checkbutton(choiseFrame,
text="Header",
variable=wl_look_head).grid(row=3,
column=0,
sticky='w')
wl_look_stub = Tix.IntVar()
WLStubCB = Tix.Checkbutton(choiseFrame, text="Stub",
variable=wl_look_stub).grid(row=4,
column=0,
sticky='w')
wl_look_super = Tix.IntVar()
WLSuperRowCB = Tix.Checkbutton(choiseFrame,
text="Super-row",
variable=wl_look_super).grid(row=5,
column=0,
sticky='w')
wl_look_data = Tix.IntVar()
WLDataCB = Tix.Checkbutton(choiseFrame, text="Data",
variable=wl_look_data).grid(row=6,
column=0,
sticky='w')
where_to_look2 = Tix.Label(
choiseFrame,
text="Where to look for black list variables?").grid(row=7,
column=0,
sticky='w')
bl_look_head = Tix.IntVar()
BLHeaderCB = Tix.Checkbutton(choiseFrame,
text="Header",
variable=bl_look_head).grid(row=8,
column=0,
sticky='w')
bl_look_stub = Tix.IntVar()
BLStubCB = Tix.Checkbutton(choiseFrame, text="Stub",
variable=bl_look_stub).grid(row=9,
column=0,
sticky='w')
bl_look_super = Tix.IntVar()
BLSuperRowCB = Tix.Checkbutton(choiseFrame,
text="Super-row",
variable=bl_look_super).grid(row=10,
column=0,
sticky='w')
bl_look_data = Tix.IntVar()
BLDataCB = Tix.Checkbutton(choiseFrame, text="Data",
variable=bl_look_data).grid(row=11,
column=0,
sticky='w')
namerule_label = Tix.Label(
itemsFrame, text="List of terms in whitelsit").grid(row=0, sticky='w')
whitelist = Tix.CheckList(itemsFrame, width=350)
whitelist.grid(row=1, sticky='w')
createSemanticWhiteList(whitelist)
whitelist.autosetmode()
namerule_label2 = Tix.Label(
itemsFrame, text="List of terms in blacklist").grid(row=2, sticky='w')
blacklist = Tix.Text(itemsFrame, height=5, width=50)
blacklist.grid(row=3, sticky='w')
whitelist_list = FileManipulationHelper.loadWhiteList(
project_name, rule_name, variable_name)
blacklist_list = FileManipulationHelper.loadBlackList(
project_name, rule_name, variable_name)
i = 1
afterWordList = False
for w in whitelist_list:
w = w.replace('\n', '')
splitted = w.split(':')
#if splitted[0]=='Type':
# if splitted[1]=='WhiteList':
# typeVar.set(type[0])
# else:
# typeVar.set(type[1])
if splitted[0] == 'Header':
wl_look_head.set(int(splitted[1]))
if splitted[0] == 'Stub':
wl_look_stub.set(int(splitted[1]))
if splitted[0] == 'Super-row':
wl_look_super.set(int(splitted[1]))
if splitted[0] == 'Data':
wl_look_data.set(int(splitted[1]))
#if splitted[0]=='All':
# look_all.set(int(splitted[1]))
if w == "SemanticTypes:":
afterWordList = True
continue
if afterWordList == True:
cur = 0
for item in semanticTypes:
if (w == item.split('.')[-1]):
whitelist.setstatus(item, "on")
cur = cur + 1
i = i + 1
afterWordList = False
for w in blacklist_list:
w = w.replace('\n', '')
splitted = w.split(':')
#if splitted[0]=='Type':
# if splitted[1]=='WhiteList':
# typeVar.set(type[0])
# else:
# typeVar.set(type[1])
if splitted[0] == 'Header':
bl_look_head.set(int(splitted[1]))
if splitted[0] == 'Stub':
bl_look_stub.set(int(splitted[1]))
if splitted[0] == 'Super-row':
bl_look_super.set(int(splitted[1]))
if splitted[0] == 'Data':
bl_look_data.set(int(splitted[1]))
#if splitted[0]=='All':
# look_all.set(int(splitted[1]))
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
blacklist.insert(str(i) + '.0', w + '\n')
i = i + 1
saveButton = Tix.Button(
itemsFrame,
text="Save",
fg="black",
command=lambda: SaveWhiteListSemanticEdit(
whitelist, blacklist.get("1.0", Tix.END), typeVar, wl_look_head,
wl_look_stub, wl_look_super, wl_look_data, bl_look_head,
bl_look_stub, bl_look_super, bl_look_data, WhiteListWindow,
project_name, rule_name)).grid(row=4, sticky='w')
pass
def GetExtractedData(project_name):
DBSettings = FileManipulationHelper.LoadDBConfigFile(project_name)
db = QueryDBClass.QueryDBCalss(DBSettings['Host'], DBSettings['User'],
DBSettings['Pass'], DBSettings['Database'])
extracted = db.getExtracted()
return extracted
def ProcessDataBase(project_name, rules):
global Source
DBSettings = FileManipulationHelper.LoadDBConfigFile(project_name)
db = QueryDBClass.QueryDBCalss(DBSettings['Host'], DBSettings['User'],
DBSettings['Pass'], DBSettings['Database'])
for rule in rules:
posSubClass = ''
print "Rule " + rule.RuleName + " executing"
WhiteWordList = []
WhiteIDList = []
WhiteDescList = []
BlackWordList = []
BlackIDList = []
BlackDescList = []
# Get different cue lists from one big list containing annotations and lexical cues
for word in rule.WhiteList:
if ('[annID]:' in word):
if (word[8:] != ''):
WhiteIDList.append(word[8:])
elif ('[annType]:' in word):
if (word[10:] != ''):
WhiteDescList.append(word[10:])
elif ('[word]:' in word):
if (word[7:] != ''):
WhiteWordList.append(word[7:])
else:
if (word != ''):
WhiteWordList.append(word)
for word in rule.BlackList:
if ('[annID]:' in word):
if (word[8:] != ''):
BlackIDList.append(word[8:])
elif ('[annType]:' in word):
if (word[10:] != ''):
BlackDescList.append(word[10:])
elif ('[word]:' in word):
if (word[7:] != ''):
BlackWordList.append(word[7:])
else:
if (word != ''):
BlackWordList.append(word)
# Get tables that contain something from white list in it
tabres = db.getRelevantTables(WhiteWordList, WhiteIDList,
WhiteDescList, rule.PragmaticClass)
tables = []
for res in tabres:
tables.append(res[0])
for table in tables:
#Get Table cells with all the annotations
cells = getCellsByTableID(table, db)
#Now the data should be filtered
for cell in cells:
extractData = True
extracted = False
selectCell = False
CueFoundInHeader = False
CueFoundInStub = False
CueFoundInSuperRow = False
CueFoundInData = False
#Check white list against data cells
if rule.wl_look_data:
for word in WhiteWordList:
if cell.Content != None:
if (word in cell.Content):
selectCell = True
CueFoundInData = True
posSubClass = word
for word in WhiteDescList:
for ann in cell.Annotations:
if ann.AnnotationDesc == word:
selectCell = True
CueFoundInData = True
posSubClass = ann.Content
for word in WhiteIDList:
for ann in cell.Annotations:
if ann.AnnotationCID == word:
selectCell = True
CueFoundInData = True
posSubClass = ann.Content
# Check white list against heades
if rule.wl_look_header:
for word in WhiteWordList:
if cell.Header != None:
if (word in cell.Header):
selectCell = True
CueFoundInHeader = True
posSubClass = word
idHeader = cell.HeaderId
heads = []
heads = getHeaderCells(cell.HeaderId, cells, heads)
for head in heads:
for word in WhiteDescList:
for ann in head.Annotations:
if ann.AnnotationDesc == word:
selectCell = True
CueFoundInHeader = True
posSubClass = ann.Content
for word in WhiteIDList:
for ann in head.Annotations:
if ann.AnnotationCID == word:
selectCell = True
CueFoundInHeader = True
posSubClass = ann.Content
# Check white list against stub
if rule.wl_look_stub:
for word in WhiteWordList:
if cell.Stub != None:
if (word in cell.Stub):
selectCell = True
CueFoundInStub = True
posSubClass = word
idStub = cell.StubId
stubs = []
stubs = getStubCells(cell.StubId, cells, stubs)
for stub in stubs:
for word in WhiteDescList:
for ann in stub.Annotations:
if ann.AnnotationDesc == word:
selectCell = True
CueFoundInStub = True
posSubClass = ann.Content
for word in WhiteIDList:
for ann in stub.Annotations:
if ann.AnnotationCID == word:
selectCell = True
CueFoundInStub = True
posSubClass = ann.Content
# Check white list against super-row
if rule.wl_look_superrow:
for word in WhiteWordList:
if cell.Super_row != None:
if (word in cell.Super_row):
selectCell = True
CueFoundInSuperRow = True
posSubClass = word
idSuperRow = cell.SuperRowId
superrows = []
superrows = getStubCells(cell.SuperRowId, cells, superrows)
for superrow in superrows:
for word in WhiteDescList:
for ann in superrow.Annotations:
if ann.AnnotationDesc == word:
selectCell = True
CueFoundInSuperRow = True
posSubClass = ann.Content
for word in WhiteIDList:
for ann in superrow.Annotations:
if ann.AnnotationCID == word:
selectCell = True
CueFoundInSuperRow = True
posSubClass = ann.Content
#=============================================================================================
# Check black list against data cells
if rule.bl_look_data:
for word in BlackWordList:
if cell.Content != None:
if (word in cell.Content):
selectCell = False
for word in BlackDescList:
for ann in cell.Annotations:
if ann.AnnotationDesc == word:
selectCell = False
for word in BlackIDList:
for ann in cell.Annotations:
if ann.AnnotationCID == word:
selectCell = False
# Check black list against heades
if rule.bl_look_header:
for word in BlackWordList:
if cell.Header != None:
if (word in cell.Header):
selectCell = False
idHeader = cell.HeaderId
heads = []
heads = getHeaderCells(cell.HeaderId, cells, heads)
for head in heads:
for word in BlackDescList:
for ann in head.Annotations:
if ann.AnnotationDesc == word:
selectCell = False
for word in BlackIDList:
for ann in head.Annotations:
if ann.AnnotationCID == word:
selectCell = False
# Check white list against stub
if rule.bl_look_stub:
for word in BlackWordList:
if cell.Stub != None:
if (word in cell.Stub):
selectCell = False
idStub = cell.StubId
stubs = []
stubs = getStubCells(cell.StubId, cells, stubs)
for stub in stubs:
for word in BlackDescList:
for ann in stub.Annotations:
if ann.AnnotationDesc == word:
selectCell = False
for word in BlackIDList:
for ann in stub.Annotations:
if ann.AnnotationCID == word:
selectCell = False
# Check white list against super-row
if rule.bl_look_superrow:
for word in BlackWordList:
if cell.Super_row != None:
if (word in cell.Super_row):
selectCell = False
idSuperRow = cell.SuperRowId
superrows = []
superrows = getStubCells(cell.SuperRowId, cells, superrows)
for superrow in superrows:
for word in BlackDescList:
for ann in superrow.Annotation:
if ann.AnnotationDesc == word:
selectCell = False
for word in BlackIDList:
for ann in superrow.Annotation:
if ann.AnnotationCID == word:
selectCell = False
if selectCell:
if ((not rule.data_in_stub) and cell.isStub):
continue
if ((not rule.data_in_data) and cell.isData):
continue
if ((not rule.data_in_header) and cell.isHeader):
continue
if ((not rule.data_in_super) and cell.isSuperRow):
continue
FoundSemantics = False
AllSemSaved = False
# Iterate trought all the patterns
for syn_rule in rule.PatternList:
if (AllSemSaved == True):
break
# check pattern
pattern = unicode(syn_rule.regex.replace('\n', ''),
'utf-8')
m = re.search(pattern, cell.Content, re.UNICODE)
# in case pattern is not found continue to the next one
if m == None:
continue
c = 0
contains_term = False
last_sem_extracted = -1
savedSomething = False
# Itterate semantics for each pattern rule (syntactic rule)
for sem in syn_rule.SemanticValues:
if contains_term and sem.Semantics == 'mean':
contains_term = False
FoundSemantics = False
continue
if (AllSemSaved == True):
break
if last_sem_extracted >= sem.position:
continue
# extract value
value = m.group(sem.position)
#Checking terms in case there are multiple semantics for certain group
if len(sem.SemTermList) > 0:
contains_term = CheckSemTermListUsingRegex(
True, True, True, False, sem.SemTermList,
cell.Header, cell.Stub, cell.Super_row,
cell.Content)
if (contains_term):
semValue = sem.Semantics
FoundSemantics = True
# Getting semantics for certain group
if len(sem.SemTermList) == 0:
semValue = sem.Semantics
FoundSemantics = True
c = c + 1
if FoundSemantics:
syn_rule_name = syn_rule.name
# Be a bit smart for generating Source
if (CueFoundInHeader and rule.data_in_data):
if cell.Super_row != None:
Source = cell.Super_row + cell.Stub
else:
Source = cell.Stub
ClassDetails = cell.Header
else:
Source = cell.Header
if cell.Super_row != None:
ClassDetails = cell.Super_row + cell.Stub
else:
ClassDetails = cell.Stub
# Get unit
SubClass = ''
if rule.RuleType == 'Categorical':
SubClass = cell.Stub
Unit = CheckUnits(cell.Header, cell.Stub,
cell.Super_row, cell.Content,
rule.DefaultUnit,
rule.PossibleUnits)
#Save the value to the database
db.SaveExtracted(cell.idArticle, cell.idTable,
cell.tableOrder, cell.idPMC,
rule.ClassName, semValue,
value, Unit, Source,
ClassDetails, rule.RuleName,
syn_rule_name, SubClass)
savedSomething = True
last_sem_extracted = sem.position
FoundSemantics = False
if (c == len(syn_rule.SemanticValues)):
AllSemSaved = True
if (savedSomething):
break
#print cells
print "Finished!!!"
print "Done!!!!"
def EditRule(project_name,Lb1):
global currentWhiteList
global currentBlackList
currentWhiteList = []
currentBlackList = []
add = Toplevel()
add.title("Edit Rule")
add.geometry('{}x{}'.format(400, 300))
itemsFrame = Frame(add,height=130)
itemsFrame.pack()
vRuleName = StringVar()
# Obtain rule/vaiable properly. The following won't work
pos = Lb1.selection()[0]
vRuleName.set(Lb1.item(pos)['text'])
vClsIn = StringVar()
vClsIn.set(Lb1.parent(pos).replace('\n',''))
namerule_label = Label(itemsFrame,text="Name of the rule").grid(row=0,column=0,sticky='w')
rulename_entry = Entry(itemsFrame,textvariable=vRuleName,state=DISABLED).grid(row=0,column=1,sticky='w')
rule_name = vRuleName.get()
cfg = FileManipulationHelper.loadRuleConfig(project_name, rule_name,vClsIn.get())
ruleType = cfg['RuleType'].replace('\n','')
ClassLabel = Label(itemsFrame,text="Class name of result",state=DISABLED).grid(row=2,column=0,sticky='w')
ClassInput = Entry(itemsFrame,textvariable=vClsIn)
ClassInput.grid(row=3,sticky='w')
vDefUnit = StringVar()
vPosUnit = StringVar()
if ruleType =='Numeric' or ruleType=="Categorical":
DefUnitLabel = Label(itemsFrame,text="Default unit")
DefUnitLabel.grid(row=4,column=0,sticky='w')
vDefUnit = StringVar()
DefUnInput = Entry(itemsFrame,textvariable=vDefUnit)
DefUnInput.grid(row=5,sticky='w')
PosUnitLabel = Label(itemsFrame,text="Possible units (comma separated)")
PosUnitLabel.grid(row=6,column=0,sticky='w')
PosUnInput = Entry(itemsFrame,textvariable=vPosUnit)
PosUnInput.grid(row=7,sticky='w')
ruleMech = cfg['RuleCreationMech'].replace('\n','')
where_to_look = Label(itemsFrame,text="Where to look for data?").grid(row=2,column=1,sticky='w')
wl_look_head = IntVar()
if('DataInHeader' in cfg.keys() and cfg['DataInHeader']!=None and cfg['DataInHeader']=='1'):
wl_look_head.set(1)
else:
wl_look_head.set(0)
WLHeaderCB = Checkbutton(itemsFrame,text="Header",variable = wl_look_head).grid(row=3,column=1,sticky='w')
wl_look_stub = IntVar()
if('DataInStub' in cfg.keys() and cfg['DataInStub']!=None and cfg['DataInStub']=='1'):
wl_look_stub.set(1)
else:
wl_look_stub.set(0)
WLStubCB = Checkbutton(itemsFrame,text="Stub",variable = wl_look_stub).grid(row=4,column=1,sticky='w')
wl_look_super = IntVar()
if('DataInSuperRow' in cfg.keys() and cfg['DataInSuperRow']!=None and cfg['DataInSuperRow']=='1'):
wl_look_super.set(1)
else:
wl_look_super.set(0)
WLSuperRowCB = Checkbutton(itemsFrame,text="Super-row",variable = wl_look_super).grid(row=5,column=1,sticky='w')
wl_look_data = IntVar()
if('DataInData' in cfg.keys() and cfg['DataInData']!=None and cfg['DataInData']=='1'):
wl_look_data.set(1)
else:
wl_look_data.set(0)
WLDataCB = Checkbutton(itemsFrame,text="Data",variable = wl_look_data).grid(row=6,column=1,sticky='w')
if ruleMech == 'Lexical':
editWhiteList = Button(itemsFrame,text="Edit Sem/Lexical Cue List",command=lambda:WhiteListWindowEdit(project_name,rule_name,vClsIn.get().replace('\n',''))).grid(row=8,column=0,sticky='w')
else:
editWhiteList = Button(itemsFrame,text="Edit Semantic Cue List",command=lambda:SemanticListWindowEdit(project_name,rule_name,vClsIn.get().replace('\n',''))).grid(row=8,column=0,sticky='w')
if ruleType != "String":
SyntacticRules = Button(itemsFrame,text="Edit Syntactic rules",command=lambda:MakeChangesToSyntacticRules(project_name,rule_name,vClsIn.get().replace('\n',''))).grid(row=9,column=0,sticky='w')
#editBlackList = Button(itemsFrame,text="Edit Black Cue List",command=lambda:BlackListWindowEdit(project_name,rule_name)).grid(row=2,column=0,sticky='w')
text_of_where_to_look = StringVar()
DBSettings = FileManipulationHelper.LoadDBConfigFile(project_name)
db = QueryDBClass.QueryDBCalss(DBSettings['Host'],DBSettings['User'],DBSettings['Pass'],DBSettings['Database'])
prags = db.GetPragmaticClasses()
prags.insert(0,"Any")
pragVar = StringVar()
pragVar.set(cfg['PragClass'])
if ruleType == 'Numeric' or ruleType == 'Categorical':
vDefUnit.set(cfg['DefUnit'])
vPosUnit.set(cfg['PosUnit'])
vClsIn.set(cfg['Class'].replace('\n',''))
PragLabel = Label(itemsFrame,text="Table type (pragmatics)").grid(row=7,column=1,sticky='w')
drop = OptionMenu(itemsFrame,pragVar,*prags)
drop.grid(row=8,column=1,sticky='w')
save = Button(itemsFrame, text="Save", fg="black",command=lambda:SaveRuleEdit(project_name,rule_name,add,vClsIn,vDefUnit,vPosUnit,pragVar,ruleType,ruleMech,wl_look_head,wl_look_stub,wl_look_super,wl_look_data)).grid(row=9,column=1,sticky='w')
def LoadFirstCfGScreen(project_name):
top = Tix.Toplevel()
top.protocol("WM_DELETE_WINDOW", on_closing)
top.title("Table InfExtractor")
top.geometry('{}x{}'.format(500, 500))
topframe = Tix.Frame(top, height=10)
topframe.pack()
frame = Tix.Frame(top)
frame.pack()
topframe2 = Tix.Frame(top, height=10)
topframe2.pack()
middleframe = Tix.Frame(top)
middleframe.pack()
bottomframe2 = Tix.Frame(top, height=10)
bottomframe2.pack(side=Tix.BOTTOM)
bottomframe = Tix.Frame(top)
bottomframe.pack(side=Tix.BOTTOM)
name = Tix.StringVar()
label_name = Tix.Label(frame, textvariable=name)
name.set("Name of task:")
label_name.pack(side=Tix.LEFT)
name2 = Tix.StringVar()
label_name2 = Tix.Label(frame, textvariable=name2)
name2.set(project_name)
label_name2.pack(side=Tix.LEFT)
ConfigureDB = Tix.Button(
frame,
text="Configure Database",
fg="black",
command=lambda: ConfigureDatabaseScreen(project_name))
ConfigureDB.pack(side=Tix.LEFT)
clearTable = Tix.Button(frame,
text="Clear DB Table",
fg="black",
command=lambda: ClearDBTables(project_name))
clearTable.pack(side=Tix.LEFT)
vars = FileManipulationHelper.loadVariables(project_name)
Lb1 = ttk.Treeview(middleframe, columns=40, height=19)
Lb1.pack()
size = Lb1.size()
for var in vars:
Lb1.insert('', 'end', var, text=var)
rules = FileManipulationHelper.loadRules(project_name, var)
for rule in rules:
Lb1.insert(var, 'end', text=rule)
#Lb1.insert(size,rule)
size = Lb1.size()
AddVariables = Tix.Button(bottomframe,
text="Add Variable",
fg="black",
command=lambda: AddVariable(project_name, Lb1))
AddVariables.pack(side=Tix.LEFT)
AddRules = Tix.Button(bottomframe,
text="Add Rule",
fg="black",
command=lambda: AddEditRule(project_name, Lb1))
AddRules.pack(side=Tix.LEFT)
DeleteRule = Tix.Button(bottomframe,
text="Delete Rule",
fg="black",
command=lambda: RemoveRule(Lb1, project_name))
DeleteRule.pack(side=Tix.LEFT)
EditRuleA = Tix.Button(bottomframe,
text="Edit Rule",
fg="black",
command=lambda: EditRule(project_name, Lb1))
EditRuleA.pack(side=Tix.LEFT)
#MoveUpRule = Tix.Button(bottomframe, text="Move Up Rule", fg="black",command=lambda:MoveRuleUp(Lb1))
#MoveUpRule.pack( side = Tix.LEFT)
#MoveDownRule =Tix.Button(bottomframe, text="Move Down Rule", fg="black",command=lambda:MoveRuleDown(Lb1))
#MoveDownRule.pack( side = Tix.LEFT)
skip_val = 0
Next = Tix.Button(
bottomframe,
text="Next",
bg="green",
command=lambda: MakeWorkingScreen(rules, top, project_name, skip_val))
Next.pack(side=Tix.LEFT)
def AddEditRule(project_name, RulesListBox):
global currentWhiteList
global currentBlackList
currentWhiteList = []
currentBlackList = []
rule = RulesListBox.selection()[0]
add = Toplevel()
#add.protocol("WM_DELETE_WINDOW", on_closing)
add.title("Add Rule")
add.geometry('{}x{}'.format(400, 350))
itemsFrame = Frame(add, height=130)
itemsFrame.pack()
namerule_label = Label(itemsFrame,
text="Name of the rule").grid(row=0,
column=0,
sticky='w')
vRule = StringVar()
rulename_entry = Entry(itemsFrame, textvariable=vRule).grid(row=0,
column=1,
sticky='w')
#editCueList = Button(itemsFrame,text="Edit Cue List",command=lambda:WhiteListWindow(project_name,rule_name)).grid(row=1,column=0,sticky='w')
ClassLabel = Label(
itemsFrame, text="Variable name (Information class)").grid(row=3,
column=0,
sticky='w')
vClsIn = StringVar()
vClsIn.set(rule)
ClassInput = Entry(itemsFrame, textvariable=vClsIn,
state=DISABLED).grid(row=4, sticky='w')
vDefUnit = StringVar()
vPosUnit = StringVar()
cfg = loadVariableConfig(project_name, rule)
vRuleType = StringVar()
vRuleType.set(cfg["VariableType"])
if (cfg["VariableType"] == "Numeric"
or cfg["VariableType"] == "Categorical"):
DefUnitLabel = Label(itemsFrame, text="Default unit").grid(row=5,
column=0,
sticky='w')
DefUnInput = Entry(itemsFrame, textvariable=vDefUnit).grid(row=6,
sticky='w')
PosUnitLabel = Label(itemsFrame,
text="Possible units (comma separated)").grid(
row=7, column=0, sticky='w')
PosUnInput = Entry(itemsFrame, textvariable=vPosUnit).grid(row=8,
sticky='w')
#if(vRuleType.get() == "Categorical"):
# PosUnitLabel = Label(itemsFrame,text="Possible categories (comma separated)").grid(row=7,column=0,sticky='w')
# vPosUnit = StringVar()
# PosUnInput = Entry(itemsFrame,textvariable=vPosUnit).grid(row=8,sticky='w')
DBSettings = FileManipulationHelper.LoadDBConfigFile(project_name)
db = QueryDBClass.QueryDBCalss(DBSettings['Host'], DBSettings['User'],
DBSettings['Pass'], DBSettings['Database'])
prags = db.GetPragmaticClasses()
prags.insert(0, "Any")
pragVar = StringVar()
pragVar.set(prags[0])
PragLabel = Label(itemsFrame,
text="Table type (pragmatics)").grid(row=9,
column=0,
sticky='w')
drop = OptionMenu(itemsFrame, pragVar, *prags)
drop.grid(row=10, column=0, sticky='w')
vLexSemRule = StringVar()
vLexSemRule.set("Lexical")
#PosUnitLabel = Label(itemsFrame,text="Select rule creation mechanism").grid(row=11,column=0,sticky='w')
#Radiobutton(itemsFrame, text="Lexical (White List+Black list)", variable=vLexSemRule, value="Lexical").grid(row=12,sticky='w')
#Radiobutton(itemsFrame, text="Semantic (UMLS Sem. type+Black list)", variable=vLexSemRule, value="Semantic").grid(row=13,sticky='w')
where_to_look = Label(itemsFrame,
text="Where to look for data?").grid(row=2,
column=1,
sticky='w')
wl_look_head = IntVar()
WLHeaderCB = Checkbutton(itemsFrame, text="Header",
variable=wl_look_head).grid(row=3,
column=1,
sticky='w')
wl_look_stub = IntVar()
WLStubCB = Checkbutton(itemsFrame, text="Stub",
variable=wl_look_stub).grid(row=4,
column=1,
sticky='w')
wl_look_super = IntVar()
WLSuperRowCB = Checkbutton(itemsFrame,
text="Super-row",
variable=wl_look_super).grid(row=5,
column=1,
sticky='w')
wl_look_data = IntVar()
WLDataCB = Checkbutton(itemsFrame, text="Data",
variable=wl_look_data).grid(row=6,
column=1,
sticky='w')
save = Button(
itemsFrame,
text="Save",
fg="black",
command=lambda: SaveRule(project_name, vRule.get(
), add, vClsIn, vDefUnit, vPosUnit, pragVar, RulesListBox, vRuleType,
vLexSemRule, wl_look_head, wl_look_stub,
wl_look_super, wl_look_data)).grid(row=14,
column=1,
sticky='w')
def LoadRulesForProcessing(project_name,before_syntactic = False):
rules = []
projectpath = "Projects/"+project_name
variable_names = FileManipulationHelper.loadVariables(project_name)
for variable_name in variable_names:
rules_names = FileManipulationHelper.loadRules(project_name,variable_name)
for rule_name in rules_names:
rule_datapath = projectpath+'/'+rule_name
black_list = FileManipulationHelper.loadBlackList(project_name, rule_name,variable_name)
white_list = FileManipulationHelper.loadWhiteList(project_name, rule_name,variable_name)
cfg = FileManipulationHelper.loadRuleConfig(project_name, rule_name,variable_name)
rule = RuleClasses_Rule.Rule()
rule.WhiteList = []
rule.BlackList = []
rule.PatternList = []
rule.PossibleUnits = []
rule.RuleName = rule_name
afterWordList= False
for w in white_list:
w = w.replace('\n','')
splitted = w.split(':')
if splitted[0]=='Type':
if splitted[1]=='WhiteList':
continue
if splitted[0]=='Header':
if int(splitted[1]) ==1:
rule.wl_look_header=True
else:
rule.wl_look_header=False
if splitted[0]=='Stub':
if int(splitted[1]) ==1:
rule.wl_look_stub=True
else:
rule.wl_look_stub=False
if splitted[0]=='Super-row':
if int(splitted[1]) ==1:
rule.wl_look_superrow=True
else:
rule.wl_look_superrow=False
if splitted[0]=='Data':
if int(splitted[1]) ==1:
rule.wl_look_data=True
else:
rule.wl_look_data=False
if splitted[0]=='All':
if int(splitted[1]) ==1:
rule.wl_look_anywhere=True
else:
rule.wl_look_anywhere=False
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
rule.WhiteList.append(w)
afterWordList= False
for w in black_list:
w = w.replace('\n','')
splitted = w.split(':')
if splitted[0]=='Type':
if splitted[1]=='BlackList':
continue
if splitted[0]=='Header':
if int(splitted[1]) ==1:
rule.bl_look_header=True
else:
rule.bl_look_header=False
if splitted[0]=='Stub':
if int(splitted[1]) ==1:
rule.bl_look_stub=True
else:
rule.bl_look_stub=False
if splitted[0]=='Super-row':
if int(splitted[1]) ==1:
rule.bl_look_superrow=True
else:
rule.bl_look_superrow=False
if splitted[0]=='Data':
if int(splitted[1]) ==1:
rule.bl_look_data=True
else:
rule.bl_look_data=False
if splitted[0]=='All':
if int(splitted[1]) ==1:
rule.bl_look_anywhere=True
else:
rule.bl_look_anywhere=False
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
rule.BlackList.append(w)
rule.RuleType = cfg['RuleType'].replace('\n','')
if(rule.RuleType == "Numeric" or rule.RuleType == "Categorical"):
rule.DefaultUnit = cfg['DefUnit']
if(rule.RuleType == "Numeric" or rule.RuleType == "Categorical"):
rule.PossibleUnits = cfg['PosUnit'].split(',')
rule.PragmaticClass = cfg['PragClass']
rule.ClassName = cfg['Class']
if(cfg["RuleCreationMech"]=="Semantic"):
rule.is_semantic = True
if('Categories' in cfg.keys()):
rule.PossibleCategories = cfg['Categories'].split(',')
if(before_syntactic==False):
patterns = []
patterns = LoadSyntacticRoles(project_name,rule_name,variable_name)
rule.PatternList = patterns
if('DataInHeader' in cfg.keys() and cfg['DataInHeader']!=None and cfg['DataInHeader']=='1'):
rule.data_in_header = True
else:
rule.data_in_header = False
if('DataInStub' in cfg.keys() and cfg['DataInStub']!=None and cfg['DataInStub']=='1'):
rule.data_in_stub = True
else:
rule.data_in_stub = False
if('DataInSuperRow' in cfg.keys() and cfg['DataInSuperRow']!=None and cfg['DataInSuperRow']=='1'):
rule.data_in_super = True
else:
rule.data_in_super = False
if('DataInData' in cfg.keys() and cfg['DataInData']!=None and cfg['DataInData']=='1'):
rule.data_in_data = True
else:
rule.data_in_data = False
rules.append(rule)
return rules
def LoadRulesForProcessing(project_name, before_syntactic=False):
rules = []
projectpath = "Projects/" + project_name
variable_names = FileManipulationHelper.loadVariables(project_name)
for variable_name in variable_names:
rules_names = FileManipulationHelper.loadRules(project_name,
variable_name)
for rule_name in rules_names:
rule_datapath = projectpath + '/' + rule_name
black_list = FileManipulationHelper.loadBlackList(
project_name, rule_name, variable_name)
white_list = FileManipulationHelper.loadWhiteList(
project_name, rule_name, variable_name)
cfg = FileManipulationHelper.loadRuleConfig(
project_name, rule_name, variable_name)
rule = RuleClasses_Rule.Rule()
rule.WhiteList = []
rule.BlackList = []
rule.PatternList = []
rule.PossibleUnits = []
rule.RuleName = rule_name
afterWordList = False
for w in white_list:
w = w.replace('\n', '')
splitted = w.split(':')
if splitted[0] == 'Type':
if splitted[1] == 'WhiteList':
continue
if splitted[0] == 'Header':
if int(splitted[1]) == 1:
rule.wl_look_header = True
else:
rule.wl_look_header = False
if splitted[0] == 'Stub':
if int(splitted[1]) == 1:
rule.wl_look_stub = True
else:
rule.wl_look_stub = False
if splitted[0] == 'Super-row':
if int(splitted[1]) == 1:
rule.wl_look_superrow = True
else:
rule.wl_look_superrow = False
if splitted[0] == 'Data':
if int(splitted[1]) == 1:
rule.wl_look_data = True
else:
rule.wl_look_data = False
if splitted[0] == 'All':
if int(splitted[1]) == 1:
rule.wl_look_anywhere = True
else:
rule.wl_look_anywhere = False
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
rule.WhiteList.append(w)
afterWordList = False
for w in black_list:
w = w.replace('\n', '')
splitted = w.split(':')
if splitted[0] == 'Type':
if splitted[1] == 'BlackList':
continue
if splitted[0] == 'Header':
if int(splitted[1]) == 1:
rule.bl_look_header = True
else:
rule.bl_look_header = False
if splitted[0] == 'Stub':
if int(splitted[1]) == 1:
rule.bl_look_stub = True
else:
rule.bl_look_stub = False
if splitted[0] == 'Super-row':
if int(splitted[1]) == 1:
rule.bl_look_superrow = True
else:
rule.bl_look_superrow = False
if splitted[0] == 'Data':
if int(splitted[1]) == 1:
rule.bl_look_data = True
else:
rule.bl_look_data = False
if splitted[0] == 'All':
if int(splitted[1]) == 1:
rule.bl_look_anywhere = True
else:
rule.bl_look_anywhere = False
if w == "WordList:":
afterWordList = True
continue
if afterWordList == True:
rule.BlackList.append(w)
rule.RuleType = cfg['RuleType'].replace('\n', '')
if (rule.RuleType == "Numeric" or rule.RuleType == "Categorical"):
rule.DefaultUnit = cfg['DefUnit']
if (rule.RuleType == "Numeric" or rule.RuleType == "Categorical"):
rule.PossibleUnits = cfg['PosUnit'].split(',')
rule.PragmaticClass = cfg['PragClass']
rule.ClassName = cfg['Class']
if (cfg["RuleCreationMech"] == "Semantic"):
rule.is_semantic = True
if ('Categories' in cfg.keys()):
rule.PossibleCategories = cfg['Categories'].split(',')
if (before_syntactic == False):
patterns = []
patterns = LoadSyntacticRoles(project_name, rule_name,
variable_name)
rule.PatternList = patterns
if ('DataInHeader' in cfg.keys() and cfg['DataInHeader'] != None
and cfg['DataInHeader'] == '1'):
rule.data_in_header = True
else:
rule.data_in_header = False
if ('DataInStub' in cfg.keys() and cfg['DataInStub'] != None
and cfg['DataInStub'] == '1'):
rule.data_in_stub = True
else:
rule.data_in_stub = False
if ('DataInSuperRow' in cfg.keys()
and cfg['DataInSuperRow'] != None
and cfg['DataInSuperRow'] == '1'):
rule.data_in_super = True
else:
rule.data_in_super = False
if ('DataInData' in cfg.keys() and cfg['DataInData'] != None
and cfg['DataInData'] == '1'):
rule.data_in_data = True
else:
rule.data_in_data = False
rules.append(rule)
return rules
