def __init__(self, testsuite_paths):
ThemedTk.__init__(self)
self.settings = Settings(default_config)
self.testsuite_paths = testsuite_paths
self.testsuites = {}
frame = tk.Frame(self)
self.scan = tk.Button(frame, text='scan .fastq files', command=self.do_scan)
self.scan.pack()
self.explore = tk.Button(frame, text='explore .json files', command=self.do_explore)
self.explore.pack()
dummy = tk.Label(frame)
dummy.pack()
self.config = tk.Button(frame, text='settings', command=self.do_config)
self.config.pack()
self.help = tk.Button(frame, text='help', command=open_help)
self.help.pack()
if logfn:
self.showlog = tk.Button(frame, text='show log file', command=self.do_showlog)
self.showlog.pack()
frame.pack(side='left', padx=10)
outer = tk.Frame(self, borderwidth=1, relief='ridge')
outer.pack(side='left', expand=True, fill='both', padx=5, pady=5)
label = tk.Label(outer, text='kvarq log output')
label.pack()
frame = tk.Frame(outer)
frame.pack(expand=True, fill='both')
self.text = tk.Text(frame) #, state=tk.DISABLED)
self.text.pack(side=tk.LEFT, fill=tk.BOTH, expand=True)
scroll = tk.Scrollbar(frame, command=self.text.yview)
scroll.pack(side=tk.RIGHT, fill=tk.Y)
self.text.config(yscrollcommand=scroll.set)
self.text.yscrollbar = scroll
def sys_exit():
if tkMessageBox.askyesno('quit KvarQ', 'really want to exit KvarQ and close all windows?'):
sys.exit(0)
self.protocol("WM_DELETE_WINDOW", sys_exit)
self.log_handler = GuiLogHandler(self.text, self.scrolldown)
lo.addHandler(self.log_handler)
lo.debug('GUI started')
def __init__(self, jpath_or_analyser, testsuites, testsuite_paths):
self.win = ThemedTk(title='json explorer', esc_closes=True,
geometry=(-200, -200))
if sys.platform == 'win32':
self.win.wm_iconbitmap(bitmap = get_root_path('res', 'TPH_DNA.ico'))
self.win.columnconfigure(0, weight=1)
self.win.columnconfigure(1, weight=0)
self.win.rowconfigure(0, weight=0)
self.win.rowconfigure(1, weight=0)
self.win.rowconfigure(2, weight=4)
if isinstance(jpath_or_analyser, Analyser):
self.analyser = jpath_or_analyser
name = os.path.basename(self.analyser.fastq.fname)
else:
try:
data = json.load(file(jpath_or_analyser))
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
self.analyser = Analyser()
self.analyser.decode(testsuites, data)
self.analyser.update_testsuites()
except Exception, e:
exc_info = sys.exc_info()
self.win.destroy()
raise exc_info[1], None, exc_info[2]
name = os.path.basename(jpath_or_analyser)
def __init__(self, dname, testsuites, testsuite_paths):
self.testsuites = testsuites
self.testsuite_paths = testsuite_paths
if dname:
self.dname = os.path.abspath(dname)
self.jpaths = glob.glob(os.path.join(self.dname, '*.json'))
else:
jpaths = askopenfilename(
initialdir=os.getcwd(),
title='Choose .json files to explore',
multiple=True,
filetypes=[('json files', '*.json')])
if not jpaths:
return
if len(jpaths) == 1:
self.do_open_json(jpaths[0])
return
self.jpaths = [os.path.abspath(jpath) for jpath in jpaths]
self.dname = os.path.dirname(self.jpaths[0])
self.win = ThemedTk(title='explore .json files', esc_closes=True,
geometry=(400, 800))
# self.menu = tk.Menu(self.win)
# filemenu = tk.Menu(self.menu)
# self.menu.add_cascade(label='KvarQ', menu=filemenu)
# filemenu.add_command(label='Help', command=open_help)
# self.win.config(menu=self.menu)
#
self.win.columnconfigure(0, weight=1)
self.win.columnconfigure(1, weight=0)
self.win.rowconfigure(0, weight=0)
self.win.rowconfigure(1, weight=1)
self.win.rowconfigure(2, weight=0)
self.dlabel = tk.Label(self.win, text='(no directory chosen)')
self.dlabel.grid(row=0, column=0, columnspan=2, sticky='ew')
self.yscroll = tk.Scrollbar(self.win, orient=tk.VERTICAL)
self.yscroll.grid(row=1, column=1, sticky='ns')
self.jlist = tk.Listbox(self.win, yscrollcommand=self.yscroll.set)
self.jlist.grid(row=1, column=0, sticky='nsew')
self.yscroll["command"] = self.jlist.yview
self.jlist.bind("<Double-Button-1>", self.open_json)
self.jlist.bind("<Return>", self.open_json)
# convert .xls button
self.convert = tk.Button(self.win, text='summarize...', command=self.summarize)
self.convert.grid(row=2, column=0, sticky='ew')
self.update()
self.jlist.activate(0)
self.jlist.selection_set(0)
self.jlist.focus_set()
def show(self):
self.win = ThemedTk(title='settings')
self.win.rowconfigure(1, weight=1)
self.win.columnconfigure(1, weight=1)
row = 0
self.win.rowconfigure(row, minsize=10)
row += 1
l = tk.Label(self.win, text='Engine configuration', font=self.win.boldfont)
l.grid(row=row, column=0, columnspan=2, sticky='w')
self.show_help = tk.Button(self.win, text='?',
command=self.launch_help)
self.show_help.grid(row=row, column=2, sticky='e')
self.entries = {}
for name in self.config.keys():
row += 1
l = tk.Label(self.win, text=name)
l.grid(row=row, column=0, sticky='w')
self.entries[name] = tk.Entry(self.win)
self.entries[name].grid(row=row, column=1, columnspan=2, sticky='ew')
self.entries[name].insert(0, self.config[name])
row += 1
self.win.rowconfigure(row, minsize=10)
row += 1
frame = tk.Frame(self.win)
frame.grid(row=row, column=0, columnspan=3)
save = tk.Button(frame, text='save', command=self.save_cb)
save.pack(side='left')
cancel = tk.Button(frame, text='cancel', command=self.cancel_cb)
cancel.pack(side='left')
self.win.bind('<Escape>', lambda x: self.win.close())
class Settings:
def __init__(self, config):
self.config = config
def show(self):
self.win = ThemedTk(title='settings')
self.win.rowconfigure(1, weight=1)
self.win.columnconfigure(1, weight=1)
row = 0
self.win.rowconfigure(row, minsize=10)
row += 1
l = tk.Label(self.win, text='Engine configuration', font=self.win.boldfont)
l.grid(row=row, column=0, columnspan=2, sticky='w')
self.show_help = tk.Button(self.win, text='?',
command=self.launch_help)
self.show_help.grid(row=row, column=2, sticky='e')
self.entries = {}
for name in self.config.keys():
row += 1
l = tk.Label(self.win, text=name)
l.grid(row=row, column=0, sticky='w')
self.entries[name] = tk.Entry(self.win)
self.entries[name].grid(row=row, column=1, columnspan=2, sticky='ew')
self.entries[name].insert(0, self.config[name])
row += 1
self.win.rowconfigure(row, minsize=10)
row += 1
frame = tk.Frame(self.win)
frame.grid(row=row, column=0, columnspan=3)
save = tk.Button(frame, text='save', command=self.save_cb)
save.pack(side='left')
cancel = tk.Button(frame, text='cancel', command=self.cancel_cb)
cancel.pack(side='left')
self.win.bind('<Escape>', lambda x: self.win.close())
def launch_help(self, e=None):
open_help(page='gui', anchor='configuring-kvarq')
def save_cb(self, e=None):
# check whether parameters have correct format
newconfig = dict(self.config)
for name in self.config.keys():
try:
newconfig[name] = int(self.entries[name].get())
except ValueError, e:
tkMessageBox.showerror(
'invalid value',
'parameter "%s" must be an integer' % name)
return
# save new settings
for name, value in newconfig.items():
self.config[name] = value
self.win.destroy()
class DirectoryExplorer:
def __init__(self, dname, testsuites, testsuite_paths):
self.testsuites = testsuites
self.testsuite_paths = testsuite_paths
if dname:
self.dname = os.path.abspath(dname)
self.jpaths = glob.glob(os.path.join(self.dname, '*.json'))
else:
jpaths = askopenfilename(
initialdir=os.getcwd(),
title='Choose .json files to explore',
multiple=True,
filetypes=[('json files', '*.json')])
if not jpaths:
return
if len(jpaths) == 1:
self.do_open_json(jpaths[0])
return
self.jpaths = [os.path.abspath(jpath) for jpath in jpaths]
self.dname = os.path.dirname(self.jpaths[0])
self.win = ThemedTk(title='explore .json files', esc_closes=True,
geometry=(400, 800))
# self.menu = tk.Menu(self.win)
# filemenu = tk.Menu(self.menu)
# self.menu.add_cascade(label='KvarQ', menu=filemenu)
# filemenu.add_command(label='Help', command=open_help)
# self.win.config(menu=self.menu)
#
self.win.columnconfigure(0, weight=1)
self.win.columnconfigure(1, weight=0)
self.win.rowconfigure(0, weight=0)
self.win.rowconfigure(1, weight=1)
self.win.rowconfigure(2, weight=0)
self.dlabel = tk.Label(self.win, text='(no directory chosen)')
self.dlabel.grid(row=0, column=0, columnspan=2, sticky='ew')
self.yscroll = tk.Scrollbar(self.win, orient=tk.VERTICAL)
self.yscroll.grid(row=1, column=1, sticky='ns')
self.jlist = tk.Listbox(self.win, yscrollcommand=self.yscroll.set)
self.jlist.grid(row=1, column=0, sticky='nsew')
self.yscroll["command"] = self.jlist.yview
self.jlist.bind("<Double-Button-1>", self.open_json)
self.jlist.bind("<Return>", self.open_json)
# convert .xls button
self.convert = tk.Button(self.win, text='summarize...', command=self.summarize)
self.convert.grid(row=2, column=0, sticky='ew')
self.update()
self.jlist.activate(0)
self.jlist.selection_set(0)
self.jlist.focus_set()
def update(self):
if len(self.dname)>30:
self.dlabel.config(text='...'+self.dname[-27:])
else:
self.dlabel.config(text=self.dname)
self.jlist.delete(0, tk.END)
for jpath in self.jpaths:
self.jlist.insert(tk.END, os.path.basename(jpath))
def open_json(self, x=None):
idxs = self.jlist.curselection()
if not idxs:
lo.warning('cannot open JsonExplorer : idxs='+str(idxs))
return
jpath = self.jpaths[int(idxs[0])]
self.do_open_json(jpath)
def do_open_json(self, jpath):
try:
je = JsonExplorer(jpath, self.testsuites, self.testsuite_paths)
except DecodingException, e:
more = ''
if isinstance(e, TestsuiteVersionConflictException):
more += '\n\nYou must load compatible versions of testsuites when ' \
'exploring a .json file; KvarQ ships with some testsuite ' \
'legacy versions (in the respectevite "legacy/" directory). ' \
'Or you may try to find old versions online at ' + DOWNLOAD_URL
if isinstance(e, VersionConflictException):
more += '\n\nSome old versions of KvarQ used a file format that ' \
'cannot be parsed with this version; you can download older ' \
'versions of KvarQ at ' + DOWNLOAD_URL
tkMessageBox.showerror(
'file format error',
'cannot load file %s : %s'%(jpath, e)
+ more)
class JsonExplorer:
# whishlist
# - file info
# - version, size, scantime
# - readlengths_hist=f(Amin), fastq_type
# - lineage
# - scores
# - resistances
# - analyse : (non) synonymous
def __init__(self, jpath_or_analyser, testsuites, testsuite_paths):
self.win = ThemedTk(title='json explorer', esc_closes=True,
geometry=(-200, -200))
if sys.platform == 'win32':
self.win.wm_iconbitmap(bitmap = get_root_path('res', 'TPH_DNA.ico'))
self.win.columnconfigure(0, weight=1)
self.win.columnconfigure(1, weight=0)
self.win.rowconfigure(0, weight=0)
self.win.rowconfigure(1, weight=0)
self.win.rowconfigure(2, weight=4)
if isinstance(jpath_or_analyser, Analyser):
self.analyser = jpath_or_analyser
name = os.path.basename(self.analyser.fastq.fname)
else:
try:
data = json.load(file(jpath_or_analyser))
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
self.analyser = Analyser()
self.analyser.decode(testsuites, data)
self.analyser.update_testsuites()
except Exception, e:
exc_info = sys.exc_info()
self.win.destroy()
raise exc_info[1], None, exc_info[2]
name = os.path.basename(jpath_or_analyser)
self.dlabel = tk.Label(self.win, text=name)
self.dlabel.grid(row=0, column=0, columnspan=2, sticky='ew')
self.menu = tk.Menu(self.win)
filemenu = tk.Menu(self.menu)
self.menu.add_cascade(label='KvarQ', menu=filemenu)
filemenu.add_command(label='Help', command=open_help)
self.win.config(menu=self.menu)
# list of analyses
self.yscroll1 = tk.Scrollbar(self.win, orient=tk.VERTICAL)
self.yscroll1.grid(row=1, column=1, sticky='ns')
self.alist = tk.Listbox(self.win, height=len(self.analyser.testsuites)+1, yscrollcommand=self.yscroll1.set)
self.alist.grid(row=1, column=0, sticky='nsew')
self.yscroll1["command"] = self.alist.yview
self.alist.bind("<Double-Button-1>", self.show_analyses)
self.alist.bind("<Return>", self.show_analyses)
# fill in list of analyses, prepare dict of coverages
self.anames = ['info']
self.alist.insert(tk.END, 'info')
for aname, testsuite in self.analyser.testsuites.items():
self.anames.append(aname)
result = self.analyser.results[aname]
if type(result)==list:
result = '; '.join(result)
self.alist.insert(tk.END, aname + ': ' + result)
# list of coverages
self.yscroll2 = tk.Scrollbar(self.win, orient=tk.VERTICAL)
self.yscroll2.grid(row=2, column=1, sticky='ns')
self.clist = tk.Listbox(self.win, yscrollcommand=self.yscroll2.set)
self.clist.grid(row=2, column=0, sticky='nsew')
self.yscroll2["command"] = self.clist.yview
self.clist.bind("<Double-Button-1>", self.show_coverage)
self.clist.bind("<Return>", self.show_coverage)
self.current = None
self.alist.activate(0)
self.alist.selection_set(0)
self.alist.focus_set()
self.after_id = None
def close_win(a=None):
if self.after_id:
self.win.after_cancel(self.after_id)
self.win.destroy()
self.win.close = close_win
self.win.protocol('WM_DELETE_WINDOW', close_win)
self.poll()