How to use get_instance method in robotframework-pageobjects
Best Python code snippet using robotframework-pageobjects_python
window.py
Source:window.py 
...32 global log_message33 global treap34 global log_list35 # Clear the old animations and reset index to zero36 animation_handler.get_instance().skip_list_graph_list.clear()37 animation_handler.get_instance().treap_graph_list.clear()38 animation_handler.get_instance().pseudocode_list.clear()39 animation_handler.get_instance().treap_pseudocode_list.clear()40 graph_list_index = 041 plot.clear()42 try:43 value = int(value_entry.get())44 except ValueError:45 if len(value_entry.get()) == 0:46 log_widget.push("ValueError: Enter a key to perfom an operation")47 log_message.config(text=log_widget.update())48 return49 else:50 log_widget.push(f"Invalid Key : {value_entry.get()}")51 log_message.config(text=log_widget.update())52 return53 # Handling the log widget:54 log_widget.push(f"search:{value}", log_list)55 log_message.config(text=log_widget.update())56 skip_list.find(value)57 treap.find(value, treap)58 skip_list_start = len(animation_handler.get_instance().skip_list_history[0])59 treap_start = len(animation_handler.get_instance().treap_history[0])60 for element in animation_handler.get_instance().skip_list_graph_list:61 animation_handler.get_instance().skip_list_history[0].append(element)62 for element in animation_handler.get_instance().pseudocode_list:63 animation_handler.get_instance().skip_list_history[1].append(element)64 for element in animation_handler.get_instance().treap_graph_list:65 animation_handler.get_instance().treap_history[0].append(element)66 for element in animation_handler.get_instance().treap_pseudocode_list:67 animation_handler.get_instance().treap_history[1].append(element)68 skip_list_end = len(animation_handler.get_instance().skip_list_history[0]) - 169 treap_end = len(animation_handler.get_instance().treap_history[0]) - 170 animation_handler.get_instance().skip_list_time_stamps.append((skip_list_start, skip_list_end))71 animation_handler.get_instance().treap_time_stamps.append((treap_start, treap_end))72 if algorithm.get() == "Skip List":73 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])74 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],75 animation_handler.get_instance().pseudocode_list[graph_list_index][1])76 elif algorithm.get() == "Treap":77 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])78 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0], # text79 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1]) # color80 value_entry.delete(0, tk.END)81def insert_command(event=None):82 global algorithm83 global animation_handler84 global graph_list_index85 global log_widget86 global log_message87 global log_list88 global treap89 # Clear the old animations and reset index to zero90 animation_handler.get_instance().skip_list_graph_list.clear()91 animation_handler.get_instance().treap_graph_list.clear()92 animation_handler.get_instance().pseudocode_list.clear()93 animation_handler.get_instance().treap_pseudocode_list.clear()94 graph_list_index = 095 plot.clear()96 try:97 value = int(value_entry.get())98 except ValueError:99 if len(value_entry.get()) == 0:100 log_widget.push("ValueError: Enter a key to perfom an operation")101 log_message.config(text=log_widget.update())102 return103 elif value_entry.get() == "jackson":104 webbrowser.open("https://youtu.be/PfrV_6yWbEg?autoplay=1&t=210", new=1)105 return106 else:107 log_widget.push(f"Invalid Key : {value_entry.get()}")108 log_message.config(text=log_widget.update())109 return110 skip_list.insert(value)111 treap.insert(value, treap)112 skip_list_start = len(animation_handler.get_instance().skip_list_history[0])113 treap_start = len(animation_handler.get_instance().treap_history[0])114 for element in animation_handler.get_instance().skip_list_graph_list:115 animation_handler.get_instance().skip_list_history[0].append(element)116 for element in animation_handler.get_instance().pseudocode_list:117 animation_handler.get_instance().skip_list_history[1].append(element)118 for element in animation_handler.get_instance().treap_graph_list:119 animation_handler.get_instance().treap_history[0].append(element)120 for element in animation_handler.get_instance().treap_pseudocode_list:121 animation_handler.get_instance().treap_history[1].append(element)122 skip_list_end = len(animation_handler.get_instance().skip_list_history[0]) - 1123 treap_end = len(animation_handler.get_instance().treap_history[0]) - 1124 animation_handler.get_instance().skip_list_time_stamps.append((skip_list_start, skip_list_end))125 animation_handler.get_instance().treap_time_stamps.append((treap_start, treap_end))126 # Handling the log widget:127 log_widget.push(f"insert:{value}", log_list)128 log_message.config(text=log_widget.update())129 if algorithm.get() == "Skip List":130 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])131 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],132 animation_handler.get_instance().pseudocode_list[graph_list_index][1])133 elif algorithm.get() == "Treap":134 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])135 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0], # text136 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1]) # color137 value_entry.delete(0, tk.END)138def delete_command(event=None):139 global algorithm140 global graph_list_index141 global animation_handler142 global treap143 global log_widget144 global log_message145 global log_list146 animation_handler.get_instance().skip_list_graph_list.clear()147 animation_handler.get_instance().treap_graph_list.clear()148 animation_handler.get_instance().pseudocode_list.clear()149 animation_handler.get_instance().treap_pseudocode_list.clear()150 graph_list_index = 0151 plot.clear()152 try:153 value = int(value_entry.get())154 except ValueError:155 if len(value_entry.get()) == 0:156 log_widget.push("ValueError: Enter a key to perfom an operation")157 log_message.config(text=log_widget.update())158 return159 else:160 log_widget.push(f"Invalid Key : {value_entry.get()}")161 log_message.config(text=log_widget.update())162 return163 skip_list.delete(value)164 treap.delete(value, treap)165 skip_list_start = len(animation_handler.get_instance().skip_list_history[0])166 treap_start = len(animation_handler.get_instance().treap_history[0])167 for element in animation_handler.get_instance().skip_list_graph_list:168 animation_handler.get_instance().skip_list_history[0].append(element)169 for element in animation_handler.get_instance().pseudocode_list:170 animation_handler.get_instance().skip_list_history[1].append(element)171 for element in animation_handler.get_instance().treap_graph_list:172 animation_handler.get_instance().treap_history[0].append(element)173 for element in animation_handler.get_instance().treap_pseudocode_list:174 animation_handler.get_instance().treap_history[1].append(element)175 skip_list_end = len(animation_handler.get_instance().skip_list_history[0]) - 1176 treap_end = len(animation_handler.get_instance().treap_history[0]) - 1177 animation_handler.get_instance().skip_list_time_stamps.append((skip_list_start, skip_list_end))178 animation_handler.get_instance().treap_time_stamps.append((treap_start, treap_end))179 # Handling the log widget:180 log_widget.push(f"delete:{value}", log_list)181 log_message.config(text=log_widget.update())182 if algorithm.get() == "Skip List":183 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])184 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],185 animation_handler.get_instance().pseudocode_list[graph_list_index][1])186 elif algorithm.get() == "Treap":187 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])188 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0],189 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1])190 value_entry.delete(0, tk.END)191def play_pause_command(event=None):192 global active193 global play_pause_button194 if play_pause_button["text"] == "Play":195 play_pause_button.config(text="Pause")196 active = True197 play_command()198 else:199 play_pause_button.config(text="Play")200 active = False201def play_command(event=None):202 global active203 global canvas204 global graph_list_index205 global animation_handler206 global algorithm207 global pseudocode_obj208 global mode209 global speed210 if active is False:211 return212 elif mode == "single_command":213 if algorithm.get() == "Skip List":214 if graph_list_index < len(animation_handler.get_instance().skip_list_graph_list) - 1:215 graph_list_index += 1216 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])217 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],218 animation_handler.get_instance().pseudocode_list[graph_list_index][1])219 root.after(1000 - speed, play_command)220 if graph_list_index == len(animation_handler.get_instance().skip_list_graph_list) - 1:221 graph_list_index = 0222 play_pause_command()223 elif algorithm.get() == "Treap":224 if graph_list_index < len(animation_handler.get_instance().treap_graph_list) - 1:225 graph_list_index += 1226 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])227 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0],228 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1])229 root.after(1000 - speed, play_command)230 if graph_list_index == len(animation_handler.get_instance().skip_list_graph_list) - 1:231 graph_list_index = 0232 play_pause_command()233 elif mode == "all_commands":234 if algorithm.get() == "Skip List":235 if graph_list_index < len(animation_handler.get_instance().skip_list_history[0]) - 1:236 graph_list_index += 1237 update_canvas(animation_handler.get_instance().skip_list_history[0][graph_list_index])238 pseudocode_obj.update(animation_handler.get_instance().skip_list_history[1][graph_list_index][0],239 animation_handler.get_instance().skip_list_history[1][graph_list_index][1])240 root.after(1000 - speed, play_command)241 if graph_list_index == len(animation_handler.get_instance().skip_list_history[0]) - 1:242 graph_list_index = 0243 play_pause_command()244 elif algorithm.get() == "Treap":245 if graph_list_index < len(animation_handler.get_instance().treap_history[0]) - 1:246 graph_list_index += 1247 update_canvas(animation_handler.get_instance().treap_history[0][graph_list_index])248 pseudocode_obj.update(animation_handler.get_instance().treap_history[1][graph_list_index][0],249 animation_handler.get_instance().treap_history[1][graph_list_index][1])250 root.after(1000 - speed, play_command)251 if graph_list_index == len(animation_handler.get_instance().treap_history[0]) - 1:252 graph_list_index = 0253 play_pause_command()254def previous_command(event=None):255 global graph_list_index256 global animation_handler257 global algorithm258 global active259 global play_pause_button260 global command_list_index261 global mode262 play_pause_button.config(text="Play")263 active = False264 if mode == "single_command":265 if algorithm.get() == "Skip List":266 if graph_list_index < len(animation_handler.get_instance().skip_list_graph_list) and graph_list_index > 0:267 graph_list_index -= 1268 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])269 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],270 animation_handler.get_instance().pseudocode_list[graph_list_index][1])271 elif algorithm.get() == "Treap":272 if graph_list_index < len(animation_handler.get_instance().treap_graph_list) and graph_list_index > 0:273 graph_list_index -= 1274 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])275 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0],276 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1])277 elif mode == "all_commands":278 if command_list_index > 0:279 command_list_index -= 1280 animation_handler.load_command(command_list_index)281 if algorithm.get() == "Skip List":282 update_canvas(animation_handler.get_instance().skip_list_graph_list[0])283 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[0][0],284 animation_handler.get_instance().pseudocode_list[0][1])285 elif algorithm.get() == "Treap":286 update_canvas(animation_handler.get_instance().treap_graph_list[0])287 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[0][0],288 animation_handler.get_instance().treap_pseudocode_list[0][1])289 else:290 return291def next_command(event=None):292 global graph_list_index293 global animation_handler294 global algorithm295 global active296 global play_pause_button297 global command_list_index298 global mode299 play_pause_button.config(text="Play")300 active = False301 if mode == "single_command":302 if algorithm.get() == "Skip List":303 if graph_list_index < len(animation_handler.get_instance().skip_list_graph_list) - 1:304 graph_list_index += 1305 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])306 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],307 animation_handler.get_instance().pseudocode_list[graph_list_index][1])308 elif algorithm.get() == "Treap":309 if graph_list_index < len(animation_handler.get_instance().treap_graph_list) - 1:310 graph_list_index += 1311 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])312 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0],313 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1])314 elif mode == "all_commands":315 if command_list_index < len(animation_handler.get_instance().treap_time_stamps) - 1:316 command_list_index += 1317 animation_handler.load_command(command_list_index)318 if algorithm.get() == "Skip List":319 update_canvas(animation_handler.get_instance().skip_list_graph_list[0])320 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[0][0],321 animation_handler.get_instance().pseudocode_list[0][1])322 elif algorithm.get() == "Treap":323 update_canvas(animation_handler.get_instance().treap_graph_list[0])324 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[0][0],325 animation_handler.get_instance().treap_pseudocode_list[0][1])326 else:327 return328def stop_command(event=None):329 global treap330 global algorithm331 global graph_list_index332 global active333 global play_pause_button334 global mode335 play_pause_button.config(text="Play")336 active = False337 graph_list_index = 0338 if mode == "single_command":339 if algorithm.get() == "Skip List":340 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])341 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],342 animation_handler.get_instance().pseudocode_list[graph_list_index][1])343 elif algorithm.get() == "Treap":344 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])345 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0],346 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1])347 elif mode == "all_commands":348 if algorithm.get() == "Skip List":349 update_canvas(animation_handler.get_instance().skip_list_history[0][graph_list_index])350 pseudocode_obj.update(animation_handler.get_instance().skip_list_history[1][graph_list_index][0],351 animation_handler.get_instance().skip_list_history[1][graph_list_index][1])352 elif algorithm.get() == "Treap":353 update_canvas(animation_handler.get_instance().treap_history[0][graph_list_index])354 pseudocode_obj.update(animation_handler.get_instance().treap_history[1][graph_list_index][0],355 animation_handler.get_instance().treap_history[1][graph_list_index][1])356def clear_command(event=None):357 global graph_list_index358 global animation_handler359 global skip_list_graph360 global treap_graph361 global algorithm362 global treap363 global skip_list364 global active365 global play_pause_button366 global log_list367 global log_widget368 global log_message369 global plot370 global canvas371 play_pause_button.config(text="Play")372 active = False373 graph_list_index = 0374 treap = tr.Treap()375 skip_list = sl.SkipList()376 animation_handler.get_instance().skip_list_graph_list.clear()377 animation_handler.get_instance().treap_graph_list.clear()378 animation_handler.get_instance().pseudocode_list.clear()379 animation_handler.get_instance().treap_pseudocode_list.clear()380 log_widget.clear()381 log_message.config(text=log_widget.update())382 log_list.clear()383 treap_graph = TreapGraph(treap)384 skip_list_graph = SkipListGraph(skip_list)385 animation_handler.get_instance().treap_graph_list.append(treap_graph.create_graph())386 animation_handler.get_instance().skip_list_graph_list.append(skip_list_graph.create_graph(skip_list))387 if algorithm.get() == "Treap":388 # update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])389 treap_graph.draw(treap_graph.treap, plot, canvas)390 else:391 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])392def switch_algorithm(string, event=None):393 global graph_list_index394 global active395 global play_pause_button396 global animation_handler397 global command_list_index398 global mode399 global canvas400 global plot401 play_pause_button.config(text="Play")402 active = False403 graph_list_index = 0404 if mode == "single_command":405 if string == "Treap":406 try:407 update_canvas(animation_handler.get_instance().treap_graph_list[0])408 except IndexError:409 treap_graph.draw(treap_graph.treap, plot, canvas)410 elif string == "Skip List":411 try:412 update_canvas(animation_handler.get_instance().skip_list_graph_list[0])413 except IndexError:414 skip_list_graph.draw(skip_list_graph.skip_list, plot, canvas)415 elif mode == "all_commands":416 if string == "Treap":417 try:418 update_canvas(animation_handler.get_instance().treap_graph_list[0])419 except IndexError:420 treap_graph.draw(treap_graph.treap, plot, canvas)421 elif string == "Skip List":422 try:423 update_canvas(animation_handler.get_instance().skip_list_graph_list[0])424 except IndexError:425 skip_list_graph.draw(skip_list_graph.skip_list, plot, canvas)426def read_data_command():427 global algorithm428 global animation_handler429 global treap430 global graph_list_index431 global data432 global log_message433 global log_widget434 graph_list_index = 0435 for command, key in data:436 animation_handler.get_instance().skip_list_graph_list.clear()437 animation_handler.get_instance().treap_graph_list.clear()438 animation_handler.get_instance().pseudocode_list.clear()439 animation_handler.get_instance().treap_pseudocode_list.clear()440 if command == "insert":441 if treap.root.key is not None:442 if treap.find_ohne(int(key)):443 continue444 if skip_list.search(int(key)):445 continue446 skip_list.insert(int(key))447 treap.insert(int(key), treap)448 skip_list_start = len(animation_handler.get_instance().skip_list_history[0])449 treap_start = len(animation_handler.get_instance().treap_history[0])450 for element in animation_handler.get_instance().skip_list_graph_list:451 animation_handler.get_instance().skip_list_history[0].append(element)452 for element in animation_handler.get_instance().pseudocode_list:453 animation_handler.get_instance().skip_list_history[1].append(element)454 for element in animation_handler.get_instance().treap_graph_list:455 animation_handler.get_instance().treap_history[0].append(element)456 for element in animation_handler.get_instance().treap_pseudocode_list:457 animation_handler.get_instance().treap_history[1].append(element)458 skip_list_end = len(animation_handler.get_instance().skip_list_history[0]) - 1459 treap_end = len(animation_handler.get_instance().treap_history[0]) - 1460 animation_handler.get_instance().skip_list_time_stamps.append((skip_list_start, skip_list_end))461 animation_handler.get_instance().treap_time_stamps.append((treap_start, treap_end))462 # Handling the log widget:463 log_widget.push(f"insert:{int(key)}", log_list)464 log_message.config(text=log_widget.update())465 if algorithm.get() == "Skip List":466 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])467 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],468 animation_handler.get_instance().pseudocode_list[graph_list_index][1])469 elif algorithm.get() == "Treap":470 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])471 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0],472 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1])473 elif command == "search":474 skip_list.find(int(key))475 treap.find(int(key), treap)476 for element in animation_handler.get_instance().skip_list_graph_list:477 animation_handler.get_instance().skip_list_history[0].append(element)478 for element in animation_handler.get_instance().pseudocode_list:479 animation_handler.get_instance().skip_list_history[1].append(element)480 for element in animation_handler.get_instance().treap_graph_list:481 animation_handler.get_instance().treap_history[0].append(element)482 for element in animation_handler.get_instance().treap_pseudocode_list:483 animation_handler.get_instance().treap_history[1].append(element)484 log_widget.push(f"search:{int(key)}", log_list)485 log_message.config(text=log_widget.update())486 if algorithm.get() == "Skip List":487 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])488 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],489 animation_handler.get_instance().pseudocode_list[graph_list_index][1])490 elif algorithm.get() == "Treap":491 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])492 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0],493 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1])494 elif command == "delete":495 skip_list.delete(int(key))496 treap.delete(int(key), treap)497 skip_list_start = len(animation_handler.get_instance().skip_list_history[0])498 treap_start = len(animation_handler.get_instance().treap_history[0])499 for element in animation_handler.get_instance().skip_list_graph_list:500 animation_handler.get_instance().skip_list_history[0].append(element)501 for element in animation_handler.get_instance().pseudocode_list:502 animation_handler.get_instance().skip_list_history[1].append(element)503 for element in animation_handler.get_instance().treap_graph_list:504 animation_handler.get_instance().treap_history[0].append(element)505 for element in animation_handler.get_instance().treap_pseudocode_list:506 animation_handler.get_instance().treap_history[1].append(element)507 skip_list_end = len(animation_handler.get_instance().skip_list_history[0]) - 1508 treap_end = len(animation_handler.get_instance().treap_history[0]) - 1509 animation_handler.get_instance().skip_list_time_stamps.append((skip_list_start, skip_list_end))510 animation_handler.get_instance().treap_time_stamps.append((treap_start, treap_end))511 log_widget.push(f"delete:{int(key)}", log_list)512 log_message.config(text=log_widget.update())513 if algorithm.get() == "Skip List":514 update_canvas(animation_handler.get_instance().skip_list_graph_list[graph_list_index])515 pseudocode_obj.update(animation_handler.get_instance().pseudocode_list[graph_list_index][0],516 animation_handler.get_instance().pseudocode_list[graph_list_index][1])517 elif algorithm.get() == "Treap":518 update_canvas(animation_handler.get_instance().treap_graph_list[graph_list_index])519 pseudocode_obj.update(animation_handler.get_instance().treap_pseudocode_list[graph_list_index][0],520 animation_handler.get_instance().treap_pseudocode_list[graph_list_index][1])521def open_file():522 global active523 global play_pause_button524 play_pause_button.config(text="Play")525 active = False526 global data527 token = False528 file = tk.filedialog.askopenfile(mode='r', title="Open file", filetypes=[('Text Files', '*.txt')])529 # check if file was opend successfully530 if file:531 # set Label with filename only if open was successful532 filename_label.config(text=file.name.split("/")[-1])533 data = []534 # append each line to DATA list, where they are stored535 for line in file:536 command = line.rstrip().split(":")537 tmp = (command[0], command[1]) # command[0] ="insert", command[1]="3"538 if tmp in data:539 continue540 else:541 data.append(tmp)542 read_data_command()543def save_graph():544 global active545 global play_pause_button546 global filename547 global fig548 play_pause_button.config(text="Play")549 active = False550 filename = ""551 filename = tk.filedialog.asksaveasfilename(title="Save File",552 filetypes=[("png files", "*.png"), ("jpeg files", "*.jpeg")])553 if filename:554 fig.savefig(filename)555def save_graph():556 global active557 global play_pause_button558 global filename559 global fig560 play_pause_button.config(text="Play")561 active = False562 filename = ""563 filename = tk.filedialog.asksaveasfilename(title="Save File",564 filetypes=[("png files", "*.png"), ("jpeg files", "*.jpeg")])565 if filename:566 fig.savefig(filename)567def callor(event):568 insert_command()569def placeholder(event):570 value_entry.delete(0, tk.END)571def github():572 webbrowser.open("https://github.com/timokilb/projektgruppe", new=1)573def donate():574 global algorithm575 if algorithm.get() == "Skip List":576 webbrowser.open("https://www.paypal.me/timokilb", new=1)577 else:578 webbrowser.open("https://www.paypal.me/denizdogan94", new=1)579def instagram():580 webbrowser.open("https://www.instagram.com/resbalar.sb/?hl=de", new=1)581def how_it_works(event=None):582 how_it_works_window = tk.Toplevel()583 how_it_works_window.title("How it works")584 how_it_works_window.minsize(300, 300)585 how_it_works_window.config(padx=20, pady=20, bg=background_color)586 how_it_works_window.resizable(height=False, width=False)587 how_it_works_frame = tk.Frame(how_it_works_window, **style_sheet["how_it_works_frame"])588 how_it_works_frame.pack(side="top", anchor="nw", fill="both", expand=1)589 explanation_text = open("./res/howto.txt", "r").read()590 explanation_message = tk.Message(master=how_it_works_frame, text=explanation_text, **style_sheet["how_it_works"])591 explanation_message.pack(anchor="nw")592def check_decision():593 global filename594 global save_decision_list595 if "save_all" and True in save_decision_list[2]:596 save_graph()597 save_log()598 filename = ""599 return600 elif "save_graph" and True in save_decision_list[0]:601 save_graph()602 filename = ""603 elif "save_log" and True in save_decision_list[1]:604 save_log()605 filename = ""606def get_frame():607 global pseudocode_frame608 return pseudocode_frame609def save_log():610 global log_list611 global filename612 if filename == "":613 filename = tk.filedialog.asksaveasfilename(title="Save File",614 filetypes=[("txt files", "*.txt")])615 tmp = open(filename + ".txt", mode="w")616 if tmp:617 for line in log_list:618 tmp.write(line + "\n")619 tmp.close()620def open_save():621 def save_decision():622 global save_decision_list623 save_decision_list.clear()624 save_decision_list.append(("save_graph", save_graph.get()))625 save_decision_list.append(("save_log", save_log.get()))626 save_decision_list.append(("save_all", (save_graph.get() and save_log.get() or (save_all.get()))))627 check_decision()628 choose_save_window.destroy()629 choose_save_window = tk.Toplevel()630 choose_save_window.title("Save")631 choose_save_window.minsize(300, 136)632 choose_save_window.resizable(width=False, height=False)633 choose_save_window.config(padx=10, pady=30, bg=background_color)634 save_graph = tk.BooleanVar()635 tk.Checkbutton(choose_save_window, text="Save Graph", variable=save_graph, **style_sheet["save_window_check"]).pack(636 side="top", anchor="w")637 save_log = tk.BooleanVar()638 tk.Checkbutton(choose_save_window, text="Save Logs", variable=save_log, **style_sheet["save_window_check"]).pack(639 side="top", anchor="w")640 save_all = tk.BooleanVar()641 tk.Checkbutton(choose_save_window, text="Save Graph and Logs", variable=save_all,642 **style_sheet["save_window_check"]).pack(side="top", anchor="w")643 tk.Button(choose_save_window, text='Save', command=save_decision, **style_sheet["save_window_button"], ).pack(644 side="left", anchor="nw", fill="x", expand=1,645 padx=2, pady=6)646 tk.Button(choose_save_window, text='Cancel', command=choose_save_window.destroy,647 **style_sheet["save_window_button"], ).pack(side="left", anchor="nw",648 fill="x", expand=1, padx=2,649 pady=6)650def set_mode(param):651 global graph_list_index652 global algorithm653 global mode654 global log_widget655 global log_message656 if algorithm.get() == "Skip List":657 if graph_list_index > len(animation_handler.get_instance().skip_list_graph_list) - 1:658 graph_list_index = 0659 elif algorithm.get() == "Treap":660 if graph_list_index > len(animation_handler.get_instance().treap_graph_list) - 1:661 graph_list_index = 0662 mode = param663 if mode == "single_command":664 log_widget.push(f"Mode: Single Command")665 log_message.config(text=log_widget.update())666 else:667 log_widget.push(f"Mode:All Commands")668 log_message.config(text=log_widget.update())669def faster_command(event=None):670 global speed671 if speed < 800:672 speed += 150673def slower_command(event=None):674 global speed...
web_transfer.py
Source:web_transfer.py
...53 "nodes/%d/info" % (get_config().NODE_ID),54 {"node_id": get_config().NODE_ID},55 {"uptime": str(self.uptime()), "load": str(self.load())},56 )57 online_iplist = ServerPool.get_instance().get_servers_iplist()58 data = []59 for port in online_iplist.keys():60 for ip in online_iplist[port]:61 data.append({"ip": ip, "user_id": self.port_uid_table[port]})62 webapi.postApi(63 "users/aliveip", {"node_id": get_config().NODE_ID}, {"data": data}64 )65 detect_log_list = ServerPool.get_instance().get_servers_detect_log()66 data = []67 for port in detect_log_list.keys():68 for rule_id in detect_log_list[port]:69 data.append(70 {"list_id": rule_id, "user_id": self.port_uid_table[port]}71 )72 webapi.postApi(73 "users/detectlog",74 {"node_id": get_config().NODE_ID},75 {"data": data},76 )77 deny_str = ""78 data = []79 if platform.system() == "Linux" and get_config().ANTISSATTACK == 1:80 wrong_iplist = ServerPool.get_instance().get_servers_wrong()81 server_ip = socket.gethostbyname(get_config().MYSQL_HOST)82 for id in wrong_iplist.keys():83 for ip in wrong_iplist[id]:84 realip = ""85 is_ipv6 = False86 if common.is_ip(ip):87 if common.is_ip(ip) == socket.AF_INET:88 realip = ip89 else:90 if common.match_ipv4_address(ip) is not None:91 realip = common.match_ipv4_address(ip)92 else:93 is_ipv6 = True94 realip = ip95 else:96 continue97 if str(realip).find(str(server_ip)) != -1:98 continue99 has_match_node = False100 for node_ip in self.node_ip_list:101 if str(realip).find(node_ip) != -1:102 has_match_node = True103 continue104 if has_match_node:105 continue106 if get_config().CLOUDSAFE == 1:107 data.append({"ip": realip})108 else:109 if not is_ipv6:110 os.system(111 "route add -host %s gw 127.0.0.1" % str(realip)112 )113 deny_str = deny_str + "\nALL: " + str(realip)114 else:115 os.system(116 "ip -6 route add ::1/128 via %s/128"117 % str(realip)118 )119 deny_str = (120 deny_str + "\nALL: [" + str(realip) + "]/128"121 )122 logging.info("Local Block ip:" + str(realip))123 if get_config().CLOUDSAFE == 0:124 deny_file = open("/etc/hosts.deny", "a")125 fcntl.flock(deny_file.fileno(), fcntl.LOCK_EX)126 deny_file.write(deny_str)127 deny_file.close()128 webapi.postApi(129 "func/block_ip",130 {"node_id": get_config().NODE_ID},131 {"data": data},132 )133 return update_transfer134 def uptime(self):135 with open("/proc/uptime", "r") as f:136 return float(f.readline().split()[0])137 def load(self):138 import os139 return os.popen(140 'cat /proc/loadavg | awk \'{ print $1" "$2" "$3 }\''141 ).readlines()[0]142 def trafficShow(self, Traffic):143 if Traffic < 1024:144 return str(round((Traffic), 2)) + "B"145 if Traffic < 1024 * 1024:146 return str(round((Traffic / 1024), 2)) + "KB"147 if Traffic < 1024 * 1024 * 1024:148 return str(round((Traffic / 1024 / 1024), 2)) + "MB"149 return str(round((Traffic / 1024 / 1024 / 1024), 2)) + "GB"150 def push_db_all_user(self):151 # æ´æ°ç¨æ·æµéå°æ°æ®åº152 last_transfer = self.last_update_transfer153 curr_transfer = ServerPool.get_instance().get_servers_transfer()154 # ä¸æ¬¡åæ¬æ¬¡çå¢é155 dt_transfer = {}156 for id in curr_transfer.keys():157 if id in last_transfer:158 if (159 curr_transfer[id][0]160 + curr_transfer[id][1]161 - last_transfer[id][0]162 - last_transfer[id][1]163 <= 0164 ):165 continue166 if (167 last_transfer[id][0] <= curr_transfer[id][0]168 and last_transfer[id][1] <= curr_transfer[id][1]169 ):170 dt_transfer[id] = [171 curr_transfer[id][0] - last_transfer[id][0],172 curr_transfer[id][1] - last_transfer[id][1],173 ]174 else:175 dt_transfer[id] = [176 curr_transfer[id][0],177 curr_transfer[id][1],178 ]179 else:180 if curr_transfer[id][0] + curr_transfer[id][1] <= 0:181 continue182 dt_transfer[id] = [curr_transfer[id][0], curr_transfer[id][1]]183 for id in dt_transfer.keys():184 last = last_transfer.get(id, [0, 0])185 last_transfer[id] = [186 last[0] + dt_transfer[id][0],187 last[1] + dt_transfer[id][1],188 ]189 self.last_update_transfer = last_transfer.copy()190 self.update_all_user(dt_transfer)191 def pull_db_all_user(self):192 global webapi193 nodeinfo = webapi.getApi("nodes/%d/info" % (get_config().NODE_ID))194 if not nodeinfo:195 rows = []196 return rows197 self.node_speedlimit = nodeinfo["node_speedlimit"]198 self.traffic_rate = nodeinfo["traffic_rate"]199 self.mu_only = nodeinfo["mu_only"]200 if nodeinfo["sort"] == 10:201 self.is_relay = True202 else:203 self.is_relay = False204 data = webapi.getApi("users", {"node_id": get_config().NODE_ID})205 if not data:206 rows = []207 return rows208 rows = data209 # 读åèç¹IP210 # SELECT * FROM `ss_node` where `node_ip` != ''211 self.node_ip_list = []212 data = webapi.getApi("nodes")213 for node in data:214 temp_list = str(node["node_ip"]).split(",")215 self.node_ip_list.append(temp_list[0])216 # 读å审计è§å,æ°æ®å
å¹é
é¨å217 self.detect_text_list = {}218 self.detect_hex_list = {}219 data = webapi.getApi("func/detect_rules")220 for rule in data:221 d = {}222 d["id"] = int(rule["id"])223 d["regex"] = str(rule["regex"])224 if int(rule["type"]) == 1:225 self.detect_text_list[d["id"]] = d.copy()226 else:227 self.detect_hex_list[d["id"]] = d.copy()228 # 读åä¸è½¬è§åï¼å¦ææ¯ä¸è½¬èç¹çè¯229 if self.is_relay:230 self.relay_rule_list = {}231 data = webapi.getApi(232 "func/relay_rules", {"node_id": get_config().NODE_ID}233 )234 for rule in data:235 d = {}236 d["id"] = int(rule["id"])237 d["user_id"] = int(rule["user_id"])238 d["dist_ip"] = str(rule["dist_ip"])239 d["port"] = int(rule["port"])240 d["priority"] = int(rule["priority"])241 self.relay_rule_list[d["id"]] = d.copy()242 return rows243 def cmp(self, val1, val2):244 if isinstance(val1, bytes):245 val1 = common.to_str(val1)246 if isinstance(val2, bytes):247 val2 = common.to_str(val2)248 return val1 == val2249 def del_server_out_of_bound_safe(self, last_rows, rows):250 # åæ¢è¶
æµéçæå¡251 # å¯å¨æ²¡è¶
æµéçæå¡252 # éè¦å¨æè½½å
¥switchruleï¼ä»¥ä¾¿å®æ¶ä¿®æ¹è§å253 try:254 switchrule = importloader.load("switchrule")255 except Exception as e:256 logging.error("load switchrule.py fail")257 cur_servers = {}258 new_servers = {}259 md5_users = {}260 self.mu_port_list = []261 for row in rows:262 if row["is_multi_user"] != 0:263 self.mu_port_list.append(int(row["port"]))264 continue265 md5_users[row["id"]] = row.copy()266 del md5_users[row["id"]]["u"]267 del md5_users[row["id"]]["d"]268 if md5_users[row["id"]]["disconnect_ip"] is None:269 md5_users[row["id"]]["disconnect_ip"] = ""270 if md5_users[row["id"]]["forbidden_ip"] is None:271 md5_users[row["id"]]["forbidden_ip"] = ""272 if md5_users[row["id"]]["forbidden_port"] is None:273 md5_users[row["id"]]["forbidden_port"] = ""274 md5_users[row["id"]]["md5"] = common.get_md5(275 str(row["id"])276 + row["passwd"]277 + row["method"]278 + row["obfs"]279 + row["protocol"]280 )281 for row in rows:282 self.port_uid_table[row["port"]] = row["id"]283 self.uid_port_table[row["id"]] = row["port"]284 if self.mu_only == 1:285 i = 0286 while i < len(rows):287 if rows[i]["is_multi_user"] == 0:288 rows.pop(i)289 i -= 1290 else:291 pass292 i += 1293 if self.mu_only == -1:294 i = 0295 while i < len(rows):296 if rows[i]["is_multi_user"] != 0:297 rows.pop(i)298 i -= 1299 else:300 pass301 i += 1302 for row in rows:303 port = row["port"]304 user_id = row["id"]305 passwd = common.to_bytes(row["passwd"])306 cfg = {"password": passwd}307 read_config_keys = [308 "method",309 "obfs",310 "obfs_param",311 "protocol",312 "protocol_param",313 "forbidden_ip",314 "forbidden_port",315 "node_speedlimit",316 "disconnect_ip",317 "is_multi_user",318 ]319 for name in read_config_keys:320 if name in row and row[name]:321 cfg[name] = row[name]322 merge_config_keys = ["password"] + read_config_keys323 for name in cfg.keys():324 if hasattr(cfg[name], "encode"):325 try:326 cfg[name] = cfg[name].encode("utf-8")327 except Exception as e:328 logging.warning(329 'encode cfg key "%s" fail, val "%s"'330 % (name, cfg[name])331 )332 if "node_speedlimit" in cfg:333 if (334 float(self.node_speedlimit) > 0.0335 or float(cfg["node_speedlimit"]) > 0.0336 ):337 cfg["node_speedlimit"] = max(338 float(self.node_speedlimit),339 float(cfg["node_speedlimit"]),340 )341 else:342 cfg["node_speedlimit"] = max(343 float(self.node_speedlimit), float(0.00)344 )345 if "disconnect_ip" not in cfg:346 cfg["disconnect_ip"] = ""347 if "forbidden_ip" not in cfg:348 cfg["forbidden_ip"] = ""349 if "forbidden_port" not in cfg:350 cfg["forbidden_port"] = ""351 if "protocol_param" not in cfg:352 cfg["protocol_param"] = ""353 if "obfs_param" not in cfg:354 cfg["obfs_param"] = ""355 if "is_multi_user" not in cfg:356 cfg["is_multi_user"] = 0357 if port not in cur_servers:358 cur_servers[port] = passwd359 else:360 logging.error(361 "more than one user use the same port [%s]" % (port,)362 )363 continue364 if cfg["is_multi_user"] != 0:365 cfg["users_table"] = md5_users.copy()366 cfg["detect_hex_list"] = self.detect_hex_list.copy()367 cfg["detect_text_list"] = self.detect_text_list.copy()368 if self.is_relay and row["is_multi_user"] != 2:369 temp_relay_rules = {}370 for id in self.relay_rule_list:371 if (372 (373 self.relay_rule_list[id]["user_id"] == user_id374 or self.relay_rule_list[id]["user_id"] == 0375 )376 or row["is_multi_user"] != 0377 ) and (378 self.relay_rule_list[id]["port"] == 0379 or self.relay_rule_list[id]["port"] == port380 ):381 has_higher_priority = False382 for priority_id in self.relay_rule_list:383 if (384 (385 (386 self.relay_rule_list[priority_id][387 "priority"388 ]389 > self.relay_rule_list[id]["priority"]390 and self.relay_rule_list[id]["id"]391 != self.relay_rule_list[priority_id][392 "id"393 ]394 )395 or (396 self.relay_rule_list[priority_id][397 "priority"398 ]399 == self.relay_rule_list[id]["priority"]400 and self.relay_rule_list[id]["id"]401 > self.relay_rule_list[priority_id][402 "id"403 ]404 )405 )406 and (407 self.relay_rule_list[priority_id][408 "user_id"409 ]410 == user_id411 or self.relay_rule_list[priority_id][412 "user_id"413 ]414 == 0415 )416 and (417 self.relay_rule_list[priority_id]["port"]418 == port419 or self.relay_rule_list[priority_id][420 "port"421 ]422 == 0423 )424 ):425 has_higher_priority = True426 continue427 if has_higher_priority:428 continue429 if (430 self.relay_rule_list[id]["dist_ip"] == "0.0.0.0"431 and row["is_multi_user"] == 0432 ):433 continue434 temp_relay_rules[id] = self.relay_rule_list[id]435 cfg["relay_rules"] = temp_relay_rules.copy()436 else:437 temp_relay_rules = {}438 cfg["relay_rules"] = temp_relay_rules.copy()439 if ServerPool.get_instance().server_is_run(port) > 0:440 cfgchange = False441 if port in ServerPool.get_instance().tcp_servers_pool:442 ServerPool.get_instance().tcp_servers_pool[443 port444 ].modify_detect_text_list(self.detect_text_list)445 ServerPool.get_instance().tcp_servers_pool[446 port447 ].modify_detect_hex_list(self.detect_hex_list)448 if port in ServerPool.get_instance().tcp_ipv6_servers_pool:449 ServerPool.get_instance().tcp_ipv6_servers_pool[450 port451 ].modify_detect_text_list(self.detect_text_list)452 ServerPool.get_instance().tcp_ipv6_servers_pool[453 port454 ].modify_detect_hex_list(self.detect_hex_list)455 if port in ServerPool.get_instance().udp_servers_pool:456 ServerPool.get_instance().udp_servers_pool[457 port458 ].modify_detect_text_list(self.detect_text_list)459 ServerPool.get_instance().udp_servers_pool[460 port461 ].modify_detect_hex_list(self.detect_hex_list)462 if port in ServerPool.get_instance().udp_ipv6_servers_pool:463 ServerPool.get_instance().udp_ipv6_servers_pool[464 port465 ].modify_detect_text_list(self.detect_text_list)466 ServerPool.get_instance().udp_ipv6_servers_pool[467 port468 ].modify_detect_hex_list(self.detect_hex_list)469 if row["is_multi_user"] != 0:470 if port in ServerPool.get_instance().tcp_servers_pool:471 ServerPool.get_instance().tcp_servers_pool[472 port473 ].modify_multi_user_table(md5_users)474 if port in ServerPool.get_instance().tcp_ipv6_servers_pool:475 ServerPool.get_instance().tcp_ipv6_servers_pool[476 port477 ].modify_multi_user_table(md5_users)478 if port in ServerPool.get_instance().udp_servers_pool:479 ServerPool.get_instance().udp_servers_pool[480 port481 ].modify_multi_user_table(md5_users)482 if port in ServerPool.get_instance().udp_ipv6_servers_pool:483 ServerPool.get_instance().udp_ipv6_servers_pool[484 port485 ].modify_multi_user_table(md5_users)486 if self.is_relay and row["is_multi_user"] != 2:487 temp_relay_rules = {}488 for id in self.relay_rule_list:489 if (490 (491 self.relay_rule_list[id]["user_id"] == user_id492 or self.relay_rule_list[id]["user_id"] == 0493 )494 or row["is_multi_user"] != 0495 ) and (496 self.relay_rule_list[id]["port"] == 0497 or self.relay_rule_list[id]["port"] == port498 ):499 has_higher_priority = False500 for priority_id in self.relay_rule_list:501 if (502 (503 (504 self.relay_rule_list[priority_id][505 "priority"506 ]507 > self.relay_rule_list[id][508 "priority"509 ]510 and self.relay_rule_list[id]["id"]511 != self.relay_rule_list[512 priority_id513 ]["id"]514 )515 or (516 self.relay_rule_list[priority_id][517 "priority"518 ]519 == self.relay_rule_list[id][520 "priority"521 ]522 and self.relay_rule_list[id]["id"]523 > self.relay_rule_list[524 priority_id525 ]["id"]526 )527 )528 and (529 self.relay_rule_list[priority_id][530 "user_id"531 ]532 == user_id533 or self.relay_rule_list[priority_id][534 "user_id"535 ]536 == 0537 )538 and (539 self.relay_rule_list[priority_id][540 "port"541 ]542 == port543 or self.relay_rule_list[priority_id][544 "port"545 ]546 == 0547 )548 ):549 has_higher_priority = True550 continue551 if has_higher_priority:552 continue553 if (554 self.relay_rule_list[id]["dist_ip"]555 == "0.0.0.0"556 and row["is_multi_user"] == 0557 ):558 continue559 temp_relay_rules[id] = self.relay_rule_list[id]560 if port in ServerPool.get_instance().tcp_servers_pool:561 ServerPool.get_instance().tcp_servers_pool[562 port563 ].push_relay_rules(temp_relay_rules)564 if port in ServerPool.get_instance().tcp_ipv6_servers_pool:565 ServerPool.get_instance().tcp_ipv6_servers_pool[566 port567 ].push_relay_rules(temp_relay_rules)568 if port in ServerPool.get_instance().udp_servers_pool:569 ServerPool.get_instance().udp_servers_pool[570 port571 ].push_relay_rules(temp_relay_rules)572 if port in ServerPool.get_instance().udp_ipv6_servers_pool:573 ServerPool.get_instance().udp_ipv6_servers_pool[574 port575 ].push_relay_rules(temp_relay_rules)576 else:577 temp_relay_rules = {}578 if port in ServerPool.get_instance().tcp_servers_pool:579 ServerPool.get_instance().tcp_servers_pool[580 port581 ].push_relay_rules(temp_relay_rules)582 if port in ServerPool.get_instance().tcp_ipv6_servers_pool:583 ServerPool.get_instance().tcp_ipv6_servers_pool[584 port585 ].push_relay_rules(temp_relay_rules)586 if port in ServerPool.get_instance().udp_servers_pool:587 ServerPool.get_instance().udp_servers_pool[588 port589 ].push_relay_rules(temp_relay_rules)590 if port in ServerPool.get_instance().udp_ipv6_servers_pool:591 ServerPool.get_instance().udp_ipv6_servers_pool[592 port593 ].push_relay_rules(temp_relay_rules)594 if port in ServerPool.get_instance().tcp_servers_pool:595 relay = ServerPool.get_instance().tcp_servers_pool[port]596 for name in merge_config_keys:597 if name in cfg and not self.cmp(598 cfg[name], relay._config[name]599 ):600 cfgchange = True601 break602 if (603 not cfgchange604 and port in ServerPool.get_instance().tcp_ipv6_servers_pool605 ):606 relay = ServerPool.get_instance().tcp_ipv6_servers_pool[607 port608 ]609 for name in merge_config_keys:610 if name in cfg and not self.cmp(611 cfg[name], relay._config[name]612 ):613 cfgchange = True614 break615 # config changed616 if cfgchange:617 self.del_server(port, "config changed")618 new_servers[port] = (passwd, cfg)619 elif ServerPool.get_instance().server_run_status(port) is False:620 # new_servers[port] = passwd621 self.new_server(port, passwd, cfg)622 for row in last_rows:623 if row["port"] in cur_servers:624 pass625 else:626 self.del_server(row["port"], "port not exist")627 if len(new_servers) > 0:628 from shadowsocks import eventloop629 self.event.wait(630 eventloop.TIMEOUT_PRECISION + eventloop.TIMEOUT_PRECISION / 2631 )632 for port in new_servers.keys():633 passwd, cfg = new_servers[port]634 self.new_server(port, passwd, cfg)635 ServerPool.get_instance().push_uid_port_table(self.uid_port_table)636 def del_server(self, port, reason):637 logging.info(638 "db stop server at port [%s] reason: %s!" % (port, reason)639 )640 ServerPool.get_instance().cb_del_server(port)641 if port in self.last_update_transfer:642 del self.last_update_transfer[port]643 for mu_user_port in self.mu_port_list:644 if mu_user_port in ServerPool.get_instance().tcp_servers_pool:645 ServerPool.get_instance().tcp_servers_pool[646 mu_user_port647 ].reset_single_multi_user_traffic(self.port_uid_table[port])648 if mu_user_port in ServerPool.get_instance().tcp_ipv6_servers_pool:649 ServerPool.get_instance().tcp_ipv6_servers_pool[650 mu_user_port651 ].reset_single_multi_user_traffic(self.port_uid_table[port])652 if mu_user_port in ServerPool.get_instance().udp_servers_pool:653 ServerPool.get_instance().udp_servers_pool[654 mu_user_port655 ].reset_single_multi_user_traffic(self.port_uid_table[port])656 if mu_user_port in ServerPool.get_instance().udp_ipv6_servers_pool:657 ServerPool.get_instance().udp_ipv6_servers_pool[658 mu_user_port659 ].reset_single_multi_user_traffic(self.port_uid_table[port])660 def new_server(self, port, passwd, cfg):661 protocol = cfg.get(662 "protocol",663 ServerPool.get_instance().config.get("protocol", "origin"),664 )665 method = cfg.get(666 "method", ServerPool.get_instance().config.get("method", "None")667 )668 obfs = cfg.get(669 "obfs", ServerPool.get_instance().config.get("obfs", "plain")670 )671 logging.info(672 "db start server at port [%s] pass [%s] protocol [%s] method [%s] obfs [%s]"673 % (port, passwd, protocol, method, obfs)674 )675 ServerPool.get_instance().new_server(port, cfg)676 @staticmethod677 def del_servers():678 global db_instance679 for port in [680 v for v in ServerPool.get_instance().tcp_servers_pool.keys()681 ]:682 if ServerPool.get_instance().server_is_run(port) > 0:683 ServerPool.get_instance().cb_del_server(port)684 if port in db_instance.last_update_transfer:685 del db_instance.last_update_transfer[port]686 for port in [687 v for v in ServerPool.get_instance().tcp_ipv6_servers_pool.keys()688 ]:689 if ServerPool.get_instance().server_is_run(port) > 0:690 ServerPool.get_instance().cb_del_server(port)691 if port in db_instance.last_update_transfer:692 del db_instance.last_update_transfer[port]693 @staticmethod694 def thread_db(obj):695 import socket696 import webapi_utils697 global db_instance698 global webapi699 timeout = 60700 socket.setdefaulttimeout(timeout)701 last_rows = []702 db_instance = obj()703 webapi = webapi_utils.WebApi()704 shell.log_shadowsocks_version()705 try:706 import resource707 logging.info(708 "current process RLIMIT_NOFILE resource: soft %d hard %d"709 % resource.getrlimit(resource.RLIMIT_NOFILE)710 )711 except:712 pass713 try:714 while True:715 load_config()716 try:717 ping = webapi.getApi("func/ping")718 if ping is None:719 logging.error(720 "something wrong with your http api, please check your config and website status and try again later."721 )722 else:723 db_instance.push_db_all_user()724 rows = db_instance.pull_db_all_user()725 db_instance.del_server_out_of_bound_safe(726 last_rows, rows727 )728 last_rows = rows729 except Exception as e:730 trace = traceback.format_exc()731 logging.error(trace)732 # logging.warn('db thread except:%s' % e)733 if (734 db_instance.event.wait(60)735 or not db_instance.is_all_thread_alive()736 ):737 break738 if db_instance.has_stopped:739 break740 except KeyboardInterrupt as e:741 pass742 db_instance.del_servers()743 ServerPool.get_instance().stop()744 db_instance = None745 @staticmethod746 def thread_db_stop():747 global db_instance748 db_instance.has_stopped = True749 db_instance.event.set()750 def is_all_thread_alive(self):751 if not ServerPool.get_instance().thread.is_alive():752 return False...
MakeDatasetRbp.py
Source:MakeDatasetRbp.py
...35 def comparison_dataset(self):36 37 38 # Create Logger instance to see the start of comparison between two datasets 39 Logger.get_instance().info( " Start of comparison datasets:..." )40 41 42 # Definition of InfoDataset arguments43 44 self.dataset_input_path = PropertyManager.get_instance().get_property( DataConstants.DATASET_INPUT_PATH_PROPERTY, True)45 self.dataset_1_file = PropertyManager.get_instance().get_property( DataConstants.DATASET_1_FILE_PROPERTY, True)46 self.dataset_2_file = PropertyManager.get_instance().get_property( DataConstants.DATASET_2_FILE_PROPERTY, True)47 self.dataset_1_index_col = PropertyManager.get_instance().get_property( DataConstants.DATASET_1_INDEX_COL_PROPERTY, True)48 self.dataset_2_index_col = PropertyManager.get_instance().get_property( DataConstants.DATASET_2_INDEX_COL_PROPERTY, True)49 self.dataset_output = PropertyManager.get_instance().get_property( DataConstants.DATASET_OUTPUT_PROPERTY, True)50 self.dataset_1_length = PropertyManager.get_instance().get_property( DataConstants.DATASET_1_LENGTH_PROPERTY, True)51 self.dataset_2_length = PropertyManager.get_instance().get_property( DataConstants.DATASET_2_LENGTH_PROPERTY, True)52 53 self.index_col = (int(self.dataset_1_index_col) , int(self.dataset_2_index_col))54 self.dataset_length = (int(self.dataset_1_length), int(self.dataset_2_length))55 56 self.path_home = Constants.PATH_HOME57 InfoDataset.global_analysis_dataset(self.path_home + self.dataset_input_path, 58 (self.dataset_1_file,59 self.dataset_2_file) ,60 self.index_col,61 self.path_home + self.dataset_output,62 length=self.dataset_length)63 64 Logger.get_instance().info( " The comparison of datasets is completed : \65two file with the common and difference \66items has been generated in \n\n " + self.dataset_output )67 68 69 # creation_list70 # ----------------71 #72 # Creation of the gene and protein list of dataset 1 in order to pass it to Ensembl method 73 # 74 def creation_list(self):75 76 77 78 Logger.get_instance().info( " Creation of gene and protein list \n " )79 80 81 # Creation of two file containing respectively the genes and protein of dataset 182 83 self.dataset_input_path = PropertyManager.get_instance().get_property( DataConstants.DATASET_INPUT_PATH_PROPERTY, True)84 self.file_dataset_1 = PropertyManager.get_instance().get_property( DataConstants.DATASET_1_FILE_PROPERTY, True)85 self.gene_index_col = PropertyManager.get_instance().get_property( DataConstants.LIST_GENE_INDEX_COL_PROPERTY, True)86 self.protein_index_col = PropertyManager.get_instance().get_property( DataConstants.LIST_PROTEIN_INDEX_COL_PROPERTY, True)87 88 89 self.list_gene_dataset_1 = PropertyManager.get_instance().get_property( DataConstants.LIST_FILE_GENE_DATASET_1_PROPERTY, True)90 self.list_protein_dataset_1 = PropertyManager.get_instance().get_property( DataConstants.LIST_FILE_PROTEIN_DATASET_1_PROPERTY, True)91 92 self.path_gene_dataset_1 = Constants.PATH_HOME + self.dataset_input_path + self.list_gene_dataset_193 self.path_protein_dataset_1 = Constants.PATH_HOME + self.dataset_input_path + self.list_protein_dataset_194 95 self.path_home = Constants.PATH_HOME96 self.path_dataset_1 = self.path_home + self.dataset_input_path + self.file_dataset_197 98 dataset_1 = FileParser.make_table(self.path_dataset_1)99 100 gene_dataset_1 = TableWrapper.get_column(dataset_1, int(self.gene_index_col), start=1)101 protein_dataset_1 = TableWrapper.get_column(dataset_1, int(self.protein_index_col), start=1)102 103 FileWriter.write_table(self.path_gene_dataset_1, gene_dataset_1)104 FileWriter.write_table(self.path_protein_dataset_1, protein_dataset_1)105 106 107 Logger.get_instance().info( " The genes and proteins file of dataset 1 have been created \108in the following path \n\n " + self.dataset_input_path )109 110 111 # connection_to_ensembl112 # ----------------------113 # 114 # Section reserved to extraction of sequences from Ensembl database 115 # DATASET 1:116 # This dataset contains the gene and protein ids then you can download directly the protein sequence117 # 118 # DATASET 2:119 # For this dataset are download only the sequences for the gene that not are also in Dataset 1 120 # That is the Differ items obtained from comparison_dataset method121 #122 def connection_to_ensembl(self):123 124 Logger.get_instance().info( " Connection to Ensembl: Starting...\n" )125 126 # DATASET 1127 # =============================================128 129 # Collection of sequences for dataset 1 130 Logger.get_instance().info( " Dataset 1 : Extraction of sequences...\n" )131 132 # Timer step133 Timer.get_instance().step(" Start of sequences extraction \n")134 135 136 # Definition of Ensembl list_get_seq arguments 137 138 self.path_home = Constants.PATH_HOME139 self.list_path = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.DATASET_INPUT_PATH_PROPERTY, True)140 141 self.gene_list_1 = PropertyManager.get_instance().get_property( DataConstants.LIST_FILE_GENE_DATASET_1_PROPERTY, True)142 self.protein_list = PropertyManager.get_instance().get_property( DataConstants.LIST_FILE_PROTEIN_DATASET_1_PROPERTY, True)143 144 self.ensembl_gene_list_1_path = self.list_path + self.gene_list_1145 self.ensembl_protein_list_1_path = self.list_path + self.protein_list146 self.type_query1_ensembl = PropertyManager.get_instance().get_property( DataConstants.ENSEMBL_TYPE_QUERY_DATASET_1_PROPERTY, True)147 148 149 self.ensembl_path_output = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.ENSEMBL_OUTPUT_PATH_SEQUENCE_PROPERTY, True)150 self.ensembl_output_dataset1 = self.ensembl_path_output + PropertyManager.get_instance().get_property( DataConstants.ENSEMBL_FILE_SEQUENCES_1_PROPERTY)151 # Calling Ensembl.list_get_seq152 Ensembl.list_get_seq(self.ensembl_gene_list_1_path, int(self.type_query1_ensembl), path_protein_list=self.ensembl_protein_list_1_path, path_output=self.ensembl_output_dataset1)153 154 155 156 # Timer step157 Timer.get_instance().step(" End of Dataset 1 Sequences Extraction\n")158 159 Logger.get_instance().info( " Extraction of sequences for the dataset 1 has been completed \n\n" )160 161 162 # END DATASET 1163 # =====================================================164 165 166 167 168 169 # DATASET 2170 # =====================================================171 172 # Collection of sequences for dataset 2 173 Logger.get_instance().info( " Dataset 2 : Extraction of sequences ....\n" )174 175 176 177 # Definition of Ensembl list_get_seq arguments 178 179 180 self.ensembl_input_list_2 = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.DATASET_OUTPUT_PROPERTY, True)181 self.gene_list_2 = Constants.FILE_DIFF182 self.ensembl_gene_list_2_path = self.ensembl_input_list_2 + self.gene_list_2183 self.type_query2_ensembl = PropertyManager.get_instance().get_property( DataConstants.ENSEMBL_TYPE_QUERY_DATASET_2_PROPERTY, True)184 185 self.ensembl_path_output = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.ENSEMBL_OUTPUT_PATH_SEQUENCE_PROPERTY, True)186 self.ensembl_output_dataset2 = self.ensembl_path_output + PropertyManager.get_instance().get_property( DataConstants.ENSEMBL_FILE_SEQUENCES_2_PROPERTY, True)187 188 189 # Calling Ensembl.list_get_seq190 Ensembl.list_get_seq(self.ensembl_gene_list_2_path, int(self.type_query2_ensembl), path_protein_list=None, path_output = self.ensembl_output_dataset2)191 192 193 # Timer step194 Timer.get_instance().step(" End of Dataset 2 Sequences Extraction\n")195 196 Logger.get_instance().info( " Extraction of sequences for the dataset 2 has been completed \n\n" )197 198 # END DATASET 2199 # =====================================================200 201 202 203 Logger.get_instance().info( " The sequences file of dataset 1 and the novel gene in dataset 2 \204have been created in the following path \n" + self.ensembl_path_output)205 206 # dictionary_identifier207 # ----------------------208 # 209 # Creation of a dictionary: gene = [ isoform1, isoform2,...isoformN] 210 # This method is necessary to select the longest isoform for each gene 211 # 212 def dictionary_identifier(self):213 214 215 Logger.get_instance().info( " Creation of a dictionary for novel gene of dataset 2\216The dictionary structure is : \n \217{gene = [ isoform1, isoform2,...isoformN]}" )218 219 self.ensembl_path_output = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.ENSEMBL_OUTPUT_PATH_SEQUENCE_PROPERTY, True)220 self.ensembl_output_dataset2 = self.ensembl_path_output + PropertyManager.get_instance().get_property( DataConstants.ENSEMBL_FILE_SEQUENCES_2_PROPERTY, True)221 222 self.dictionary_output = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.DICTIONARY_PATH_OUTPUT_PROPERTY, True)223 self.dictionary_namefile = self.dictionary_output + PropertyManager.get_instance().get_property( DataConstants.DICTIONARY_NAME_FILE_PROPERTY, True) 224 225 dict_identifier = InfoFasta.make_dictionary(self.ensembl_output_dataset2)226 227 file_dict = FileUtils.open_text_w(self.dictionary_namefile)228 229 pickle.dump(dict_identifier, file_dict)230 231 232 Logger.get_instance().info( " The creation of a dictionary for novel gene in dataset 2 is completed \n\n")233 234 # longest_sequence235 # ----------------236 # 237 # this method find the longest isoform for each gene (see the principals of LengthSeq method)238 # 239 def longest_sequence(self):240 241 242 Logger.get_instance().info( " Start of the selection of longest sequences of novel dataset \n")243 244 245 246 # Definition of arguments247 self.path_sequences = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.LONGEST_PATH_SEQUENCE_PROPERTY, True)248 self.file_sequences = self.path_sequences + PropertyManager.get_instance().get_property( DataConstants.LONGEST_PROT_FILE_SEQUENCES_2_PROPERTY, True)249 self.path_dictionary_identifier = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.LONGEST_PATH_DICTIONARY_PROPERTY, True)250 self.file_dictionary = self.path_dictionary_identifier + PropertyManager.get_instance().get_property( DataConstants.LONGEST_DICTIONARY_NAME_FILE_PROPERTY, True)251 252 self.path_output_longest = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.LONGEST_PATH_OUTPUT_PROPERTY, True)253 254 self.path_file_longest = self.path_output_longest + PropertyManager.get_instance().get_property( DataConstants.LONGEST_FILE_PROPERTY, True)255 self.path_file_isoform = self.path_output_longest + PropertyManager.get_instance().get_property( DataConstants.ISOFORM_FILE_PROPERTY, True)256 257 258 # Extraction the longest sequences from dataset 2 sequences (isoforms) 259 LengthSeq.longest_seq(self.file_sequences, self.file_dictionary, self.path_file_longest, self.path_file_isoform)260 261 262 # Timer step263 Timer.get_instance().step(" End of selection of the longest sequences in dataset 2 \n")264 265 266 Logger.get_instance().info( " End of selection of the longest sequences: \n \267two file have been generated one with longest sequences and the other one containing the isoform with same length ")268 269 270 271 272 # isoform_sequences 273 # --------------------------274 #275 # like explained in LengthSeq method a file containing isoform with same length is created276 #277 # In this section occurs the Random Selection of isoforms sequences278 # 279 def isoform_sequences(self):280 281 282 Logger.get_instance().info( " Starting the random selection of isoforms with same length \n")283 Logger.get_instance().info( " The following headers are the proteins randomly selected \n")284 285 self.path_output_longest = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.LONGEST_PATH_OUTPUT_PROPERTY, True)286 287 288 self.path_file_isoform = self.path_output_longest + PropertyManager.get_instance().get_property( DataConstants.ISOFORM_FILE_PROPERTY, True)289 self.path_file_selected_isoform = self.path_output_longest + PropertyManager.get_instance().get_property( DataConstants.RANDOM_ISOFORM_SEQ_PROPERTY, True)290 291 # The headers of a Isoform fasta file are taken by InfoFasta class292 # You make sure that the arg text is equal to False because the input object is a file and not a list293 294 295 self.headers = InfoFasta.get_header(self.path_file_isoform, text=False)296 297 # Extraction of genes form headers line298 # This vector contains double gene because the file contains some isoform of the same gene299 300 gene_isoform = []301 for header in self.headers:302 gene = header[1:16]303 gene_isoform.append(gene)304 305 # gene set creation 306 unique_gene = set(gene_isoform)307 308 # This for loop flows on the unique gene 309 #310 random_header = []311 old_num_isoform = 0312 for gene in unique_gene:313 # For each gene counts how many isoform has 314 num_isoform = gene_isoform.count(gene)315 item = range(0,num_isoform)316 # Select one isoform randomly317 sel = random.choice(item)318 # The header selected randomly are stored in array319 random_header.append(self.headers[old_num_isoform : old_num_isoform + num_isoform][sel])320 old_num_isoform = old_num_isoform + num_isoform321 322 323 self.file_random_seq = FileUtils.open_text_a(self.path_file_selected_isoform)324 325 # The sequences corresponding to header selected are extracted from isoform file 326 327 for header in random_header:328 Logger.get_instance().info('Header selected : ' + header)329 identifier = header[33:48]330 sequence = InfoFasta.get_seq(self.path_file_isoform, identifier)331 fasta_seq = SeqToFasta.give_fasta(header, sequence)332 self.file_random_seq.write(fasta_seq)333 334 335 Logger.get_instance().info( " End of selection random sequences \n ")336 337 338 339 # merger_sequences340 # --------------------341 #342 # This method merges:343 # - the Longest sequences and the random isoform (dataset 2)344 # - FinalSeqDataset2 + SequencesDataset1345 # 346 # The output is the final fasta file of dataset that can be gived as input to DisorderAnalysis347 # 348 def merger_sequences(self):349 350 Logger.get_instance().info( " Union of the longest sequences and the random selected isoform ")351 352 # Input variables to merge the longest Novel sequences and random selected isoform of dataset 2353 354 self.path_input_longest = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.FUSION_PATH_INPUT_PROPERTY, True)355 self.path_file_longest = self.path_input_longest + PropertyManager.get_instance().get_property( DataConstants.LONGEST_FILE_PROPERTY, True)356 self.path_file_isoform = self.path_input_longest + PropertyManager.get_instance().get_property( DataConstants.SELECTED_ISOFORM_FILE_PROPERTY, True)357 358 self.path_output_seq = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.FUSION_PATH_OUTPUT_PROPERTY, True)359 self.path_file_seq_dataset_2 = self.path_output_seq + PropertyManager.get_instance().get_property( DataConstants.FUSION_FILE_SEQ_DATASET_2_PROPERTY, True)360 361 362 FileParser.merge_file(self.path_file_longest, self.path_file_isoform, self.path_file_seq_dataset_2)363 364 365 # Input variables to merge the sequences datasets (Novel_JProteomics and NatRevGenetics)366 367 self.path_input_seq_dataset1 = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.FUSION_PATH_INPUT_DATASET_1_PROPERTY, True)368 self.path_file_dataset1 = self.path_input_seq_dataset1 + PropertyManager.get_instance().get_property( DataConstants.FUSION_FILE_DATASET_1_PROPERTY, True)369 370 self.path_file_dataset12 = self.path_output_seq + PropertyManager.get_instance().get_property( DataConstants.FUSION_DATASET_12_PROPERTY, True)371 372 373 374 Logger.get_instance().info( " Union of sequences respectively of dataset 1 and the novel dataset 2 proteins \n ")375 376 FileParser.merge_file(self.path_file_dataset1, self.path_file_seq_dataset_2, self.path_file_dataset12)377 378 379 Logger.get_instance().info( " The New RBP Dataset has been created\n ")380 381 382 # This part checks if there are pseudo genes inside dataset 2383 # Make the comparison between the original genes gived as an input and the genes obtained after 384 # connection to Ensembl 385 # This check allows to find genes that are not anymore available or that are pseudogenes386 387 Logger.get_instance().info( " Comparison between original genes and Ensembl output ")388 self.path_home = Constants.PATH_HOME389 self.path_input_original_file = self.dataset_output = PropertyManager.get_instance().get_property( DataConstants.DATASET_OUTPUT_PROPERTY, True)390 self.original_file = self.path_home + self.path_input_original_file + Constants.FILE_DIFF391 392 original_genes = FileParser.read_file(self.original_file)393 394 395 self.path_output_seq = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.FUSION_PATH_OUTPUT_PROPERTY, True)396 self.path_file_seq_dataset_2 = self.path_output_seq + PropertyManager.get_instance().get_property( DataConstants.FUSION_FILE_SEQ_DATASET_2_PROPERTY, True)397 398 final_headers = InfoFasta.get_header(self.path_file_seq_dataset_2)399 final_genes = [item[1:16] for item in final_headers]400 401 out_comparison = InfoDataset.comparison_dataset(original_genes, final_genes, header=False)402 403 genes = '\n'.join(out_comparison[1])404 405 Logger.get_instance().info(" The genes lost during the request to Ensembl are : \n" + genes)406 407 408 409 410 411 412 # method that delete the append file in order to run again the whole workflow413 def delet_append_file(self):414 415 416 self.del_ensembl_input = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.DEL_ENSEMBL_PATH_PROPERTY, True)417 self.del_ensembl_file1 = self.del_ensembl_input + PropertyManager.get_instance().get_property( DataConstants.DEL_ENSEMBL_FILE1_PROPERTY, True)418 self.del_ensembl_file2 = self.del_ensembl_input + PropertyManager.get_instance().get_property( DataConstants.DEL_ENSEMBL_FILE2_PROPERTY, True)419 420 self.del_longest_input = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.DEL_LONGEST_PATH_PROPERTY, True)421 self.del_longest_file = self.del_longest_input + PropertyManager.get_instance().get_property( DataConstants.DEL_LONGEST_FILE_PROPERTY, True)422 self.del_isoform_file = self.del_longest_input + PropertyManager.get_instance().get_property( DataConstants.DEL_ISOFORM_FILE_PROPERTY, True)423 self.del_random_isoform_file = self.del_longest_input + PropertyManager.get_instance().get_property( DataConstants.DEL_RANDOM_ISOFORM_FILE_PROPERTY, True)424 425 self.del_fusion_path = Constants.PATH_HOME + PropertyManager.get_instance().get_property( DataConstants.DEL_FUSION_PATH_PROPERTY, True)426 self.del_fusion_file_longest = self.del_fusion_path + PropertyManager.get_instance().get_property( DataConstants.DEL_FUSION_DATASET_LONGEST_PROPERTY, True)427 self.del_fusion_file_dataset12 = self.del_fusion_path + PropertyManager.get_instance().get_property( DataConstants.DEL_FUSION_DATASET12_PROPERTY, True)428 429 files = [self.del_ensembl_file1, 430 self.del_ensembl_file2,431 self.del_longest_file,432 self.del_isoform_file,433 self.del_random_isoform_file,434 self.del_fusion_file_longest,435 self.del_fusion_file_dataset12]436 437 for namefile in files:438 RemoveFile.delete_file(namefile)439 440 441 442 # whole_procedure443 # ----------------444 # 445 # This method allows to select just some of previously methods446 #447 448 @staticmethod449 def whole_procedure():450 451 452 # start chrono453 Timer.get_instance().start_chrono()454 Logger.get_instance().info("Start of the creation of RBP dataset.....\n ")455 456 M = MakeDatasetRbp()457 458 #M.delet_append_file()459 460 #M.comparison_dataset()461 #M.creation_list()462 #M.connection_to_ensembl()463 #M.dictionary_identifier()464 #M.longest_sequence()465 #M.isoform_sequences()466 #M.merger_sequences()467 M.split_dataset()468 469 Timer.get_instance().stop_chrono(' End of the creation of RBP dataset')470 471 472 473if __name__ == '__main__':474 475 OptionManager.get_instance().initialize()476 477 # Retrieve the MakeDatasetRbp properties478 PropertyManager.get_instance().read_properties( OptionManager.get_instance().get_option( OptionConstants.OPTION_MAKEDATASETRBP_PROPERTIES_PATH, True))479 480 MakeDatasetRbp.whole_procedure()481 482 483 484 485 486 487 488 489 490 491 492 ...
MotifsAnalysis.py
Source:MotifsAnalysis.py
...19 20 def __init__(self):21 22 self.path_home = Constants.PATH_HOME23 self.protein_list_file = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_PROTEIN_FILE_PROPERTY, True)24 self.protein_list = FileParser.read_file(self.protein_list_file)25 self.motif_folder = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_FOLDER_PROPERTY, True)26 self.domain_region_file = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_DOMAIN_REGION_FILE_PROPERTY, True)27 28 # iupred_motifs29 # ----------------------------30 #31 # This method calls the GlobalOverlapRegionAnalysis for iupred tool 32 #33 # Output: 34 # - The result of motifs overlap analysis will be saved in some files in output folder 35 #36 def iupred_motifs(self):37 38 Logger.get_instance().info( " .....Start of IUPred motifs analysis.....\n")39 40 self.iupred_folder = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_IUPRED_FOLDER_PROPERTY,True)41 42 # Iupred Analysis at threshold value of 0.443 44 Timer.get_instance().step(" Start of IUPred motifs analysis - threshold = 0.4 \n")45 46 self.threshold_1 = Constants.MOTIFS_THRESHOLD_147 self.output_folder_1 = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_IUP_OUTPUT_FOLDER_1_PROPERTY, True)48 49 GlobalOverlapRegionAnalysis.iupred_overlap_analysis(self.protein_list,self.iupred_folder, self.output_folder_1, self.threshold_1,50 self.motif_folder,self.domain_region_file)51 52 Timer.get_instance().step(" End of IUPred motifs analysis - threshold = 0.4 \n")53 54 55 # Iupred Analysis at threshold value of 0.556 57 Timer.get_instance().step(" Start of IUPred motifs analysis - threshold = 0.5 \n")58 self.threshold_2 = Constants.MOTIFS_THRESHOLD_259 self.output_folder_2 = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_IUP_OUTPUT_FOLDER_2_PROPERTY, True)60 61 GlobalOverlapRegionAnalysis.iupred_overlap_analysis(self.protein_list,self.iupred_folder, self.output_folder_2, self.threshold_2,62 self.motif_folder,self.domain_region_file)63 64 Timer.get_instance().step(" End of IUPred motifs analysis - threshold = 0.5 \n")65 66 Logger.get_instance().info( " .....End of IUPred motifs analysis.....\n")67 68 69 # anchor_motifs70 # ----------------------------71 #72 # This method calls the GlobalOverlapRegionAnalysis for anchor tool 73 #74 # Output: 75 # - The result of motifs overlap analysis will be saved in some files in output folder 76 # 77 def anchor_motifs(self):78 79 Logger.get_instance().info( " .....Start of IUPred motifs analysis.....\n")80 81 self.anchor_folder = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_ANCHOR_FOLDER_PROPERTY, True)82 self.anchor_output_folder = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_ANCHOR_OUTPUT_FOLDER_PROPERTY, True)83 84 Timer.get_instance().step(" Start of ANCHOR motifs analysis \n")85 86 GlobalOverlapRegionAnalysis.anchor_overlap_analysis(self.protein_list,self.anchor_folder,self.anchor_output_folder,87 self.motif_folder,self.domain_region_file)88 89 90 Timer.get_instance().step(" End of IUPred motifs analysis \n")91 92 Logger.get_instance().info( " .....End of ANCHOR motifs analysis.....\n")93 94 95 # disordp_motifs96 # ----------------------------97 #98 # This method calls the GlobalOverlapRegionAnalysis for disordpbind tool 99 #100 # Output: 101 # - The result of motifs overlap analysis will be saved in some files in output folder 102 103 def disordp_motifs(self):104 105 Logger.get_instance().info( " .....Start of DisoRDPbind motifs analysis.....\n")106 107 self.disordp_folder = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_DISORDP_FOLDER_PROPERTY, True)108 self.disordp_output_folder = self.path_home + PropertyManager.get_instance().get_property( DataConstants.MOTIFS_DISORDP_OUTPUT_FOLDER_PROPERTY, True)109 self.filename = PropertyManager.get_instance().get_property( DataConstants.MOTIFS_DISORDP_FILE_PROPERTY,True)110 111 Timer.get_instance().step(" Start of DisoRDPbind motifs analysis \n")112 113 GlobalOverlapRegionAnalysis.disordp_overlap_analysis(self.protein_list, self.disordp_folder, self.filename, self.motif_folder,114 self.domain_region_file,self.disordp_output_folder)115 116 117 118 Timer.get_instance().step(" End of DisoRDPbind motifs analysis \n")119 Logger.get_instance().info( " .....End of DisoRDPbind motifs analysis.....\n")120 121 122 # whole_procedure123 # ----------------124 # 125 # This method allows to select just some of previously methods126 #127 @staticmethod128 def whole_procedure():129 130 dataset_type = PropertyManager.get_instance().get_property( DataConstants.MOTIFS_DATASET_TYPE_PROPERTY, True)131 132 # start chrono133 Timer.get_instance().start_chrono()134 Logger.get_instance().info(" ........Start of " + dataset_type + " Motifs Analysis.....\n ")135 136 motifs = MotifsAnalysis()137 motifs.iupred_motifs()138 motifs.anchor_motifs()139 motifs.disordp_motifs()140 141 Timer.get_instance().stop_chrono(" End of " + dataset_type + " Motifs Analysis")142if __name__ == '__main__':143 144 OptionManager.get_instance().initialize()145 146 # Set the level of verbosity147 Logger.get_instance().set_level( OptionManager.get_instance().get_option( OptionConstants.OPTION_VERBOSITY))148 PropertyManager.get_instance().read_properties( OptionManager.get_instance().get_option( OptionConstants.OPTION_MOTIFS_ANALYSIS_PROPERTY_PATH, True))149 150 MotifsAnalysis.whole_procedure()...
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