Kivy: debug, understand adblog| adb log© Malik Brahimi
 0 Posted Updated Python / Kivy13 minutes read (About 1900 words)

Kivy: debug, understand adblog| adb log

Adblog cat

A standard adblog catout is adb logcat. But I do not suggest you do this since there is too much unrelated information

If you have are familiar with adb, you may add a filter-args like adb logcat *:W. But this is not the case for Kivy because most of the information is in *:I level.

As a result, pipeline adblog with grep is the best choice which could solve most of your problem. Here is my advice:

# it could cover 99% cases
adb logcat| grep -i python

# it could help you access a more elegant result which cover the most of errors.
adb logcat| grep -w "I python"

adb logcat| grep -i python could access all information containing python.
grep -w "I python" should more focus on the running log of python-android.

Python for Android Ended

This piece of information always one line a heading before the code Python for android ended. So, you can find it very easily with:

adb logcat| grep -B 1 -w "Python for android ended"

ModuleNotFoundError

  04-27 23:19:06.229 25804 25854 I python  : [INFO   ] [Logger      ] Record log in /data/user/0/org.sirfanas.filechooser.filechooser/files/app/.kivy/logs/kivy_21-04-27_3.txt
  04-27 23:19:06.229 25804 25854 I python  : [INFO   ] [Kivy        ] v1.11.1
  04-27 23:19:06.229 25804 25854 I python  : [INFO   ] [Kivy        ] Installed at "/data/user/0/org.sirfanas.filechooser.filechooser/files/app/_python_bundle/site-packages/kivy/__init__.pyc"
  04-27 23:19:06.229 25804 25854 I python  : [INFO   ] [Python      ] v3.7.5 (default, Apr 21 2021, 11:10:26)
  04-27 23:19:06.229 25804 25854 I python  : [Clang 8.0.2 (https://android.googlesource.com/toolchain/clang 40173bab62ec7462
  04-27 23:19:06.229 25804 25854 I python  : [INFO   ] [Python      ] Interpreter at "android_python"
  04-27 23:19:06.287  2208  2469 I WindowManager: Removing Window{8e822e1 u0 Splash Screen org.sirfanas.filechooser.filechooser} from AppWindowToken{8ef4121 token=Token{7fb7980 ActivityRecord{8ef4191 u0 org.sirfanas.filechooser.filechooser/org.kivy.android.PythonActivity t13316}}}
  04-27 23:19:06.390  2208  4223 I WindowManager: Animation done in AppWindowToken{8ef4121 token=Token{7fb7980 ActivityRecord{8ef4191 u0 org.sirfanas.filechooser.filechooser/org.kivy.android.PythonActivity t13316}}} isHidden:false hiddenRequested:false
  04-27 23:19:06.587 25804 25854 I python  : [INFO   ] [Factory     ] 184 symbols loaded
  04-27 23:19:06.730 25804 25854 I python  : [INFO   ] [Image       ] Providers: img_tex, img_dds, img_sdl2, img_pil, img_gif (img_ffpyplayer ignored)
  04-27 23:19:06.745 25804 25854 I python  : [INFO   ] [Text        ] Provider: sdl2
  04-27 23:19:06.761 25804 25854 I python  : [INFO   ] [Window      ] Provider: sdl2
  04-27 23:19:06.776 25804 25854 I python  : [INFO   ] [GL          ] Using the "OpenGL ES 2" graphics system
  04-27 23:19:06.777 25804 25854 I python  : [INFO   ] [GL          ] Backend used 
  04-27 23:19:06.777 25804 25854 I python  : [INFO   ] [GL          ] OpenGL version 
  04-27 23:19:06.777 25804 25854 I python  : [INFO   ] [GL          ] OpenGL vendor 
  04-27 23:19:06.777 25804 25854 I python  : [INFO   ] [GL          ] OpenGL renderer 
  04-27 23:19:06.777 25804 25854 I python  : [INFO   ] [GL          ] OpenGL parsed version: 3, 2
  04-27 23:19:06.777 25804 25854 I python  : [INFO   ] [GL          ] Texture max size <8192>
  04-27 23:19:06.777 25804 25854 I python  : [INFO   ] [GL          ] Texture max units <16>
  04-27 23:19:06.780  2208  4460 I DebugKeepScreenOn: Acquiring screen wakelock due to Window{888d929 u0 org.sirfanas.filechooser.filechooser/org.kivy.android.PythonActivity}
  04-27 23:19:06.787 25804 25854 I python  : [INFO   ] [Window      ] auto add sdl2 input provider
  04-27 23:19:06.788 25804 25854 I python  : [INFO   ] [Window      ] virtual keyboard not allowed, single mode, not docked
  04-27 23:19:06.848 25804 25854 I python  : [INFO   ] [Video       ] Provider: null(['video_ffmpeg', 'video_ffpyplayer'] ignored)
  04-27 23:19:06.849 25804 25854 I python  :  Traceback (most recent call last):
  04-27 23:19:06.849 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/app/main.py", line 64, in 
  04-27 23:19:06.849 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/app.py", line 828, in run
  04-27 23:19:06.849 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/app.py", line 599, in load_kv
  04-27 23:19:06.849 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/lang/builder.py", line 301, in load_file
  04-27 23:19:06.849 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/lang/builder.py", line 405, in load_string
  04-27 23:19:06.850 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/lang/builder.py", line 659, in _apply_rule
  04-27 23:19:06.850 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/lang/builder.py", line 659, in _apply_rule
  04-27 23:19:06.850 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/lang/builder.py", line 616, in _apply_rule
  04-27 23:19:06.850 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/factory.py", line 142, in __getattr__
  04-27 23:19:06.850 25804 25854 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/uix/rst.py", line 81, in 
  04-27 23:19:06.850 25804 25854 I python  :    ModuleNotFoundError: No module named 'docutils'
  04-27 23:19:06.850 25804 25854 I python  : Python for android ended.
  04-27 23:19:06.943  2208  2664 W InputDispatcher: channel '888d929 org.sirfanas.filechooser.filechooser/org.kivy.android.PythonActivity (server)' ~ Consumer closed input channel or an error occurred.  events=0x9
  04-27 23:19:06.943  2208  2664 E InputDispatcher: channel '888d929 org.sirfanas.filechooser.filechooser/org.kivy.android.PythonActivity (server)' ~ Channel is unrecoverably broken and will be disposed!

What you want to know is this: ModuleNotFoundError: No module named 'docutils'

As it’s who below, we can get the info by:

AttributeError

  04-30 16:22:14.236  6326  6417 I python  : [INFO   ] [Base        ] Start application main loop
  04-30 16:22:14.236  6326  6417 I python  : [INFO   ] [Base        ] Leaving application in progress...
  04-30 16:22:14.237  6326  6417 I python  :  Traceback (most recent call last):
  04-30 16:22:14.237  6326  6417 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/app/main.py", line 111, in 
  04-30 16:22:14.237  6326  6417 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/app.py", line 855, in run
  04-30 16:22:14.237  6326  6417 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/base.py", line 504, in runTouchApp
  04-30 16:22:14.237  6326  6417 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/core/window/window_sdl2.py", line 747, in mainloop
  04-30 16:22:14.237  6326  6417 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/core/window/window_sdl2.py", line 479, in _mainloop
  04-30 16:22:14.237  6326  6417 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/base.py", line 339, in idle
  04-30 16:22:14.238  6326  6417 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/clock.py", line 591, in tick
  04-30 16:22:14.238  6326  6417 I python  :    File "kivy/_clock.pyx", line 384, in kivy._clock.CyClockBase._process_events
  04-30 16:22:14.238  6326  6417 I python  :    File "kivy/_clock.pyx", line 414, in kivy._clock.CyClockBase._process_events
  04-30 16:22:14.238  6326  6417 I python  :    File "kivy/_clock.pyx", line 412, in kivy._clock.CyClockBase._process_events
  04-30 16:22:14.238  6326  6417 I python  :    File "kivy/_clock.pyx", line 154, in kivy._clock.ClockEvent.tick
  04-30 16:22:14.238  6326  6417 I python  :    File "kivy/_clock.pyx", line 88, in kivy._clock.ClockEvent.get_callback
  04-30 16:22:14.239  6326  6417 I python  :    File "/media/ken/Data/Kivy/.buildozer/android/platform/build-armeabi-v7a/build/python-installs/filechooser/kivy/weakmethod.py", line 47, in __call__
  04-30 16:22:14.239  6326  6417 I python  :  AttributeError: 'WebviewLauncher' object has no attribute 'f2'
  04-30 16:22:14.239  6326  6417 I python  : Python for android ended.

Check the class WebviewLauncher and figure out what is f2 in it.

Buildozer Error

  Non-user install due to --prefix or --target option
  Created temporary directory: /tmp/pip-target-nnpo4wye
  Created temporary directory: /tmp/pip-ephem-wheel-cache-hjzhdyqg
  Created temporary directory: /tmp/pip-req-tracker-nryx6lee
  Initialized build tracking at /tmp/pip-req-tracker-nryx6lee
  Created build tracker: /tmp/pip-req-tracker-nryx6lee
  Entered build tracker: /tmp/pip-req-tracker-nryx6lee
  Created temporary directory: /tmp/pip-install-xivbs0bw
  Collecting https://github.com/kivymd/kivymd/archive/master.zip (from -r requirements.txt (line 1))
    Created temporary directory: /tmp/pip-req-build-6lx7kxss
    Created temporary directory: /tmp/pip-unpack-cr7m7azt
    Looking up "https://github.com/kivymd/kivymd/archive/master.zip" in the cache
    No cache entry available
    Starting new HTTPS connection (1): github.com:443
    Incremented Retry for (url='/kivymd/kivymd/archive/master.zip'): Retry(total=4, connect=None, read=None, redirect=None, status=None)
    WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='github.com', port=443): Read timed out. (read timeout=15)")': /kivymd/kivymd/archive/master.zip
    Starting new HTTPS connection (2): github.com:443
    Incremented Retry for (url='/kivymd/kivymd/archive/master.zip'): Retry(total=3, connect=None, read=None, redirect=None, status=None)
    WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to github.com timed out. (connect timeout=15)')': /kivymd/kivymd/archive/master.zip
    Starting new HTTPS connection (3): github.com:443
    Incremented Retry for (url='/kivymd/kivymd/archive/master.zip'): Retry(total=2, connect=None, read=None, redirect=None, status=None)
    WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to github.com timed out. (connect timeout=15)')': /kivymd/kivymd/archive/master.zip
    Starting new HTTPS connection (4): github.com:443
    Incremented Retry for (url='/kivymd/kivymd/archive/master.zip'): Retry(total=1, connect=None, read=None, redirect=None, status=None)
    WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /kivymd/kivymd/archive/master.zip
    Starting new HTTPS connection (5): github.com:443
    Incremented Retry for (url='/kivymd/kivymd/archive/master.zip'): Retry(total=0, connect=None, read=None, redirect=None, status=None)
    WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to github.com timed out. (connect timeout=15)')': /kivymd/kivymd/archive/master.zip
    Starting new HTTPS connection (6): github.com:443
  ERROR: Could not install packages due to an OSError.
  Traceback (most recent call last):
    File "/media/ken/Data/Kivy_env/Kivy2Py3.8.1MD0.104.2.dev0/.buildozer/android/platform/build-armeabi-v7a/build/venv/lib/python3.8/site-packages/pip/_vendor/urllib3/connection.py", line 169, in _new_conn
      conn = connection.create_connection(
    File "/media/ken/Data/Kivy_env/Kivy2Py3.8.1MD0.104.2.dev0/.buildozer/android/platform/build-armeabi-v7a/build/venv/lib/python3.8/site-packages/pip/_vendor/urllib3/util/connection.py", line 96, in create_connection
      raise err
    File "/media/ken/Data/Kivy_env/Kivy2Py3.8.1MD0.104.2.dev0/.buildozer/android/platform/build-armeabi-v7a/build/venv/lib/python3.8/site-packages/pip/_vendor/urllib3/util/connection.py", line 86, in create_connection
      sock.connect(sa)
  socket.timeout: timed out

  During handling of the above exception, another exception occurred:

Key error: Starting new HTTPS connection (5): github.com:443
Reason: Github didn’t response.
Resolution: Try builder again or connect your terminal to VPN.

Errors

requests
Found by adb logcat| grep -i python
Resolution:

buildozer.spec
requirements =  openssl, requests, Urllib3, chardet, certifi, idna
  05-09 19:24:20.139 23571 23629 I python  :    File "kivy/_event.pyx", line 709, in kivy._event.EventDispatcher.dispatch
  05-09 19:24:20.140 23571 23629 I python  :    File "/media/ken/Data/Kivy_env/Kivy2Py3.8.1MD0.104.2.dev0/.buildozer/android/app/libWidget/Seq.py", line 25, in align
  05-09 19:24:20.141 23571 23629 I python  :    File "/media/ken/Data/Kivy_env/Kivy2Py3.8.1MD0.104.2.dev0/.buildozer/android/app/bin/clustalo.py", line 35, in 
  05-09 19:24:20.141 23571 23629 I python  :  ModuleNotFoundError: No module named 'requests'
  05-09 19:24:20.141 23571 23629 I python  : Python for android ended.

def fasta_read(FA):
fasta = {}
with open("clusttmp/result.aln-fasta.fasta") as file_one:
    for line in file_one:
        line = line.strip()
        if not line:
            continue
        if line.startswith(">"):
            print(line)
            active_sequence_name = line[1:]
            if active_sequence_name not in fasta:
                fasta[active_sequence_name] = []
            continue
        sequence = line
        fasta[active_sequence_name].append(sequence)

print(fasta)
      return fasta

from collections import defaultdict #this will make your life simpler
f = open("clusttmp/result.aln-fasta.fasta",'r')
list=defaultdict(str)
name = ''
for line in f:
    #if your line starts with a > then it is the name of the following sequence
    if line.startswith('>'):
        name = line[1:-1]
        continue #this means skips to the next line
    #This code is only executed if it is a sequence of bases and not a name.
    list[name]+=line.strip()


d = {}

with open("clusttmp/result.aln-fasta.fasta") as f:
    for line in f:
        if len(line) > 1:
            if '%Labelinf' in line:
                key = line.strip()
                d[key] = ""
            else:
                d[key] += line.strip() + "+"

d = {key: d[key][:-1] for key in d}
print d

Kivy: debug, understand adblog| adb log

https://karobben.github.io/2021/04/30/Python/kivy_adblog/

Author

Karobben

Posted on

2021-04-30

Updated on

2023-06-06

Licensed under

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