Opened 4 years ago

Closed 4 years ago

#5186 closed defect (fixed)

UniProt ID arg: can't hand empty text to next_token()

Reported by: jonathan.sheehan@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.3.dev202108260719 (2021-08-26 07:19:00 UTC)
Description
I clicked on "predict" in the Alphafold tool.

Log:
UCSF ChimeraX version: 1.3.dev202108260719 (2021-08-26)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 181, in _predict  
self._run_command('predict')  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 204, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2812, in run  
prev_annos = self._process_positional_arguments()  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2588, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2447, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\atomic\args.py", line 161, in parse  
value, used, rest = SequencesArg.parse(text, session)  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\atomic\args.py", line 141, in parse  
elif is_uniprot_id(text):  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\atomic\args.py", line 179, in is_uniprot_id  
id, text, rest = next_token(text)  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1774, in next_token  
assert text and not text[0].isspace()  
AssertionError  
  
AssertionError  
  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1774, in next_token  
assert text and not text[0].isspace()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 24.20.100.6286
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude 7490
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 34,233,217,024
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Cc: Greg Couch added
Component: Unassigned → Sequence
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → UniProt ID arg: can't hand empty text to next_token()

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Pressed AlphaFold panel Predict button without providing a UniProt id. This gave a traceback. Now it gives a simple message that you didn't specify the sequence.

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