AlphaFold unzipping of results: expected str, bytes or os.PathLike object, not NoneType

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3.dev202109170828 (2021-09-17 08:28:14 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7639 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.3.dev202109170828 (2021-09-17)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/there/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show AlphaFold

> alphafold predict #1

[Repeated 1 time(s)]Running AlphaFold prediction  
[Repeated 1 time(s)]

> alphafold predict
> MAPPAAAPELGSCCICLDAITGAARALPCLHAFCLACIRRWLEGRPTCPLCKAPVQSLIHSVASDECFEEIPVGGGPGADGALEPDAAVIWGEDYDAGPIDLTAADGEASGAGGEAGAADGSEAGGGAGGAEEAGEARGAGAGRAAGAAGGRAGRGADAAQEFIDRVARGPRLPLLPNTPEHGPGAPYLRRVVEWVEGALVGSFAVTARELAAMTDYVMAMLAECGFDDDGLADAMEPLIGEDDAPAFVRSLLFVAARCVTVGPSHLIPQQSAPPGGRGVVFLDTSDSDSEGSEDDSWSESEESSSGLSTSDLTAIDDTETEPETDAEVESRRTRGASGAARARRPAERQYVSTRGRQTPAVQPAPRSLARRPCGRAAAVSAPPSSRSRGGRRDPRLPAAPRAAPAAQARACSPEPREEGRGAGLGVAAGETAGWGAGSEEGRGERRARLLGEAGPPRVQARRRRRTELDRAPTPAPAPAPAPAPISTVIDLTANAPARPADPAPAAAPGPASAGAQIGTPAAAAAVTAAAAAPSVARSSAPSPAVTAAATSTAAAISTRAPTPSPAGRAPAADPRRAGAPALAGAARAEVGRNGNPGRERRPASAMARGDLDPGPESSVAAWVRESLLGTPRRSSAALAPQPGGRQGPSLAGLLGRCSGGSAWRQ

[Repeated 1 time(s)]Running AlphaFold prediction  
[Repeated 1 time(s)] Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in C:\Users\there/Downloads\ChimeraX\AlphaFold\prediction_7  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\alphafold\predict.py", line 159, in _unzip_results  
path = join(self._download_directory, 'results.zip')  
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\ntpath.py", line
78, in join  
path = os.fspath(path)  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\ntpath.py", line
78, in join  
path = os.fspath(path)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.7639
OpenGL renderer: Intel(R) Iris(R) Plus Graphics 640
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Laptop
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 8,503,017,472
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-7660U CPU @ 2.50GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
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[Tom Goddard]

Appears the user clicked the AlphaFold tool predict button twice for model #1 and twice for a specified sequence.

The AlphaFold tool has a "running" flag it checks and is supposed to give an error starting a second run when one is already running. But the code never sets running = True, so it simply tries to run the next job. Not clear what that does, but it looks like it would simply replace the current run since we use just one Colab browser instance. This behavior might be better than if the running flag worked, because the running flag would prevent canceling the current job and replacing it.

If only the most recent run proceeds then I don't see how the reported error happened. The reported error is because the download directory where results.zip was downloaded was not not set. The only way the unzip routine can be called is if the download directory is set. So it was set. But after an unzip the download directory is set to None so the next run uses a new directory. So it looks like two unzip calls were made with the first setting download directory to None and the second then giving this error.

To get the unzip method called twice there need to be two download requests of results.zip both made before either download finishes. Maybe the run completed and the download request was made and the user then clicked the play button on the Colab window which quickly made another download request before the first one was complete. I think that would generate this error, but the timing would be hard to achieve since the results.zip download should be pretty fast.

[Tom Goddard]

Maybe a double-click on the AlphaFold tool button does queue up two runs and the second is very quick since all the files are already cached and so two results.zip downloads happen before either completes. I am testing this now.

[Tom Goddard]

Looks like I really should have a way to quit the current prediction and start a new one. Currently even if it does start the second job, I think it will use the cached files from the first job which is for a different sequence!

[Tom Goddard]

Current colab script checks if sequence has changed and moves the results directory and starts over. So running a second prediction should correctly recompute with the new sequence.

[Tom Goddard]

The log shows "Results in C:\Users\there/Downloads\ChimeraX\AlphaFold\prediction_7" so the results were downloaded once and download directory set to None and then the second results.zip download happened giving the error.

[Tom Goddard]

Double clicking the predict button did not cause an error when results were downloaded. Pressing the predict button again after completed also did not cause any error. So it seems it required precise timing to get two results.zip downloads going at once. I can simply not unzip the results if the download directory is not set, suppressing this error. Or I can leave it as is -- I don't think it is likely to be seen again. Suppressing will also not show the best fit for that second try. I think it is better leave the error.

Maybe the download directory should not be cleared until a new run is started. Seems not great since the user can press the colab play button and cause a second results download which will then go to the same directory and get a different file suffix.

Another approach is to pass the downloads directory into the unzip routine instead of using an instance attribute. I didn't do this before because multiple downloads go to the directory, the best model pdb and results.zip, but I since eliminated the pdb since it is in results.zip. But in the future we may also want multiple downloads.

[Tom Goddard]

If you manage to get two downloads of results.zip the second will have an altered file name. So I think it is probably reasonable to not try to unzip it, the first copy was already unzipped. So I guess it is ok to put in the check for download directory = None and ignore that zip file.

[Tom Goddard]

Fixed.

In case user manages to start two results.zip downloads before one completes I put in code to only unzip the first and avoid the reported error.