String decoding of BLAST results no longer necessary

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-10)
Description
blast protein AttributeError: 'str' object has no attribute 'decode'

open 1www
blastprotein /V database pdb cutoff 1e-3 matrix BLOSUM62 max_hits 100 tool_id 7

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> open presets.cxc

> alias cardef car style modeh def arrows t arrowshelix f arrowscale 2 wid 2
thick 0.4 sides 12 div 20; car style ~(nucleic|strand) x round; car style
(nucleic|strand) x rect

> alias nospheres style (protein|nucleic|solvent) & @@draw_mode=0 stick

> alias nucrib cardef; car style nucleic x round width 1.6 thick 1.6

> alias cylinders cardef; car style protein modeh tube rad 2 sides 24 thick
0.6

> alias licorice cardef; car style protein modeh default arrows f x round
width 1 thick 1

> alias cartoon1 surf hide; nospheres; cartoon; cardef; nuc tube/slab shape
box

> alias cartoon2 surf hide; nospheres; cartoon; cylinders; car style nucleic x
round width 1.6 thick 1.6; nuc stubs

> alias cartoon3 surf hide; nospheres; cartoon; licorice; car style nucleic x
round width 1.6 thick 1.6; nuc tube/slab shape ellipsoid

> alias surfw nospheres; surface; color white targ s trans 80

> alias surfat nospheres; surface; color fromatoms targ s trans 70

> alias surfc nospheres; surface; color bychain targ s trans 0

> alias surfm nospheres; surface; color bymodel targ s trans 0

> alias pub set bgcolor white silhouettes t

> alias unpub ~set bgcolor; set silhouettes f

executed presets.cxc  
executed startup.cxc  
UCSF ChimeraX version: 0.9 (2019-04-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1www format mmCIF fromDatabase pdb

1www title:  
NGF In complex with domain 5 of the TRKA receptor [more info...]  
  
Chain information for 1www #1  
---  
Chain | Description  
V W | protein (nerve growth factor)  
X Y | protein (TRKA receptor)  
  
  

> toolshed show '"Blast Protein"'

> blastprotein /V database pdb cutoff 1e-3 matrix BLOSUM62 max_hits 100
tool_id 7

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1555365801200572598610  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1555365801200572598610  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 536, in customEvent  
func(*args, **kw)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 81, in on_finish  
results = self.get_file(self.RESULTS_FILENAME).decode("utf-8")  
AttributeError: 'str' object has no attribute 'decode'  
  
AttributeError: 'str' object has no attribute 'decode'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 81, in on_finish  
results = self.get_file(self.RESULTS_FILENAME).decode("utf-8")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

Conrad fixed this yesterday