Opened 5 years ago

Last modified 5 years ago

#4023 accepted enhancement

Better error handling on web service failure

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Web Services Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-126-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/ly/maps_hfn180/hfn180ice_11k_refined_model.pdb

Chain information for hfn180ice_11k_refined_model.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | No description available  
  

> open /home/ly/maps_hfn180/hfn180N_11k_refined_model.pdb

Chain information for hfn180N_11k_refined_model.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | No description available  
  

> open /home/ly/maps_hfn180/hfn180normal_11k_refined_model.pdb

Chain information for hfn180normal_11k_refined_model.pdb #3  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | No description available  
  

> open /home/ly/maps_hfn180/hfn180normal_27_refined.pdb

Chain information for hfn180normal_27_refined.pdb #4  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | No description available  
  

> hide cartoons

> show atoms

> style stick

Changed 132864 atom styles  

> style ball

Changed 132864 atom styles  

> mlp

Map values for surface "hfn180ice_11k_refined_model.pdb_U SES surface":
minimum -27.19, mean -4.301, maximum 21.62  
Map values for surface "hfn180ice_11k_refined_model.pdb_A SES surface":
minimum -27.88, mean -4.264, maximum 21.78  
Map values for surface "hfn180ice_11k_refined_model.pdb_B SES surface":
minimum -27.9, mean -4.311, maximum 21.32  
Map values for surface "hfn180ice_11k_refined_model.pdb_C SES surface":
minimum -25.93, mean -4.293, maximum 21.55  
Map values for surface "hfn180ice_11k_refined_model.pdb_D SES surface":
minimum -26.35, mean -4.285, maximum 21.29  
Map values for surface "hfn180ice_11k_refined_model.pdb_E SES surface":
minimum -25.22, mean -4.299, maximum 21.49  
Map values for surface "hfn180ice_11k_refined_model.pdb_F SES surface":
minimum -26.28, mean -4.281, maximum 21.32  
Map values for surface "hfn180ice_11k_refined_model.pdb_G SES surface":
minimum -27.99, mean -4.321, maximum 21.93  
Map values for surface "hfn180ice_11k_refined_model.pdb_H SES surface":
minimum -28.26, mean -4.308, maximum 21.95  
Map values for surface "hfn180ice_11k_refined_model.pdb_I SES surface":
minimum -28.16, mean -4.279, maximum 21.96  
Map values for surface "hfn180ice_11k_refined_model.pdb_J SES surface":
minimum -28.13, mean -4.282, maximum 21.96  
Map values for surface "hfn180ice_11k_refined_model.pdb_K SES surface":
minimum -28.05, mean -4.363, maximum 21.65  
Map values for surface "hfn180ice_11k_refined_model.pdb_L SES surface":
minimum -25.86, mean -4.281, maximum 21.56  
Map values for surface "hfn180ice_11k_refined_model.pdb_M SES surface":
minimum -26.31, mean -4.283, maximum 21.33  
Map values for surface "hfn180ice_11k_refined_model.pdb_N SES surface":
minimum -27.83, mean -4.311, maximum 21.84  
Map values for surface "hfn180ice_11k_refined_model.pdb_O SES surface":
minimum -28.26, mean -4.317, maximum 21.95  
Map values for surface "hfn180ice_11k_refined_model.pdb_P SES surface":
minimum -27.89, mean -4.259, maximum 21.7  
Map values for surface "hfn180ice_11k_refined_model.pdb_Q SES surface":
minimum -25.96, mean -4.292, maximum 21.54  
Map values for surface "hfn180ice_11k_refined_model.pdb_R SES surface":
minimum -26.35, mean -4.295, maximum 21.3  
Map values for surface "hfn180ice_11k_refined_model.pdb_S SES surface":
minimum -26.17, mean -4.289, maximum 21.33  
Map values for surface "hfn180ice_11k_refined_model.pdb_T SES surface":
minimum -25.86, mean -4.275, maximum 21.57  
Map values for surface "hfn180ice_11k_refined_model.pdb_V SES surface":
minimum -26.36, mean -4.279, maximum 21.3  
Map values for surface "hfn180ice_11k_refined_model.pdb_W SES surface":
minimum -27.9, mean -4.265, maximum 21.71  
Map values for surface "hfn180ice_11k_refined_model.pdb_X SES surface":
minimum -25.92, mean -4.284, maximum 21.55  
Map values for surface "hfn180N_11k_refined_model.pdb_U SES surface": minimum
-27.67, mean -4.414, maximum 22.01  
Map values for surface "hfn180N_11k_refined_model.pdb_A SES surface": minimum
-27.39, mean -4.41, maximum 21.93  
Map values for surface "hfn180N_11k_refined_model.pdb_B SES surface": minimum
-24.94, mean -4.293, maximum 21.36  
Map values for surface "hfn180N_11k_refined_model.pdb_C SES surface": minimum
-25.35, mean -4.282, maximum 21.97  
Map values for surface "hfn180N_11k_refined_model.pdb_D SES surface": minimum
-27.02, mean -4.308, maximum 22.35  
Map values for surface "hfn180N_11k_refined_model.pdb_E SES surface": minimum
-25.72, mean -4.274, maximum 21.82  
Map values for surface "hfn180N_11k_refined_model.pdb_F SES surface": minimum
-26.83, mean -4.41, maximum 22  
Map values for surface "hfn180N_11k_refined_model.pdb_G SES surface": minimum
-24.59, mean -4.325, maximum 21.39  
Map values for surface "hfn180N_11k_refined_model.pdb_H SES surface": minimum
-25.11, mean -4.386, maximum 21.34  
Map values for surface "hfn180N_11k_refined_model.pdb_I SES surface": minimum
-24.65, mean -4.328, maximum 21.4  
Map values for surface "hfn180N_11k_refined_model.pdb_J SES surface": minimum
-24.63, mean -4.322, maximum 21.4  
Map values for surface "hfn180N_11k_refined_model.pdb_K SES surface": minimum
-27.37, mean -4.39, maximum 22.05  
Map values for surface "hfn180N_11k_refined_model.pdb_L SES surface": minimum
-25.7, mean -4.28, maximum 21.91  
Map values for surface "hfn180N_11k_refined_model.pdb_M SES surface": minimum
-26.86, mean -4.418, maximum 21.99  
Map values for surface "hfn180N_11k_refined_model.pdb_N SES surface": minimum
-27.43, mean -4.421, maximum 22.14  
Map values for surface "hfn180N_11k_refined_model.pdb_O SES surface": minimum
-25.11, mean -4.382, maximum 21.34  
Map values for surface "hfn180N_11k_refined_model.pdb_P SES surface": minimum
-27.43, mean -4.401, maximum 21.9  
Map values for surface "hfn180N_11k_refined_model.pdb_Q SES surface": minimum
-25.28, mean -4.302, maximum 21.95  
Map values for surface "hfn180N_11k_refined_model.pdb_R SES surface": minimum
-27.01, mean -4.297, maximum 22.36  
Map values for surface "hfn180N_11k_refined_model.pdb_S SES surface": minimum
-26.71, mean -4.402, maximum 22.06  
Map values for surface "hfn180N_11k_refined_model.pdb_T SES surface": minimum
-25.64, mean -4.263, maximum 21.91  
Map values for surface "hfn180N_11k_refined_model.pdb_V SES surface": minimum
-27.01, mean -4.296, maximum 22.35  
Map values for surface "hfn180N_11k_refined_model.pdb_W SES surface": minimum
-27.43, mean -4.375, maximum 21.93  
Map values for surface "hfn180N_11k_refined_model.pdb_X SES surface": minimum
-25.44, mean -4.279, maximum 22.02  
Map values for surface "hfn180normal_11k_refined_model.pdb_U SES surface":
minimum -26.21, mean -4.379, maximum 21.47  
Map values for surface "hfn180normal_11k_refined_model.pdb_A SES surface":
minimum -25.33, mean -4.249, maximum 21.46  
Map values for surface "hfn180normal_11k_refined_model.pdb_B SES surface":
minimum -28.51, mean -4.281, maximum 21.7  
Map values for surface "hfn180normal_11k_refined_model.pdb_C SES surface":
minimum -26.5, mean -4.333, maximum 21.49  
Map values for surface "hfn180normal_11k_refined_model.pdb_D SES surface":
minimum -27.33, mean -4.355, maximum 21.18  
Map values for surface "hfn180normal_11k_refined_model.pdb_E SES surface":
minimum -25.95, mean -4.317, maximum 21.44  
Map values for surface "hfn180normal_11k_refined_model.pdb_F SES surface":
minimum -27.07, mean -4.338, maximum 21.21  
Map values for surface "hfn180normal_11k_refined_model.pdb_G SES surface":
minimum -25.85, mean -4.317, maximum 21.5  
Map values for surface "hfn180normal_11k_refined_model.pdb_H SES surface":
minimum -25.47, mean -4.259, maximum 21.54  
Map values for surface "hfn180normal_11k_refined_model.pdb_I SES surface":
minimum -25.94, mean -4.312, maximum 21.46  
Map values for surface "hfn180normal_11k_refined_model.pdb_J SES surface":
minimum -25.94, mean -4.313, maximum 21.47  
Map values for surface "hfn180normal_11k_refined_model.pdb_K SES surface":
minimum -26.17, mean -4.314, maximum 21.18  
Map values for surface "hfn180normal_11k_refined_model.pdb_L SES surface":
minimum -27.01, mean -4.357, maximum 21.26  
Map values for surface "hfn180normal_11k_refined_model.pdb_M SES surface":
minimum -27.11, mean -4.356, maximum 21  
Map values for surface "hfn180normal_11k_refined_model.pdb_N SES surface":
minimum -25.98, mean -4.214, maximum 21.54  
Map values for surface "hfn180normal_11k_refined_model.pdb_O SES surface":
minimum -25.47, mean -4.251, maximum 21.56  
Map values for surface "hfn180normal_11k_refined_model.pdb_P SES surface":
minimum -25.43, mean -4.242, maximum 21.46  
Map values for surface "hfn180normal_11k_refined_model.pdb_Q SES surface":
minimum -26.58, mean -4.356, maximum 21.35  
Map values for surface "hfn180normal_11k_refined_model.pdb_R SES surface":
minimum -27.34, mean -4.376, maximum 21.18  
Map values for surface "hfn180normal_11k_refined_model.pdb_S SES surface":
minimum -26.9, mean -4.345, maximum 21.22  
Map values for surface "hfn180normal_11k_refined_model.pdb_T SES surface":
minimum -27.14, mean -4.363, maximum 21.23  
Map values for surface "hfn180normal_11k_refined_model.pdb_V SES surface":
minimum -27.35, mean -4.354, maximum 21.17  
Map values for surface "hfn180normal_11k_refined_model.pdb_W SES surface":
minimum -25.39, mean -4.245, maximum 21.45  
Map values for surface "hfn180normal_11k_refined_model.pdb_X SES surface":
minimum -27.07, mean -4.344, maximum 21.32  
Map values for surface "hfn180normal_27_refined.pdb_U SES surface": minimum
-27.09, mean -4.382, maximum 22.18  
Map values for surface "hfn180normal_27_refined.pdb_A SES surface": minimum
-27.05, mean -4.403, maximum 22.12  
Map values for surface "hfn180normal_27_refined.pdb_B SES surface": minimum
-26.11, mean -4.327, maximum 22.56  
Map values for surface "hfn180normal_27_refined.pdb_C SES surface": minimum
-25.28, mean -4.356, maximum 21.97  
Map values for surface "hfn180normal_27_refined.pdb_D SES surface": minimum
-25.14, mean -4.381, maximum 22.19  
Map values for surface "hfn180normal_27_refined.pdb_E SES surface": minimum
-24.41, mean -4.362, maximum 22.53  
Map values for surface "hfn180normal_27_refined.pdb_F SES surface": minimum
-24.3, mean -4.378, maximum 22.32  
Map values for surface "hfn180normal_27_refined.pdb_G SES surface": minimum
-27.3, mean -4.402, maximum 22.02  
Map values for surface "hfn180normal_27_refined.pdb_H SES surface": minimum
-26.81, mean -4.428, maximum 21.95  
Map values for surface "hfn180normal_27_refined.pdb_I SES surface": minimum
-27.29, mean -4.403, maximum 21.99  
Map values for surface "hfn180normal_27_refined.pdb_J SES surface": minimum
-27.29, mean -4.408, maximum 21.98  
Map values for surface "hfn180normal_27_refined.pdb_K SES surface": minimum
-27.03, mean -4.389, maximum 22.2  
Map values for surface "hfn180normal_27_refined.pdb_L SES surface": minimum
-24.52, mean -4.381, maximum 22.02  
Map values for surface "hfn180normal_27_refined.pdb_M SES surface": minimum
-24.31, mean -4.388, maximum 22.32  
Map values for surface "hfn180normal_27_refined.pdb_N SES surface": minimum
-27.35, mean -4.43, maximum 22.26  
Map values for surface "hfn180normal_27_refined.pdb_O SES surface": minimum
-26.82, mean -4.425, maximum 21.95  
Map values for surface "hfn180normal_27_refined.pdb_P SES surface": minimum
-27.04, mean -4.416, maximum 22.13  
Map values for surface "hfn180normal_27_refined.pdb_Q SES surface": minimum
-25.2, mean -4.372, maximum 22.01  
Map values for surface "hfn180normal_27_refined.pdb_R SES surface": minimum
-25.14, mean -4.381, maximum 22.19  
Map values for surface "hfn180normal_27_refined.pdb_S SES surface": minimum
-24.26, mean -4.385, maximum 22.41  
Map values for surface "hfn180normal_27_refined.pdb_T SES surface": minimum
-24.35, mean -4.369, maximum 22.34  
Map values for surface "hfn180normal_27_refined.pdb_V SES surface": minimum
-25.16, mean -4.38, maximum 22.19  
Map values for surface "hfn180normal_27_refined.pdb_W SES surface": minimum
-27.03, mean -4.411, maximum 22.14  
Map values for surface "hfn180normal_27_refined.pdb_X SES surface": minimum
-25.32, mean -4.367, maximum 21.92  
Alignment identifier is 1  

> hide surfaces

> ui tool show Distances

> ui tool show Clashes

> ui tool show "Blast Protein"

> blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

> blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

> blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

> blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

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: appBlastProtein2Service1607180434869-177239169  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1607180434869-177239169  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/client.py", line
115, in __init__  
self.wsdl = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/reader.py", line
150, in open  
d = self.fn(url, self.options)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/reader.py", line
74, in open  
d = self.download(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/reader.py", line
94, in download  
content = fp.read()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/http/client.py", line 464, in read  
return self._readall_chunked()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/http/client.py", line 574, in
_readall_chunked  
value.append(self._safe_read(chunk_left))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/http/client.py", line 620, in
_safe_read  
chunk = self.fp.read(min(amt, MAXAMOUNT))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
socket.timeout: timed out  
  
Exception in thread 2:  
socket.timeout: timed out  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/client.py", line
115, in __init__  
self.wsdl = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/reader.py", line
150, in open  
d = self.fn(url, self.options)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/reader.py", line
74, in open  
d = self.download(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/reader.py", line
94, in download  
content = fp.read()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/http/client.py", line 464, in read  
return self._readall_chunked()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/http/client.py", line 574, in
_readall_chunked  
value.append(self._safe_read(chunk_left))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/http/client.py", line 620, in
_safe_read  
chunk = self.fp.read(min(amt, MAXAMOUNT))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
socket.timeout: timed out  
  
Exception in thread 1:  
socket.timeout: timed out  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/client.py", line
115, in __init__  
self.wsdl = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/reader.py", line
150, in open  
d = self.fn(url, self.options)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/reader.py", line
74, in open  
d = self.download(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/suds/reader.py", line
94, in download  
content = fp.read()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/http/client.py", line 464, in read  
return self._readall_chunked()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/http/client.py", line 574, in
_readall_chunked  
value.append(self._safe_read(chunk_left))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/http/client.py", line 620, in
_safe_read  
chunk = self.fp.read(min(amt, MAXAMOUNT))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
socket.timeout: timed out  
  
Exception in thread 3:  
socket.timeout: timed out  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  
BlastProtein finished.  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 604, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 82, in on_finish  
out = self.get_file("stdout.txt")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  
BlastProtein finished.  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 604, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 82, in on_finish  
out = self.get_file("stdout.txt")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  
BlastProtein finished.  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 604, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 82, in on_finish  
out = self.get_file("stdout.txt")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 18.0.5
OpenGL renderer: Mesa DRI Intel(R) Haswell Desktop 
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: Dell Inc.
Model: OptiPlex 9020
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        5.1G        3.1G        1.3G        7.4G        8.8G
	Swap:          3.7G         78M        3.6G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics Controller [8086:0412] (rev 06)	
	DeviceName:  Onboard IGD	
	Subsystem: Dell Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics Controller [1028:05a4]
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Tom Goddard, 5 years ago

Component: Unassigned → Sequence
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → BLAST Protein: socket.timeout: timed out

Maybe the blast web service was down 2 days ago. The code should give a sensible error message in that case like "Can't reach BLAST web server ​https://xxx".

comment:2 by pett, 5 years ago

Component: Sequence → Web Services
Status: assigned → accepted
Summary: BLAST Protein: socket.timeout: timed out → Better error handling on web service failure
Type: defect → enhancement

It's tricky because the failure is happening in a thread, but will try to do something.

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