Opened 7 years ago

Closed 7 years ago

#1847 closed defect (duplicate)

Either: Tempy broken, or Registration internal error -- dealer's choice

Reported by: chimerax-bug-report@… Owned by: Conrad Huang
Priority: normal Milestone:
Component: Infrastructure Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-46-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.8 (2018-11-28)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-11-28)  
How to cite UCSF ChimeraX  

> open
/home/ricardo/tilipo33_publicação/dock_files/yasara/tilipo33_model-1.yob

Unrecognized file suffix '.yob'  

Unrecognized file suffix '.yob'  

> open
/home/ricardo/tilipo33_publicação/dock_files/yasara/tilipo33_model-1.pdb

Summary of feedback from opening
/home/ricardo/tilipo33_publicação/dock_files/yasara/tilipo33_model-1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK YASARA *************************************************************  
  
Ignored bad PDB record found on line 2  
REMARK YASARA * *  
  
Ignored bad PDB record found on line 3  
REMARK YASARA * Y A S A R A *  
  
Ignored bad PDB record found on line 4  
REMARK YASARA * *  
  
Ignored bad PDB record found on line 5  
REMARK YASARA * Yet Another Scientific Artificial Reality Application *  
  
14 messages similar to the above omitted  
  
Chain information for tilipo33_model-1.pdb #1  
---  
Chain | Description  
A | biogenic amine-binding protein  
  

> ~select #1

Nothing selected  

> select #1

2617 atoms, 2644 bonds selected  

> ~select #1

Nothing selected  

> hide selAtoms ribbons

> toolshed show "Blast Protein"

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: appBlastProtein2Service15553544029431093310020  
Opal status URL:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15553544029431093310020  
BlastProtein finished.  

> hide selAtoms ribbons

> show selAtoms

> show selAtoms ribbons

> hide selAtoms ribbons

> show selAtoms ribbons

> hide selAtoms

> show selAtoms

> lighting full

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting simple

> hide selAtoms ribbons

> ui mousemode rightMode rotate and select

> ui mousemode rightMode translate

> ui mousemode rightMode select

> ui mousemode rightMode clip

> ui mousemode rightMode distance

> ui mousemode rightMode tug

> ui mousemode rightMode minimize

> hide selAtoms ribbons

> hide selAtoms

> show selAtoms ribbons

Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.3.1 ChimeraX-ISOLDE-1.0b2  
Installed ChimeraX-Clipper (0.3.1)  
Installed ChimeraX-ISOLDE (1.0b2)  
Downloading bundle ChimeraX_Cytoscape-0.1-py3-none-any.whl  
Successfully installed ChimeraX-Cytoscape-0.1  
Installed ChimeraX-Cytoscape (0.1)  
Downloading bundle ChimeraX_Stringdb-0.1-py3-none-any.whl  
Successfully installed ChimeraX-Stringdb-0.1  
Installed ChimeraX-Stringdb (0.1)  
Downloading bundle ChimeraX_Stringdb-0.1-py3-none-any.whl  
unloading module chimerax.stringdb  
Successfully installed ChimeraX-Stringdb-0.1  
Installed ChimeraX-Stringdb (0.1)  
Downloading bundle ChimeraX_BlastProtein-0.1-py3-none-any.whl  
unloading module chimerax.blastprotein  
Successfully installed ChimeraX-BlastProtein-0.1  
Installed ChimeraX-BlastProtein (0.1)  
Downloading bundle ChimeraX_Tempy-0.6.0-py3-none-any.whl  
unloading module chimerax.tempy  
Successfully installed ChimeraX-Tempy-0.6.0  
Installed ChimeraX-Tempy (0.6.0)  

> toolshed show "Blast Protein"

> toolshed show "Density Map Toolbar"

> close session

> open "/media/ricardo/New
Volume/home/ricardo/aati/pedro_aati/AaTI/Refine_299/AaTI_Structure_refine_299.pdb"

Chain information for AaTI_Structure_refine_299.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open "/media/ricardo/New
Volume/home/ricardo/aati/pedro_aati/AaTI/Refine_299/AaTI_Structure_refine_data.mtz"

Must specify a structure model to associate with crystallographic data  

Must specify a structure model to associate with crystallographic data  

> volume selMaps style solid

No volumes specified  

No volumes specified  

> toolshed show Tempy

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 575, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1185, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/__init__.py", line 16, in start_tool  
from .tool import ToolUI  
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/tool.py", line 14, in <module>  
from . import tool_scores  
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/tool_scores.py", line 8, in <module>  
from . import tool_select  
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/tool_select.py", line 8, in <module>  
from chimerax.core.map.volume import Volume  
ModuleNotFoundError: No module named 'chimerax.core.map'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 922, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 581, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Tempy in
bundle ChimeraX-Tempy:  
No module named 'chimerax.core.map'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Tempy in
bundle ChimeraX-Tempy:  
No module named 'chimerax.core.map'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 581, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  

> volume selMaps style mesh

No volumes specified  

No volumes specified  

> select #1

927 atoms, 844 bonds selected  

> volume selMaps style solid

No volumes specified  

No volumes specified  

> ~select #1

Nothing selected  

> toolshed show Registration

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 529, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/gui.py", line 67, in handle_scheme  
self.session.ui.thread_safe(self._register, url)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 286, in thread_safe  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/gui.py", line 121, in _register  
join_announcements=values["join_announcements"])  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/cmd.py", line 76, in register  
funding, funding_other, comment)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/cmd.py", line 120, in _get_registration  
with urlopen(RegistrationURL, urlencode(params).encode()) as f:  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 223,
in urlopen  
return opener.open(url, data, timeout)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 532,
in open  
response = meth(req, response)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 642,
in http_response  
'http', request, response, code, msg, hdrs)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 570,
in error  
return self._call_chain(*args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 504,
in _call_chain  
result = func(*args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 650,
in http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 500: Registration internal error  
  
urllib.error.HTTPError: HTTP Error 500: Registration internal error  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 650,
in http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
  
See log for complete Python traceback.  
  
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
ricardojstorquato@gmail.com is subscribed to the ChimeraX discussion list  
ricardojstorquato@gmail.com is subscribed to the ChimeraX announcements list  

> show all

> volume selMaps style solid

No volumes specified  

No volumes specified  

> volume selMaps step 1

No volumes specified  

No volumes specified  

> open "/media/ricardo/New
Volume/home/ricardo/aati/pedro_aati/AaTI/Refine_299/AaTI_Structure_refine_299.mtz"

Must specify a structure model to associate with crystallographic data  

Must specify a structure model to associate with crystallographic data  

> close session

Must specify a structure model to associate with crystallographic data  

Must specify a structure model to associate with crystallographic data  

> toolshed show ISOLDE

> toolshed show Tempy

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 575, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1185, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/__init__.py", line 16, in start_tool  
from .tool import ToolUI  
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/tool.py", line 14, in <module>  
from . import tool_scores  
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/tool_scores.py", line 8, in <module>  
from . import tool_select  
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/tool_select.py", line 8, in <module>  
from chimerax.core.map.volume import Volume  
ModuleNotFoundError: No module named 'chimerax.core.map'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 922, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 581, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Tempy in
bundle ChimeraX-Tempy:  
No module named 'chimerax.core.map'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Tempy in
bundle ChimeraX-Tempy:  
No module named 'chimerax.core.map'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 581, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: Quadro K4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 7 years ago

Cc: Tom Goddard added
Component: Unassigned → Infrastructure
Owner: set to Conrad Huang
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Either: Tempy broken, or Registration internal error -- dealer's choice

comment:2 by pett, 7 years ago

Resolution: → duplicate
Status: assigned → closed

dup of #1846

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