Opened 7 years ago

Closed 6 years ago

#1836 closed defect (duplicate)

"toolshed uninstall": JSONDecodeError

Reported by: tic20@… Owned by: Conrad Huang
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.9 (2019-04-09)
Description
Due to the vagaries of PyBind11 I can't currently rebuild Clipper while an existing version is loading (ChimeraX's command framework invokes Clipper's __init__.py, which loads some compiled objects, then the builder's test suite tries to load the new versions of same and bails out). Since the ChimeraX shell switches still don't work for me in Windows (see #1563) I do the builds from within the GUI. Anyway, all that's leading to why I attempted to run 'toolshed uninstall Clipper' - which yields this traceback. 

No immediate concern on my part - I can still move forward by simply deleting ChimeraX's AppData/Local and cache folders, and I suppose with a bit of rearrangement of imports I can avoid the problem entirely.

Log:
UCSF ChimeraX version: 0.9 (2019-04-09)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed uninstall Clipper

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\metadata.py",
line 730, in __init__  
self._data = json.loads(data)  
File "C:\Program Files\ChimeraX\bin\lib\json\\__init__.py", line 348, in loads  
return _default_decoder.decode(s)  
File "C:\Program Files\ChimeraX\bin\lib\json\decoder.py", line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
File "C:\Program Files\ChimeraX\bin\lib\json\decoder.py", line 355, in
raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 253, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2628, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\toolshed.py", line 254, in toolshed_uninstall  
deps = bi.dependents(logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 665, in dependents  
for d in DistributionPath().get_distributions():  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\database.py",
line 213, in get_distributions  
self._generate_cache()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\database.py",
line 167, in _generate_cache  
for dist in self._yield_distributions():  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\database.py",
line 148, in _yield_distributions  
metadata = Metadata(fileobj=stream, scheme='legacy')  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\metadata.py",
line 741, in __init__  
self.validate()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\metadata.py",
line 958, in validate  
missing, warnings = self._legacy.check(True)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\metadata.py",
line 522, in check  
self.set_metadata_version()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\metadata.py",
line 289, in set_metadata_version  
self._fields['Metadata-Version'] = _best_version(self._fields)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\metadata.py",
line 167, in _best_version  
raise MetadataConflictError('Unknown metadata set')  
distlib.metadata.MetadataConflictError: Unknown metadata set  
  
distlib.metadata.MetadataConflictError: Unknown metadata set  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\distlib\metadata.py",
line 167, in _best_version  
raise MetadataConflictError('Unknown metadata set')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 398.11
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 7 years ago

Component: UnassignedTool Shed
Owner: set to Conrad Huang
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submission"toolshed uninstall": JSONDecodeError

comment:2 by Conrad Huang, 6 years ago

Resolution: duplicate
Status: assignedclosed

Same as #2043.

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