Opened 6 years ago
Closed 6 years ago
#3017 closed defect (duplicate)
cellPACK: Collada scheme failure
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Higher-Order Structure | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 0.92 (2020-03-06)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.92 (2020-03-06)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Missing or invalid "filename" argument: Expected a file name
> open HIV-1_0.1.6_6
Unrecognized file suffix '.6_6'
> open noprefs nowildcard cellpackID HIV-1_0.1.6_6
Missing filename suffix noprefs
> open nowildcard cellpackID HIV-1_0.1.6_6
Missing filename suffix nowildcard
> open cellpackID HIV-1_0.1.6_6
Missing filename suffix cellpackID
Missing or invalid "filename" argument: Expected a file name
Unknown command: ?
> open ?
Missing filename suffix ?
> open cellpack:HIV-1_0.1.6_6 fromDatabase cellpack format cellpack
Summary of feedback from opening HIV-1_0.1.6_6 fetched from cellpack
---
notes | Fetching compressed results HIV-1_0.1.6_6 from
https://github.com/mesoscope/cellPACK_data/raw/master/cellPACK_database_1.1.0/results/HIV-1_0.1.6_6.apr.json
Fetching compressed recipe for HIV-1_0.1.6_6 from
https://github.com/mesoscope/cellPACK_data/raw/master/cellPACK_database_1.1.0/recipes/HIV-1_0.1.6-6.json
Fetching compressed compartment bounds HIV1_capsid_3j3q_PackInner_0_1_1.dae
from
https://github.com/mesoscope/cellPACK_data/raw/master/cellPACK_database_1.1.0/geometries/HIV1_capsid_3j3q_PackInner_0_1_1.dae
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 23, in fetch_cellpack
surf = fetch_autopack(session, path, cellpack_id, database, ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 65, in fetch_autopack
slist, msg = read_collada_surfaces(session, geom_path, 'geometry')
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\collada.py", line 15, in read_collada_surfaces
from collada import Collada
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\\__init__.py",
line 48, in <module>
from collada import schema
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\schema.py", line
27, in <module>
'resources/schema-1.4.1.xml').decode('utf-8'))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1158, in resource_string
self, resource_name
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1402, in get_resource_string
return self._get(self._fn(self.module_path, resource_name))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1617, in _get
with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\\Program
Files\\\ChimeraX\\\bin\\\lib\\\site-
packages\\\collada\\\resources\\\schema-1.4.1.xml'
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 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 44, in open
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 153, in _fetch_from_database
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 438, in fetch_from_database
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 501, in fetch
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 383, in fetch_cb
return fetch_shim(session, identifier, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in fetch_shim
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\\__init__.py", line 22, in fetch_from_database
return fetch_cellpack(session, identifier, ignore_cache=ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
NameError: name 'results_name' is not defined
NameError: name 'results_name' is not defined
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
See log for complete Python traceback.
> open cellpack:HIV-1_0.1.6_6 fromDatabase cellpack format cellpack
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 23, in fetch_cellpack
surf = fetch_autopack(session, path, cellpack_id, database, ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 65, in fetch_autopack
slist, msg = read_collada_surfaces(session, geom_path, 'geometry')
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\collada.py", line 15, in read_collada_surfaces
from collada import Collada
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\\__init__.py",
line 48, in <module>
from collada import schema
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\schema.py", line
27, in <module>
'resources/schema-1.4.1.xml').decode('utf-8'))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1158, in resource_string
self, resource_name
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1402, in get_resource_string
return self._get(self._fn(self.module_path, resource_name))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1617, in _get
with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\\Program
Files\\\ChimeraX\\\bin\\\lib\\\site-
packages\\\collada\\\resources\\\schema-1.4.1.xml'
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 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 44, in open
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 153, in _fetch_from_database
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 438, in fetch_from_database
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 501, in fetch
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in fetch_shim
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\\__init__.py", line 22, in fetch_from_database
return fetch_cellpack(session, identifier, ignore_cache=ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
NameError: name 'results_name' is not defined
NameError: name 'results_name' is not defined
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
See log for complete Python traceback.
> open cellpack:HIV-1_0.1.6_6 fromDatabase cellpack format cellpack
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 23, in fetch_cellpack
surf = fetch_autopack(session, path, cellpack_id, database, ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 65, in fetch_autopack
slist, msg = read_collada_surfaces(session, geom_path, 'geometry')
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\collada.py", line 15, in read_collada_surfaces
from collada import Collada
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\\__init__.py",
line 48, in <module>
from collada import schema
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\schema.py", line
27, in <module>
'resources/schema-1.4.1.xml').decode('utf-8'))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1158, in resource_string
self, resource_name
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1402, in get_resource_string
return self._get(self._fn(self.module_path, resource_name))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1617, in _get
with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\\Program
Files\\\ChimeraX\\\bin\\\lib\\\site-
packages\\\collada\\\resources\\\schema-1.4.1.xml'
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 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 44, in open
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 153, in _fetch_from_database
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 438, in fetch_from_database
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 501, in fetch
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in fetch_shim
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\\__init__.py", line 22, in fetch_from_database
return fetch_cellpack(session, identifier, ignore_cache=ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
NameError: name 'results_name' is not defined
NameError: name 'results_name' is not defined
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
See log for complete Python traceback.
> open cellpack:HIV-1_0.1.6_6 fromDatabase cellpack format cellpack
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 23, in fetch_cellpack
surf = fetch_autopack(session, path, cellpack_id, database, ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 65, in fetch_autopack
slist, msg = read_collada_surfaces(session, geom_path, 'geometry')
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\collada.py", line 15, in read_collada_surfaces
from collada import Collada
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\\__init__.py",
line 48, in <module>
from collada import schema
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\schema.py", line
27, in <module>
'resources/schema-1.4.1.xml').decode('utf-8'))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1158, in resource_string
self, resource_name
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1402, in get_resource_string
return self._get(self._fn(self.module_path, resource_name))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1617, in _get
with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\\Program
Files\\\ChimeraX\\\bin\\\lib\\\site-
packages\\\collada\\\resources\\\schema-1.4.1.xml'
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 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 44, in open
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 153, in _fetch_from_database
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 438, in fetch_from_database
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 501, in fetch
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in fetch_shim
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\\__init__.py", line 22, in fetch_from_database
return fetch_cellpack(session, identifier, ignore_cache=ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
NameError: name 'results_name' is not defined
NameError: name 'results_name' is not defined
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
See log for complete Python traceback.
> open C:/Users/cgm/Downloads/ChimeraX/cellPACK/HIV-1_0.1.6_6.apr.json
Unrecognized file suffix '.json'
> open
> C:/Users/cgm/Downloads/ChimeraX/cellPACK/HIV1_capsid_3j3q_PackInner_0_1_1.dae
[Errno 2] No such file or directory: 'C:\\\Program
Files\\\ChimeraX\\\bin\\\lib\\\site-
packages\\\collada\\\resources\\\schema-1.4.1.xml'
> open cellpack:HIV-1_0.1.6_5 fromDatabase cellpack format cellpack
Summary of feedback from opening HIV-1_0.1.6_5 fetched from cellpack
---
notes | Fetching compressed results HIV-1_0.1.6_5 from
https://github.com/mesoscope/cellPACK_data/raw/master/cellPACK_database_1.1.0/results/HIV-1_0.1.6_5.apr.json
Fetching compressed recipe for HIV-1_0.1.6_5 from
https://github.com/mesoscope/cellPACK_data/raw/master/cellPACK_database_1.1.0/recipes/HIV-1_0.1.6-5.json
Fetching compressed compartment bounds HIV1_capsid_3j3q_PackInner_0_1_0.dae
from
https://github.com/mesoscope/cellPACK_data/raw/master/cellPACK_database_1.1.0/geometries/HIV1_capsid_3j3q_PackInner_0_1_0.dae
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 23, in fetch_cellpack
surf = fetch_autopack(session, path, cellpack_id, database, ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 65, in fetch_autopack
slist, msg = read_collada_surfaces(session, geom_path, 'geometry')
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\collada.py", line 15, in read_collada_surfaces
from collada import Collada
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\\__init__.py",
line 48, in <module>
from collada import schema
File "C:\Program Files\ChimeraX\bin\lib\site-packages\collada\schema.py", line
27, in <module>
'resources/schema-1.4.1.xml').decode('utf-8'))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1158, in resource_string
self, resource_name
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1402, in get_resource_string
return self._get(self._fn(self.module_path, resource_name))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 1617, in _get
with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\\Program
Files\\\ChimeraX\\\bin\\\lib\\\site-
packages\\\collada\\\resources\\\schema-1.4.1.xml'
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 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 44, in open
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 153, in _fetch_from_database
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 438, in fetch_from_database
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 501, in fetch
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in fetch_shim
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\\__init__.py", line 22, in fetch_from_database
return fetch_cellpack(session, identifier, ignore_cache=ignore_cache)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
NameError: name 'results_name' is not defined
NameError: name 'results_name' is not defined
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cellpack\fetch_cellpack.py", line 26, in fetch_cellpack
raise UserError('Unknown cellPACK id "%s"\n\n%s' % (results_name, str(e)))
See log for complete Python traceback.
OpenGL version: 3.3.13560 Core Profile Forward-Compatible Context 26.20.11030.9002
OpenGL renderer: AMD Radeon(TM) Vega 3 Graphics
OpenGL vendor: ATI Technologies Inc.
Change History (2)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Higher-Order Structure |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → cellPACK: Collada scheme failure |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #3016