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