Opened 10 years ago

Closed 10 years ago

Last modified 7 years ago

#211 closed defect (fixed)

Problem opening 4v41 (template fetching)

Reported by: pett Owned by: Greg Couch
Priority: blocker Milestone:
Component: Input/Output Version:
Keywords: Cc: chimera-programmers@…, meng@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Traceback (most recent call last):
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 121, in on_enter
cmd.execute()
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1798, in execute
results.append(ci.function(session, kw_args))
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py", line 40, in open
format=format, name=name)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/fetch.py", line 201, in fetch_from_database
models, status = df.fetch(session, id, format=format)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/fetch.py", line 236, in fetch
return fetch(session, database_id)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/mmcif.py", line 65, in fetch_mmcif
models, status = io.open_data(session, filename, format = 'mmcif', name = pdb_id)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 508, in open_data
models, status = open_func(session, stream, dname,
kw)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/mmcif.py", line 35, in open_mmcif
pointers = _mmcif.parse_mmCIF_file(filename, _additional_categories, log)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/mmcif.py", line 34, in <lambda>
_mmcif.set_Python_locate_function(lambda name: _get_template(name, session.app_dirs, log))
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/mmcif.py", line 87, in _get_template
"User-Agent": utils.html_user_agent(app_dirs),
AttributeError: module 'chimerax.core.utils' has no attribute 'html_user_agent'

Change History (2)

comment:1 by Tom Goddard, 10 years ago

Resolution: fixed
Status: newclosed

Fixed. Change to core/mmcif.py pushed.

I moved the the html_user_agent() routine from utils.py to fetch.py but missed one place it was used in fetching mmcif templates.

comment:2 by pett, 7 years ago

Component: mmCIF Reader/WriterInput/Output

reducing # of categories, so lumping into I/O category

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