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Opened 10 years ago
Closed 10 years ago
#263 closed defect (fixed)
Traceback opening unknown pdb id code
| Reported by: | Tom Goddard | Owned by: | Greg Couch |
|---|---|---|---|
| Priority: | major | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
Opening a pdb id code that doesn't exist should give a simple error message -- getting a traceback now.
open 555z
Traceback (most recent call last):
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 120, in on_enter
cmd.run(cmd_text)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2122, in run
results.append(ci.function(session, kw_args))
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py", line 53, in open
format=format, name=name, ignore_cache=ignore_cache)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/fetch.py", line 212, in fetch_from_database
models, status = df.fetch(session, id, format=format, ignore_cache=ignore_cache)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/fetch.py", line 247, in fetch
return fetch(session, database_id, ignore_cache=ignore_cache)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/mmcif.py", line 64, in fetch_mmcif
models, status = io.open_data(session, filename, format = 'mmcif', name = pdb_id)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 513, in open_data
models, status = open_func(session, stream, dname, kw)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/mmcif.py", line 33, in open_mmcif
pointers = _mmcif.parse_mmCIF_file(filename, _additional_categories, session.logger)
_mmcif.error: unexpected data value on line 1
Added code to see if returned mmCIF data from PDB URL is actually a mmCIF file instead of an HTML error message (why it doesn't return an HTTP error is unknown).