| 1 | from chimerax.core.toolshed import NewerVersionQuery
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| 2 | NewerVersionQuery.SESSION_SAVE=False
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| 3 |
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| 4 | from chimerax.core.commands import run
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| 5 | run(session, "save /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_linux.cxs")
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| 6 | ---------------------------------------------------------------------------
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| 7 | RuntimeError Traceback (most recent call last)
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| 8 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:262, in _SaveManager.discovery(self, containers)
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| 9 | 261 try:
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| 10 | --> 262 self.processed[key] = self.process(obj, parents)
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| 11 | 263 except UserError:
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| 12 |
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| 13 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:299, in _SaveManager.process(self, obj, parents)
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| 14 | 298 return add_obj(obj, parents)
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| 15 | --> 299 return copy_state(data, convert=convert)
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| 16 |
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| 17 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:219, in copy_state(data, convert)
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| 18 | 217 return convert(data)
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| 19 | --> 219 return _copy(data)
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| 20 |
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| 21 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:204, in copy_state.<locals>._copy(data)
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| 22 | 203 if isinstance(data, Mapping):
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| 23 | --> 204 items = [(_copy(k), _copy(v)) for k, v in data.items()]
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| 24 | 205 elif isinstance(data, numpy.ndarray):
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| 25 |
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| 26 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:204, in <listcomp>(.0)
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| 27 | 203 if isinstance(data, Mapping):
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| 28 | --> 204 items = [(_copy(k), _copy(v)) for k, v in data.items()]
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| 29 | 205 elif isinstance(data, numpy.ndarray):
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| 30 |
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| 31 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:204, in copy_state.<locals>._copy(data)
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| 32 | 203 if isinstance(data, Mapping):
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| 33 | --> 204 items = [(_copy(k), _copy(v)) for k, v in data.items()]
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| 34 | 205 elif isinstance(data, numpy.ndarray):
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| 35 |
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| 36 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:204, in <listcomp>(.0)
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| 37 | 203 if isinstance(data, Mapping):
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| 38 | --> 204 items = [(_copy(k), _copy(v)) for k, v in data.items()]
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| 39 | 205 elif isinstance(data, numpy.ndarray):
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| 40 |
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| 41 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:217, in copy_state.<locals>._copy(data)
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| 42 | 215 else:
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| 43 | 216 # Use state methods to convert object to primitives
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| 44 | --> 217 return convert(data)
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| 45 |
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| 46 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:298, in _SaveManager.process.<locals>.convert(obj, parents, add_obj)
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| 47 | 297 def convert(obj, parents=parents + (obj,), add_obj=self._add_obj):
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| 48 | --> 298 return add_obj(obj, parents)
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| 49 |
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| 50 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:270, in _SaveManager._add_obj(self, obj, parents)
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| 51 | 269 def _add_obj(self, obj, parents=()):
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| 52 | --> 270 uid = _UniqueName.from_obj(self.session, obj)
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| 53 | 271 self._found_objs.append(uid)
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| 54 |
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| 55 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:143, in _UniqueName.from_obj(cls, session, obj)
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| 56 | 142 if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
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| 57 | --> 143 raise RuntimeError(
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| 58 | 144 'Unable to restore objects of %s class in %s bundle'
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| 59 | 145 ' because the class name is not listed in the name to class table'
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| 60 | 146 ' for session restore' %
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| 61 | 147 (obj_cls.__name__, bundle_info.name))
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| 62 | 149 if not known_class and bundle_info != 'builtin':
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| 63 |
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| 64 | RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore
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| 65 |
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| 66 | During handling of the above exception, another exception occurred:
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| 67 |
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| 68 | ValueError Traceback (most recent call last)
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| 69 | Cell In[2], line 2
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| 70 | 1 from chimerax.core.commands import run
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| 71 | ----> 2 run(session, "save /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_linux.cxs")
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| 72 |
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| 73 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py:38, in run(session, text, log, downgrade_errors, return_json, return_list)
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| 74 | 36 command = Command(session)
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| 75 | 37 try:
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| 76 | ---> 38 results = command.run(text, log=log, return_json=return_json)
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| 77 | 39 except UserError as err:
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| 78 | 40 if downgrade_errors:
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| 79 |
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| 80 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py:2897, in Command.run(self, text, log, log_only, return_json, _used_aliases)
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| 81 | 2895 kw_args['log'] = log
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| 82 | 2896 try:
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| 83 | -> 2897 result = ci.function(session, **kw_args)
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| 84 | 2898 except CancelOperation:
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| 85 | 2899 if not self._ci.self_logging:
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| 86 |
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| 87 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py:75, in cmd_save(session, file_name, rest_of_line, log)
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| 88 | 73 session.logger.info(more_log_info, is_html=True)
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| 89 | 74 raise
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| 90 | ---> 75 Command(session, registry=registry).run(provider_cmd_text, log=log)
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| 91 |
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| 92 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py:2897, in Command.run(self, text, log, log_only, return_json, _used_aliases)
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| 93 | 2895 kw_args['log'] = log
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| 94 | 2896 try:
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| 95 | -> 2897 result = ci.function(session, **kw_args)
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| 96 | 2898 except CancelOperation:
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| 97 | 2899 if not self._ci.self_logging:
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| 98 |
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| 99 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py:90, in provider_save(session, file_name, format, **provider_kw)
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| 100 | 88 try:
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| 101 | 89 saver_info = provider_info.bundle_info.run_provider(session, provider_info.format_name, mgr)
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| 102 | ---> 90 saver_info.save(session, path, **provider_kw)
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| 103 | 91 except (IOError, PermissionError, OSError) as e:
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| 104 | 92 raise UserError("Cannot save '%s': %s" % (file_name, e))
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| 105 |
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| 106 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core_formats/__init__.py:84, in _SessionAPI.run_provider.<locals>.Info.save(self, session, path, **kw)
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| 107 | 82 def save(self, session, path, **kw):
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| 108 | 83 from chimerax.core.session import save as cxs_save
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| 109 | ---> 84 return cxs_save(session, path, **kw)
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| 110 |
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| 111 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:901, in save(session, path, version, compress, include_maps)
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| 112 | 899 session.session_file_path = path
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| 113 | 900 try:
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| 114 | --> 901 session.save(output, version=version, include_maps=include_maps)
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| 115 | 902 except Exception:
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| 116 | 903 if open_func is not None:
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| 117 |
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| 118 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:625, in Session.save(self, stream, version, include_maps)
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| 119 | 621 fserialize(stream, metadata)
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| 120 | 622 # guarantee that bundles are serialized first, so on restoration,
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| 121 | 623 # all of the related code will be loaded before the rest of the
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| 122 | 624 # session is restored
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| 123 | --> 625 mgr.discovery(self._state_containers)
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| 124 | 626 fserialize(stream, mgr.bundle_infos())
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| 125 | 627 # TODO: collect OrderDAGError exceptions from walk and analyze
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| 126 |
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| 127 | File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:266, in _SaveManager.discovery(self, containers)
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| 128 | 264 raise # For example map size is larger than 4 Gbyte msgpack limit.
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| 129 | 265 except Exception as e:
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| 130 | --> 266 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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| 131 | 267 self.graph[key] = self._found_objs
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| 132 |
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| 133 | ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at 0x7f71a2b0a690>: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore
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