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Unable to view or install Mothur suite #2539

Closed blankenberg closed 4 years ago

blankenberg commented 8 years ago

You encounter a recursion error on the (test) toolshed:

View: https://testtoolshed.g2.bx.psu.edu/repository/browse_repositories?sort=name&operation=view_or_manage_repository&f-free-text-search=mothur&id=85391b8d5d7ad39d

Install (in frame): https://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=85391b8d5d7ad39d&changeset_revision=1aa5c8a48cb9

I tried resetting metadata directly by URL, but encountered a recursion error as well, when the repo tried to display (metadata reset was successful).

Error - <type 'exceptions.RuntimeError'>: maximum recursion depth exceeded while getting the str of an object
URL: https://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=85391b8d5d7ad39d&changeset_revision=1aa5c8a48cb9
File 'lib/galaxy/web/framework/middleware/error.py', line 151 in __call__
  app_iter = self.application(environ, sr_checker)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__
  return self.application(environ, start_response)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__
  return self.application(environ, start_response)
File 'lib/galaxy/web/framework/base.py', line 131 in __call__
  return self.handle_request( environ, start_response )
File 'lib/galaxy/web/framework/base.py', line 190 in handle_request
  body = method( trans, **kwargs )
File 'lib/galaxy/webapps/tool_shed/controllers/repository.py', line 2442 in preview_tools_in_changeset
  repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 154 in get_repository_dependencies_for_changeset_revision
  self.handle_current_repository_dependency( current_repository_key )
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 254 in handle_current_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 154 in get_repository_dependencies_for_changeset_revision
  self.handle_current_repository_dependency( current_repository_key )
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 254 in handle_current_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 160 in get_repository_dependencies_for_changeset_revision
  self.handle_next_repository_dependency()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 296 in handle_next_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 154 in get_repository_dependencies_for_changeset_revision
  self.handle_current_repository_dependency( current_repository_key )
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 254 in handle_current_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 160 in get_repository_dependencies_for_changeset_revision
  self.handle_next_repository_dependency()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 296 in handle_next_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 154 in get_repository_dependencies_for_changeset_revision
  self.handle_current_repository_dependency( current_repository_key )
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 254 in handle_current_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()

...

File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 296 in handle_next_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 158 in get_repository_dependencies_for_changeset_revision
  self.handle_next_repository_dependency()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 296 in handle_next_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 158 in get_repository_dependencies_for_changeset_revision
  self.handle_next_repository_dependency()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 296 in handle_next_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 160 in get_repository_dependencies_for_changeset_revision
  self.handle_next_repository_dependency()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 296 in handle_next_repository_dependency
  return self.get_repository_dependencies_for_changeset_revision()
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 146 in get_repository_dependencies_for_changeset_revision
  repository_dependencies_dict )
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 378 in populate_repository_dependency_objects_for_processing
  self.get_updated_changeset_revisions_for_repository_dependencies( current_repository_key_rd_dicts )
File 'lib/tool_shed/dependencies/repository/relation_builder.py', line 184 in get_updated_changeset_revisions_for_repository_dependencies
  repository = suc.get_repository_by_name_and_owner( self.app, rd_name, rd_owner )
File 'lib/tool_shed/util/shed_util_common.py', line 563 in get_repository_by_name_and_owner
  app.model.Repository.table.c.user_id == user.id ) ) \
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py', line 2445 in first
  ret = list(self[0:1])
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py', line 2281 in __getitem__
  return list(res)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py', line 2516 in __iter__
  return self._execute_and_instances(context)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py', line 2531 in _execute_and_instances
  result = conn.execute(querycontext.statement, self._params)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py', line 914 in execute
  return meth(self, multiparams, params)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py', line 323 in _execute_on_connection
  return connection._execute_clauseelement(self, multiparams, params)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py', line 1003 in _execute_clauseelement
  inline=len(distilled_params) > 1)
File '<string>', line 1 in <lambda>
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py', line 494 in compile
  return self._compiler(dialect, bind=bind, **kw)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py', line 500 in _compiler
  return dialect.statement_compiler(dialect, self, **kw)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 392 in __init__
  Compiled.__init__(self, dialect, statement, **kwargs)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 190 in __init__
  self.string = self.process(self.statement, **compile_kwargs)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 213 in process
  return obj._compiler_dispatch(self, **kwargs)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py', line 81 in _compiler_dispatch
  return meth(self, **kw)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 1602 in visit_select
  text, select, inner_columns, froms, byfrom, kwargs)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 1699 in _compose_select_body
  t = select._whereclause._compiler_dispatch(self, **kwargs)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py', line 93 in _compiler_dispatch
  return meth(self, **kw)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 745 in visit_clauselist
  for c in clauselist.clauses)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 742 in <genexpr>
  s for s in
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 745 in <genexpr>
  for c in clauselist.clauses)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py', line 93 in _compiler_dispatch
  return meth(self, **kw)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 921 in visit_binary
  return self._generate_generic_binary(binary, opstring, **kw)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 938 in _generate_generic_binary
  binary.right._compiler_dispatch(self, **kw)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py', line 93 in _compiler_dispatch
  return meth(self, **kw)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 1067 in visit_bindparam
  name = self._truncate_bindparam(bindparam)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 1123 in _truncate_bindparam
  bind_name = self._truncated_identifier("bindparam", bind_name)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 1134 in _truncated_identifier
  anonname = name.apply_map(self.anon_map)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py', line 3630 in apply_map
  return self % map_
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/util/_collections.py', line 728 in __missing__
  self[key] = val = self.creator(key)
File '/srv/toolshed/test/venv/local/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py', line 1153 in _process_anon
  return derived + "_" + str(anonymous_counter)
RuntimeError: maximum recursion depth exceeded while getting the str of an object
martenson commented 7 years ago

This also prevents the suite from being installed.

mvdbeek commented 4 years ago

Installation by API seems to work now, and the linked view displays fine.