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galaxy.jobs.runners ERROR 2020-07-22 15:15:32,060 (1) Failure preparing job
Traceback (most recent call last):
File "/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 236, in prepare_job
job_wrapper.prepare()
File "/galaxy-central/lib/galaxy/jobs/__init__.py", line 1096, in prepare
tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
File "/galaxy-central/lib/galaxy/tools/evaluation.py", line 119, in set_compute_environment
out_data=out_data, tool=self.tool, param_dict=incoming)
File "/galaxy-central/lib/galaxy/tools/__init__.py", line 1838, in call_hook
return code(*args, **kwargs)
File "/galaxy-central/database/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_manual/0bed5ee5b74a/data_manager_manual/data_manager/data_manager_manual.py", line 61, in exec_before_job
target_dir, tool_path, relative_target_dir = tdtm.get_target_install_dir(tool_shed_repository)
File "/galaxy-central/lib/galaxy/tool_shed/tools/data_table_manager.py", line 112, in get_target_install_dir
tool_path, relative_target_dir = tool_shed_repository.get_tool_relative_path(self.app)
File "/galaxy-central/lib/galaxy/model/tool_shed_install/__init__.py", line 103, in get_tool_relative_path
shed_conf_dict = self.get_shed_config_dict(app)
File "/galaxy-central/lib/galaxy/model/tool_shed_install/__init__.py", line 95, in get_shed_config_dict
if self.shed_config_filename:
File "/galaxy-central/lib/galaxy/model/tool_shed_install/__init__.py", line 84, in shed_config_filename
return self.metadata.get('shed_config_filename')
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/attributes.py", line 286, in __get__
return self.impl.get(instance_state(instance), dict_)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/attributes.py", line 720, in get
value = callable_(state, passive)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/strategies.py", line 439, in __call__
return strategy._load_for_state(state, passive)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/strategies.py", line 412, in _load_for_state
% (orm_util.state_str(state), self.key)
sqlalchemy.orm.exc.DetachedInstanceError: Error in 'Manual Data Manager' hook 'exec_before_job', original message: Parent instance <ToolShedRepository at 0x7fb5b70a2c88> is not bound to a Session; deferred load operation of attribute 'metadata' cannot proceed (Background on this error at: http://sqlalche.me/e/bhk3)
I think we've fixed this for good in #12390, which will be part of 21.09. I'm gonna close this but feel free to open again if you see this after updating to 21.09.
Hi,
Found an error with latest data_manager_manual and galaxy 20.05 while testing biomaj2galaxy with 20.05:
I guess Galaxy has problems executing this code: https://github.com/galaxyproject/tools-iuc/blob/master/data_managers/data_manager_manual/data_manager/data_manager_manual.py#L35
Any idea if it's a data_manager_manual or galaxy problem?
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