Galaxy |

export_remote in error's stderr message

Listed in descending order by number of error of each type

Tool error	Number of error like this	Date of this error
Traceback (most recent call last): File "/srv/galaxy/server/tools/data_export/export_remote.py", line 79, in ... File "/srv/galaxy/server/lib/galaxy/files/sources/nels.py", line 125, in _write_from dirname = fs.path.dirname(target_path) NameError: name 'fs' is not defined ------------------------- Extended error ------------------------- Traceback (most recent call last): File "/srv/galaxy/server/tools/data_export/export_remote.py", line 79, in main() File "/srv/galaxy/server/tools/data_export/export_remote.py", line 56, in main if write_if_not_exists(file_sources, target_uri, real_data_path): File "/srv/galaxy/server/tools/data_export/export_remote.py", line 35, in write_if_not_exists file_source.write_from(file_source_path.path, real_data_path) File "/srv/galaxy/server/lib/galaxy/files/sources/__init__.py", line 158, in write_from self._write_from(target_path, native_path, user_context=user_context) File "/srv/galaxy/server/lib/galaxy/files/sources/nels.py", line 125, in _write_from dirname = fs.path.dirname(target_path) NameError: name 'fs' is not defined ------------------------------------------------------------------	3	2024-04-02
Traceback (most recent call last): File "/srv/galaxy/server/lib/galaxy/files/sources/nels.py", line 134, in _write_from ... File "/srv/galaxy/server/lib/galaxy/files/sources/nels.py", line 140, in _write_from if (h): UnboundLocalError: local variable 'h' referenced before assignment ------------------------- Extended error ------------------------- Traceback (most recent call last): File "/srv/galaxy/server/lib/galaxy/files/sources/nels.py", line 134, in _write_from h = self._open_fs(user_context=user_context, opts=opts) File "/srv/galaxy/server/lib/galaxy/files/sources/nels.py", line 156, in _open_fs [host,nelsUser,sshKey] = self._get_nels_ssh_credentials(username,config['API_URL'],config['CLIENT_KEY'],config['CLIENT_SECRET']) File "/srv/galaxy/server/lib/galaxy/files/sources/nels.py", line 199, in _get_nels_ssh_credentials raise Exception("NeLS Storage API error: HTTP response code %s [%s]" % (str(response.status_code),url)) Exception: NeLS Storage API error: HTTP response code 502 [https://test-fe.cbu.uib.no/nels-storage2/federated/siljeo@test.feide.no] During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/srv/galaxy/server/tools/data_export/export_remote.py", line 79, in main() File "/srv/galaxy/server/tools/data_export/export_remote.py", line 56, in main if write_if_not_exists(file_sources, target_uri, real_data_path): File "/srv/galaxy/server/tools/data_export/export_remote.py", line 35, in write_if_not_exists file_source.write_from(file_source_path.path, real_data_path) File "/srv/galaxy/server/lib/galaxy/files/sources/__init__.py", line 310, in write_from self._write_from(target_path, native_path, user_context=user_context, opts=opts) File "/srv/galaxy/server/lib/galaxy/files/sources/nels.py", line 140, in _write_from if (h): UnboundLocalError: local variable 'h' referenced before assignment ------------------------------------------------------------------	2	2024-03-31
Traceback (most recent call last): File "/srv/galaxy/server/tools/data_export/export_remote.py", line 79, in ... File "/srv/galaxy/server/lib/galaxy/files/sources/s3fs.py", line 25, in __init__ raise Exception("Package s3fs unavailable but required for this file source plugin.") Exception: Package s3fs unavailable but required for this file source plugin. ------------------------- Extended error ------------------------- Traceback (most recent call last): File "/srv/galaxy/server/tools/data_export/export_remote.py", line 79, in main() File "/srv/galaxy/server/tools/data_export/export_remote.py", line 43, in main file_sources = get_file_sources(args.file_sources) File "/srv/galaxy/server/tools/data_export/export_remote.py", line 13, in get_file_sources file_sources = ConfiguredFileSources.from_dict(file_sources_as_dict) File "/srv/galaxy/server/lib/galaxy/files/__init__.py", line 179, in from_dict return ConfiguredFileSources(file_sources_config, conf_dict=sources_as_dict) File "/srv/galaxy/server/lib/galaxy/files/__init__.py", line 30, in __init__ file_sources = self._parse_plugin_source(plugin_source) File "/srv/galaxy/server/lib/galaxy/files/__init__.py", line 75, in _parse_plugin_source dict_to_list_key="id", File "/srv/galaxy/server/lib/galaxy/util/plugin_config.py", line 39, in load_plugins dict_to_list_key=dict_to_list_key, File "/srv/galaxy/server/lib/galaxy/util/plugin_config.py", line 95, in __load_plugins_from_dicts plugin = plugins_dict[plugin_type](**plugin_kwds) File "/srv/galaxy/server/lib/galaxy/files/sources/s3fs.py", line 25, in __init__ raise Exception("Package s3fs unavailable but required for this file source plugin.") Exception: Package s3fs unavailable but required for this file source plugin. ------------------------------------------------------------------	1	2023-04-13
Traceback (most recent call last): File "/srv/galaxy/server/tools/data_export/export_remote.py", line 79, in ... File "/srv/galaxy/server/lib/galaxy/files/sources/s3fs.py", line 23, in __init__ raise Exception("Package s3fs unavailable but required for this file source plugin.") Exception: Package s3fs unavailable but required for this file source plugin. ------------------------- Extended error ------------------------- Traceback (most recent call last): File "/srv/galaxy/server/tools/data_export/export_remote.py", line 79, in main() File "/srv/galaxy/server/tools/data_export/export_remote.py", line 43, in main file_sources = get_file_sources(args.file_sources) File "/srv/galaxy/server/tools/data_export/export_remote.py", line 13, in get_file_sources file_sources = ConfiguredFileSources.from_dict(file_sources_as_dict) File "/srv/galaxy/server/lib/galaxy/files/__init__.py", line 179, in from_dict return ConfiguredFileSources(file_sources_config, conf_dict=sources_as_dict) File "/srv/galaxy/server/lib/galaxy/files/__init__.py", line 30, in __init__ file_sources = self._parse_plugin_source(plugin_source) File "/srv/galaxy/server/lib/galaxy/files/__init__.py", line 75, in _parse_plugin_source dict_to_list_key="id", File "/srv/galaxy/server/lib/galaxy/util/plugin_config.py", line 39, in load_plugins dict_to_list_key=dict_to_list_key, File "/srv/galaxy/server/lib/galaxy/util/plugin_config.py", line 95, in __load_plugins_from_dicts plugin = plugins_dict[plugin_type](**plugin_kwds) File "/srv/galaxy/server/lib/galaxy/files/sources/s3fs.py", line 23, in __init__ raise Exception("Package s3fs unavailable but required for this file source plugin.") Exception: Package s3fs unavailable but required for this file source plugin. ------------------------------------------------------------------	1	2023-04-13