tools-iuc
tools-iuc copied to clipboard
Published
20 hours ago •
galaxyproject
galaxyproject
data_manager_fetch_genome_dbkeys_all_fasta cannot populate dbkey table
Hello, I don't know if the issue is the tool wrapper or galaxy.
I used the data_manager 'data_manager_fetch_genome_dbkeys_all_fasta' version 0.0.5. And the datamanager populates the table all_fasta.loc but not the 'dbkeys.loc'. The job is in error state because exec_after_process hook failed. If I check the journalctl I have:
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: During handling of the above exception, another exception occurred: 18:05:48 [0/1951]
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: Traceback (most recent call last):
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/jobs/__init__.py", line 2048, in finish
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: task_wrapper = self.tool.exec_after_process(
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/tools/__init__.py", line 3162, in exec_after_process
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: data_manager.process_result(out_data)
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/tools/data_manager/manager.py", line 235, in process_result
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: updated_data_tables = tool_data_tables.process_bundle(
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/tool_util/data/__init__.py", line 1174, in process_bundle
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: return _process_bundle(out_data, bundle, options, self)
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/tool_util/data/__init__.py", line 1311, in _process_bundle
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: _process_move(
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/tool_util/data/__init__.py", line 1410, in _process_move
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: fill_template(
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/util/template.py", line 115, in fill_template
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: return fill_template(
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: ^^^^^^^^^^^^^^
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/util/template.py", line 115, in fill_template
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: return fill_template(
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: ^^^^^^^^^^^^^^
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/util/template.py", line 115, in fill_template
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: return fill_template(
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: ^^^^^^^^^^^^^^
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: [Previous line repeated 7 more times]
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/util/template.py", line 123, in fill_template
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: raise first_exception or e
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: return unicodify(t, log_exception=False)
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: value = str(value)
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: ^^^^^^^^^^
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/venv/lib/python3.12/site-packages/Cheetah/Template.py", line 1053, in __unicode__
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: return getattr(self, mainMethName)()
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "cheetah_DynamicallyCompiledCheetahTemplate_1743181323_7225928_37719.py", line 87, in respond
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/venv/lib/python3.12/site-packages/Cheetah/NameMapper.py", line 293, in valueFromSearchList
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: _raiseNotFoundException(key, searchList)
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: File "/data/galaxy/galaxy/venv/lib/python3.12/site-packages/Cheetah/NameMapper.py", line 178, in _raiseNotFoundException
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: raise NotFound(excString)
Mar 28 18:05:47 workstationduboule galaxyctl[2847543]: Cheetah.NameMapper.NotFound: cannot find 'dbkey'
I am running galaxy release 24.1 and the playbook is here: https://github.com/lldelisle/galaxyduboule-infrastructure/tree/setup_cdf
The server is ubuntu 24.04.2
python 3.12.
