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TypeError: 'NoneType' object does not support item assignment
File "galaxy/jobs/runners/__init__.py", line 297, in prepare_job
job_wrapper.prepare()
File "galaxy/jobs/__init__.py", line 1249, in prepare
tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
File "galaxy/tools/evaluation.py", line 171, in set_compute_environment
self.execute_tool_hooks(inp_data=inp_data, out_data=out_data, incoming=incoming)
File "galaxy/tools/evaluation.py", line 176, in execute_tool_hooks
self.tool.exec_before_job(self.app, inp_data, out_data, self.param_dict)
File "galaxy/tools/__init__.py", line 2849, in exec_before_job
json_wrap(self.inputs, param_dict, self.profile, job, handle_files="OBJECT")
File "galaxy/tools/parameters/wrapped_json.py", line 31, in json_wrap
json_value = _json_wrap_input(input, value_wrapper, profile, handle_files=handle_files)
File "galaxy/tools/parameters/wrapped_json.py", line 141, in _json_wrap_input
json_value["contents"] = fh.read(input.load_contents).decode("utf-8", errors="replace")
json_value here is None, which I think is a valid input, but it looks like a this was part of a workflow that failed early on, including a proper workflow invocation error message, so this might not be a high-priority bug.
The text was updated successfully, but these errors were encountered:
If that is the case, this leads to a different error down the road:
galaxy.tool_util.output_checker INFO 2024-04-19 18:07:59,295 [pN:main.1,p:583932,tN:LocalRunner.work_thread-1] Job failed because of contents in the standard error stream: [Traceback (most recent call last):
File "/home/dlopez/sandbox/data-gx/24.0/jobs_directory/000/416/_evaluate_expression_.py", line 1, in <module>
from galaxy_ext.expressions.handle_job import run; run()
^^^^^
File "/home/dlopez/dev/gx-version/24.0/lib/galaxy_ext/expressions/handle_job.py", line 54, in run
output_value = expression.interpolate(from_expression, result)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dlopez/dev/gx-version/24.0/.venv/lib/python3.11/site-packages/cwl_utils/expression.py", line 215, in interpolate
e = evaluator(
^^^^^^^^^^
File "/home/dlopez/dev/gx-version/24.0/.venv/lib/python3.11/site-packages/cwl_utils/expression.py", line 164, in evaluator
raise JavascriptException(
cwl_utils.errors.JavascriptException: Syntax error in parameter reference 'output': output is not defined. This could be due to using Javascript code without specifying InlineJavascriptRequirement.
]
galaxy.jobs DEBUG 2024-04-19 18:07:59,337 [pN:main.1,p:583932,tN:LocalRunner.work_thread-1] (416) setting dataset 417 state to ERROR
So I guess we need to return something else as output, right? 🤔
from https://sentry.galaxyproject.org/share/issue/021c4d3c646149eab718d9ceea5487ea/.
json_value
here is None, which I think is a valid input, but it looks like a this was part of a workflow that failed early on, including a proper workflow invocation error message, so this might not be a high-priority bug.The text was updated successfully, but these errors were encountered: