Fix boolean to select bugs in msconvert #755
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Fixes
```
NotFound: cannot find 'input_ident' while searching for 'data_processing.precursor_refinement.input_ident.ext'
File "galaxy/jobs/runners/__init__.py", line 297, in prepare_job
job_wrapper.prepare()
File "galaxy/jobs/__init__.py", line 1256, in prepare
) = tool_evaluator.build()
File "galaxy/tools/evaluation.py", line 588, in build
global_tool_logs(self._build_command_line, config_file, "Building Command Line")
File "galaxy/tools/evaluation.py", line 98, in global_tool_logs
raise e
File "galaxy/tools/evaluation.py", line 94, in global_tool_logs
return func()
File "galaxy/tools/evaluation.py", line 611, in _build_command_line
command_line = fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 115, in fill_template
return fill_template(
File "galaxy/util/template.py", line 123, in fill_template
raise first_exception or e
File "galaxy/util/template.py", line 87, in fill_template
return unicodify(t, log_exception=False)
File "galaxy/util/__init__.py", line 1196, in unicodify
value = str(value)
File "Cheetah/Template.py", line 1053, in __unicode__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1712898486_6070771_49370.py", line 146, in respond
```
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Really can't tell what the problem is here, step 5 is even missing from the log archive. |
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Any chance we could merge this ? AFAICT the CI runs out of disk space. I've just fixed this again before I noticed I already came here to fix it. |
bgruening
approved these changes
Jul 26, 2024
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I hope it gets deployed, lets see. Thanks @mvdbeek! |
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I think this didn't get deployed @bgruening: https://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert/545054b15d7c |
|
Manually uploaded. Thanks. |
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Fixes
which broke in 79947db.
@bebatut is there a chance that you could go over your recent EDAM related commits and see if this has happened elsewhere ?