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Slightly improve workflow warnings/errors logging. #4396

merged 3 commits into from Aug 18, 2017


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commented Aug 9, 2017

  • Better assertion message for unknown module types.
  • Warn in the logs if an input connection is defined but unused while connecting up things for tool execution.

More small usability improvements from the CWL branch.

@@ -965,7 +977,7 @@ def from_dict( self, trans, d, **kwargs ):
Return module initialized from the data in dictionary `d`.
type = d['type']
assert type in self.module_types
assert type in self.module_types, "Unexpected workflow step type [%s] not found in [%s]"% (type, self.module_types.keys())

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nsoranzo Aug 9, 2017


lib/galaxy/workflow/ E225 missing whitespace around operator

@@ -810,6 +810,9 @@ def execute( self, trans, progress, invocation, step ):
# TODO: Move next step into copy()
execution_state.inputs = make_dict_copy( execution_state.inputs )

expected_replacement_keys = set(step.input_connections_by_name.keys())
found_replacement_keys = set([])

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nsoranzo Aug 9, 2017


set() should be equivalent to set([])

jmchilton added a commit to jmchilton/galaxy that referenced this pull request Aug 9, 2017

@jmchilton jmchilton force-pushed the jmchilton:workflow_warnings branch from f71a000 to 7bf7f39 Aug 17, 2017

@nsoranzo nsoranzo merged commit 784e6f5 into galaxyproject:dev Aug 18, 2017

6 checks passed

api test Build finished. 281 tests run, 0 skipped, 0 failed.
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framework test Build finished. 153 tests run, 0 skipped, 0 failed.
integration test Build finished. 44 tests run, 0 skipped, 0 failed.
lgtm analysis: JavaScript No alert changes
toolshed test Build finished. 579 tests run, 0 skipped, 0 failed.
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