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Fix missing tools wf editor alternative #4552

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merged 4 commits into from Sep 5, 2017
Merged

Fix missing tools wf editor alternative #4552

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686cb48
Alternative fix for workflow editor hang with missing tools
mvdbeek Sep 5, 2017
33defd1
Revert "Properly raise Exception if tool not found"
mvdbeek Sep 5, 2017
09c96da
Fix extra-space (thx @nsoranzo)
mvdbeek Sep 5, 2017
40c9ca5
Log warning for missing tools when building workflow modules
mvdbeek Sep 5, 2017
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3 changes: 3 additions & 0 deletions lib/galaxy/managers/workflows.py
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Expand Up @@ -568,6 +568,9 @@ def _workflow_to_dict_export(self, trans, stored=None, workflow=None):
module = module_factory.from_workflow_step(trans, step)
if not module:
return None
if module.type == 'tool' and not module.tool:
msg = "Cannot download workflow because the tool '%s' is missing in step %s." % (step.tool_id, step.order_index)
raise exceptions.ToolMissingException(msg)
# Get user annotation.
annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
content_id = module.get_content_id()
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3 changes: 1 addition & 2 deletions lib/galaxy/workflow/modules.py
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Expand Up @@ -618,8 +618,7 @@ def from_workflow_step(Class, trans, step, **kwds):
log.debug(message)
module.version_changes.append(message)
else:
# The tool is not installed
raise ToolMissingException("Tool %s missing. Cannot build workflow module." % tool_id)
log.warning("The tool '%s' is missing. Cannot build workflow module." % tool_id)
return module

# ---- Saving in various forms ------------------------------------------
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