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Fixes for finding tools installed from a tool shed when building workflows from the current history or running workflows, and the workflow in question references tools using the old tool_id.

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Greg Von Kuster
2011-10-28 16:13:21 -04:00
parent 2e750be904
commit 20f01fcb8f
1 changed files with 20 additions and 2 deletions
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lib/galaxy/web/controllers/workflow.py
+20 -2
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@@ -1296,7 +1296,16 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
for job_id in job_ids:
assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
job = jobs_by_id[ job_id ]
tool = trans.app.toolbox.tools_by_id[ job.tool_id ]
try:
tool = trans.app.toolbox.tools_by_id[ job.tool_id ]
except KeyError, e:
# Handle the case where the workflow requires a tool not available in the local Galaxy instance.
# The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id
# attribute should contain what we're looking for.
for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
if job.tool_id == available_tool.old_id:
tool = available_tool
break
param_values = job.get_param_values( trans.app )
associations = cleanup_param_values( tool.inputs, param_values )
# Doing it this way breaks dynamic parameters, backed out temporarily.
@@ -1463,7 +1472,16 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
# Execute module
job = None
if step.type == 'tool' or step.type is None:
tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
try:
tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
except KeyError, e:
# Handle the case where the workflow requires a tool not available in the local Galaxy instance.
# The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id
# attribute should contain what we're looking for.
for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
if step.tool_id == available_tool.old_id:
tool = available_tool
break
input_values = step.state.inputs
# Connect up
def callback( input, value, prefixed_name, prefixed_label ):