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Merge pull request #14624 from davelopez/fix_invocation_export_with_celery

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Fix `toolbox` access in invocation export
This commit is contained in:
Björn Grüning
2022-09-15 18:20:12 +02:00
committed by GitHub
parent a887fc894d 07b38ba429
commit 89803553db
1 changed files with 14 additions and 8 deletions
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lib/galaxy/workflow/modules.py
+14 -8
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@@ -1437,9 +1437,11 @@ class ToolModule(WorkflowModule):
self.tool_id = tool_id
self.tool_version = str(tool_version) if tool_version else None
self.tool_uuid = tool_uuid
self.tool = trans.app.toolbox.get_tool(
tool_id, tool_version=tool_version, exact=exact_tools, tool_uuid=tool_uuid
)
self.tool = None
if getattr(trans.app, "toolbox", None):
self.tool = trans.app.toolbox.get_tool(
tool_id, tool_version=tool_version, exact=exact_tools, tool_uuid=tool_uuid
)
if self.tool:
current_tool_id = self.tool.id
current_tool_version = str(self.tool.version)
@@ -1789,7 +1791,12 @@ class ToolModule(WorkflowModule):
input_connections = kwds.get("input_connections", {})
expected_replacement_keys = input_connections.keys()
def augment(expected_replacement_key, inputs, inputs_states):
def augment(expected_replacement_key, inputs_states):
if self.tool is None:
raise ToolMissingException(
f"Tool {self.tool_id} missing. Cannot augment tool state for input connections.",
tool_id=self.tool_id,
)
if "|" not in expected_replacement_key:
return
@@ -1817,12 +1824,11 @@ class ToolModule(WorkflowModule):
if repeat_instance_state:
# TODO: untest branch - no test case for nested repeats yet...
augment(rest, repeat.inputs, repeat_instance_state)
augment(rest, repeat_instance_state)
for expected_replacement_key in expected_replacement_keys:
inputs_states = self.state.inputs
inputs = self.tool.inputs
augment(expected_replacement_key, inputs, inputs_states)
augment(expected_replacement_key, inputs_states)
def get_runtime_state(self):
state = DefaultToolState()
@@ -2097,7 +2103,7 @@ class WorkflowModuleFactory:
def from_workflow_step(self, trans, step, **kwargs):
"""
Return module initializd from the WorkflowStep object `step`.
Return module initialized from the WorkflowStep object `step`.
"""
type = step.type
return self.module_types[type].from_workflow_step(trans, step, **kwargs)