diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 2c14748468d..caed4b979c5 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -617,7 +617,7 @@ class WorkflowContentsManager(UsesAnnotations):
continue
if step.upgrade_messages:
has_upgrade_messages = True
- if step.type == 'tool' or step.type is None:
+ if step.type in ('tool', 'subworkflow', None):
if step.module.version_changes:
step_version_changes.extend(step.module.version_changes)
step_errors = step.module.get_errors()
@@ -805,7 +805,7 @@ class WorkflowContentsManager(UsesAnnotations):
# Fix any missing parameters
upgrade_message_dict = module.check_and_update_state() or {}
if hasattr(module, "version_changes") and module.version_changes:
- upgrade_message_dict[module.tool.name] = "\n".join(module.version_changes)
+ upgrade_message_dict[module.get_name()] = "\n".join(module.version_changes)
# Get user annotation.
config_form = module.get_config_form(step=step)
annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 6ab39d1f6b8..262593afc9e 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -761,21 +761,6 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
return True
return False
- def get_tool_id(self, tool_id):
- """ Take a tool id - potentially from a different Galaxy instance or that
- is no longer loaded - and find the closest match to the currently loaded
- tools (using get_tool for inexact matches which currently returns the oldest
- tool shed installed tool with the same short id).
- """
- if tool_id not in self._tools_by_id:
- tool = self.get_tool(tool_id)
- if tool:
- tool_id = tool.id
- else:
- tool_id = None
- # else exact match - leave unmodified.
- return tool_id
-
def get_loaded_tools_by_lineage(self, tool_id):
"""Get all loaded tools associated by lineage to the tool whose id is tool_id."""
tool_lineage = self._lineage_map.get(tool_id)
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 8400f42114b..2463fcf1d02 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -398,6 +398,7 @@ class SubWorkflowModule(WorkflowModule):
# - Second pass actually turn RuntimeInputs into inputs if possible.
type = "subworkflow"
name = "Subworkflow"
+ _modules = None
@classmethod
def from_dict(Class, trans, d, **kwds):
@@ -455,7 +456,21 @@ class SubWorkflowModule(WorkflowModule):
return inputs
def get_modules(self):
- return [module_factory.from_workflow_step(self.trans, step) for step in self.subworkflow.steps]
+ if self._modules is None:
+ self._modules = [module_factory.from_workflow_step(self.trans, step) for step in self.subworkflow.steps]
+ return self._modules
+
+ @property
+ def version_changes(self):
+ version_changes = []
+ for m in self.get_modules():
+ if hasattr(m, 'version_changes'):
+ version_changes.extend(m.version_changes)
+ return version_changes
+
+ def check_and_update_state(self):
+ states = (m.check_and_update_state() for m in self.get_modules())
+ return [upgrade_message for upgrade_message in states if upgrade_message] or None
def get_errors(self, **kwargs):
errors = (module.get_errors(include_tool_id=True) for module in self.get_modules())
@@ -1244,13 +1259,15 @@ class ToolModule(WorkflowModule):
def __init__(self, trans, tool_id, tool_version=None, exact_tools=True, tool_uuid=None, **kwds):
super().__init__(trans, content_id=tool_id, **kwds)
self.tool_id = tool_id
- self.tool_version = str(tool_version)
+ 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)
if self.tool:
- if tool_version and exact_tools and str(self.tool.version) != tool_version:
- safe_version = WORKFLOW_SAFE_TOOL_VERSION_UPDATES.get(tool_id)
- if safe_version and safe_version.current_version >= packaging.version.parse(tool_version) >= safe_version.min_version:
+ current_tool_id = self.tool.id
+ current_tool_version = str(self.tool.version)
+ if tool_version and exact_tools and self.tool_version != current_tool_version:
+ safe_version = WORKFLOW_SAFE_TOOL_VERSION_UPDATES.get(current_tool_id)
+ if safe_version and safe_version.current_version >= packaging.version.parse(current_tool_id) >= safe_version.min_version:
self.tool = trans.app.toolbox.get_tool(tool_id, tool_version=tool_version, exact=False, tool_uuid=tool_uuid)
else:
log.info(f"Exact tool specified during workflow module creation for [{tool_id}] but couldn't find correct version [{tool_version}].")
@@ -1299,22 +1316,19 @@ class ToolModule(WorkflowModule):
@classmethod
def from_workflow_step(Class, trans, step, **kwds):
- if step.tool_id is not None:
- tool_id = trans.app.toolbox.get_tool_id(step.tool_id) or step.tool_id
- else:
- tool_id = None
tool_version = step.tool_version
tool_uuid = step.tool_uuid
- module = super().from_workflow_step(trans, step, tool_id=tool_id, tool_version=tool_version, tool_uuid=tool_uuid, **kwds)
+ kwds['exact_tools'] = False
+ module = super().from_workflow_step(trans, step, tool_id=step.tool_id, tool_version=tool_version, tool_uuid=tool_uuid, **kwds)
module.workflow_outputs = step.workflow_outputs
module.post_job_actions = {}
for pja in step.post_job_actions:
module.post_job_actions[pja.action_type] = pja
if module.tool:
message = ""
- if step.tool_id and step.tool_id != module.tool_id: # This means the exact version of the tool is not installed. We inform the user.
+ if step.tool_id and step.tool_id != module.tool.id or step.tool_version and step.tool_version != module.tool.version: # This means the exact version of the tool is not installed. We inform the user.
old_tool_shed = step.tool_id.split("/repos/")[0]
- if old_tool_shed not in tool_id: # Only display the following warning if the tool comes from a different tool shed
+ if old_tool_shed not in module.tool.id: # Only display the following warning if the tool comes from a different tool shed
old_tool_shed_url = get_tool_shed_url_from_tool_shed_registry(trans.app, old_tool_shed)
if not old_tool_shed_url: # a tool from a different tool_shed has been found, but the original tool shed has been deactivated
old_tool_shed_url = "http://" + old_tool_shed # let's just assume it's either http, or a http is forwarded to https.
@@ -1324,12 +1338,12 @@ class ToolModule(WorkflowModule):
message += f"The tool \'{module.tool.name}\', version {tool_version} by the owner {module.tool.repository_owner} installed from {old_tool_shed_url} is not available. "
message += f"A derivation of this tool installed from {new_tool_shed_url} will be used instead. "
if step.tool_version and (step.tool_version != module.tool.version):
- message += f"Using version '{module.tool.version}' instead of version '{step.tool_version}' specified in this workflow. "
+ message += f"Using version '{module.tool.version}' instead of version '{step.tool_version}' specified in this workflow. "
if message:
log.debug(message)
module.version_changes.append(message)
else:
- log.warning("The tool '%s' is missing. Cannot build workflow module." % tool_id)
+ log.warning("The tool '%s' is missing. Cannot build workflow module." % step.tool_id)
return module
# ---- Saving in various forms ------------------------------------------