Fill in needed state defaults when importing manually curated workflows.

lib/galaxy/managers/workflows.py

@@ -244,6 +244,7 @@ def build_workflow_from_dict(
         publish=False,
         create_stored_workflow=True,
         exact_tools=True,
+        fill_defaults=False,
     ):
         # Put parameters in workflow mode
         trans.workflow_building_mode = workflow_building_modes.ENABLED
@@ -257,6 +258,7 @@ def build_workflow_from_dict(
             data,
             name=name,
             exact_tools=exact_tools,
+            fill_defaults=fill_defaults,
         )
         if 'uuid' in data:
             workflow.uuid = data['uuid']
@@ -298,14 +300,15 @@ def build_workflow_from_dict(
             missing_tools=missing_tool_tups
         )
 
-    def update_workflow_from_dict(self, trans, stored_workflow, workflow_data):
+    def update_workflow_from_dict(self, trans, stored_workflow, workflow_data, **kwds):
         # Put parameters in workflow mode
         trans.workflow_building_mode = workflow_building_modes.ENABLED
 
         workflow, missing_tool_tups = self._workflow_from_dict(
             trans,
             workflow_data,
             name=stored_workflow.name,
+            **kwds
         )
 
         if missing_tool_tups:

lib/galaxy/web/base/controller.py

@@ -1237,7 +1237,7 @@ def _import_shared_workflow(self, trans, stored):
         session.flush()
         return imported_stored
 
-    def _workflow_from_dict(self, trans, data, source=None, add_to_menu=False, publish=False, exact_tools=True):
+    def _workflow_from_dict(self, trans, data, source=None, add_to_menu=False, publish=False, exact_tools=True, fill_defaults=False):
         """
         Creates a workflow from a dict. Created workflow is stored in the database and returned.
         """
@@ -1250,6 +1250,7 @@ def _workflow_from_dict(self, trans, data, source=None, add_to_menu=False, publi
             add_to_menu=add_to_menu,
             publish=publish,
             exact_tools=exact_tools,
+            fill_defaults=fill_defaults,
         )
         return created_workflow.stored_workflow, created_workflow.missing_tools
 

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -515,10 +515,12 @@ def update(self, trans, id, payload, **kwds):
 
             if 'steps' in workflow_dict:
                 try:
+                    from_dict_kwds = self.__import_or_update_kwds(payload)
                     workflow, errors = self.workflow_contents_manager.update_workflow_from_dict(
                         trans,
                         stored_workflow,
                         workflow_dict,
+                        **from_dict_kwds
                     )
                 except workflows.MissingToolsException:
                     raise exceptions.MessageException("This workflow contains missing tools. It cannot be saved until they have been removed from the workflow or installed.")
@@ -578,18 +580,17 @@ def __api_import_new_workflow(self, trans, payload, **kwd):
         import_tools = util.string_as_bool(payload.get("import_tools", False))
         if import_tools and not trans.user_is_admin():
             raise exceptions.AdminRequiredException()
+
+        from_dict_kwds = self.__import_or_update_kwds(payload)
+
         publish = util.string_as_bool(payload.get("publish", False))
         # If 'publish' set, default to importable.
         importable = util.string_as_bool(payload.get("importable", publish))
-        # Galaxy will try to upgrade tool versions that don't match exactly during import,
-        # this prevents that.
-        exact_tools = util.string_as_bool(payload.get("exact_tools", True))
+
         if publish and not importable:
             raise exceptions.RequestParameterInvalidException("Published workflow must be importable.")
-        from_dict_kwds = dict(
-            publish=publish,
-            exact_tools=exact_tools,
-        )
+
+        from_dict_kwds["publish"] = publish
         workflow, missing_tool_tups = self._workflow_from_dict(trans, data, **from_dict_kwds)
         if importable:
             self._make_item_accessible(trans.sa_session, workflow)
@@ -629,6 +630,20 @@ def __api_import_new_workflow(self, trans, payload, **kwd):
                             payload)
         return item
 
+    def __import_or_update_kwds(self, payload):
+        # Galaxy will try to upgrade tool versions that don't match exactly during import,
+        # this prevents that.
+        exact_tools = util.string_as_bool(payload.get("exact_tools", True))
+
+        # Fill in missing tool state for hand built so the workflow can run, default of this
+        # should become True at some point in the future I imagine.
+        fill_defaults = util.string_as_bool(payload.get("fill_defaults", False))
+
+        return {
+            'exact_tools': exact_tools,
+            'fill_defaults': fill_defaults,
+        }
+
     @expose_api
     def import_shared_workflow_deprecated(self, trans, payload, **kwd):
         """

lib/galaxy/workflow/modules.py

@@ -77,7 +77,7 @@ def __init__(self, trans, content_id=None, **kwds):
     @classmethod
     def from_dict(Class, trans, d, **kwds):
         module = Class(trans, **kwds)
-        module.recover_state(d.get("tool_state"))
+        module.recover_state(d.get("tool_state"), **kwds)
         module.label = d.get("label")
         return module
 
@@ -848,6 +848,18 @@ def get_post_job_actions(self, incoming):
 
     # ---- Run time ---------------------------------------------------------
 
+    def recover_state(self, state, **kwds):
+        """ Recover state `dict` from simple dictionary describing configuration
+        state (potentially from persisted step state).
+
+        Sub-classes should supply a `default_state` method which contains the
+        initial state `dict` with key, value pairs for all available attributes.
+        """
+        super(ToolModule, self).recover_state(state, **kwds)
+        if kwds.get("fill_defaults", False) and self.tool:
+            self.compute_runtime_state(self.trans, step_updates=None)
+            self.tool.check_and_update_param_values(self.state.inputs, self.trans, workflow_building_mode=True)
+
     def get_runtime_state(self):
         state = DefaultToolState()
         state.inputs = self.state.inputs

test/api/test_workflows_from_yaml.py

@@ -3,6 +3,7 @@
 import json
 import os
 
+from base.populators import uses_test_history
 from base.workflow_fixtures import (
     WORKFLOW_RUNTIME_PARAMETER_SIMPLE,
 )
@@ -300,6 +301,39 @@ def test_implicit_connections(self):
         workflow = self._get("workflows/%s/download" % workflow_id).json()
         print(workflow)
 
+    @uses_test_history()
+    def test_conditional_ints(self, history_id):
+        self._run_jobs("""
+class: GalaxyWorkflow
+steps:
+  - label: test_input
+    tool_id: disambiguate_cond
+    state:
+      p3:
+        use: true
+      files:
+        attach_files: false
+""", test_data={}, history_id=history_id)
+        content = self.dataset_populator.get_history_dataset_content(history_id)
+        assert "no file specified" in content
+        assert "7 7 4" in content
+
+        self._run_jobs("""
+class: GalaxyWorkflow
+steps:
+  - label: test_input
+    tool_id: disambiguate_cond
+    state:
+      p3:
+        use: true
+        p3v: 5
+      files:
+        attach_files: false
+""", test_data={}, history_id=history_id)
+        content = self.dataset_populator.get_history_dataset_content(history_id)
+        assert "no file specified" in content
+        assert "7 7 5" in content
+
     def _steps_by_label(self, workflow_as_dict):
         by_label = {}
         assert "steps" in workflow_as_dict, workflow_as_dict

test/base/populators.py

@@ -570,7 +570,7 @@ def invoke_workflow(self, history_id, workflow_id, inputs={}, request={}, assert
         if inputs:
             request["inputs"] = json.dumps(inputs)
             request["inputs_by"] = 'step_index'
-        invocation_response = self.invoke_workflow_raw(request)
+        invocation_response = self.invoke_workflow_raw(workflow_id, request)
         if assert_ok:
             api_asserts.assert_status_code_is(invocation_response, 200)
             invocation_id = invocation_response.json()["id"]

test/base/workflows_format_2/main.py

@@ -35,7 +35,10 @@ def convert_and_import_workflow(has_workflow, **kwds):
         workflow["name"] = name
     publish = kwds.get("publish", False)
     exact_tools = kwds.get("exact_tools", False)
-    import_kwds = {}
+    fill_defaults = kwds.get("fill_defaults", True)
+    import_kwds = {
+        "fill_defaults": fill_defaults
+    }
     if publish:
         import_kwds["publish"] = True
     if exact_tools:

test/functional/tools/disambiguate_cond.xml

@@ -1,6 +1,11 @@
 <tool id="disambiguate_cond" name="disambiguate_cond">
     <command>
-        echo "$p1.p1v $p2.p2v $p3.p3v" > $out_file1; cat "$files.p4.file" >> $out_file1;
+        echo "$p1.p1v $p2.p2v $p3.p3v" > $out_file1;
+        #if $files.attach_files
+        cat "$files.p4.file" >> $out_file1;
+        #else
+        echo "no file specified" >> $out_file1;
+        #end if
     </command>
     <inputs>
         <conditional name="p1">