Merge pull request #17271 from bernt-matthias/topic/null-exec-post

Consider Null inputs

lib/galaxy/tools/__init__.py

@@ -2864,6 +2864,8 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
             if val.output_type == "data":
                 with open(out_data[key].get_file_name()) as f:
                     src = json.load(f)
+                if src is None:
+                    continue
                 assert isinstance(src, dict), f"Expected dataset 'src' to be a dictionary - actual type is {type(src)}"
                 dataset_id = src["id"]
                 copy_object = None

test/integration/test_workflow_invocation.py

@@ -7,6 +7,48 @@
 from galaxy_test.base.uses_shed_api import UsesShedApi
 from galaxy_test.driver import integration_util
 
+OPTIONAL_INPUT_BOOL_WORKFLOW = """
+class: GalaxyWorkflow
+inputs:
+  optional_data:
+    optional: true
+    type: data
+steps:
+  optional_data_to_boolean:
+    tool_id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
+    tool_state:
+      input_param_type:
+        mappings:
+        - from: null
+          to: false
+        type: data
+      output_param_type: boolean
+      unmapped:
+        default_value: true
+        on_unmapped: default
+    in:
+      input_param_type|input_param: optional_data
+  optional_to_non_optional:
+    tool_id: pick_value
+    tool_state:
+      style_cond:
+        pick_style: first
+        type_cond:
+          param_type: data
+    in:
+      style_cond|type_cond|pick_from_0|value:
+        source: optional_data
+  cat1:
+    tool_id: cat1
+    when: $(inputs.when)
+    in:
+      input1: optional_to_non_optional/data_param
+      when: optional_data_to_boolean/output_param_boolean
+outputs:
+  cat1:
+    outputSource: cat1/out_file1
+"""
+
 
 class TestWorkflowInvocation(integration_util.IntegrationTestCase, UsesShedApi):
     dataset_populator: DatasetPopulator
@@ -18,6 +60,33 @@ def setUp(self):
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
         self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
 
+    def test_run_workflow_optional_data_skips_step(self) -> None:
+        self.install_repository("iuc", "map_param_value", "5ac8a4bf7a8d")
+        with self.dataset_populator.test_history() as history_id:
+            summary = self.workflow_populator.run_workflow(OPTIONAL_INPUT_BOOL_WORKFLOW, history_id=history_id)
+            invocation_details = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True)
+            for step in invocation_details["steps"]:
+                if step["workflow_step_label"] == "cat1":
+                    assert sum(1 for j in step["jobs"] if j["state"] == "skipped") == 1
+
+    def test_run_workflow_optional_data_provided_runs_step(self) -> None:
+        self.install_repository("iuc", "map_param_value", "5ac8a4bf7a8d")
+        with self.dataset_populator.test_history() as history_id:
+            summary = self.workflow_populator.run_workflow(
+                OPTIONAL_INPUT_BOOL_WORKFLOW,
+                test_data={
+                    "optional_data": {
+                        "value": "1.bed",
+                        "type": "File",
+                    }
+                },
+                history_id=history_id,
+            )
+            invocation_details = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True)
+            for step in invocation_details["steps"]:
+                if step["workflow_step_label"] == "cat1":
+                    assert sum(1 for j in step["jobs"] if j["state"] == "ok") == 1, step["jobs"]
+
     def test_run_workflow_with_missing_tool(self):
         self.install_repository("iuc", "compose_text_param", "feb3acba1e0a")  # 0.1.0
         with self.dataset_populator.test_history() as history_id: