Merge pull request #1305 from lldelisle/fix_autoupdate_error

Don't fail planemo autoupdate if tool version not found in tool shed

planemo/autoupdate.py

@@ -295,6 +295,9 @@ def check_tool_step(step, ts):  # return a dict with current and newest tool ver
         except Exception:
             ctx.log(f"The ToolShed returned an error when searching for the most recent version of {step['tool_id']}")
             return {}
+        if len(repos) == 0:
+            ctx.log(f"The tool {step['tool_id']} is not in the toolshed (may have been tagged as invalid).")
+            return {}
         base_id = "/".join(step["tool_id"].split("/")[:-1])
         tool_ids_found = {
             tool["guid"] for repo in repos.values() if type(repo) == dict for tool in repo.get("tools", [])

tests/data/wf_repos/autoupdate_tests/workflow_with_unexisting_version_of_tool.ga

@@ -0,0 +1,92 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "",
+    "format-version": "0.1",
+    "name": "Workflow with unexisting version of tool",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "input"
+                }
+            ],
+            "label": "input",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 0
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "62da4422-2462-40d8-a4f6-35b0fd1156f4",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "070bf2da-a153-4b1e-a38c-55fc164ca4f9"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/0.1.0",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "infile": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Select first",
+                    "name": "infile"
+                }
+            ],
+            "label": "fake tool",
+            "name": "Select first",
+            "outputs": [
+                {
+                    "name": "outfile",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 281,
+                "top": 47
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/0.1.0",
+            "tool_shed_repository": {
+                "changeset_revision": "adf54b12c295",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"complement\": \"\", \"count\": \"10\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.1.0",
+            "type": "tool",
+            "uuid": "c15c0342-6bde-4c83-9399-3b8597de6a83",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "outfile",
+                    "uuid": "61762374-8db1-46bc-8446-0eaca9ab8e92"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "e75d0ddc-b376-456f-b5e3-a8afbb7b85ed",
+    "version": 1
+}

tests/test_cmd_autoupdate.py

@@ -100,3 +100,13 @@ def test_autoupdate_workflow(self):
             assert wf["steps"][0]["tool_id"] == "toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0"
             assert wf["steps"][1]["run"]["steps"][0]["tool_version"] == "3.7+galaxy0"
             assert wf["release"] == "0.1.1"
+
+    def test_autoupdate_workflow_unexisting_version(self):
+        """Test autoupdate command for a workflow where the version of the tool is not in the toolshed."""
+        with self._isolate_with_test_data("wf_repos/autoupdate_tests") as f:
+            wf_file = os.path.join(f, "workflow_with_unexisting_version_of_tool.ga")
+            autoupdate_command = ["autoupdate", wf_file]
+            self._runner.invoke(self._cli.planemo, autoupdate_command)
+            # We just want to be sure planemo autoupdate do not raise an error
+            # Currently it would write to the output that no update are available
+            # In future versions it could be great that it gives the last valid version.