Fix HistoryClient.show_dataset_provenance() not passing the follow parameter

Author: nsoranzo

CHANGELOG.md

@@ -12,9 +12,20 @@
 
 * Added ``get_or_create_user_apikey()`` method to ``UserClient``.
 
+* Added ``require_exact_tool_versions`` parameter to
+  ``WorkflowClient.invoke_workflow()`` method (thanks to
+  [cat-bro](https://github.com/cat-bro)).
+
 * Remove unused methods from ``bioblend.config.Config``. If needed, use the
   methods inherited from `configparser.ConfigParser` instead.
 
+* Allowed any 2XX HTTP response status code in ``Client._delete()`` to correctly
+  support history purging via Celery (thanks to
+  [Nolan Woods](https://github.com/innovate-invent)).
+
+* Fixed bug in ``HistoryClient.show_dataset_provenance()`` where the ``follow``
+  parameter was not passed to the Galaxy API.
+
 * BioBlend.objects: Added ``delete()`` abstract method to ``DatasetContainer``
   class.
 

bioblend/_tests/GalaxyTestBase.py

@@ -1,6 +1,11 @@
 import os
 import unittest
-from typing import Any
+from typing import (
+    Any,
+    Dict,
+)
+
+from typing_extensions import Literal
 
 import bioblend
 from bioblend.galaxy import GalaxyInstance
@@ -30,3 +35,19 @@ def _wait_and_verify_dataset(
     ) -> None:
         dataset_contents = self.gi.datasets.download_dataset(dataset_id, maxwait=timeout_seconds)
         assert dataset_contents == expected_contents
+
+    def _run_random_lines1(
+        self, history_id: str, dataset_id: str, input_format: Literal["21.01", "legacy"] = "legacy"
+    ) -> Dict[str, Any]:
+        tool_inputs = {
+            "num_lines": "1",
+            "input": {"src": "hda", "id": dataset_id},
+        }
+        if input_format == "21.01":
+            tool_inputs.update({"seed_source": {"seed_source_selector": "set_seed", "seed": "asdf"}})
+        else:
+            # legacy format
+            tool_inputs.update({"seed_source|seed_source_selector": "set_seed", "seed_source|seed": "asdf"})
+        return self.gi.tools.run_tool(
+            history_id=history_id, tool_id="random_lines1", tool_inputs=tool_inputs, input_format=input_format
+        )

bioblend/_tests/TestGalaxyHistories.py

@@ -140,12 +140,26 @@ def test_show_dataset(self):
         assert not dataset["deleted"]
         assert dataset["visible"]
 
-    def test_show_dataset_provenance(self):
+    @test_util.skip_unless_galaxy("release_22.01")
+    def test_show_dataset_provenance(self) -> None:
+        MINIMAL_PROV_KEYS = ("id", "uuid")
+        OTHER_PROV_KEYS = ("job_id", "parameters", "stderr", "stdout", "tool_id")
+        ALL_PROV_KEYS = MINIMAL_PROV_KEYS + OTHER_PROV_KEYS
         history_id = self.history["id"]
         dataset1_id = self._test_dataset(history_id)
-        prov = self.gi.histories.show_dataset_provenance(history_id, dataset1_id)
-        for key in ["id", "job_id", "parameters", "stderr", "stdout", "tool_id"]:
+        dataset2_id = self._run_random_lines1(history_id, dataset1_id)["outputs"][0]["id"]
+        prov = self.gi.histories.show_dataset_provenance(history_id, dataset2_id)
+        for key in ALL_PROV_KEYS:
             assert key in prov
+        for key in MINIMAL_PROV_KEYS:
+            assert key in prov["parameters"]["input"]
+        for key in OTHER_PROV_KEYS:
+            assert key not in prov["parameters"]["input"]
+        recursive_prov = self.gi.histories.show_dataset_provenance(history_id, dataset2_id, follow=True)
+        for key in ALL_PROV_KEYS:
+            assert key in recursive_prov
+        for key in ALL_PROV_KEYS:
+            assert key in recursive_prov["parameters"]["input"]
 
     def test_delete_dataset(self):
         history_id = self.history["id"]

bioblend/_tests/TestGalaxyJobs.py

@@ -227,16 +227,4 @@ def test_cancel_job(self):
         assert job["state"] in ("deleted", "deleting")
 
     def _run_tool(self, input_format: Literal["21.01", "legacy"] = "legacy") -> dict:
-        tool_inputs = {
-            "num_lines": "1",
-            "input": {"src": "hda", "id": self.dataset_id},
-        }
-        if input_format == "21.01":
-            tool_inputs.update({"seed_source": {"seed_source_selector": "set_seed", "seed": "asdf"}})
-        else:
-            # legacy format
-            tool_inputs.update({"seed_source|seed_source_selector": "set_seed", "seed_source|seed": "asdf"})
-
-        return self.gi.tools.run_tool(
-            history_id=self.history_id, tool_id="random_lines1", tool_inputs=tool_inputs, input_format=input_format
-        )
+        return super()._run_random_lines1(self.history_id, self.dataset_id, input_format=input_format)

bioblend/galaxy/histories/__init__.py

@@ -426,7 +426,8 @@ def show_dataset_provenance(self, history_id: str, dataset_id: str, follow: bool
              'uuid': '5c0c43f5-8d93-44bd-939d-305e82f213c6'}
         """
         url = "/".join((self._make_url(history_id, contents=True), dataset_id, "provenance"))
-        return self._get(url=url)
+        params = {"follow": follow}
+        return self._get(url=url, params=params)
 
     def update_history(self, history_id: str, **kwargs: Any) -> Dict[str, Any]:
         """