Migrate some tool-on-deferred tests to newer style execute tests.

Author: jmchilton

lib/galaxy_test/api/test_tool_execute.py

@@ -613,3 +613,23 @@ def test_null_to_text_tool_with_validation(required_tool: RequiredTool, tool_inp
     required_tool.execute.with_inputs(tool_input_format.when.any({})).assert_fails()
     required_tool.execute.with_inputs(tool_input_format.when.any({"parameter": None})).assert_fails()
     required_tool.execute.with_inputs(tool_input_format.when.any({"parameter": ""})).assert_fails()
+
+
+@requires_tool_id("cat|cat1")
+def test_deferred_basic(required_tool: RequiredTool, target_history: TargetHistory):
+    has_src_dict = target_history.with_deferred_dataset_for_test_file("1.bed", ext="bed")
+    inputs = {
+        "input1": has_src_dict.src_dict,
+    }
+    output = required_tool.execute.with_inputs(inputs).assert_has_single_job.with_single_output
+    output.assert_contains("chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-")
+
+
+@requires_tool_id("metadata_bam")
+def test_deferred_with_metadata_options_filter(required_tool: RequiredTool, target_history: TargetHistory):
+    has_src_dict = target_history.with_deferred_dataset_for_test_file("1.bam", ext="bam")
+    inputs = {
+        "input_bam": has_src_dict.src_dict,
+        "ref_names": "chrM",
+    }
+    required_tool.execute.with_inputs(inputs).assert_has_single_job.with_single_output.with_contents_stripped("chrM")

lib/galaxy_test/api/test_tools.py

@@ -2826,38 +2826,6 @@ def test_group_tag_selection_multiple(self, history_id):
         output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
         assert output_content.strip() == "123\n456\n456\n0ab"
 
-    @skip_without_tool("cat1")
-    def test_run_deferred_dataset(self, history_id):
-        details = self.dataset_populator.create_deferred_hda(
-            history_id, "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed", ext="bed"
-        )
-        inputs = {
-            "input1": dataset_to_param(details),
-        }
-        outputs = self._cat1_outputs(history_id, inputs=inputs)
-        output = outputs[0]
-        details = self.dataset_populator.get_history_dataset_details(
-            history_id, dataset=output, wait=True, assert_ok=True
-        )
-        assert details["state"] == "ok"
-        output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
-        assert output_content.startswith("chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-")
-
-    @skip_without_tool("metadata_bam")
-    def test_run_deferred_dataset_with_metadata_options_filter(self, history_id):
-        details = self.dataset_populator.create_deferred_hda(
-            history_id, "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bam", ext="bam"
-        )
-        inputs = {"input_bam": dataset_to_param(details), "ref_names": "chrM"}
-        run_response = self.dataset_populator.run_tool(tool_id="metadata_bam", inputs=inputs, history_id=history_id)
-        output = run_response["outputs"][0]
-        output_details = self.dataset_populator.get_history_dataset_details(
-            history_id, dataset=output, wait=True, assert_ok=True
-        )
-        assert output_details["state"] == "ok"
-        output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
-        assert output_content.startswith("chrM")
-
     @skip_without_tool("pileup")
     def test_metadata_validator_on_deferred_input(self, history_id):
         deferred_bam_details = self.dataset_populator.create_deferred_hda(

lib/galaxy_test/base/populators.py

@@ -4137,6 +4137,31 @@ def with_dataset(
         )
         return HasSrcDict("hda", new_dataset)
 
+    def with_deferred_dataset(
+        self,
+        uri: str,
+        named: Optional[str] = None,
+        ext: Optional[str] = None,
+    ) -> "HasSrcDict":
+        kwd = {}
+        if named is not None:
+            kwd["name"] = named
+        new_dataset = self._dataset_populator.create_deferred_hda(
+            history_id=self._history_id,
+            uri=uri,
+            ext=ext,
+        )
+        return HasSrcDict("hda", new_dataset)
+
+    def with_deferred_dataset_for_test_file(
+        self,
+        filename: str,
+        named: Optional[str] = None,
+        ext: Optional[str] = None,
+    ) -> "HasSrcDict":
+        base64_url = self._dataset_populator.base64_url_for_test_file(filename)
+        return self.with_deferred_dataset(base64_url, named=named, ext=ext)
+
     def with_unpaired(self) -> "HasSrcDict":
         return self._fetch_response(
             self._dataset_collection_populator.create_unpaired_in_history(self._history_id, wait=True)