Migrate various tool execute tests to more declarative style.

lib/galaxy_test/api/test_tool_execute.py

@@ -0,0 +1,189 @@
+"""Test tool execution pieces.
+
+Longer term ideally we would separate all the tool tests in test_tools.py that
+describe tool execution into this file and make sure we have parallel or matching
+tests for both the legacy tool execution API and the tool request API. We would then
+keep things like testing other tool APIs in ./test_tools.py (index, search, tool test
+files, etc..).
+"""
+
+from galaxy_test.base.decorators import requires_tool_id
+from galaxy_test.base.populators import (
+    RequiredTool,
+    TargetHistory,
+)
+
+
+@requires_tool_id("multi_data_param")
+def test_multidata_param(target_history: TargetHistory, required_tool: RequiredTool):
+    hda1 = target_history.with_dataset("1\t2\t3").src_dict
+    hda2 = target_history.with_dataset("4\t5\t6").src_dict
+    execution = required_tool.execute.with_inputs(
+        {
+            "f1": {"batch": False, "values": [hda1, hda2]},
+            "f2": {"batch": False, "values": [hda2, hda1]},
+        }
+    )
+    execution.assert_has_job(0).with_output("out1").with_contents("1\t2\t3\n4\t5\t6\n")
+    execution.assert_has_job(0).with_output("out2").with_contents("4\t5\t6\n1\t2\t3\n")
+
+
+@requires_tool_id("expression_forty_two")
+def test_galaxy_expression_tool_simplest(required_tool: RequiredTool):
+    required_tool.execute.assert_has_single_job.with_single_output.with_contents("42")
+
+
+@requires_tool_id("expression_parse_int")
+def test_galaxy_expression_tool_simple(required_tool: RequiredTool):
+    execution = required_tool.execute.with_inputs({"input1": "7"})
+    execution.assert_has_single_job.with_single_output.with_contents("7")
+
+
+@requires_tool_id("expression_log_line_count")
+def test_galaxy_expression_metadata(target_history: TargetHistory, required_tool: RequiredTool):
+    hda1 = target_history.with_dataset("1\n2\n3\n4\n5\n6\n7\n8\n9\n10\n11\n12\n13\n14").src_dict
+    execution = required_tool.execute.with_inputs({"input1": hda1})
+    execution.assert_has_single_job.with_single_output.with_contents("3")
+
+
+@requires_tool_id("multi_select")
+def test_multi_select_as_list(required_tool: RequiredTool):
+    execution = required_tool.execute.with_inputs({"select_ex": ["--ex1", "ex2"]})
+    execution.assert_has_single_job.with_output("output").with_contents("--ex1,ex2")
+
+
+@requires_tool_id("multi_select")
+def test_multi_select_optional(required_tool: RequiredTool):
+    execution = required_tool.execute.with_inputs(
+        {
+            "select_ex": ["--ex1"],
+            "select_optional": None,
+        }
+    )
+    job = execution.assert_has_single_job
+    job.assert_has_output("output").with_contents("--ex1")
+    job.assert_has_output("output2").with_contents_stripped("None")
+
+
+@requires_tool_id("identifier_single")
+def test_identifier_outside_map(target_history: TargetHistory, required_tool: RequiredTool):
+    hda = target_history.with_dataset("123", named="Plain HDA")
+    execute = required_tool.execute.with_inputs({"input1": hda.src_dict})
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("Plain HDA")
+
+
+@requires_tool_id("identifier_multiple")
+def test_identifier_in_multiple_reduce(target_history: TargetHistory, required_tool: RequiredTool):
+    hdca = target_history.with_pair(["123", "456"])
+    execute = required_tool.execute.with_inputs({"input1": hdca.src_dict})
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("forward\nreverse")
+
+
+@requires_tool_id("identifier_in_conditional")
+def test_identifier_map_over_multiple_input_in_conditional_legacy_format(
+    target_history: TargetHistory, required_tool: RequiredTool
+):
+    hdca = target_history.with_pair(["123", "456"])
+    execute = required_tool.execute.with_inputs(
+        {
+            "outer_cond|input1": hdca.src_dict,
+        }
+    )
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("forward\nreverse")
+
+
+@requires_tool_id("identifier_in_conditional")
+def test_identifier_map_over_multiple_input_in_conditional_21_01_format(
+    target_history: TargetHistory, required_tool: RequiredTool
+):
+    hdca = target_history.with_pair(["123", "456"])
+    execute = required_tool.execute.with_nested_inputs(
+        {
+            "outer_cond": {
+                "multi_input": True,
+                "input1": hdca.src_dict,
+            },
+        }
+    )
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("forward\nreverse")
+
+
+@requires_tool_id("identifier_multiple_in_repeat")
+def test_identifier_multiple_reduce_in_repeat_new_payload_form(
+    target_history: TargetHistory, required_tool: RequiredTool
+):
+    hdca = target_history.with_pair(["123", "456"])
+    execute = required_tool.execute.with_nested_inputs(
+        {
+            "the_repeat": [{"the_data": {"input1": hdca.src_dict}}],
+        }
+    )
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("forward\nreverse")
+
+
+@requires_tool_id("output_action_change_format")
+def test_map_over_with_output_format_actions(target_history: TargetHistory, required_tool: RequiredTool):
+    hdca = target_history.with_pair(["123", "456"])
+    for use_action in ["do", "dont"]:
+        execute = required_tool.execute.with_inputs(
+            {
+                "input_cond|dispatch": use_action,
+                "input_cond|input": {"batch": True, "values": [hdca.src_dict]},
+            }
+        )
+        execute.assert_has_n_jobs(2).assert_creates_n_implicit_collections(1)
+        expected_extension = "txt" if (use_action == "do") else "data"
+        execute.assert_has_job(0).with_single_output.with_file_ext(expected_extension)
+        execute.assert_has_job(1).with_single_output.with_file_ext(expected_extension)
+
+
+@requires_tool_id("output_action_change_format_paired")
+def test_map_over_with_nested_paired_output_format_actions(target_history: TargetHistory, required_tool: RequiredTool):
+    hdca = target_history.with_example_list_of_pairs()
+    execute = required_tool.execute.with_inputs(
+        {"input": {"batch": True, "values": [dict(map_over_type="paired", **hdca.src_dict)]}}
+    )
+    execute.assert_has_n_jobs(2).assert_creates_n_implicit_collections(1)
+    execute.assert_has_job(0).with_single_output.with_file_ext("txt")
+    execute.assert_has_job(1).with_single_output.with_file_ext("txt")
+
+
+@requires_tool_id("identifier_collection")
+def test_identifier_with_data_collection(target_history: TargetHistory, required_tool: RequiredTool):
+    contents = [("foo", "text for foo element"), ("bar", "more text for bar element")]
+    hdca = target_history.with_list(contents)
+    execute = required_tool.execute.with_inputs({"input1": hdca.src_dict})
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("foo\nbar")
+
+
+@requires_tool_id("identifier_in_actions")
+def test_identifier_in_actions(target_history: TargetHistory, required_tool: RequiredTool):
+    contents = [("foo", "text for foo element"), ("bar", "more text for bar element")]
+    hdca = target_history.with_list(contents)
+
+    execute = required_tool.execute.with_inputs({"input": {"batch": True, "values": [hdca.src_dict]}})
+
+    output = execute.assert_has_job(0).assert_has_single_output
+    assert output.details["metadata_column_names"][1] == "foo", output.details
+
+    output = execute.assert_has_job(1).assert_has_single_output
+    assert output.details["metadata_column_names"][1] == "bar", output.details
+
+
+@requires_tool_id("cat1")
+def test_map_over_empty_collection(target_history: TargetHistory, required_tool: RequiredTool):
+    hdca = target_history.with_list([])
+    inputs = {
+        "input1": {"batch": True, "values": [hdca.src_dict]},
+    }
+    execute = required_tool.execute.with_inputs(inputs)
+    execute.assert_has_n_jobs(0)
+    execute.assert_creates_implicit_collection(0).named("Concatenate datasets on collection 1")
+
+
+@requires_tool_id("gx_repeat_boolean_min")
+def test_optional_repeats_with_mins_filled_id(target_history: TargetHistory, required_tool: RequiredTool):
+    # we have a tool test for this but I wanted to verify it wasn't just the
+    # tool test framework filling in a default. Creating a raw request here
+    # verifies that currently select parameters don't require a selection.
+    required_tool.execute.assert_has_single_job.with_single_output.containing("false").containing("length: 2")