adding unit tests for rdf tool

Author: Jgmedina95

mdagent/tools/base_tools/analysis_tools/rdf_tool.py

@@ -50,6 +50,9 @@ class RDFTool(BaseTool):
     args_schema = RDFToolInput
     path_registry: Optional[PathRegistry]
 
+    # def __init__(self, path_registry: PathRegistry):
+    #    self.path_registry = path_registry
+
     def _run(self, input):
         try:
             inputs = self.validate_input(input)

tests/test_rdftool.py

@@ -0,0 +1,115 @@
+import json
+
+import pytest
+
+from mdagent.tools.base_tools.analysis_tools.rdf_tool import RDFTool
+
+# TODO add dcd files in testing file for testing
+
+
+@pytest.fixture(scope="module")
+def rdf_input_good_string():
+    return """
+    {
+        "trajectory_fileid": "rec0_142404",
+        "topology_fileid": "top_sim0_142401",
+        "stride": 2,
+        "selections": ["protein", "water"]
+    }
+    """
+
+
+@pytest.fixture(scope="module")
+def rdf_input_wrong_string_1():
+    return """
+    {
+        "topology_fileid": "top_sim0_142401",
+        "stride": 2,
+        "selections": [["protein", "water", "lipid"]]
+    }
+    """
+
+
+@pytest.fixture(scope="module")
+def rdf_input_wrong_string_2():
+    return """
+    {
+        "trajectory_fileid": "rec0_142404",
+        "topology_fileid": "top_sim0_142401",
+        "stride": "half",
+        "selections": [["protein", "water", "lipid"]]
+    }
+    """
+
+
+@pytest.fixture(scope="module")
+def rdf_input_wrong_string_3():
+    return """
+    {
+        "trajectory_fileid": "rec0_142404Wrong",
+        "topology_fileid": "top_sim0_142401",
+        "stride": 2,
+        "selections": [["protein", "water"]]
+    }
+    """
+
+
+def test_rdf_tool_init(get_registry):
+    registry = get_registry("raw", False)
+    tool = RDFTool(path_registry=registry)
+    assert tool.name == "RDFTool"
+    assert tool.path_registry == registry
+
+
+class MockRegistryResponse:
+    # mock json() method always returns a specific testing dictionary
+    dictionary = {
+        "rec0_142404": "files/records/TRAJ_sim0123456_142404.dcd",
+        "top_sim0_142401": "files/records/TOP_sim0123456_142401.pdb",
+    }
+
+    @staticmethod
+    def get_mapped_path(self, fileid):
+        return self.dictionary[fileid]
+
+    def list_path_names(self):
+        return "rec0_142404", "top_sim0_142401"
+
+
+def test_rdf_tool_validation(
+    monkeypatch,
+    rdf_input_good_string,
+    rdf_input_wrong_string_1,
+    rdf_input_wrong_string_2,
+    rdf_input_wrong_string_3,
+    get_registry,
+):
+    registry = get_registry("raw", False)
+    tool = RDFTool(path_registry=registry)
+
+    def mock_get_mapped_path(fileid):
+        return MockRegistryResponse.dictionary[fileid]
+
+    def mock_list_path_names():
+        return "rec0_142404", "top_sim0_142401"
+
+    monkeypatch.setattr(tool.path_registry, "get_mapped_path", mock_get_mapped_path)
+    monkeypatch.setattr(tool.path_registry, "list_path_names", mock_list_path_names)
+    # assert that a valueerror was raised
+    with pytest.raises(ValueError) as error:
+        inputs = tool.validate_input(json.loads(rdf_input_wrong_string_1))
+        assert str(error.value) == "Missing Inputs: Trajectory file ID is required"
+        inputs = tool.validate_input(json.loads(rdf_input_wrong_string_2))
+        assert str(error.value) == (
+            "Incorrect Inputs: Stride must be an integer "
+            "or None for default value of 1"
+        )
+        inputs = tool.validate_input(json.loads(rdf_input_wrong_string_3))
+        assert str(error.value) == "Trajectory File ID not in path registry"
+
+    inputs = tool.validate_input(json.loads(rdf_input_good_string))
+
+    assert inputs["trajectory_fileid"] == "rec0_142404"
+    assert inputs["topology_fileid"] == "top_sim0_142401"
+    assert inputs["stride"] == 2
+    # assert inputs["selections"] == ["protein", "water"]