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openmmdl/tests/test_setup_options.py

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+import pytest
+from typing import List, Dict
+from flask import session
+from werkzeug.datastructures import ImmutableMultiDict
+from openmmdl.openmmdl_setup.setup_options import SetupOptionsConfigurator, SessionDict, RequestSessionManager
+
+@pytest.fixture
+def default_session() -> SessionDict:
+    """
+    Provides a default mock session with minimal required data for testing.
+    """
+    return {
+        "fileType": "pdb",
+        "waterModel": "explicit",
+    }
+
+@pytest.fixture
+def configurator(default_session: SessionDict) -> SetupOptionsConfigurator:
+    """
+    Provides a SetupOptionsConfigurator instance initialized with the default session.
+    """
+    return SetupOptionsConfigurator(session=default_session)
+
+def test_configure_default_options(configurator: SetupOptionsConfigurator, default_session: SessionDict):
+    """
+    Test the `configure_default_options` method to ensure default values are properly set.
+    """
+    configurator.configure_default_options()
+
+    assert default_session["restart_checkpoint"] is False
+    assert default_session["mdtraj_output"] == "mdtraj_pdb_dcd"
+    assert default_session["mda_output"] == "mda_pdb_dcd"
+    assert default_session["analysis_selection"] == "analysis_all"
+    assert default_session["binding_mode"] == "40"
+    assert default_session["ensemble"] == "npt"  # since waterModel is 'explicit'
+    assert default_session["platform"] == "CUDA"
+    assert default_session["precision"] == "mixed"
+    assert default_session["cutoff"] == "1.0"  # as waterModel is not 'implicit'
+    assert default_session["hmr"] is True
+    assert default_session["writeDCD"] is True
+    assert default_session["dataFields"] == ["step", "speed", "progress", "potentialEnergy", "temperature"]
+    assert default_session["writeCheckpoint"] is True
+
+def test_configure_default_options_with_implicit_water(configurator: SetupOptionsConfigurator, default_session: SessionDict):
+    """
+    Test `configure_default_options` when the water model is set to implicit.
+    """
+    default_session["waterModel"] = "implicit"
+    configurator.configure_default_options()
+
+    assert default_session["ensemble"] == "nvt"  # should switch to nvt due to implicit water
+    assert default_session["cutoff"] == "2.0"  # cutoff should change
+    assert default_session["nonbondedMethod"] == "CutoffNonPeriodic"
+
+def test_configure_default_amber_options(configurator: SetupOptionsConfigurator, default_session: SessionDict):
+    """
+    Test the `configureDefaultAmberOptions` method to ensure Amber options are set correctly.
+    """
+    configurator.configureDefaultAmberOptions()
+
+    assert default_session["lig_ff"] == "gaff2"
+    assert default_session["charge_value"] == "0"
+    assert default_session["charge_method"] == "bcc"
+    assert default_session["prot_ff"] == "ff19SB"
+    assert default_session["dna_ff"] == "OL15"
+    assert default_session["rna_ff"] == "OL3"
+    assert default_session["carbo_ff"] == "GLYCAM_06j"
+    assert default_session["addType"] == "addWater"
+    assert default_session["boxType"] == "cube"
+    assert default_session["lipid_tp"] == "POPC"
+    assert default_session["dist2Border"] == "15"
+    assert default_session["water_ff"] == "opc"
+    assert default_session["pos_ion"] == "Na+"
+    assert default_session["neg_ion"] == "Cl-"
+    assert default_session["ionConc"] == "0.15"
+
+
+@pytest.fixture
+def app_context():
+    """
+    Provides a Flask test request context for session management.
+    """
+    from flask import Flask
+
+    app = Flask(__name__)
+    app.secret_key = 'test_secret_key'  # Required to use sessions
+    with app.test_request_context():
+        yield
+
+@pytest.fixture
+def default_form() -> ImmutableMultiDict:
+    """
+    Provides default mock form data for testing.
+    """
+    return ImmutableMultiDict({
+        "rcpType": "protein",
+        "prot_ff": "ff14SB",
+        "other_prot_ff_input": "custom_prot_ff",
+        "dna_ff": "OL15",
+        "other_dna_ff_input": "custom_dna_ff",
+        "rna_ff": "OL3",
+        "other_rna_ff_input": "custom_rna_ff",
+        "carbo_ff": "GLYCAM_06j",
+        "addType": "addWater",
+        "boxType": "geometry",
+        "geomPadding": "10",
+        "ionicstrength": "0.15",
+        "positiveion": "Na+",
+        "negativeion": "Cl-",
+        "forcefield": "amber14",
+        "ml_forcefield": "openff",
+        "waterModel": "tip3p",
+        "smallMoleculeForceField": "gaff",
+        "ligandMinimization": "Yes",
+        "ligandSanitization": "Yes",
+        "writeDCD": "True",
+        "writeData": "True",
+        "writeCheckpoint": "True",
+        "dataFields": "step,speed,temperature",
+        "hmr": "True",
+    })
+
+@pytest.fixture
+def request_manager(default_form) -> RequestSessionManager:
+    """
+    Provides a RequestSessionManager instance initialized with the default form data.
+    """
+    return RequestSessionManager(form=default_form)
+
+def test_set_amber_options_rcp_session(request_manager: RequestSessionManager, app_context):
+    """
+    Test the `setAmberOptions_rcp_session` method.
+    """
+    request_manager.setAmberOptions_rcp_session()
+
+    assert session["rcpType"] == "protein"
+    assert session["prot_ff"] == "ff14SB"
+    assert session["other_prot_ff_input"] == "custom_prot_ff"
+    assert session["dna_ff"] == "OL15"
+    assert session["other_dna_ff_input"] == "custom_dna_ff"
+    assert session["rna_ff"] == "OL3"
+    assert session["other_rna_ff_input"] == "custom_rna_ff"
+    assert session["carbo_ff"] == "GLYCAM_06j"
+
+def test_set_amber_options_water_membrane_session(request_manager: RequestSessionManager, app_context):
+    """
+    Test the `setAmberOptions_water_membrane_session` method.
+    """
+    request_manager.setAmberOptions_water_membrane_session()
+
+    assert session["addType"] == "addWater"
+    assert session["boxType"] == "geometry"
+    assert session["dist"] == ""
+    assert session["lipid_tp"] == ""
+    assert session["other_lipid_tp_input"] == ""
+    assert session["lipid_ratio"] == ""
+    assert session["lipid_ff"] == ""
+    assert session["dist2Border"] == ""
+    assert session["padDist"] == ""
+
+def test_simulationoptions_add_general_settings(request_manager: RequestSessionManager, app_context):
+    """
+    Test the `simulationoptions_add_general_settings` method to ensure general simulation settings are correctly added to the session.
+    """
+    request_manager.simulationoptions_add_general_settings()
+
+    assert session["forcefield"] == "amber14"
+    assert session["ml_forcefield"] == "openff"
+    assert session["waterModel"] == "tip3p"
+    assert session["smallMoleculeForceField"] == "gaff"
+    assert session["ligandMinimization"] == "Yes"
+    assert session["ligandSanitization"] == "Yes"
+    assert session["writeDCD"] is True
+    assert session["writeData"] is True
+    assert session["writeCheckpoint"] is True
+    assert session["dataFields"] == ["step,speed,temperature"]
+    assert session["hmr"] is True
+
+def test_configure_files_add_forcefield_ligand_settings(request_manager: RequestSessionManager, app_context):
+    """
+    Test the `configureFiles_add_forcefield_ligand_settings` method to ensure forcefield and ligand settings are added to the session.
+    """
+    request_manager.configureFiles_add_forcefield_ligand_settings()
+
+    assert session["forcefield"] == "amber14"
+    assert session["ml_forcefield"] == "openff"
+    assert session["waterModel"] == "tip3p"
+    assert session["smallMoleculeForceField"] == "gaff"
+    assert session["ligandMinimization"] == "Yes"
+    assert session["ligandSanitization"] == "Yes"
+
+def test_parse_float(request_manager: RequestSessionManager):
+    """
+    Test the `_parse_float` helper function.
+    """
+    assert request_manager._parse_float("10.5") == 10.5
+    assert request_manager._parse_float(None) is None
+    assert request_manager._parse_float("invalid") is None