adding metabolism tests for CART cells

test/arcade/patch/agent/process/PatchProcessMetabolismCARTTest.java

@@ -1,2 +1,319 @@
+package arcade.patch.agent.process;
+
+import java.lang.reflect.Field;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import ec.util.MersenneTwisterFast;
+import arcade.core.sim.Simulation;
+import arcade.core.util.Parameters;
+import arcade.patch.agent.cell.PatchCellCART;
+import arcade.patch.env.location.PatchLocation;
+import static org.junit.jupiter.api.Assertions.*;
+import static org.mockito.Mockito.*;
+import static arcade.core.ARCADETestUtilities.randomDoubleBetween;
+
 public class PatchProcessMetabolismCARTTest {
+
+    private PatchCellCART mockCell;
+    private Parameters mockParameters;
+    private PatchProcessMetabolismCART metabolism;
+    private PatchLocation mockLocation;
+
+    @BeforeEach
+    public void setUp() {
+        mockCell = mock(PatchCellCART.class);
+        mockParameters = mock(Parameters.class);
+        mockLocation = mock(PatchLocation.class);
+
+        when(mockCell.getParameters()).thenReturn(mockParameters);
+        when(mockParameters.getDouble(anyString())).thenReturn(1.0);
+        when(mockCell.getLocation()).thenReturn(mockLocation);
+        when(mockCell.getVolume()).thenReturn(randomDoubleBetween(165, 180));
+        when(mockLocation.getPerimeter(anyDouble()))
+                .thenReturn(randomDoubleBetween(0, 1.0) * 6 * 30 / Math.sqrt(3));
+        when(mockLocation.getArea()).thenReturn(3.0 / 2.0 / Math.sqrt(3.0) * 30 * 30);
+        when(mockLocation.getVolume()).thenReturn(3.0 / 2.0 / Math.sqrt(3.0) * 30 * 30 * 8.7);
+    }
+
+    @Test
+    public void testConstructorInitializesFields()
+            throws NoSuchFieldException, IllegalAccessException {
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+
+        assertNotNull(metabolism);
+
+        Field metaPrefField = PatchProcessMetabolismCART.class.getDeclaredField("metaPref");
+        metaPrefField.setAccessible(true);
+        assertEquals(1.0, metaPrefField.get(metabolism));
+
+        Field conversionFractionField =
+                PatchProcessMetabolismCART.class.getDeclaredField("conversionFraction");
+        conversionFractionField.setAccessible(true);
+        assertEquals(1.0, conversionFractionField.get(metabolism));
+
+        Field fracMassField = PatchProcessMetabolismCART.class.getDeclaredField("fracMass");
+        fracMassField.setAccessible(true);
+        assertEquals(1.0, fracMassField.get(metabolism));
+
+        Field ratioGlucosePyruvateField =
+                PatchProcessMetabolismCART.class.getDeclaredField("ratioGlucosePyruvate");
+        ratioGlucosePyruvateField.setAccessible(true);
+        assertEquals(1.0, ratioGlucosePyruvateField.get(metabolism));
+
+        Field lactateRateField = PatchProcessMetabolismCART.class.getDeclaredField("lactateRate");
+        lactateRateField.setAccessible(true);
+        assertEquals(1.0, lactateRateField.get(metabolism));
+
+        Field autophagyRateField =
+                PatchProcessMetabolismCART.class.getDeclaredField("autophagyRate");
+        autophagyRateField.setAccessible(true);
+        assertEquals(1.0, autophagyRateField.get(metabolism));
+
+        Field glucUptakeRateField =
+                PatchProcessMetabolismCART.class.getDeclaredField("glucUptakeRate");
+        glucUptakeRateField.setAccessible(true);
+        assertEquals(1.0, glucUptakeRateField.get(metabolism));
+
+        Field metabolicPreference_IL2Field =
+                PatchProcessMetabolismCART.class.getDeclaredField("metabolicPreference_IL2");
+        metabolicPreference_IL2Field.setAccessible(true);
+        assertEquals(1.0, metabolicPreference_IL2Field.get(metabolism));
+
+        Field metabolicPreference_activeField =
+                PatchProcessMetabolismCART.class.getDeclaredField("metabolicPreference_active");
+        metabolicPreference_activeField.setAccessible(true);
+        assertEquals(1.0, metabolicPreference_activeField.get(metabolism));
+
+        Field glucoseUptakeRate_IL2Field =
+                PatchProcessMetabolismCART.class.getDeclaredField("glucoseUptakeRate_IL2");
+        glucoseUptakeRate_IL2Field.setAccessible(true);
+        assertEquals(1.0, glucoseUptakeRate_IL2Field.get(metabolism));
+
+        Field glucoseUptakeRate_activeField =
+                PatchProcessMetabolismCART.class.getDeclaredField("glucoseUptakeRate_active");
+        glucoseUptakeRate_activeField.setAccessible(true);
+        assertEquals(1.0, glucoseUptakeRate_activeField.get(metabolism));
+
+        Field minimumMassFraction_activeField =
+                PatchProcessMetabolismCART.class.getDeclaredField("minimumMassFraction_active");
+        minimumMassFraction_activeField.setAccessible(true);
+        assertEquals(1.0, minimumMassFraction_activeField.get(metabolism));
+
+        Field timeDelayField = PatchProcessMetabolismCART.class.getDeclaredField("timeDelay");
+        timeDelayField.setAccessible(true);
+        assertEquals(1, timeDelayField.get(metabolism));
+    }
+
+    @Test
+    public void testStepProcess() throws NoSuchFieldException, IllegalAccessException {
+        // set up metabolism class
+        when(mockParameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE")).thenReturn(1.12);
+        when(mockParameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION")).thenReturn(0.05);
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+        Field fraction = PatchProcessMetabolism.class.getDeclaredField("f");
+        fraction.setAccessible(true);
+        fraction.set(metabolism, 1.0);
+
+        // set up simulation
+        MersenneTwisterFast random = new MersenneTwisterFast();
+        Simulation sim = mock(Simulation.class);
+
+        // mock inflammation process
+        PatchProcessInflammation inflammation = spy(new PatchProcessInflammationCD4(mockCell));
+        when(mockCell.getProcess(any())).thenReturn(inflammation);
+        when(mockCell.getActivationStatus()).thenReturn(true);
+
+        metabolism.stepProcess(random, sim);
+
+        assertTrue(metabolism.intAmts[PatchProcessMetabolismCART.GLUCOSE] >= 0);
+        assertTrue(metabolism.intAmts[PatchProcessMetabolismCART.PYRUVATE] >= 0);
+    }
+
+    @Test
+    public void testStepProcessWithZeroInitialGlucose() {
+        // set up metabolism class
+        when(mockParameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE")).thenReturn(1.12);
+        when(mockParameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION")).thenReturn(0.0);
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+
+        // set up simulation
+        MersenneTwisterFast random = new MersenneTwisterFast();
+        Simulation sim = mock(Simulation.class);
+
+        // mock inflammation process
+        PatchProcessInflammation inflammation = spy(new PatchProcessInflammationCD4(mockCell));
+        when(mockCell.getProcess(any())).thenReturn(inflammation);
+        when(mockCell.getActivationStatus()).thenReturn(true);
+
+        metabolism.stepProcess(random, sim);
+
+        assertEquals(0.0, metabolism.intAmts[PatchProcessMetabolismCART.GLUCOSE]);
+    }
+
+    @Test
+    public void testStepProcessWithMaxGlucoseConcentration() {
+        // set up metabolism class
+        when(mockParameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE")).thenReturn(1.12);
+        when(mockParameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION"))
+                .thenReturn(Double.MAX_VALUE);
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+
+        // set up simulation
+        MersenneTwisterFast random = new MersenneTwisterFast();
+        Simulation sim = mock(Simulation.class);
+
+        // mock inflammation process
+        PatchProcessInflammation inflammation = spy(new PatchProcessInflammationCD4(mockCell));
+        when(mockCell.getProcess(any())).thenReturn(inflammation);
+        when(mockCell.getActivationStatus()).thenReturn(true);
+
+        metabolism.stepProcess(random, sim);
+
+        assertTrue(metabolism.intAmts[PatchProcessMetabolismCART.GLUCOSE] <= Double.MAX_VALUE);
+    }
+
+    @Test
+    public void testStepProcessWithNegativeGlucoseConcentration() {
+        // set up metabolism class
+        when(mockParameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE")).thenReturn(1.12);
+        when(mockParameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION")).thenReturn(-1.0);
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+
+        // set up simulation
+        MersenneTwisterFast random = new MersenneTwisterFast();
+        Simulation sim = mock(Simulation.class);
+
+        // mock inflammation process
+        PatchProcessInflammation inflammation = spy(new PatchProcessInflammationCD4(mockCell));
+        when(mockCell.getProcess(any())).thenReturn(inflammation);
+        when(mockCell.getActivationStatus()).thenReturn(true);
+
+        metabolism.stepProcess(random, sim);
+
+        assertTrue(metabolism.intAmts[PatchProcessMetabolismCART.GLUCOSE] >= 0);
+    }
+
+    @Test
+    public void testStepProcessWithZeroOxygenConcentration() {
+        // set up metabolism class
+        when(mockParameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE")).thenReturn(1.12);
+        when(mockParameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION")).thenReturn(0.05);
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+
+        // set up simulation
+        MersenneTwisterFast random = new MersenneTwisterFast();
+        Simulation sim = mock(Simulation.class);
+
+        // mock inflammation process
+        PatchProcessInflammation inflammation = spy(new PatchProcessInflammationCD4(mockCell));
+        when(mockCell.getProcess(any())).thenReturn(inflammation);
+        when(mockCell.getActivationStatus()).thenReturn(true);
+
+        metabolism.extAmts[PatchProcessMetabolismCART.OXYGEN] = 0.0;
+
+        metabolism.stepProcess(random, sim);
+
+        assertEquals(0.0, metabolism.extAmts[PatchProcessMetabolismCART.OXYGEN]);
+    }
+
+    @Test
+    public void testStepProcessWithMaxOxygenConcentration() {
+        // set up metabolism class
+        when(mockParameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE")).thenReturn(1.12);
+        when(mockParameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION")).thenReturn(0.05);
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+
+        // set up simulation
+        MersenneTwisterFast random = new MersenneTwisterFast();
+        Simulation sim = mock(Simulation.class);
+
+        // mock inflammation process
+        PatchProcessInflammation inflammation = spy(new PatchProcessInflammationCD4(mockCell));
+        when(mockCell.getProcess(any())).thenReturn(inflammation);
+        when(mockCell.getActivationStatus()).thenReturn(true);
+
+        metabolism.extAmts[PatchProcessMetabolismCART.OXYGEN] = Double.MAX_VALUE;
+
+        metabolism.stepProcess(random, sim);
+
+        assertTrue(metabolism.extAmts[PatchProcessMetabolismCART.OXYGEN] <= Double.MAX_VALUE);
+    }
+
+    @Test
+    public void testActivatedMetabolicPreference()
+            throws IllegalAccessException, NoSuchFieldException {
+        // set up metabolism class
+        when(mockParameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE")).thenReturn(1.12);
+        when(mockParameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION")).thenReturn(0.05);
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+
+        // set up simulation
+        MersenneTwisterFast random = new MersenneTwisterFast();
+        Simulation sim = mock(Simulation.class);
+
+        // mock inflammation process
+        PatchProcessInflammation inflammation = spy(new PatchProcessInflammationCD4(mockCell));
+        Field activeTicker = PatchProcessInflammation.class.getDeclaredField("activeTicker");
+        activeTicker.setAccessible(true);
+        activeTicker.set(inflammation, 1);
+        when(mockCell.getProcess(any())).thenReturn(inflammation);
+        when(mockCell.getActivationStatus()).thenReturn(true);
+
+        metabolism.stepProcess(random, sim);
+
+        double expectedMetabolicPreference = 1.0 + 1.0; // base + active
+        assertEquals(expectedMetabolicPreference, metabolism.getFinalMetabolicPreference());
+    }
+
+    @Test
+    public void testActivatedGlucoseUptakeRate()
+            throws IllegalAccessException, NoSuchFieldException {
+        // set up metabolism class
+        when(mockParameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE")).thenReturn(1.12);
+        when(mockParameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION")).thenReturn(0.05);
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+
+        // set up simulation
+        MersenneTwisterFast random = new MersenneTwisterFast();
+        Simulation sim = mock(Simulation.class);
+
+        // mock inflammation process
+        PatchProcessInflammation inflammation = spy(new PatchProcessInflammationCD4(mockCell));
+        Field activeTicker = PatchProcessInflammation.class.getDeclaredField("activeTicker");
+        activeTicker.setAccessible(true);
+        activeTicker.set(inflammation, 1);
+        when(mockCell.getProcess(any())).thenReturn(inflammation);
+        when(mockCell.getActivationStatus()).thenReturn(true);
+
+        metabolism.stepProcess(random, sim);
+
+        double expectedGlucoseUptakeRate = 1.12 + 1.0; // base + active
+        assertEquals(expectedGlucoseUptakeRate, metabolism.getFinalGlucoseUptakeRate());
+    }
+
+    @Test
+    public void testActivatedMinimumMassFraction()
+            throws NoSuchFieldException, IllegalAccessException {
+        // set up metabolism class
+        when(mockParameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE")).thenReturn(1.12);
+        when(mockParameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION")).thenReturn(0.05);
+        metabolism = new PatchProcessMetabolismCART(mockCell);
+
+        // set up simulation
+        MersenneTwisterFast random = new MersenneTwisterFast();
+        Simulation sim = mock(Simulation.class);
+
+        // mock inflammation process
+        PatchProcessInflammation inflammation = spy(new PatchProcessInflammationCD4(mockCell));
+        Field activeTicker = PatchProcessInflammation.class.getDeclaredField("activeTicker");
+        activeTicker.setAccessible(true);
+        activeTicker.set(inflammation, 1);
+        when(mockCell.getProcess(any())).thenReturn(inflammation);
+        when(mockCell.getActivationStatus()).thenReturn(true);
+
+        metabolism.stepProcess(random, sim);
+
+        double expectedMinimumMassFraction = 1.0 + 1.0; // base + active
+        assertEquals(expectedMinimumMassFraction, metabolism.getFinalMinimumMassFraction());
+    }
 }