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changing T cell tests to accomodate for cell death due to age
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@allison-li-1016
allison-li-1016 committed Dec 31, 2024
1 parent 93d3303 commit 0413b6c
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Showing 2 changed files with 30 additions and 24 deletions.
27 changes: 15 additions & 12 deletions test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package arcade.patch.agent.cell;

import java.lang.reflect.Field;
import java.util.ArrayList;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
Expand Down Expand Up @@ -32,16 +33,17 @@ public class PatchCellCARTCD4Test {
private Parameters parameters;

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java#L33 <com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck> 

'VARIABLE_DEF' should be separated from previous line.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java:33:5: error: 'VARIABLE_DEF' should be separated from previous line. (com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck)
private PatchLocation location;

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java#L34 <com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck> 

'VARIABLE_DEF' should be separated from previous line.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java:34:5: error: 'VARIABLE_DEF' should be separated from previous line. (com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck)
private PatchCellContainer container;

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java#L35 <com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck> 

'VARIABLE_DEF' should be separated from previous line.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java:35:5: error: 'VARIABLE_DEF' should be separated from previous line. (com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck)
private PatchCellCARTCD4 cell;

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java#L36 <com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck> 

'VARIABLE_DEF' should be separated from previous line.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java:36:5: error: 'VARIABLE_DEF' should be separated from previous line. (com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck)

@BeforeEach

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java#L38 <com.puppycrawl.tools.checkstyle.checks.design.DesignForExtensionCheck> 

Class 'PatchCellCARTCD4Test' looks like designed for extension (can be subclassed), but the method 'setUp' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PatchCellCARTCD4Test' final or making the method 'setUp' static/final/abstract/empty, or adding allowed annotation for the method.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java:38:5: error: Class 'PatchCellCARTCD4Test' looks like designed for extension (can be subclassed), but the method 'setUp' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PatchCellCARTCD4Test' final or making the method 'setUp' static/final/abstract/empty, or adding allowed annotation for the method. (com.puppycrawl.tools.checkstyle.checks.design.DesignForExtensionCheck)
public void setUp() {
public void setUp() throws NoSuchFieldException, IllegalAccessException {
parameters = mock(Parameters.class);
location = mock(PatchLocation.class);

int id = 1;
int parentId = 1;
int pop = 1;
int age = randomIntBetween(1, 100800);
int age = randomIntBetween(1, 120950);
int divisions = 10;
double volume = randomDoubleBetween(100, 200);
double height = randomDoubleBetween(4, 10);
Expand Down Expand Up @@ -87,7 +89,18 @@ public void setUp() {
when(parameters.getInt("MAX_ANTIGEN_BINDING")).thenReturn(10);
when(parameters.getInt("CARS")).thenReturn(50000);

when(parameters.getInt("APOPTOSIS_AGE")).thenReturn(120960);
when(parameters.getInt("MAX_DENSITY")).thenReturn(54);

patchCellCART = new PatchCellCARTCD4(container, location, parameters);
cell = spy(new PatchCellCARTCD4(container, location, parameters));
Field apoptosisAge = PatchCell.class.getDeclaredField("apoptosisAge");
apoptosisAge.setAccessible(true);
apoptosisAge.set(cell, 120958);

Field maxDensity = PatchCell.class.getDeclaredField("maxDensity");
maxDensity.setAccessible(true);
maxDensity.set(cell, 54);
}

@Test
Expand Down Expand Up @@ -208,7 +221,6 @@ public void testBindTarget() {
@Test
public void testStepIncreasesAge() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -238,7 +250,6 @@ public void testStepIncreasesAge() {
@Test
public void testStepSetsStateToApoptoticWhenEnergyIsLow() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -272,7 +283,6 @@ public void testStepSetsStateToApoptoticWhenEnergyIsLow() {
@Test
public void testStepSetsStateToStarvedWhenEnergyIsNegativeAndMoreThanThreshold() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -305,7 +315,6 @@ public void testStepSetsStateToStarvedWhenEnergyIsNegativeAndMoreThanThreshold()
@Test
public void testStepSetsStateToApoptoticWhenEnergyIsNegativeAndLessThanThreshold() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -337,7 +346,6 @@ public void testStepSetsStateToApoptoticWhenEnergyIsNegativeAndLessThanThreshold
@Test
public void testStepSetsStateToSenescentWhenDivisionsAreZero() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -371,7 +379,6 @@ public void testStepSetsStateToSenescentWhenDivisionsAreZero() {
@Test
public void testStepSetsStateToAnergicWhenBoundToBothAntigenAndSelf() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -405,7 +412,6 @@ public void testStepSetsStateToAnergicWhenBoundToBothAntigenAndSelf() {
@Test
public void testStepSetsStateToCytotoxicWhenBoundToAntigen() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -444,7 +450,6 @@ public void testStepSetsStateToCytotoxicWhenBoundToAntigen() {
@Test
public void testStepSetsStateToProliferativeWhenActivated() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -476,7 +481,6 @@ public void testStepSetsStateToProliferativeWhenActivated() {
@Test
public void testStepSetsStateToMigratoryWhenNotActivated() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -508,7 +512,6 @@ public void testStepSetsStateToMigratoryWhenNotActivated() {
@Test
public void testStepSetsStatetoExhaustedWhenOverstimulated() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD4 cell = spy(new PatchCellCARTCD4(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down
27 changes: 15 additions & 12 deletions test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package arcade.patch.agent.cell;

import java.lang.reflect.Field;
import java.util.ArrayList;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
Expand Down Expand Up @@ -29,19 +30,20 @@
public class PatchCellCARTCD8Test {

private PatchCellCARTCD8 patchCellCART;
private PatchCellCARTCD8 cell;

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java#L33 <com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck> 

'VARIABLE_DEF' should be separated from previous line.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java:33:5: error: 'VARIABLE_DEF' should be separated from previous line. (com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck)
private Parameters parameters;

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java#L34 <com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck> 

'VARIABLE_DEF' should be separated from previous line.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java:34:5: error: 'VARIABLE_DEF' should be separated from previous line. (com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck)
private PatchLocation location;

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java#L35 <com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck> 

'VARIABLE_DEF' should be separated from previous line.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java:35:5: error: 'VARIABLE_DEF' should be separated from previous line. (com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck)
private PatchCellContainer container;

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java#L36 <com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck> 

'VARIABLE_DEF' should be separated from previous line.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java:36:5: error: 'VARIABLE_DEF' should be separated from previous line. (com.puppycrawl.tools.checkstyle.checks.whitespace.EmptyLineSeparatorCheck)

@BeforeEach

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[checkstyle] test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java#L38 <com.puppycrawl.tools.checkstyle.checks.design.DesignForExtensionCheck> 

Class 'PatchCellCARTCD8Test' looks like designed for extension (can be subclassed), but the method 'setUp' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PatchCellCARTCD8Test' final or making the method 'setUp' static/final/abstract/empty, or adding allowed annotation for the method.
Raw output 
/github/workspace/./test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java:38:5: error: Class 'PatchCellCARTCD8Test' looks like designed for extension (can be subclassed), but the method 'setUp' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PatchCellCARTCD8Test' final or making the method 'setUp' static/final/abstract/empty, or adding allowed annotation for the method. (com.puppycrawl.tools.checkstyle.checks.design.DesignForExtensionCheck)
public void setUp() {
public void setUp() throws NoSuchFieldException, IllegalAccessException {
parameters = mock(Parameters.class);
location = mock(PatchLocation.class);

int id = 1;
int parentId = 1;
int pop = 1;
int age = randomIntBetween(1, 100800);
int age = randomIntBetween(1, 120950);
int divisions = 10;
double volume = randomDoubleBetween(100, 200);
double height = randomDoubleBetween(4, 10);
Expand Down Expand Up @@ -86,8 +88,19 @@ public void setUp() {
when(parameters.getDouble("CONTACT_FRAC")).thenReturn(7.8E-6);
when(parameters.getInt("MAX_ANTIGEN_BINDING")).thenReturn(10);
when(parameters.getInt("CARS")).thenReturn(50000);
when(parameters.getInt("APOPTOSIS_AGE")).thenReturn(120960);
when(parameters.getInt("MAX_DENSITY")).thenReturn(54);

patchCellCART = new PatchCellCARTCD8(container, location, parameters);

cell = spy(new PatchCellCARTCD8(container, location, parameters));
Field apoptosisAge = PatchCell.class.getDeclaredField("apoptosisAge");
apoptosisAge.setAccessible(true);
apoptosisAge.set(cell, 120958);

Field maxDensity = PatchCell.class.getDeclaredField("maxDensity");
maxDensity.setAccessible(true);
maxDensity.set(cell, 54);
}

@Test
Expand Down Expand Up @@ -208,7 +221,6 @@ public void testBindTarget() {
@Test
public void testStepIncreasesAge() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -238,7 +250,6 @@ public void testStepIncreasesAge() {
@Test
public void testStepSetsStateToApoptoticWhenEnergyIsLow() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -272,7 +283,6 @@ public void testStepSetsStateToApoptoticWhenEnergyIsLow() {
@Test
public void testStepSetsStateToStarvedWhenEnergyIsNegativeAndMoreThanThreshold() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -305,7 +315,6 @@ public void testStepSetsStateToStarvedWhenEnergyIsNegativeAndMoreThanThreshold()
@Test
public void testStepSetsStateToApoptoticWhenEnergyIsNegativeAndLessThanThreshold() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -337,7 +346,6 @@ public void testStepSetsStateToApoptoticWhenEnergyIsNegativeAndLessThanThreshold
@Test
public void testStepSetsStateToSenescentWhenDivisionsAreZero() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -371,7 +379,6 @@ public void testStepSetsStateToSenescentWhenDivisionsAreZero() {
@Test
public void testStepSetsStateToAnergicWhenBoundToBothAntigenAndSelf() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -405,7 +412,6 @@ public void testStepSetsStateToAnergicWhenBoundToBothAntigenAndSelf() {
@Test
public void testStepSetsStateToCytotoxicWhenBoundToAntigen() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -442,7 +448,6 @@ public void testStepSetsStateToCytotoxicWhenBoundToAntigen() {
@Test
public void testStepSetsStateToProliferativeWhenActivated() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -474,7 +479,6 @@ public void testStepSetsStateToProliferativeWhenActivated() {
@Test
public void testStepSetsStateToMigratoryWhenNotActivated() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down Expand Up @@ -506,7 +510,6 @@ public void testStepSetsStateToMigratoryWhenNotActivated() {
@Test
public void testStepSetsStatetoExhaustedWhenOverstimulated() {
PatchSimulation sim = mock(PatchSimulation.class);
PatchCellCARTCD8 cell = spy(new PatchCellCARTCD8(container, location, parameters));
cell.processes.put(Domain.METABOLISM, mock(PatchProcessMetabolism.class));
cell.processes.put(Domain.SIGNALING, mock(PatchProcessSignaling.class));
cell.processes.put(Domain.INFLAMMATION, mock(PatchProcessInflammation.class));
Expand Down

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