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refactor: Overfitting detection as an AbstractRepairStep component #1208

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merged 2 commits into from
Apr 19, 2021
Merged

refactor: Overfitting detection as an AbstractRepairStep component #1208

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c686059
Overfitting detection as an AbstractRepairStep component. Closes #1135
andre15silva Apr 6, 2021
c92c9a5
Remove patch ranking code
andre15silva Apr 9, 2021
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91 changes: 80 additions & 11 deletions src/repairnator-core/src/main/java/fr/inria/spirals/repairnator/LauncherUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -132,8 +132,19 @@ public static void registerCommonArgs(JSAP jsap) throws JSAPException {
// --sequencerRepair
jsap.registerParameter(LauncherUtils.defineArgSequencerRepairMode());

// --patchRankingMode
jsap.registerParameter(LauncherUtils.defineArgPatchRankingMode());
// --patchClassification
jsap.registerParameter(LauncherUtils.defineArgPatchClassification());
// --patchClassificationMode
jsap.registerParameter(LauncherUtils.defineArgPatchClassificationMode());

// --patchFiltering
jsap.registerParameter(LauncherUtils.defineArgPatchFiltering());
// --patchFilteringMode
jsap.registerParameter(LauncherUtils.defineArgPatchFilteringMode());

// --odsPath
jsap.registerParameter(LauncherUtils.defineArgODSPath());

}

public static void initCommonConfig(RepairnatorConfig config, JSAPResult arguments) {
Expand Down Expand Up @@ -229,7 +240,12 @@ public static void initCommonConfig(RepairnatorConfig config, JSAPResult argumen
config.setNPEScope(LauncherUtils.getArgNPEScope(arguments));
config.setNPERepairStrategy(LauncherUtils.getArgNPERepairStrategy(arguments));

config.setPatchRankingMode(LauncherUtils.getArgPatchRankingMode(arguments));
config.setPatchClassificationMode(LauncherUtils.getArgPatchClassificationMode(arguments));
config.setPatchClassification(LauncherUtils.getArgPatchClassification(arguments));
config.setPatchFiltering(LauncherUtils.getArgPatchFiltering(arguments));
config.setPatchFilteringMode(LauncherUtils.getArgPatchFilteringMode(arguments));

config.setODSPath(LauncherUtils.getArgODSPath(arguments).getAbsolutePath());
}

public static Switch defineArgHelp() {
Expand Down Expand Up @@ -947,17 +963,71 @@ public static String getArgNPERepairStrategy(JSAPResult arguments) {
return arguments.getString("npeRepairStrategy");
}

public static FlaggedOption defineArgPatchRankingMode() {
FlaggedOption opt = new FlaggedOption("patchRankingMode");
opt.setLongFlag("patchRankingMode");
public static FlaggedOption defineArgODSPath() {
FlaggedOption opt = new FlaggedOption("odsPath");
opt.setLongFlag("odsPath");
opt.setDefault("./repairnator-output/ODSPatches");
opt.setStringParser(JSAP.STRING_PARSER);
opt.setDefault(RepairnatorConfig.PATCH_RANKING_MODE.NONE.name());
opt.setHelp("Possible string values NONE, OVERFITTING.");
opt.setHelp("Path for ODS output");
return opt;
}

public static String getArgPatchRankingMode(JSAPResult arguments) {
return arguments.getString("patchRankingMode");
public static File getArgODSPath(JSAPResult arguments) {
File output = new File(arguments.getString("odsPath"));
if (!output.exists()) {
output.mkdirs();
}
return output;
}

public static Switch defineArgPatchClassification() {
Switch sw = new Switch("patchClassification");
sw.setLongFlag("patchClassification");
sw.setDefault("false");
sw.setHelp("Classify repair patches using the defined mode.");
return sw;
}

public static boolean getArgPatchClassification(JSAPResult arguments) {
return arguments.getBoolean("patchClassification");
}

public static FlaggedOption defineArgPatchClassificationMode() {
FlaggedOption opt = new FlaggedOption("patchClassificationMode");
opt.setLongFlag("patchClassificationMode");
opt.setStringParser(JSAP.STRING_PARSER);
opt.setDefault(RepairnatorConfig.PATCH_CLASSIFICATION_MODE.NONE.name());
opt.setHelp("Possible string values NONE, ODS.");
return opt;
}

public static RepairnatorConfig.PATCH_CLASSIFICATION_MODE getArgPatchClassificationMode(JSAPResult arguments) {
return RepairnatorConfig.PATCH_CLASSIFICATION_MODE.valueOf(arguments.getString("patchClassificationMode"));
}

public static Switch defineArgPatchFiltering() {
Switch sw = new Switch("patchFiltering");
sw.setLongFlag("patchFiltering");
sw.setDefault("false");
sw.setHelp("Filter repair patches using the defined mode.");
return sw;
}

public static boolean getArgPatchFiltering(JSAPResult arguments) {
return arguments.getBoolean("patchFiltering");
}

public static FlaggedOption defineArgPatchFilteringMode() {
FlaggedOption opt = new FlaggedOption("patchFilteringMode");
opt.setLongFlag("patchFilteringMode");
opt.setStringParser(JSAP.STRING_PARSER);
opt.setDefault(RepairnatorConfig.PATCH_FILTERING_MODE.NONE.name());
opt.setHelp("Possible string values NONE, ODS_CORRECT.");
return opt;
}

public static RepairnatorConfig.PATCH_FILTERING_MODE getArgPatchFilteringMode(JSAPResult arguments) {
return RepairnatorConfig.PATCH_FILTERING_MODE.valueOf(arguments.getString("patchFilteringMode"));
}

public static void checkPushUrlArg(JSAP jsap, JSAPResult arguments, LauncherType launcherType) {
Expand All @@ -969,7 +1039,6 @@ public static void checkPushUrlArg(JSAP jsap, JSAPResult arguments, LauncherType
}
}


public static void printUsage(JSAP jsap, LauncherType launcherType) {
String moduleName = "repairnator-" + launcherType.name().toLowerCase();
System.err.println("Usage: java <" + moduleName + " name> [option(s)]");
Expand Down
85 changes: 48 additions & 37 deletions ...repairnator-core/src/main/java/fr/inria/spirals/repairnator/config/RepairnatorConfig.java
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Original file line number Diff line number Diff line change
Expand Up @@ -49,14 +49,14 @@ public String getKlass() {
}
}

public enum PATCH_RANKING_MODE {
public enum PATCH_CLASSIFICATION_MODE {
NONE,
OVERFITTING
ODS
}

public enum PATCH_CLASSIFICATION_MODE {
public enum PATCH_FILTERING_MODE {
NONE,
ODS
ODS_CORRECT
}

/**
Expand Down Expand Up @@ -116,6 +116,7 @@ public enum SORALD_REPAIR_MODE {
private String localMavenRepository;
private String jTravisEndpoint;
private String travisToken;
private String ODSPath;

private String gitRepositoryUrl;
private String gitRepositoryBranch;
Expand All @@ -134,10 +135,10 @@ public enum SORALD_REPAIR_MODE {
private String npeScope;
private String npeRepairStrategy;

private PATCH_RANKING_MODE patchRankingMode;

private PATCH_CLASSIFICATION_MODE patchClassificationMode;

private PATCH_FILTERING_MODE patchFilteringMode;
private boolean patchClassification;
private boolean patchFiltering;

// Dockerpool
private String dockerImageName;
Expand Down Expand Up @@ -808,35 +809,6 @@ public void setNPERepairStrategy(String npeRepairStrategy) {
this.npeRepairStrategy = npeRepairStrategy;
}

public PATCH_RANKING_MODE getPatchRankingMode() {
return patchRankingMode;
}


public void setPatchRankingMode(String patchRankingMode) {
for (PATCH_RANKING_MODE mode: PATCH_RANKING_MODE.values()) {
if (patchRankingMode.equals(mode.name())) {
this.patchRankingMode = PATCH_RANKING_MODE.valueOf(patchRankingMode);
return;
}
}
throw new RuntimeException("unknown patch ranking mode: " + patchRankingMode);
}

public PATCH_CLASSIFICATION_MODE getPatchClassificationMode() {
return patchClassificationMode;
}

public void setPatchClassificationMode(String patchClassificationMode) {
for (PATCH_CLASSIFICATION_MODE mode: PATCH_CLASSIFICATION_MODE.values()) {
if (patchClassificationMode.equals(mode.name())) {
this.patchClassificationMode = PATCH_CLASSIFICATION_MODE.valueOf(patchClassificationMode);
return;
}
}
throw new RuntimeException("unknown patch classification mode: " + patchClassificationMode);
}

@Override
public String toString() {
String ghToken = this.getGithubToken();
Expand Down Expand Up @@ -907,7 +879,6 @@ public String toString() {
", mavenHome=" + mavenHome +
", localMavenRepository=" + localMavenRepository +
", noTravisRepair=" + noTravisRepair +
", rankPatches=" + patchRankingMode +
", jTravisEndpoint=" + jTravisEndpoint +
", travisToken=" + travisToken +
'}';
Expand Down Expand Up @@ -1006,4 +977,44 @@ public String getTravisToken() {
public void setTravisToken(String travisToken) {
this.travisToken = travisToken;
}

public String getODSPath() {
return ODSPath;
}

public void setODSPath(String ODSPath) {
this.ODSPath = ODSPath;
}

public PATCH_CLASSIFICATION_MODE getPatchClassificationMode() {
return patchClassificationMode;
}

public void setPatchClassificationMode(PATCH_CLASSIFICATION_MODE patchClassificationMode) {
this.patchClassificationMode = patchClassificationMode;
}

public boolean isPatchClassification() {
return patchClassification;
}

public void setPatchClassification(boolean patchClassification) {
this.patchClassification = patchClassification;
}

public PATCH_FILTERING_MODE getPatchFilteringMode() {
return patchFilteringMode;
}

public void setPatchFilteringMode(PATCH_FILTERING_MODE patchFilteringMode) {
this.patchFilteringMode = patchFilteringMode;
}

public boolean isPatchFiltering() {
return patchFiltering;
}

public void setPatchFiltering(boolean patchFiltering) {
this.patchFiltering = patchFiltering;
}
}
2 changes: 0 additions & 2 deletions src/repairnator-core/src/main/java/fr/inria/spirals/repairnator/config/SequencerConfig.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@ public enum RAW_URL_SOURCE {
public final String collectorPath;
public final int contextSize;
public final RAW_URL_SOURCE rawURLSource;
public final String ODSPath;

private static SequencerConfig instance;

Expand All @@ -31,7 +30,6 @@ private SequencerConfig(){
this.collectorPath = getEnvOrDefault("SEQUENCER_COLLECTOR_PATH",
System.getProperty("user.home") + "/continuous-learning-data");
this.contextSize = Integer.parseInt(getEnvOrDefault("SEQUENCER_CONTEXT_SIZE", "3"));
this.ODSPath = (getEnvOrDefault("SEQUENCER_ODS_PATH", RepairnatorConfig.getInstance().getOutputPath() + "/ODSPatches"));
this.rawURLSource = parseRawURLSource();

}
Expand Down
3 changes: 1 addition & 2 deletions ...core/src/main/java/fr/inria/spirals/repairnator/dockerpool/RunnablePipelineContainer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,6 @@ public RunnablePipelineContainer(DockerPoolManager poolManager, String imageId,
this.envValues.add("SEQUENCER_THREADS=" + sequencerConfig.threads);
this.envValues.add("SEQUENCER_BEAM_SIZE=" + sequencerConfig.beamSize);
this.envValues.add("SEQUENCER_TIMEOUT=" + sequencerConfig.timeout);
this.envValues.add("SEQUENCER_ODS_PATH=" + sequencerConfig.ODSPath);
}
}

Expand Down Expand Up @@ -167,7 +166,7 @@ public void run() {
.appendBinds(HostConfig.Bind
.builder()
.from(ODSVolume)
.to(SequencerConfig.getInstance().ODSPath)
.to(RepairnatorConfig.getInstance().getODSPath())
.build())
.build();

Expand Down
22 changes: 1 addition & 21 deletions ...tor-pipeline/src/main/java/fr/inria/spirals/repairnator/process/inspectors/JobStatus.java
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Original file line number Diff line number Diff line change
@@ -1,19 +1,16 @@
package fr.inria.spirals.repairnator.process.inspectors;

import com.google.gson.JsonElement;
import fr.inria.spirals.repairnator.config.RepairnatorConfig;
import fr.inria.spirals.repairnator.config.RepairnatorConfig.PATCH_RANKING_MODE;
import fr.inria.spirals.repairnator.process.inspectors.properties.Properties;
import fr.inria.spirals.repairnator.process.inspectors.properties.features.Features;
import fr.inria.spirals.repairnator.process.inspectors.properties.tests.FailureDetail;
import fr.inria.spirals.repairnator.process.step.StepStatus;
import fr.inria.spirals.repairnator.process.testinformation.FailureLocation;
import fr.inria.spirals.repairnator.states.PushState;
import org.apache.maven.model.Plugin;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import org.apache.maven.model.Plugin;

import java.io.File;
import java.net.URL;
import java.util.*;
Expand Down Expand Up @@ -276,23 +273,6 @@ public List<RepairPatch> getAllPatches() {
return allPatches;
}

public List<RepairPatch> getRankedPatches() {
return getRankedPatches(Features.P4J);
}

protected List<RepairPatch> getRankedPatches(Features features) {
List<RepairPatch> allPatches = getAllPatches();
PATCH_RANKING_MODE patchRankingMode = RepairnatorConfig.getInstance().getPatchRankingMode();

switch (patchRankingMode){
case OVERFITTING:
allPatches.sort(RepairPatch.rankByOverfittingWithFeatures(features));
break;
}
return allPatches;
}


protected List<RepairPatch> getCorrectnessLabeledPatches(Features features, String buildId) {
List<RepairPatch> allPatches = getAllPatches();
return RepairPatch.classifyByODSWithFeatures(allPatches, buildId);
Expand Down
18 changes: 8 additions & 10 deletions ...r-pipeline/src/main/java/fr/inria/spirals/repairnator/process/inspectors/RepairPatch.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import fr.inria.coming.codefeatures.RepairnatorFeatures;
import fr.inria.coming.codefeatures.RepairnatorFeatures.ODSLabel;
import fr.inria.coming.main.ComingProperties;
import fr.inria.spirals.repairnator.config.RepairnatorConfig;
import fr.inria.spirals.repairnator.config.SequencerConfig;
import fr.inria.spirals.repairnator.process.inspectors.properties.features.Features;
import fr.inria.spirals.repairnator.process.inspectors.properties.features.Overfitting;
Expand All @@ -23,7 +24,6 @@

public class RepairPatch {

static final String ODSPath = SequencerConfig.getInstance().ODSPath;
protected static Logger log = Logger.getLogger(Thread.currentThread().getName());

/**
Expand Down Expand Up @@ -145,11 +145,6 @@ public int hashCode() {
return Objects.hash(toolname, filePath, diff);
}

// ranking algorithms
public static Comparator<RepairPatch> rankByOverfittingWithFeatures(Features features) {
return (x, y) -> overfittingSort(x, y, features);
}

private static int overfittingSort(RepairPatch patch1, RepairPatch patch2, Features features) { // ascending
double score1 = patch1.getOverfittingScore(features);
double score2 = patch2.getOverfittingScore(features);
Expand All @@ -164,9 +159,11 @@ private static int overfittingSort(RepairPatch patch1, RepairPatch patch2, Featu

// ODS classification
public static List<RepairPatch> classifyByODSWithFeatures(List<RepairPatch> allPatches, String buildId) {
String ODSPath = RepairnatorConfig.getInstance().getODSPath();

File f = new File(ODSPath);
f.mkdir();
f.mkdirs();


int len = allPatches.size();

Expand All @@ -192,8 +189,9 @@ public static List<RepairPatch> classifyByODSWithFeatures(List<RepairPatch> allP
}

private ODSLabel computeODSLabel(int patchId, String buildId) {

ODSLabel label = ODSLabel.UNKNOWN;
String ODSPath = RepairnatorConfig.getInstance().getODSPath();

ODSLabel label = ODSLabel.UNKNOWN;

try {
File buggyFile = new File(filePath);
Expand All @@ -218,7 +216,7 @@ private ODSLabel computeODSLabel(int patchId, String buildId) {

// create a directory to store the patch: "patches/"+buildId+patchId
String buggyClassName = buggyFile.getName().replace(".java", "");
String odsFilesPath = SequencerConfig.getInstance().ODSPath;
String odsFilesPath = ODSPath;

String patchPath = odsFilesPath + "/" + buildId + "-" + patchId;
Path path = Paths.get(patchPath + '/' + buggyClassName);
Expand Down
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