a bit of 💙 for Coming (#257)

.github/workflows/maven.yml

@@ -27,9 +27,16 @@ jobs:
         java-version: '17'
         distribution: 'temurin'
         cache: maven
+    - name: Set up maven settings.xml
+      uses: s4u/maven-settings-action@v2.3.0
+      with:
+        servers: |
+          [{
+              "id": "brufulascam",
+              "username": "monperrus",
+              "password": "${{ secrets.GHTOKEN_READPACKAGES }}"
+          }]
+    - name: Clone test resource
+      run: git clone https://github.com/SpoonLabs/repogit4testv0
     - name: Build with Maven
       run: mvn -B package --file pom.xml
-
-    # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive
-    - name: Update dependency graph
-      uses: advanced-security/maven-dependency-submission-action@571e99aab1055c2e71a1e2309b9691de18d6b7d6

README.md

@@ -1,25 +1,49 @@
-[![Travis Build Status](https://travis-ci.org/SpoonLabs/coming.svg?branch=master)](https://travis-ci.org/SpoonLabs/coming)
-
 Coming
 =======
-Coming is a tool for mining git repositories.
+Coming is a tool for commit analysis in git repositories.
 
-If you use Coming, please cite one of: 
+If you use Coming, please cite: 
 
-* [Coming: a Tool for Mining Change Pattern Instances from Git Commits](http://arxiv.org/pdf/1810.08532). M. Martinez, M. Monperrus, Proceedings of ICSE - Demo track, 2019 ([doi:10.1109/ICSE-Companion.2019.00043](https://doi.org/10.1109/ICSE-Companion.2019.00043)). [bibtex](https://www.monperrus.net/martin/bibtexbrowser.php?key=arXiv-1810.08532&bib=monperrus.bib)
-* [Accurate Extraction of Bug Fix Pattern Occurrences using Abstract Syntax Tree Analysis](https://hal.archives-ouvertes.fr/hal-01075938/file/bug-fix-pattern-identification.pdf) (Matias Martinez, Laurence Duchien and Martin Monperrus), Technical report hal-01075938, Inria, 2014 [bibtex](https://www.monperrus.net/martin/bibtexbrowser.php?key=martinez%3Ahal-01075938&bib=monperrus.bib)
-* [Automatically Extracting Instances of Code Change Patterns with AST Analysis](https://hal.inria.fr/hal-00861883/file/paper-short.pdf) (Martinez, M.; Duchien, L.; Monperrus, M.) IEEE International Conference on Software Maintenance (ICSM), pp.388-391, 2013, doi: 10.1109/ICSM.2013.54 [bibtex](https://www.monperrus.net/martin/bibtexbrowser.php?key=martinez%3Ahal-00861883&bib=monperrus.bib)
+* [Coming: a Tool for Mining Change Pattern Instances from Git Commits](http://arxiv.org/pdf/1810.08532). M. Martinez, M. Monperrus, Proceedings of ICSE, 2019 ([doi:10.1109/ICSE-Companion.2019.00043](https://doi.org/10.1109/ICSE-Companion.2019.00043)). [bibtex](https://www.monperrus.net/martin/bibtexbrowser.php?key=1810.08532&bib=monperrus.bib)
 
 Contact: 
 
 [Matias Martinez](http://www.martinezmatias.com/), [Martin Monperrus](http://www.monperrus.net/martin/)
 
 ## Install
 
-Please install a JDK 1.8 and configure Maven or your IDE to use it.
+Coming is deployed on Maven Central, see [past versions](https://repo1.maven.org/maven2/com/github/spoonlabs/coming/).
+
+To build yourself, the procedure is as follows.
+
+Add a github token in `.m2/settings.xml`.
+
+```xml
+<settings>
+  <servers>
+    <server>
+      <id>br.ufu.lascam</id>
+      <username>yourlogin</username>
+      <!-- your github token with scope read:packages -->
+      <password>FOOBAR</password>
+    </server>
+  </servers>
+</settings>
+```
+
+
+Install a JDK 17 and configure Maven or your IDE to use it.
+
 
 ```
- mvn install -DskipTests
+$ export JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64/
+$ mvn -version
+Apache Maven 3.6.3
+Maven home: /usr/share/maven
+Java version: 17.0.9, vendor: Private Build, runtime: /usr/lib/jvm/java-17-openjdk-amd64
+
+# now installing
+$ mvn install -DskipTests
 ```
 
 Tests:
@@ -82,6 +106,8 @@ In the following command we change the value of two properties: `max_nb_hunks` a
 
 When running Coming in mode `-mode mineinstance` the output is a file name `instances_found.json` , which shows the different instances of the pattern passed as parameter.
 
+* [Automatically Extracting Instances of Code Change Patterns with AST Analysis](https://hal.inria.fr/hal-00861883/file/paper-short.pdf) (Martinez, M.; Duchien, L.; Monperrus, M.) IEEE International Conference on Software Maintenance (ICSM), pp.388-391, 2013, doi: 10.1109/ICSM.2013.54 [bibtex](https://www.monperrus.net/martin/bibtexbrowser.php?key=martinez%3Ahal-00861883&bib=monperrus.bib)
+
 
 #### Mining Simple Changes (i.e., with exactly one change)
 
@@ -313,6 +339,11 @@ Example, the previous json file shows
 which means that there are 2 changes that update binary operators inside an if condition (i.e., the parent).
 
 ### Mode Repairability
+
+This is a mode to find commits which look like automated program repair commits, see paper ["Estimating the Potential of Program Repair Search Spaces with Commit Analysis"](http://arxiv.org/pdf/2007.06986) (Khashayar Etemadi, Niloofar Tarighat, Siddharth Yadav, Matias Martinez and Martin Monperrus, Journal of Systems and Software, 2022).
+
+Note that the results are sensitive to the underlying diff algorithm. If you run repairibility analysis today, you'll get results that are different from the paper. For exact reproduction, use commit [1cad74323bacad65f06ddf80ab53971d38957507](https://github.com/SpoonLabs/coming/commit/1cad74323bacad65f06ddf80ab53971d38957507) and Java 8.
+
 When running Coming in mode `-mode repairibility`, the output is a file named `all_instances_found.json` , which shows the possible tool creating the commits. You can choose tools of interest by including the option:  `-repairtool All,Jkali,..`
 
 An example of the content of such file is:
@@ -376,10 +407,12 @@ Last 100 commits of the repository are analyzed by default, you can change this
 
 ### Mode Code Features
 
-Coming has an option to compute the features associated to the code changed by a commit.
+Coming can be used to compute features associated to the code changed by a commit.
 This functionality can be used with the argument `-mode features`.
 Coming writes in the folder specified in the `-output` a JSON file for each commit.
 
+See [Automated Classification of Overfitting Patches with Statically Extracted Code Features](http://arxiv.org/pdf/1910.12057) (He Ye, Jian Gu, Matias Martinez, Thomas Durieux and Martin Monperrus), In IEEE Transactions on Software Engineering, 2021.
+
 ## Input Types
 
 Coming read the input from the folder indicated by the argument `-location`. The kind of input depends on the argument `-input`. 

pom.xml

@@ -68,13 +68,16 @@
 			<artifactId>commons-io</artifactId>
 			<version>2.4</version>
 		</dependency>
+
 
-		<dependency><!-- must come before gumtree-spoon -->
+		<!-- must come before gumtree-spoon  --> 
+
+		<dependency>
 			<groupId>br.ufu.lascam</groupId>
 			<artifactId>automatic-diff-dissection</artifactId>
-			<version>1.1-SNAPSHOT</version>
+			<version>1.1</version>
 		</dependency>
-
+		
 		<dependency>
 			<groupId>fr.inria.gforge.spoon.labs </groupId>
 			<artifactId>gumtree-spoon-ast-diff</artifactId>
@@ -170,13 +173,18 @@
 
 		<dependency>
 		    <groupId>ml.dmlc</groupId>
-		    <artifactId>xgboost4j</artifactId>
-		    <version>0.72</version>
+		    <artifactId>xgboost4j_2.12</artifactId>
+		    <version>2.0.3</version>
 		</dependency>
 
 	</dependencies>
 
 	<repositories>
+		<repository>
+			<id>brufulascam</id>
+			<url>https://maven.pkg.github.com/lascam-UFU/automatic-diff-dissection</url>
+		</repository>
+
 		<repository>
 			<id>tdurieux.github.io/maven-repository/snapshots/</id>
 			<name>tdurieux.github.io maven-repository</name>
@@ -189,11 +197,7 @@
 			<url>https://tdurieux.github.io/maven-repository/releases/</url>
 		</repository>
 
-		<repository>
-			<id>maven.inria.fr-snapshot</id>
-			<name>Maven Repository for Spoon Snapshots</name>
-			<url>http://maven.inria.fr/artifactory/spoon-public-snapshot</url>
-		</repository>
+
 	</repositories>
 
 	<build>
@@ -311,6 +315,7 @@
 			<id>ossrh</id>
 			<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
 		</repository>
+
 		<snapshotRepository>
 			<id>ossrh-snapshot</id>
 			<url>https://oss.sonatype.org/repositories/snapshots</url>

src/main/java/fr/inria/coming/changeminer/analyzer/instancedetector/MegaDiff.java

@@ -25,7 +25,7 @@ public class MegaDiff implements Diff {
 	/**
 	 * the mapping of this diff
 	 */
-	private MappingStore _mappingsComp = new MappingStore();
+	private MappingStore _mappingsComp;
 	/**
 	 * Context of the spoon diff.
 	 */
@@ -37,7 +37,7 @@ public void merge(Diff anotherDiff) {
 		this.rootOperations.addAll(anotherDiff.getRootOperations());
 
 		for (Mapping map : anotherDiff.getMappingsComp().asSet()) {
-			_mappingsComp.link(map.getFirst(), map.getSecond());
+			_mappingsComp = new MappingStore(map.first, map.second);
 		}
 
 		// context.
@@ -101,6 +101,11 @@ public boolean containsOperations(List<Operation> operations, OperationKind kind
 		return false;
 	}
 
+	@Override
+	public boolean containsOperations(List<Operation> list, OperationKind operationKind, String s) {
+		return containsOperations(list, operationKind, s,"EMPTY");
+	}
+
 	@Override
 	public void debugInformation() {
 

src/main/java/fr/inria/coming/codefeatures/RepairnatorFeatures.java

@@ -59,6 +59,7 @@ public ODSLabel getLabel(File pairFolder) throws Exception {
 		File tempFile = null;
 		try {
 			tempFile = File.createTempFile("test", ".txt");
+			System.out.println("tempFile: "+tempFile);
 		} catch (Exception e) {
 			log.error("ODS cannot create a feature file test.txt in the disk ");
 			return ODSLabel.UNKNOWN;

src/main/java/fr/inria/coming/codefeatures/codeanalyze/AbstractCodeAnalyzer.java

@@ -4,8 +4,8 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
-import com.github.gumtreediff.tree.ITree;
 
+import com.github.gumtreediff.tree.Tree;
 import fr.inria.coming.codefeatures.Cntx;
 import fr.inria.coming.codefeatures.CodeElementInfo;
 import fr.inria.coming.codefeatures.CodeFeatures;
@@ -69,7 +69,7 @@ public void writeGroupedInfo(Cntx<Object> context, String key, CodeFeatures prop
 	public String adjustIdentifyInJson(CtElement spoonElement) {
 
 		if (spoonElement.getAllMetadata().containsKey("gtnode")) {
-			ITree gumtreeObject = (ITree) spoonElement.getMetadata("gtnode");
+			Tree gumtreeObject = (Tree) spoonElement.getMetadata("gtnode");
 
 			return gumtreeObject.getLabel();
 		} else {

src/main/java/fr/inria/coming/codefeatures/sec/SecAnalysis.java

@@ -3,7 +3,7 @@
 import java.util.List;
 import java.util.Map;
 
-import com.github.gumtreediff.tree.ITree;
+import com.github.gumtreediff.tree.Tree;
 import com.google.gson.JsonArray;
 import com.google.gson.JsonObject;
 
@@ -71,7 +71,7 @@ public static JsonObject createJSonOfOperation(MapList<Operation, Operation> ope
 						operation.getAction().getNode());
 				change.add("ast_node_updated_previous", ast);
 
-				ITree dest = iDiff.getMappingsComp().getDst(operation.getAction().getNode());
+				Tree dest = iDiff.getMappingsComp().getDstForSrc(operation.getAction().getNode());
 				JsonObject ast_dst = jsongen.getJSONasJsonObject(((DiffImpl) iDiff).getContext(), dest);
 				change.add("ast_node_updated_post", ast_dst);
 

src/main/java/fr/inria/coming/core/engine/git/RepositoryPGit.java

@@ -56,6 +56,9 @@ public RepositoryPGit(String pathOfRepo, String branch) {
 	 *            The branch to analyze
 	 */
 	public RepositoryPGit(String pathOfRepo, String branch, Collection<String> filter) {
+		if (!new File(pathOfRepo).exists()) {
+			throw new RuntimeException("repository path (arg --location) does not exist");
+		}
 		FileRepositoryBuilder builder = new FileRepositoryBuilder();
 		this.filter = filter;
 		String path = pathOfRepo;

src/main/java/fr/inria/coming/core/entities/output/JSonPatternInstanceOutput.java

@@ -99,7 +99,9 @@ public void getInstancesOfRevision(RevisionResult revisionResult, JsonArray inst
 						opjson.add("concrete_change", getJSONFromOperator(op));
 
 						if (op.getNode().getPosition() != null) {
-							opjson.addProperty("file", op.getNode().getPosition().getFile().getAbsolutePath());
+							final String repoPath = new File(ComingProperties.getProperty("location")).getAbsolutePath();
+							final String relativePath = op.getNode().getPosition().getFile().getAbsolutePath().replace(new File(System.getProperty("user.dir")).getAbsolutePath(), "");
+							opjson.addProperty("file", repoPath+File.separator+ relativePath);
 							opjson.addProperty("line", op.getNode().getPosition().getLine());
 						}
 						ops.add(opjson);

src/main/java/fr/inria/coming/main/ComingMain.java

@@ -238,13 +238,7 @@ private void loadFilters() {
 	private void loadOutput() {
 		String outputs = ComingProperties.getProperty("outputprocessor");
 		if (outputs == null) {
-			if (Boolean.valueOf(System.getProperty("executed_by_travis"))) {
-				navigatorEngine.getOutputProcessors().add(0, new NullOutput());
-				System.out.println("****EXECUTED_BY_TRAVIS****");
-			} else {
-				navigatorEngine.getOutputProcessors().add(0, new StdOutput());
-				System.out.println("**NOT_EXECUTED_BY_TRAVIS**");
-			}
+			navigatorEngine.getOutputProcessors().add(0, new NullOutput());
 		} else {
 			loadOutputProcessors(outputs);
 		}

src/main/java/fr/inria/coming/repairability/repairtools/Arja.java

@@ -11,8 +11,8 @@
 
 import com.github.gumtreediff.actions.model.Insert;
 import com.github.gumtreediff.matchers.MappingStore;
-import com.github.gumtreediff.tree.ITree;
 
+import com.github.gumtreediff.tree.Tree;
 import fr.inria.coming.changeminer.analyzer.instancedetector.ChangePatternInstance;
 import fr.inria.coming.changeminer.analyzer.patternspecification.ChangePatternSpecification;
 import fr.inria.coming.changeminer.entity.IRevision;
@@ -82,7 +82,7 @@ public boolean filter(ChangePatternInstance instance, IRevision revision, Diff d
 				return true;
 			} else if (op instanceof InsertOperation) {
 				MappingStore mapping = diff.getMappingsComp();
-				if (!mapping.hasSrc(((Insert) op.getAction()).getParent()))
+				if (!mapping.isSrcMapped(((Insert) op.getAction()).getParent()))
 					return false;
 
 				CtElement parentOfInsertedNode = ((InsertOperation) op).getParent();
@@ -102,18 +102,18 @@ public boolean filter(ChangePatternInstance instance, IRevision revision, Diff d
 			CtElement affectedNode, srcNode;
 			if (op instanceof InsertOperation) {
 				MappingStore mapping = diff.getMappingsComp();
-				if (!mapping.hasSrc(((Insert) op.getAction()).getParent()))
+				if (!mapping.isSrcMapped(((Insert) op.getAction()).getParent()))
 					return false;
 
 				affectedNode = op.getSrcNode().getParent();
 				srcNode = ((InsertOperation) op).getParent();
 			} else if (op instanceof DeleteOperation) {
 				MappingStore mapping = diff.getMappingsComp();
 
-				if (!mapping.hasSrc(op.getAction().getNode().getParent()))
+				if (!mapping.isSrcMapped(op.getAction().getNode().getParent()))
 					return false;
 
-				ITree dstTree = mapping.getDst(op.getAction().getNode().getParent());
+				Tree dstTree = mapping.getDstForSrc(op.getAction().getNode().getParent());
 				affectedNode = (CtElement) dstTree.getMetadata("spoon_object");
 				srcNode = op.getSrcNode();
 			} else if (op instanceof UpdateOperation) {
@@ -137,10 +137,13 @@ public boolean filter(ChangePatternInstance instance, IRevision revision, Diff d
 					delOp = getActionFromDelInsInstance(instance, "DEL");
 
 			MappingStore mapping = diff.getMappingsComp();
-			if (!mapping.hasSrc(((Insert) op.getAction()).getParent()))
+			if (!mapping.isSrcMapped(((Insert) op.getAction()).getParent()))
 				// the inserted node is a part of a parent inserted node
 				return false;
-
+
+			if (!(insOp instanceof InsertOperation)) {
+				return false;
+			}
 			CtElement insertedNodeParent = ((InsertOperation)insOp).getParent();
 
 			if(insertedNodeParent == null)