Enable detection of Inline Variable in commit

pmd/pmd@07516ee
Support comment multi-mappings in commit
jOOQ/jOOQ@58a4e74
Fix bug in the generation of line-comment groups
Add tests for comment multi-mappings

src/main/java/gr/uom/java/xmi/decomposition/AbstractCodeMapping.java

@@ -540,6 +540,20 @@ public void temporaryVariableAssignment(AbstractCodeFragment statement,
 							}
 						}
 					}
+					else if(initializer != null && initializer.toString().equals(before)) {
+						ExtractVariableRefactoring ref = new ExtractVariableRefactoring(declaration, operation1, operation2, insideExtractedOrInlinedMethod);
+						List<LeafExpression> subExpressions = getFragment1().findExpression(before);
+						for(LeafExpression subExpression : subExpressions) {
+							LeafMapping leafMapping = new LeafMapping(subExpression, initializer, operation1, operation2);
+							ref.addSubExpressionMapping(leafMapping);
+						}
+						processExtractVariableRefactoring(ref, refactorings);
+						checkForNestedExtractVariable(ref, refactorings, nonMappedLeavesT2, insideExtractedOrInlinedMethod);
+						if(identical()) {
+							identicalWithExtractedVariable = true;
+						}
+						return;
+					}
 				}
 				else if(after.startsWith("()" + JAVA.LAMBDA_ARROW + variableName + ".")) {
 					int extraLength = "()".length() + JAVA.LAMBDA_ARROW.length();
@@ -836,6 +850,19 @@ public void inlinedVariableAssignment(AbstractCodeFragment statement,
 							}
 						}
 					}
+					else if(initializer != null && initializer.toString().equals(after)) {
+						InlineVariableRefactoring ref = new InlineVariableRefactoring(declaration, operation1, operation2, insideExtractedOrInlinedMethod);
+						List<LeafExpression> subExpressions = getFragment2().findExpression(after);
+						for(LeafExpression subExpression : subExpressions) {
+							LeafMapping leafMapping = new LeafMapping(initializer, subExpression, operation1, operation2);
+							ref.addSubExpressionMapping(leafMapping);
+						}
+						processInlineVariableRefactoring(ref, refactorings);
+						if(identical()) {
+							identicalWithInlinedVariable = true;
+						}
+						return;
+					}
 				}
 				else if(before.startsWith("()" + JAVA.LAMBDA_ARROW + variableName + ".")) {
 					int extraLength = "()".length() + JAVA.LAMBDA_ARROW.length();

src/main/java/gr/uom/java/xmi/decomposition/UMLOperationBodyMapper.java

@@ -2651,13 +2651,23 @@ else if(streamAPIStatements1.size() > 0 && streamAPIStatements2.size() == 0) {
 				inlinedVariableAssignment(statement, nonMappedLeavesT2);
 			}
 			if(parentMapper != null && parentMapper.commentListDiff != null) {
-				List<UMLComment> deletedComments = new ArrayList<UMLComment>();
-				deletedComments.addAll(parentMapper.commentListDiff.getDeletedComments());
+				AbstractCodeMapping parentMapping = findParentMappingContainingOperationInvocation();
+				Set<UMLComment> deletedComments = new LinkedHashSet<UMLComment>();
+				if(parentMapping != null) {
+					for(UMLComment deletedComment : parentMapper.commentListDiff.getDeletedComments()) {
+						if(parentMapping.getFragment1().getLocationInfo().subsumes(deletedComment.getLocationInfo())) {
+							deletedComments.add(deletedComment);
+						}
+					}
+				}
+				else {
+					deletedComments.addAll(parentMapper.commentListDiff.getDeletedComments());
+				}
 				for(UMLOperationBodyMapper childMapper : parentMapper.getChildMappers()) {
 					if(childMapper.commentListDiff != null)
 						deletedComments.addAll(childMapper.commentListDiff.getDeletedComments());
 				}
-				this.commentListDiff = new UMLCommentListDiff(deletedComments, container2.getComments());
+				this.commentListDiff = new UMLCommentListDiff(new ArrayList<>(deletedComments), container2.getComments());
 				checkUnmatchedStatementsBeingCommented();
 			}
 		}
@@ -3041,13 +3051,23 @@ else if(streamAPIStatements1.size() > 0 && streamAPIStatements2.size() == 0) {
 				inlinedVariableAssignment(statement, nonMappedLeavesT2);
 			}
 			if(parentMapper != null && parentMapper.commentListDiff != null) {
-				List<UMLComment> addedComments = new ArrayList<UMLComment>();
-				addedComments.addAll(parentMapper.commentListDiff.getAddedComments());
+				AbstractCodeMapping parentMapping = findParentMappingContainingOperationInvocation();
+				Set<UMLComment> addedComments = new LinkedHashSet<UMLComment>();
+				if(parentMapping != null) {
+					for(UMLComment addedComment : parentMapper.commentListDiff.getAddedComments()) {
+						if(parentMapping.getFragment2().getLocationInfo().subsumes(addedComment.getLocationInfo())) {
+							addedComments.add(addedComment);
+						}
+					}
+				}
+				else {
+					addedComments.addAll(parentMapper.commentListDiff.getAddedComments());
+				}
 				for(UMLOperationBodyMapper childMapper : parentMapper.getChildMappers()) {
 					if(childMapper.commentListDiff != null)
 						addedComments.addAll(childMapper.commentListDiff.getAddedComments());
 				}
-				this.commentListDiff = new UMLCommentListDiff(container1.getComments(), addedComments);
+				this.commentListDiff = new UMLCommentListDiff(container1.getComments(), new ArrayList<>(addedComments));
 				checkUnmatchedStatementsBeingCommented();
 			}
 		}

src/main/java/gr/uom/java/xmi/diff/UMLCommentListDiff.java

@@ -177,17 +177,32 @@ private List<UMLCommentGroup> createCommentGroups(List<UMLComment> commentsBefor
 						}
 						else {
 							//make new group
-							groups.add(new UMLCommentGroup(currentGroup.getGroup()));
+							if (currentGroup.getGroup().size() > 0) {
+								groups.add(new UMLCommentGroup(currentGroup.getGroup()));
+							}
 							currentGroup = new UMLCommentGroup();
 							currentGroup.addComment(current);
 						}
 					}
+					else {
+						//make new group
+						if (currentGroup.getGroup().size() > 0) {
+							groups.add(new UMLCommentGroup(currentGroup.getGroup()));
+						}
+						currentGroup = new UMLCommentGroup();
+						currentGroup.addComment(current);
+					}
 				}
 				else {
 					//this is the first line comment
 					currentGroup.addComment(current);
 				}
 			}
+			else if (currentGroup.getGroup().size() > 0) {
+				//there is a comment of different type
+				groups.add(new UMLCommentGroup(currentGroup.getGroup()));
+				currentGroup = new UMLCommentGroup();
+			}
 		}
 		if(!currentGroup.getGroup().isEmpty())
 			groups.add(currentGroup);

src/test/java/org/refactoringminer/test/TestAllRefactorings.java

@@ -15,6 +15,6 @@ public void testAllRefactorings() throws Exception {
 		GitHistoryRefactoringMinerImpl detector = new GitHistoryRefactoringMinerImpl();
 		TestBuilder test = new TestBuilder(detector, REPOS, Refactorings.All.getValue());
 		RefactoringPopulator.feedRefactoringsInstances(Refactorings.All.getValue(), Systems.FSE.getValue(), test);
-		test.assertExpectationsWithGitHubAPI(12265, 20, 233);
+		test.assertExpectationsWithGitHubAPI(12269, 20, 233);
 	}
 }

src/test/java/org/refactoringminer/test/TestJavadocDiff.java

@@ -14,6 +14,7 @@
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.CsvSource;
+import org.refactoringminer.api.Refactoring;
 import org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl;
 import org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl.ChangedFileInfo;
 
@@ -22,6 +23,8 @@
 import gr.uom.java.xmi.UMLDocElement;
 import gr.uom.java.xmi.UMLModel;
 import gr.uom.java.xmi.decomposition.UMLOperationBodyMapper;
+import gr.uom.java.xmi.diff.ExtractOperationRefactoring;
+import gr.uom.java.xmi.diff.InlineOperationRefactoring;
 import gr.uom.java.xmi.diff.UMLClassDiff;
 
 public class TestJavadocDiff {
@@ -113,6 +116,47 @@ public void testMethodCommentMappings(String url, String commitId, String classN
 		Assertions.assertTrue(expected.size() == actual.size() && expected.containsAll(actual) && actual.containsAll(expected));
 	}
 
+	@ParameterizedTest
+	@CsvSource({
+		"https://github.com/jOOQ/jOOQ.git, 58a4e74d28073e7c6f15d1f225ac1c2fd9aa4357, org.jooq.tools.Convert.ConvertAll, jOOQ-58a4e74d28073e7c6f15d1f225ac1c2fd9aa4357-comments.txt",
+		"https://github.com/thymeleaf/thymeleaf.git, 378ba37750a9cb1b19a6db434dfa59308f721ea6, org.thymeleaf.templateparser.reader.BlockAwareReader, thymeleaf-378ba37750a9cb1b19a6db434dfa59308f721ea6-comments.txt",
+		"https://github.com/eclipse-vertx/vert.x.git, 32a8c9086040fd6d6fa11a214570ee4f75a4301f, io.vertx.core.http.impl.HttpServerImpl.ServerHandler, vertx-32a8c9086040fd6d6fa11a214570ee4f75a4301f-comments.txt"
+	})
+	public void testMethodCommentMultiMappings(String url, String commitId, String className, String testResultFileName) throws Exception {
+		final List<String> actual = new ArrayList<>();
+		UMLClassDiff classDiff = generateClassDiff(url, commitId, new File(REPOS), className);
+		classDiff.process();
+		List<Refactoring> refactorings = classDiff.getRefactorings();
+		List<UMLOperationBodyMapper> parentMappers = new ArrayList<>();
+		for (Refactoring ref : refactorings) {
+			if(ref instanceof ExtractOperationRefactoring) {
+				ExtractOperationRefactoring ex = (ExtractOperationRefactoring)ref;
+				UMLOperationBodyMapper bodyMapper = ex.getBodyMapper();
+				if(!bodyMapper.isNested()) {
+					if(!parentMappers.contains(bodyMapper.getParentMapper())) {
+						parentMappers.add(bodyMapper.getParentMapper());
+					}
+				}
+				commentInfo(bodyMapper, actual);
+			}
+			else if(ref instanceof InlineOperationRefactoring) {
+				InlineOperationRefactoring ex = (InlineOperationRefactoring)ref;
+				UMLOperationBodyMapper bodyMapper = ex.getBodyMapper();
+				if(!bodyMapper.isNested()) {
+					if(!parentMappers.contains(bodyMapper.getParentMapper())) {
+						parentMappers.add(bodyMapper.getParentMapper());
+					}
+				}
+				commentInfo(bodyMapper, actual);
+			}
+		}
+		for(UMLOperationBodyMapper parentMapper : parentMappers) {
+			commentInfo(parentMapper, actual);
+		}
+		List<String> expected = IOUtils.readLines(new FileReader(EXPECTED_PATH + testResultFileName));
+		Assertions.assertTrue(expected.size() == actual.size() && expected.containsAll(actual) && actual.containsAll(expected));
+	}
+
 	private UMLClassDiff generateClassDiff(String cloneURL, String commitId, File rootFolder, String className) throws Exception {
 		Set<String> repositoryDirectoriesBefore = ConcurrentHashMap.newKeySet();
 		Set<String> repositoryDirectoriesCurrent = ConcurrentHashMap.newKeySet();

src/test/resources/mappings/jOOQ-58a4e74d28073e7c6f15d1f225ac1c2fd9aa4357-comments.txt

@@ -0,0 +1,53 @@
+public from(from Object) : U -> private millis(temporal Temporal) : long
+line range:573-573==line range:1057-1057
+line range:584-584==line range:1068-1068
+line range:589-589==line range:1073-1073
+public from(from Object) : U -> private millis(temporal Temporal) : long
+line range:666-666==line range:1057-1057
+line range:677-677==line range:1068-1068
+line range:682-682==line range:1073-1073
+public from(from Object) : U -> public from(from Object) : U
+line range:449-449==line range:450-450
+line range:450-450==line range:451-451
+line range:475-475==line range:476-476
+line range:476-476==line range:477-477
+line range:943-943==line range:918-918
+line range:944-944==line range:919-919
+line range:964-964==line range:939-939
+line range:965-965==line range:940-940
+line range:453-453==line range:454-454
+line range:458-458==line range:459-459
+line range:470-470==line range:471-471
+line range:481-481==line range:482-482
+line range:484-484==line range:485-485
+line range:489-489==line range:490-490
+line range:498-498==line range:499-499
+line range:507-507==line range:508-508
+line range:569-569==line range:570-570
+line range:594-594==line range:574-574
+line range:604-604==line range:584-584
+line range:662-662==line range:642-642
+line range:687-687==line range:646-646
+line range:697-697==line range:656-656
+line range:779-779==line range:738-738
+line range:789-789==line range:748-748
+line range:799-799==line range:758-758
+line range:809-809==line range:768-768
+line range:814-814==line range:773-773
+line range:818-818==line range:777-777
+line range:820-820==line range:779-779
+line range:825-825==line range:784-784
+line range:829-829==line range:788-788
+line range:831-831==line range:790-790
+line range:841-841==line range:800-800
+line range:851-851==line range:810-810
+line range:861-861==line range:820-820
+line range:864-864==line range:823-823
+line range:880-880==line range:839-839
+line range:896-896==line range:855-855
+line range:912-912==line range:871-871
+line range:928-928==line range:887-887
+line range:941-941==line range:916-916
+line range:954-954==line range:929-929
+line range:971-1008==line range:946-983
+line range:1010-1010==line range:985-985

src/test/resources/mappings/thymeleaf-378ba37750a9cb1b19a6db434dfa59308f721ea6-comments.txt

@@ -0,0 +1,26 @@
+public read(cbuf char[], off int, len int) : int -> private matchOverflow(structure char[]) : boolean
+line range:165-165==line range:271-271
+line range:180-180==line range:271-271
+public read(cbuf char[], off int, len int) : int -> private matchOverflow(structure char[]) : boolean
+line range:165-165==line range:271-271
+line range:180-180==line range:271-271
+public read(cbuf char[], off int, len int) : int -> public read(cbuf char[], off int, len int) : int
+line range:127-127==line range:127-127
+line range:128-128==line range:128-128
+line range:159-159==line range:159-159
+line range:160-160==line range:160-160
+line range:194-194==line range:172-172
+line range:195-195==line range:173-173
+line range:196-196==line range:174-174
+line range:197-197==line range:175-175
+line range:73-73==line range:73-73
+line range:80-80==line range:80-80
+line range:85-85==line range:85-85
+line range:94-94==line range:94-94
+line range:117-117==line range:117-117
+line range:152-152==line range:152-152
+line range:154-154==line range:154-154
+line range:168-168==line range:163-163
+line range:171-171==line range:167-167
+line range:183-183==line range:163-163
+line range:186-186==line range:167-167

src/test/resources/mappings/vertx-32a8c9086040fd6d6fa11a214570ee4f75a4301f-comments.txt

@@ -0,0 +1,11 @@
+private handleHttp(conn ServerConnection, ch Channel, msg Object) : void -> protected doMessageReceived(conn ServerConnection, ctx ChannelHandlerContext, msg Object) : void
+line range:539-539==line range:525-525
+private handleExpectWebsockets(conn ServerConnection, ctx ChannelHandlerContext, msg Object) : void -> protected doMessageReceived(conn ServerConnection, ctx ChannelHandlerContext, msg Object) : void
+line range:511-511==line range:549-549
+line range:512-512==line range:550-550
+line range:495-495==line range:533-533
+line range:506-506==line range:544-544
+private handleHttp(conn ServerConnection, ch Channel, msg Object) : void -> protected doMessageReceived(conn ServerConnection, ctx ChannelHandlerContext, msg Object) : void
+line range:539-539==line range:525-525
+line range:539-539==line range:575-575
+protected doMessageReceived(conn ServerConnection, ctx ChannelHandlerContext, msg Object) : void -> protected doMessageReceived(conn ServerConnection, ctx ChannelHandlerContext, msg Object) : void

src/test/resources/oracle/data.json

@@ -3242,6 +3242,13 @@
         "validation": "TP",
         "detectionTools": "RefactoringMiner",
         "validators": null
+    }, {
+        "type": "Inline Variable",
+        "description": "Inline Variable handlers : Map<String,LoggingHandlerImpl> in method public getChildren() : Collection<? extends AbstractTreeNode> from class com.intellij.remoteServer.impl.runtime.ui.tree.ServersTreeStructure.DeploymentNodeImpl",
+        "comment": null,
+        "validation": "TP",
+        "detectionTools": "RefactoringMiner",
+        "validators": null
     }],
     "refDiffExecutionTime": 14854
 }, {
@@ -90732,6 +90739,13 @@
         "validation": "TP",
         "detectionTools": "RefactoringMiner",
         "validators": null
+    }, {
+        "type": "Extract Variable",
+        "description": "Extract Variable entry : ConnectorMetadataEntry in method public beginInsert(session Session, tableHandle TableHandle) : InsertTableHandle from class com.facebook.presto.metadata.MetadataManager",
+        "comment": null,
+        "validation": "TP",
+        "detectionTools": "RefactoringMiner",
+        "validators": null
     }],
     "refDiffExecutionTime": 9866
 }, {
@@ -101590,6 +101604,13 @@
         "validation": "TP",
         "detectionTools": "RefactoringMiner",
         "validators": null
+    }, {
+        "type": "Inline Variable",
+        "description": "Inline Variable temporal : Temporal in method public from(from Object) : U from class org.jooq.tools.Convert.ConvertAll",
+        "comment": null,
+        "validation": "TP",
+        "detectionTools": "RefactoringMiner",
+        "validators": null
     }],
     "refDiffExecutionTime": 1574
 }, {
@@ -103683,6 +103704,13 @@
         "validation": "TP",
         "detectionTools": "RefactoringMiner",
         "validators": null
+    }, {
+        "type": "Inline Variable",
+        "description": "Inline Variable values : List<Object> in method public getParameters() : List<Object> from class org.jbpm.query.jpa.data.QueryCriteria",
+        "comment": null,
+        "validation": "TP",
+        "detectionTools": "RefactoringMiner",
+        "validators": null
     }],
     "refDiffExecutionTime": 3454
 }, {

src/test/resources/oracle/expected.txt

@@ -234,7 +234,7 @@ ecd0ad5ab99b8d14f28881cf4f49ec01f2221776, 6, 0, 0
 cfea606b129dbfc5703eb279d4803185afc99c58, 13, 0, 3
 83cfa21578e63956bca0715eefee2860c3b6d39a, 9, 0, 0
 a739d16d301f0e89ab0b9dfa56b4585bbad6b793, 15, 0, 0
-58a4e74d28073e7c6f15d1f225ac1c2fd9aa4357, 2, 0, 0
+58a4e74d28073e7c6f15d1f225ac1c2fd9aa4357, 3, 0, 0
 f01d8610b9ceebc1de59d42f569b8af3efbe0a0f, 2, 0, 0
 72f61ec9b85a740fd09d10ad711e275d2ec2e564, 3, 0, 0
 227254cf769f3e821ed1b2ef2d88c4ec6b20adea, 9, 0, 0
@@ -314,7 +314,7 @@ d5f10a4958f5e870680be906689d92d1efb42480, 6, 0, 0
 2bd1557bc293cb8c2348374771aad832befbe26f, 2, 0, 0
 72b5348307d86b1a118e546c24d97f1ac1895bdb, 73, 0, 1
 7ccbd4693288dbdbc2e6844aa0877640d63fbd04, 12, 0, 0
-11048642b1e6b0e35efefab9e4e693b09c8753f5, 265, 0, 0
+11048642b1e6b0e35efefab9e4e693b09c8753f5, 266, 0, 0
 0b6ea757e34a63b1421b77ed5fbb61398377aab1, 6, 0, 0
 2b89553db5081fe4e55b7b34d636d0ea2acf71c5, 6, 0, 0
 b25d3f32ed2e2da86f5c746098686445c2e2a314, 6, 1, 0
@@ -360,7 +360,7 @@ d69e5cb21c04d9eede314aaa9ad059fc603fb025, 4, 0, 1
 ea96643364e91125f560e9508a5cbcdb776bde64, 28, 0, 0
 ba5e6d44526a2491a7004423ca2ad780c6992c46, 3, 0, 0
 b9a17665b158955ad28ef7f50cc0a8585460f053, 6, 0, 0
-3815f293ba9338f423315d93a373608c95002b15, 134, 0, 3
+3815f293ba9338f423315d93a373608c95002b15, 135, 0, 3
 b8929ccb4057c74ac64679216487a4abcd3ae1c3, 4, 0, 0
 3d5e343df6a39ce3b41624b90974d83e9899541e, 2, 0, 0
 0b93231025f51c7ec62fd8588985c5dc807854e4, 1, 0, 0
@@ -451,7 +451,7 @@ e1f0dbc2f09541fc64ce88ee22d8f8f4648004fe, 2, 0, 0
 484038e916dc40bf87eca10c77889d79eca96c4d, 2, 0, 0
 97811cf971f7ccf6a5fc5e90a491db2f58d49da1, 9, 0, 0
 e1625136ba12907696ef4c6e922ce073293f3a2c, 3, 0, 0
-219d6ddfd1db62c11efb57e0216436874e087834, 25, 0, 0
+219d6ddfd1db62c11efb57e0216436874e087834, 26, 0, 0
 7655200f58293e5a30bf8b3cbb29ebadae374564, 16, 0, 0
 8d7a26edd1fedb9505b4f2b4fe57b2d2958b4dd9, 5, 0, 0
 cc0eaf7faa408a04b68e2b5820f3ebcc75420b5b, 5, 0, 0