[WIP] On-going work by Henry

.travis.yml

@@ -28,7 +28,9 @@ cache:
 before_install:
 - sudo apt-get update
 - sudo apt-get install python3
-
+# Pull Mongodb image to test
+- docker pull mongo:latest
+- docker run -d --net=host mongo:latest
 install:
 - export DSPOT_VERSION=`grep '<version>' dspot/pom.xml | head -n 1 | sed -e 's/<version>//' -e 's/<\\/version>//' -e 's/ *//g'`
 - export MAVEN_HOME=`mvn --version | grep 'Maven home' | sed -e 's/Maven h.* //'`

dspot/pom.xml

@@ -157,7 +157,11 @@
                <artifactId>junit-vintage-engine</artifactId>
                <version>5.3.2</version>
        </dependency>
-
+       <dependency>
+            <groupId>org.mongodb</groupId>
+            <artifactId>mongodb-driver</artifactId>
+            <version>3.2.2</version>
+        </dependency>
 
 
     </dependencies>

dspot/src/main/java/eu/stamp_project/Main.java

@@ -8,6 +8,7 @@
 import eu.stamp_project.utils.report.error.ErrorReportImpl;
 import eu.stamp_project.utils.report.output.OutputReportImpl;
 import eu.stamp_project.utils.report.output.selector.TestSelectorReportImpl;
+import eu.stamp_project.mongodb.MongodbManager;
 import org.apache.commons.io.FileUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -59,6 +60,10 @@ public static void run() {
 		// global report handling
 		Main.GLOBAL_REPORT.output();
 		Main.GLOBAL_REPORT.reset();
+		// Send info to Mongodb
+		if (MongodbManager.getInstance().getDbConnectable()) {
+			MongodbManager.getInstance().sendInfoToDb();
+		}
 	}
 
 	public static void createOutputDirectories() {

dspot/src/main/java/eu/stamp_project/dspot/selector/JacocoCoverageSelector.java

@@ -1,5 +1,7 @@
 package eu.stamp_project.dspot.selector;
 
+import org.bson.Document;
+import eu.stamp_project.mongodb.MongodbManager;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 import eu.stamp_project.utils.report.output.selector.TestSelectorElementReport;
@@ -47,6 +49,8 @@ public class JacocoCoverageSelector extends TakeAllSelector {
 
     private TestSelectorElementReport lastReport;
 
+    private Document infoDoc;
+
     @Override
     public boolean init() {
         super.init();
@@ -185,7 +189,11 @@ public TestSelectorElementReport report() {
                 .append(this.selectedAmplifiedTest.size())
                 .append(" amplified tests.")
                 .append(AmplificationHelper.LINE_SEPARATOR);
-
+        /*Sending info to Mongodb, format original/newkills/percentage*/
+        if (MongodbManager.getInstance().getDbConnectable()) {
+            infoDoc = new Document();
+            infoDoc.append("initialCoverage","" + this.initialCoverage.getInstructionsCovered());
+        }
         // compute the new coverage obtained by the amplification
         final CtType<?> clone = this.currentClassTestToBeAmplified.clone();
         this.currentClassTestToBeAmplified.getPackage().addType(clone);
@@ -222,6 +230,15 @@ public TestSelectorElementReport report() {
                     .append("%")
                     .append(AmplificationHelper.LINE_SEPARATOR);
             lastReport = new TestSelectorElementReportImpl(report.toString(), jsonReport(coverageResults));
+            /*Sending data to Mongodb*/
+            if (MongodbManager.getInstance().getDbConnectable()) {
+                String s = this.currentClassTestToBeAmplified.getQualifiedName();
+                infoDoc.append("ampCoverage","" + coverageResults.getInstructionsCovered());
+                infoDoc.append("totalCoverage","" + coverageResults.getInstructionsTotal());
+
+                MongodbManager.getInstance().jacocoSelectorDocs.add(new Document(s.replace(".","/D/"),infoDoc));
+            }
+
             return lastReport;
         } catch (TimeoutException e) {
             throw new RuntimeException(e);

dspot/src/main/java/eu/stamp_project/dspot/selector/PitMutantScoreSelector.java

@@ -1,5 +1,7 @@
 package eu.stamp_project.dspot.selector;
 
+import org.bson.Document;
+import eu.stamp_project.mongodb.MongodbManager;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 import eu.stamp_project.Main;
@@ -53,6 +55,8 @@ public enum OutputFormat {XML, CSV}
 
     private TestSelectorElementReport lastReport;
 
+    private Document infoDoc;
+
     public PitMutantScoreSelector() {
         this(OutputFormat.XML);
     }
@@ -235,6 +239,14 @@ public TestSelectorElementReport report() {
     }
 
     private String reportStdout() {
+        if (MongodbManager.getInstance().getDbConnectable()) {
+            String s = this.currentClassTestToBeAmplified.getQualifiedName();
+            infoDoc = new Document();
+            infoDoc.append("originalKilledMutants","" + this.originalKilledMutants.size());
+            infoDoc.append("NewMutantKilled","" + getNbTotalNewMutantKilled());
+            MongodbManager.getInstance().pitMutantScoreSelectorDocs.add(new Document(s.replace(".","/D/"),infoDoc));
+        }
+
         return "Test class that has been amplified: " + this.currentClassTestToBeAmplified.getQualifiedName() +
                 AmplificationHelper.LINE_SEPARATOR +
                 "The original test suite kills " +

dspot/src/main/java/eu/stamp_project/mongodb/MongodbManager.java

@@ -0,0 +1,192 @@
+package eu.stamp_project.mongodb;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import com.mongodb.*;
+
+import com.mongodb.MongoClient;
+import com.mongodb.MongoClientURI;
+
+import com.mongodb.client.MongoCollection;
+import com.mongodb.client.MongoDatabase;
+import static com.mongodb.client.model.Filters.*;
+import static com.mongodb.client.model.Projections.*;
+import static com.mongodb.client.model.Updates.*;
+import org.bson.Document;
+
+
+/*Parsing date*/
+import java.util.Date;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import java.nio.file.Files;
+import java.nio.charset.StandardCharsets;
+import java.nio.charset.Charset;
+import java.nio.file.Paths;
+import java.io.IOException;
+
+public class MongodbManager {
+	private static final Logger LOGGER = LoggerFactory.getLogger(MongodbManager.class);
+	/*Format of date for saving in Mongodb*/
+	private static final DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
+	private static MongodbManager single_instance = null;
+
+	private static MongoClient mongoClient;
+	private static String mongoUrl;
+	private static String dbName;
+	private static String repoSlug;
+	private static String repoBranch;
+	private static String colName;
+	private static boolean dbConnectable;
+	private static boolean restful;
+
+	/*Jacoco Selector*/
+	public List<Document> jacocoSelectorDocs;
+
+	/*PitMutantScoreSelector*/
+	public List<Document> pitMutantScoreSelectorDocs;/*
+
+	/*Argumets from input*/
+	public Document argsDoc;
+
+	/*Output paths for java files*/
+	public List<String> javaPathList;
+
+	private MongodbManager () {
+		this.jacocoSelectorDocs = new ArrayList<Document>();
+		this.pitMutantScoreSelectorDocs = new ArrayList<Document>();
+		this.argsDoc = new Document();
+		this.javaPathList = new ArrayList<String>();
+		this.dbConnectable = testConnectionToDb();
+	}
+
+	public static MongodbManager getInstance() {
+		if (single_instance == null) {
+			single_instance = new MongodbManager();
+		}
+		return single_instance;
+	}
+
+	public static void initMongodbManager (String mongoUrl_ln, String dbName_ln, String colName_ln, String repoSlug_ln, String repoBranch_ln, boolean restful_ln) {
+		mongoUrl = mongoUrl_ln;
+		dbName = dbName_ln;
+		colName = colName_ln;
+		repoSlug = repoSlug_ln;
+		repoBranch = repoBranch_ln;
+		restful = restful_ln;
+		dbConnectable = testConnectionToDb();
+	}
+
+	public static MongoClient connectToMongo (String mongoUrl) {
+		return new MongoClient(new MongoClientURI(mongoUrl));
+	}
+
+	public static MongoDatabase getDatabase (String dbName , MongoClient mongoClient) {
+		return mongoClient.getDatabase(dbName);
+	}
+
+	public static MongoCollection<Document> getCollection (String colName,MongoDatabase database) {
+		return database.getCollection(colName);
+	}
+
+	private static boolean testConnectionToDb() {
+		try {
+			mongoClient = new MongoClient(new MongoClientURI(mongoUrl));
+			mongoClient.close();
+			LOGGER.warn("Mongodb connection Successful");
+			return true;
+		}catch (Exception e) {
+			LOGGER.warn("failed to connect to mongodb, No information will be submitted at the end");
+			return false;
+		}
+	}
+
+	public boolean getDbConnectable() {
+		return dbConnectable;
+	}
+
+	public void sendInfoToDb() {
+		try {
+		    mongoClient = connectToMongo(this.mongoUrl);
+			MongoDatabase database = getDatabase(this.dbName,mongoClient);
+			MongoCollection<Document> coll = getCollection(this.colName,database);
+
+
+			Document mainDoc;
+			if (!restful) {
+				mainDoc = new Document("RepoSlug", this.repoSlug)
+				.append("RepoBranch",this.repoBranch)
+				.append("Date",this.getCurrentDate());
+        		mainDoc.append("AmpOptions",argsDoc);
+			}else {
+				mainDoc = coll.find(and(eq("RepoSlug",this.repoSlug),eq("RepoBranch",this.repoBranch),eq("State","pending"))).projection(fields(excludeId())).first();
+				if (mainDoc != null) {
+					mainDoc.append("State","recent");
+				}
+			}
+			System.out.println(mainDoc.toString());
+			if (mainDoc != null) {
+				if (argsDoc.get("test-criterion").equals("JacocoCoverageSelector")) {
+        		Document mergedDoc = new Document();
+        		for (Document doc : jacocoSelectorDocs) {
+        			mergedDoc.putAll(doc);
+        		}
+        		mainDoc.append("AmpResult",mergedDoc);
+	        	}else if (argsDoc.get("test-criterion").equals("PitMutantScoreSelector")) {
+	        		Document mergedDoc = new Document();
+	        		for (Document doc : pitMutantScoreSelectorDocs) {
+	        			mergedDoc.putAll(doc);
+	        		}
+	        		mainDoc.append("AmpResult",mergedDoc);
+	        	}
+
+
+	        	Document ampFiles = new Document();
+	        	for (String path : javaPathList) {
+	        		String fileName = this.getFileNameGivenPath(path).replace(".java","");
+	        		String content = this.readFile(path,StandardCharsets.US_ASCII).replace(".","/D/");
+	        		LOGGER.warn("fileName: " + fileName);
+	        		LOGGER.warn("content: " + content);
+	        		ampFiles.append(fileName,content);
+	        	}
+	        	mainDoc.append("AmpTestFiles",ampFiles);
+	        	if (!restful) {
+	        		coll.insertOne(mainDoc);
+	        	} else {
+	        		// Set the previous recent repo as old
+	        		coll.updateOne(and(eq("RepoSlug",this.repoSlug),eq("RepoBranch",this.repoBranch),eq("State","recent")),new Document("$set",new Document("State","old")));
+	        		coll.updateOne(and(eq("RepoSlug",this.repoSlug),eq("RepoBranch",this.repoBranch),eq("State","pending")),new Document("$set",mainDoc));
+	        	}
+			}else {
+				LOGGER.warn("Main document for submitting is not initialized, No document found in restful mode.");
+			}
+
+			mongoClient.close();
+		}catch (Exception e) {
+			System.out.println("failed to connect to mongodb");
+		}
+	}
+
+	private static String readFile(String path, Charset encoding) {
+		try {
+			byte[] encoded = Files.readAllBytes(Paths.get(path));
+			return new String(encoded, encoding);
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	private String getCurrentDate() {
+		Date date = new Date();
+		return this.dateFormat.format(date);
+	}
+
+	private String getFileNameGivenPath(String path) {
+		String[] bits = path.split("/");
+		return bits[bits.length - 1];
+	}
+}

dspot/src/main/java/eu/stamp_project/utils/DSpotUtils.java

@@ -1,6 +1,7 @@
 package eu.stamp_project.utils;
 
 import eu.stamp_project.Main;
+import eu.stamp_project.mongodb.MongodbManager;
 import eu.stamp_project.utils.compilation.DSpotCompiler;
 import eu.stamp_project.utils.program.InputConfiguration;
 import eu.stamp_project.utils.report.error.Error;
@@ -107,6 +108,13 @@ public static void printAndCompileToCheck(CtType<?> type, File directory) {
         final String pathname =
                 directory.getAbsolutePath() + File.separator +
                         type.getQualifiedName().replaceAll("\\.", regex) + ".java";
+
+        // Save path to mongodb.
+        if (MongodbManager.getInstance().getDbConnectable()) {
+            MongodbManager.getInstance().javaPathList.add(pathname);
+            LOGGER.warn("Henry- Pathname : " + pathname);
+        }
+
         final CtType<?> existingAmplifiedTestClass;
         if (new File(pathname).exists()) {
             existingAmplifiedTestClass = getExistingClass(type, pathname);//FIXME: analyse for optimisation (16% total execution time)