[WAYANG-32] More general corrections, comments, and Readme update

wayang-commons/pom.xml

@@ -214,14 +214,15 @@
             <dependency>
                 <groupId>com.google.code.gson</groupId>
                 <artifactId>gson</artifactId>
-                <version>2.2.4</version>
+                <version>2.8.8</version>
             </dependency>
         </dependencies>
     </dependencyManagement>
 
     <modules>
         <module>wayang-core</module>
         <module>wayang-basic</module>
+        <module>wayang-utils</module>
     </modules>
 
 </project>

wayang-commons/wayang-utils/wayang-profile-db/readme.md

@@ -1,3 +1,30 @@
-Base on
+This code is based on the implementation you can find in the following repository:
 
-https://github.com/sekruse/profiledb-java.git
+- https://github.com/sekruse/profiledb-java.git
+
+The code there does not have regular maintenance. Wayang will require new functionalities to deal with serialization of UDFs and storage in other platforms.
+
+The classes below has not been modified:
+
+    MeasurementDeserializer
+    MeasurementSerializer
+    Experiment
+    Measurement
+    Subject
+    TimeMeasurement
+    Type
+
+The classes below has been added/modified to provide an abstraction over different Storage methods:
+
+    ProfileDB
+    Storage
+    FileStorage
+    JDBCStorage
+
+The code that is based on the mentioned repository starts and ends with the commits indicated below:
+
+- start: [5344336f68bb9038e701435e9859321b6e8cbcfc](https://github.com/apache/incubator-wayang/commit/5344336f68bb9038e701435e9859321b6e8cbcfc)
+
+- end: 
+
+All the code that has been added after those commits is totally independent of the mentioned repository. 

wayang-commons/wayang-utils/wayang-profile-db/src/main/java/profiledb/ProfileDB.java

@@ -40,30 +40,74 @@ public class ProfileDB {
      */
     private Gson gson;
 
+    /**
+     * Receive an array of {@link Experiment}s and persist them
+     *
+     * @param experiments Array of {@link Experiment}s to be persisted
+     * @throws IOException
+     */
     public void save(Experiment... experiments) throws IOException {
         this.storage.save(experiments);
     }
 
+    /**
+     * Receive a Collection of {@link Experiment}s and persist them
+     *
+     * @param experiments Collection of {@link Experiment}s to be persisted
+     * @throws IOException
+     */
     public void save(Collection<Experiment> experiments) throws IOException {
         this.storage.save(experiments);
     }
 
+    /**
+     * Receive a Collection of {@link Experiment}s and persist them
+     *
+     * @param experiments Collection of {@link Experiment}s to be persisted
+     * @param outputStream Indicates where the data must to be written
+     * @throws IOException
+     */
     public void save(Collection<Experiment> experiments, OutputStream outputStream) throws IOException {
         this.storage.save(experiments, outputStream);
     }
 
+    /**
+     * Related to file based storage, Receive an array of {@link Experiment}s and persist them at the end of a file
+     *
+     * @param experiments Array of {@link Experiment}s to be persisted
+     * @throws IOException
+     */
     public void append(Experiment... experiments) throws IOException {
         this.storage.append(experiments);
     }
 
+    /**
+     * Related to file based storage, Receive a Collection of {@link Experiment}s and persist them at the end of a file
+     *
+     * @param experiments Collection of {@link Experiment}s to be persisted
+     * @throws IOException
+     */
     public void append(Collection<Experiment> experiments) throws IOException {
         this.storage.append(experiments);
     }
 
+    /**
+     * Bring {@link Experiment}s from current Storage to local variable
+     *
+     * @return Collection of {@link Experiment}s
+     * @throws IOException
+     */
     public Collection<Experiment> load() throws IOException {
         return this.storage.load();
     }
 
+    /**
+     * Bring {@link Experiment}s from current Storage to local variable
+     *
+     * @param inputStream Data to be read
+     * @return Collection of {@link Experiment}s
+     * @throws IOException
+     */
     public Collection<Experiment> load(InputStream inputStream) throws IOException {
         return this.storage.load(inputStream);
     }

wayang-commons/wayang-utils/wayang-profile-db/src/main/java/profiledb/storage/Storage.java

@@ -32,6 +32,8 @@ public Storage(URI uri){
         this.storageFile = uri;
     }
 
+
+
     /**
      * Sets the ProfileDB for this instance that manages all the Measurement subclasses
      * */
@@ -47,18 +49,48 @@ public void changeLocation(URI uri){
         this.storageFile = uri;
     }
 
-    public void save(Experiment... experiments) throws IOException {
-        System.out.println("llegue");
-    }
+    /**
+     * Receive an array of {@link Experiment}s and persist them
+     *
+     * @param experiments Array of {@link Experiment}s to be persisted
+     * @throws IOException
+     */
+    public abstract void save(Experiment... experiments) throws IOException;
 
-    public void save(Collection<Experiment> experiments) throws IOException {}
+    /**
+     * Receive a Collection of {@link Experiment}s and persist them
+     *
+     * @param experiments Collection of {@link Experiment}s to be persisted
+     * @throws IOException
+     */
+    public abstract void save(Collection<Experiment> experiments) throws IOException;
 
-    public void append(Experiment... experiments) throws IOException {}
+    /**
+     * Related to file based storage, Receive an array of {@link Experiment}s and persist them at the end of a file
+     *
+     * @param experiments Array of {@link Experiment}s to be persisted
+     * @throws IOException
+     */
+    public abstract void append(Experiment... experiments) throws IOException;
 
-    public void append(Collection<Experiment> experiments) throws IOException {}
+    /**
+     * Related to file based storage, Receive a Collection of {@link Experiment}s and persist them at the end of a file
+     *
+     * @param experiments Collection of {@link Experiment}s to be persisted
+     * @throws IOException
+     */
+    public abstract void append(Collection<Experiment> experiments) throws IOException ;
+
+    /**
+     * Bring {@link Experiment}s from current Storage to local variable
+     *
+     * @return Collection of {@link Experiment}s
+     * @throws IOException
+     */
+    public abstract Collection<Experiment> load() throws IOException;
 
-    public Collection<Experiment> load() throws IOException { return null; }
 
+    //TODO The following methods should be moved to file storage implementation
     /**
      * Write {@link Experiment}s to an {@link OutputStream}.
      *

wayang-commons/wayang-utils/wayang-profile-db/src/test/java/profiledb/ProfileDBTest.java

@@ -15,7 +15,9 @@
 import java.io.IOException;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.net.URL;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.*;
 
@@ -25,32 +27,28 @@ public class ProfileDBTest {
     public void testPolymorphSaveAndLoad() throws IOException {
 
         try {
-            URI uri = new URI("file:///Users/rodrigopardomeza/Desktop/random/myfile.txt");
+            Path temp = Files.createTempFile("", ".tmp");
+
+            String absolutePath = temp.toString();
+            System.out.println("Temp file : " + absolutePath);
+
+            URI uri = new URI("my-file4");
+
             FileStorage store = new FileStorage(uri);
 
             ProfileDB profileDB = new ProfileDB(store)
                     .registerMeasurementClass(TestMemoryMeasurement.class)
                     .registerMeasurementClass(TestTimeMeasurement.class);
 
-            /**
-             * Esto es lo que se espera del codigo del cliente
-             * Tiene que usar la API para registrar medidas
-             */
-            // crea un experimento falso
             final Experiment experiment = new Experiment("test-xp", new Subject("PageRank", "1.0"), "test experiment");
 
-            // Agrega medidas falsas hardcoded
             Measurement timeMeasurement = new TestTimeMeasurement("exec-time", 12345L);
             Measurement memoryMeasurement = new TestMemoryMeasurement("exec-time", System.currentTimeMillis(), 54321L);
 
-            /*Agrega las medidas al experimento*/
             experiment.addMeasurement(timeMeasurement);
             experiment.addMeasurement(memoryMeasurement);
 
             // Save the experiment.
-            /**
-             * Guarda el experimento en memoria
-             */
             byte[] buffer;
             ByteArrayOutputStream bos = new ByteArrayOutputStream();
             profileDB.save(Collections.singleton(experiment), bos);
@@ -59,9 +57,6 @@ public void testPolymorphSaveAndLoad() throws IOException {
             System.out.println("Buffer contents: " + new String(buffer, "UTF-8"));
 
             // Load the experiment.
-            /**
-             * Lee el experimento desde el buffer en memoria
-             */
             ByteArrayInputStream bis = new ByteArrayInputStream(buffer);
             Collection<Experiment> loadedExperiments = profileDB.load(bis);
 
@@ -86,7 +81,7 @@ public void testPolymorphSaveAndLoad() throws IOException {
     @Test
     public void testRecursiveSaveAndLoad() throws IOException {
         try {
-            URI uri = new URI("file:///Users/rodrigopardomeza/Desktop/random/myfile.txt");
+            URI uri = new URI("my-file2");
             FileStorage store = new FileStorage(uri);
 
             ProfileDB profileDB = new ProfileDB(store)
@@ -128,78 +123,64 @@ public void testRecursiveSaveAndLoad() throws IOException {
 
     @Test
     public void testFileOperations() throws IOException {
-
-        try {
-            URI uri = new URI("file:///Users/rodrigopardomeza/Desktop/random/myfile.txt");
-            FileStorage store = new FileStorage(uri);
-
-            ProfileDB profileDB = new ProfileDB(store)
-                    .registerMeasurementClass(TestMemoryMeasurement.class)
-                    .registerMeasurementClass(TestTimeMeasurement.class);
-
-            // Create example experiments.
-            final Experiment experiment1 = new Experiment("xp1", new Subject("PageRank", "1.0"), "test experiment 1");
-            experiment1.addMeasurement(new TestTimeMeasurement("exec-time", 1L));
-            final Experiment experiment2 = new Experiment("xp2", new Subject("KMeans", "1.1"), "test experiment 2");
-            experiment2.addMeasurement(new TestTimeMeasurement("exec-time", 2L));
-            final Experiment experiment3 = new Experiment("xp3", new Subject("Apriori", "2.0"), "test experiment 3");
-            experiment3.addMeasurement(new TestMemoryMeasurement("ram", System.currentTimeMillis(), 3L));
-
-            // Save the experiments.
-            File tempDir = Files.createTempDirectory("profiledb").toFile();
-            //File dir = Files.createTempDirectory(Paths.get("/Users/rodrigopardomeza/Desktop/random/"), "profiledb").toFile();
-            //File dir = Paths.get("/Users/rodrigopardomeza/Desktop/random/").toFile();
-            File file = new File(tempDir, "profiledb.json");
-            file.createNewFile();
-            profileDB.save(experiment1);
-            profileDB.append(experiment2, experiment3);
-
-            System.out.println("File plat" + file.toPath().toUri().toString());
-            Files.lines(file.toPath()).forEach(System.out::println);
-
-            // Load and compare.
-            final Set<Experiment> loadedExperiments = new HashSet<>(profileDB.load());
-            final List<Experiment> expectedExperiments = Arrays.asList(experiment1, experiment2, experiment3);
-            Assert.assertEquals(expectedExperiments.size(), loadedExperiments.size());
-            Assert.assertEquals(new HashSet<>(expectedExperiments), new HashSet<>(loadedExperiments));
-        } catch (URISyntaxException e) {
-            e.printStackTrace();
-        }
+        File tempDir = Files.createTempDirectory("profiledb").toFile();
+        File file = new File(tempDir, "profiledb.json");
+        file.createNewFile();
+        FileStorage store = new FileStorage(file.toURI());
+
+        ProfileDB profileDB = new ProfileDB(store)
+                .registerMeasurementClass(TestMemoryMeasurement.class)
+                .registerMeasurementClass(TestTimeMeasurement.class);
+
+        // Create example experiments.
+        final Experiment experiment1 = new Experiment("xp1", new Subject("PageRank", "1.0"), "test experiment 1");
+        experiment1.addMeasurement(new TestTimeMeasurement("exec-time", 1L));
+        final Experiment experiment2 = new Experiment("xp2", new Subject("KMeans", "1.1"), "test experiment 2");
+        experiment2.addMeasurement(new TestTimeMeasurement("exec-time", 2L));
+        final Experiment experiment3 = new Experiment("xp3", new Subject("Apriori", "2.0"), "test experiment 3");
+        experiment3.addMeasurement(new TestMemoryMeasurement("ram", System.currentTimeMillis(), 3L));
+
+        // Save the experiments.
+        profileDB.save(experiment1);
+        profileDB.append(experiment2, experiment3);
+
+        Files.lines(file.toPath()).forEach(System.out::println);
+
+        // Load and compare.
+        final Set<Experiment> loadedExperiments = new HashSet<>(profileDB.load());
+        final List<Experiment> expectedExperiments = Arrays.asList(experiment1, experiment2, experiment3);
+        Assert.assertEquals(expectedExperiments.size(), loadedExperiments.size());
+        Assert.assertEquals(new HashSet<>(expectedExperiments), new HashSet<>(loadedExperiments));
     }
 
     @Test
     public void testAppendOnNonExistentFile() throws IOException {
 
-        try {
-            URI uri = new URI("file:///Users/rodrigopardomeza/Desktop/random/myfile.txt");
-            FileStorage store = new FileStorage(uri);
+        File tempDir = Files.createTempDirectory("profiledb").toFile();
+        File file = new File(tempDir, "new-profiledb.json");
+        file.createNewFile();
+        FileStorage store = new FileStorage(file.toURI());
 
-            // This seems to be an issue on Linux.
-            ProfileDB profileDB = new ProfileDB(store)
-                    .registerMeasurementClass(TestMemoryMeasurement.class)
-                    .registerMeasurementClass(TestTimeMeasurement.class);
+        // This seems to be an issue on Linux.
+        ProfileDB profileDB = new ProfileDB(store)
+                .registerMeasurementClass(TestMemoryMeasurement.class)
+                .registerMeasurementClass(TestTimeMeasurement.class);
 
-            // Create example experiments.
-            final Experiment experiment1 = new Experiment("xp1", new Subject("PageRank", "1.0"), "test experiment 1");
-            experiment1.addMeasurement(new TestTimeMeasurement("exec-time", 1L));
+        // Create example experiments.
+        final Experiment experiment1 = new Experiment("xp1", new Subject("PageRank", "1.0"), "test experiment 1");
+        experiment1.addMeasurement(new TestTimeMeasurement("exec-time", 1L));
 
-            // Save the experiments.
-            File tempDir = Files.createTempDirectory("profiledb").toFile();
-            File file = new File(tempDir, "new-profiledb.json");
-            file.createNewFile();
-            Assert.assertTrue(!file.exists() || file.delete());
-            profileDB.append(experiment1);
+        // Save the experiments.
+        Assert.assertTrue(!file.exists() || file.delete());
+        profileDB.append(experiment1);
 
-            Files.lines(file.toPath()).forEach(System.out::println);
+        Files.lines(file.toPath()).forEach(System.out::println);
 
-            // Load and compare.
-            final Set<Experiment> loadedExperiments = new HashSet<>(profileDB.load());
-            final List<Experiment> expectedExperiments = Collections.singletonList(experiment1);
-            Assert.assertEquals(expectedExperiments.size(), loadedExperiments.size());
-            Assert.assertEquals(new HashSet<>(expectedExperiments), new HashSet<>(loadedExperiments));
-        } catch (URISyntaxException e) {
-            e.printStackTrace();
-        }
+        // Load and compare.
+        final Set<Experiment> loadedExperiments = new HashSet<>(profileDB.load());
+        final List<Experiment> expectedExperiments = Collections.singletonList(experiment1);
+        Assert.assertEquals(expectedExperiments.size(), loadedExperiments.size());
+        Assert.assertEquals(new HashSet<>(expectedExperiments), new HashSet<>(loadedExperiments));
     }
 
 }