Release v1.3.0 (PR #146)

Merging release/1.3.0 into master
dice-group · Feb 21, 2018 · 50de898 · 50de898
2 parents 09e4ffe + ebc4e6a
commit 50de898
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diff --git a/Dockerfile b/Dockerfile
@@ -25,5 +25,7 @@ WORKDIR /limes
 COPY --from=builder /limes/limes.jar limes.jar
 # set default java flags
 ENV JAVA_OPTS="-Xmx2G"
+# expose port
+EXPOSE 8080
 # assign start command
 CMD ["java", "-jar", "limes.jar", "-s"]
diff --git a/README.md b/README.md
@@ -1,6 +1,8 @@
 # LIMES - Link Discovery Framework for Metric Spaces.
 
-[![Build Status](https://travis-ci.org/dice-group/LIMES.svg?branch=master)](https://travis-ci.org/dice-group/LIMES) [![Join the chat at https://gitter.im/dice_limes/Lobby](https://badges.gitter.im/dice_limes/Lobby.svg)](https://gitter.im/dice_limes/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Build Status](https://travis-ci.org/dice-group/LIMES.svg?branch=dev)](https://travis-ci.org/dice-group/LIMES)
+
+Development branch for LIMES - Link Discovery Framework for Metric Spaces.
 
 ## Generating Jar File (Headless)
 installing use:

diff --git a/git-hooks/pre-push b/git-hooks/pre-push
diff --git a/git-hooks/setup.sh b/git-hooks/setup.sh
diff --git a/limes-core/pom.xml b/limes-core/pom.xml
@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.aksw.limes</groupId>
         <artifactId>limes-full</artifactId>
-        <version>1.2.4</version>
+        <version>1.3.0</version>
     </parent>
 
     <scm>
@@ -95,17 +95,13 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>2.17</version>
+                <version>2.20.1</version>
                 <configuration>
                     <forkMode>pertest</forkMode>
-                    <argLine>${argLine} -Xms256m -Xmx512m</argLine>
+                    <argLine>@{argLine} -Xms256m -Xmx512m</argLine>
                     <testFailureIgnore>false</testFailureIgnore>
                     <skipTests>false</skipTests>
                     <useManifestOnlyJar>false</useManifestOnlyJar>
-                    <!-- used to debug one only package via CLI (mvn test -DtestGroup=org/aksw/limes/...) -->
-                    <!-- <includes>
-                        <include>**/${testGroup}/*Test.java</include>
-                    </includes> -->
                 </configuration>
             </plugin>
 
@@ -140,28 +136,10 @@
                 </configuration>
             </plugin>
 
-            <plugin>
-                <artifactId>exec-maven-plugin</artifactId>
-                <groupId>org.codehaus.mojo</groupId>
-                <executions>
-                    <execution><!-- symlink hooks to git -->
-                        <id>Git-Hooks-Setup</id>
-                        <phase>install</phase>
-                        <goals>
-                            <goal>exec</goal>
-                        </goals>
-                        <configuration>
-                            <executable>${basedir}/../git-hooks/setup.sh</executable>
-                            <workingDirectory>${basedir}/../git-hooks</workingDirectory>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
-
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-checkstyle-plugin</artifactId>
-                <version>2.17</version>
+                <version>3.0.0</version>
                 <executions>
                     <execution>
                         <id>validate</id>
@@ -207,7 +185,7 @@
                                         </goals>
                                     </pluginExecutionFilter>
                                     <action>
-                                        <ignore></ignore>
+                                        <ignore/>
                                     </action>
                                 </pluginExecution>
                             </pluginExecutions>
@@ -223,12 +201,12 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>findbugs-maven-plugin</artifactId>
-                <version>3.0.3</version>
+                <version>3.0.5</version>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-pmd-plugin</artifactId>
-                <version>3.6</version>
+                <version>3.9.0</version>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>

diff --git a/limes-core/src/main/java/org/aksw/limes/core/controller/Controller.java b/limes-core/src/main/java/org/aksw/limes/core/controller/Controller.java
@@ -8,7 +8,9 @@
 import org.aksw.limes.core.execution.planning.planner.ExecutionPlannerFactory;
 import org.aksw.limes.core.execution.rewriter.RewriterFactory;
 //import org.aksw.limes.core.gui.LimesGUI;
+import org.aksw.limes.core.io.cache.ACache;
 import org.aksw.limes.core.io.cache.HybridCache;
+import org.aksw.limes.core.io.cache.MemoryCache;
 import org.aksw.limes.core.io.config.Configuration;
 import org.aksw.limes.core.io.config.reader.AConfigurationReader;
 import org.aksw.limes.core.io.config.reader.rdf.RDFConfigurationReader;
@@ -28,17 +30,20 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.function.Function;
+
 /**
  * This is the default LIMES Controller used to run the software as CLI.
  *
  * @author Kevin Dreßler
  */
 public class Controller {
 
-    public static final String DEFAULT_LOGGING_PATH = "limes.log";
+    private static final String DEFAULT_LOGGING_PATH = "limes.log";
     private static final int MAX_ITERATIONS_NUMBER = 10;
     private static Logger logger = null;
-    private static int serverPort = 8080;
+    private static int defaultPort = 8080;
+    private static int defaultLimit = -1;
     private static Options options = getOptions();
 
     /**
@@ -61,9 +66,11 @@ public static void main(String[] args) {
 //            LimesGUI.startGUI(new String[0]);
 //            System.exit(0);
         } else if (cmd.hasOption('s')){
-            int port = serverPort;
+            int port = defaultPort;
             if (cmd.hasOption('p')) port = Integer.parseInt(cmd.getOptionValue('p'));
-            SimpleServer.startServer(port);
+            int limit = defaultLimit;
+            if (cmd.hasOption('l')) limit = Integer.parseInt(cmd.getOptionValue('l'));
+            SimpleServer.startServer(port, limit);
         } else {
             // III. Has Arguments?
             if (cmd.getArgs().length < 1) {
@@ -78,7 +85,7 @@ public static void main(String[] args) {
         }
     }
 
-    public static CommandLine parseCommandLine(String[] args) {
+    private static CommandLine parseCommandLine(String[] args) {
         CommandLineParser parser = new BasicParser();
         CommandLine cl = null;
         try {
@@ -135,13 +142,27 @@ public static Configuration getConfig(CommandLine cmd) {
      *
      */
     public static ResultMappings getMapping(Configuration config) {
+        return  getMapping(config, -1);
+    }
+
+
+    static ResultMappings getMapping(Configuration config, int limit) {
         if (logger == null)
             logger = LoggerFactory.getLogger(Controller.class);
         AMapping results = null;
 
         // 3. Fill Caches
-        HybridCache sourceCache = HybridCache.getData(config.getSourceInfo());
-        HybridCache targetCache = HybridCache.getData(config.getTargetInfo());
+        ACache sourceCache = HybridCache.getData(config.getSourceInfo());
+        ACache targetCache = HybridCache.getData(config.getTargetInfo());
+        if (limit > 0) {
+            Function<ACache, ACache> getSubCache = c -> {
+                ACache reducedCache = new MemoryCache();
+                c.getAllInstances().subList(0, limit).forEach(reducedCache::addInstance);
+                return reducedCache;
+            };
+            sourceCache = getSubCache.apply(sourceCache);
+            targetCache = getSubCache.apply(targetCache);
+        }
 
         // 4. Machine Learning or Planning
         StopWatch stopWatch = new StopWatch();
@@ -202,7 +223,7 @@ private static Options getOptions() {
         options.addOption("f", true, "Optionally configure format of <config_file_or_uri>, either \"xml\" (default) or " +
                 "\"rdf\". If not specified, LIMES tries to infer the format from file ending.");
         options.addOption("p", true, "Optionally configure HTTP server port. Only effective if -s is specified. Default port is 8080.");
-        // options.addOption("s", false, "Silent run");
+        options.addOption("l", true, "Optionally configure a limit for source and target resources processed by LIMES Server. Only effective if -s is specified. Default value is -1 (no limit).");
         // options.addOption("v", false, "Verbose run");
         return options;
     }

diff --git a/limes-core/src/main/java/org/aksw/limes/core/controller/MLPipeline.java b/limes-core/src/main/java/org/aksw/limes/core/controller/MLPipeline.java
@@ -61,7 +61,7 @@ public static AMapping execute(
                 mls.init(learningParameters, source, target);
                 mls.getMl().setConfiguration(configuration);
                 mlm = mls.learn(trainingDataMap);
-                logger.info(mlm.getLinkSpecification().toStringOneLine());
+                logger.info("Learned: " + mlm.getLinkSpecification().getFullExpression() + " with threshold: " + mlm.getLinkSpecification().getThreshold());
                 return mls.predict(source, target, mlm);
             case SUPERVISED_ACTIVE:
                 // for active learning, need to reiterate and prompt the user for evaluation of examples:
@@ -109,6 +109,7 @@ public static AMapping execute(
                     }
                     mlm = mla.activeLearn(nextExamples);
                 }
+                logger.info("Learned: " + mlm.getLinkSpecification().getFullExpression() + " with threshold: " + mlm.getLinkSpecification().getThreshold());
                 return mla.predict(source, target, mlm);
             case UNSUPERVISED:
                 UnsupervisedMLAlgorithm mlu = new UnsupervisedMLAlgorithm(clazz);
@@ -119,6 +120,7 @@ public static AMapping execute(
                     pfm = (PseudoFMeasure) EvaluatorFactory.create(pfmType);
                 }
                 mlm = mlu.learn(pfm);
+                logger.info("Learned: " + mlm.getLinkSpecification().getFullExpression() + " with threshold: " + mlm.getLinkSpecification().getThreshold());
                 return mlu.predict(source, target, mlm);
             default:
                 throw new UnsupportedMLImplementationException(clazz.getName());

diff --git a/limes-core/src/main/java/org/aksw/limes/core/controller/SimpleServer.java b/limes-core/src/main/java/org/aksw/limes/core/controller/SimpleServer.java
@@ -34,10 +34,12 @@ public class SimpleServer {
     private static final String LOCK_DIR_PATH = "/lock/";
     private static final String QUERY_PARAM_RESULT_TYPE = "result_type";
     private static final String QUERY_PARAM_JOB_ID = "job_id";
-    public static final String CONFIG_FILE_PREFIX = "limes_server_cfg_";
+    private static final String CONFIG_FILE_PREFIX = "limes_server_cfg_";
     private static ConcurrentMap<Long, Integer> jobs = new ConcurrentHashMap<>();
+    private static int limit;
 
-    public static void startServer(int port) {
+    public static void startServer(int port, int limit) {
+        SimpleServer.limit = limit;
         HttpServer server = null;
         logger.info("Attempting to start LIMES server at port " + port + "...");
         try {
@@ -54,10 +56,16 @@ public static void startServer(int port) {
         logger.info("Server has been started! Waiting for requests...");
     }
 
+    private static void addCORSHeaders(Headers headers) {
+        headers.add("Access-Control-Allow-Origin", "*");
+        headers.add("Access-Control-Allow-Methods", "GET, POST, OPTIONS");
+    }
+
     private static class ExecuteHandler implements HttpHandler {
 
         @Override
         public void handle(HttpExchange t) throws IOException {
+            addCORSHeaders(t.getResponseHeaders());
             if (t.getRequestMethod().equals("POST")) {
                 Headers headers = t.getRequestHeaders();
                 String boundary = "boundary=";
@@ -79,7 +87,7 @@ public void handle(HttpExchange t) throws IOException {
                 AConfigurationReader reader = new XMLConfigurationReader(STORAGE_DIR_PATH + CONFIG_FILE_PREFIX + id + ".xml");
                 Configuration config = reader.read();
                 jobs.put(Long.parseLong(id), 1);
-                ResultMappings mappings = Controller.getMapping(config);
+                ResultMappings mappings = Controller.getMapping(config, limit);
                 String outputFormat = config.getOutputFormat();
                 ISerializer output = SerializerFactory.createSerializer(outputFormat);
                 output.setPrefixes(config.getPrefixes());
@@ -100,6 +108,10 @@ public void handle(HttpExchange t) throws IOException {
                 _acceptanceFile.renameTo(acceptanceFile);
                 lockDir.delete();
                 jobs.put(Long.parseLong(id), 2);
+            } else if (t.getRequestMethod().equals("OPTIONS")) {
+                // we only accept POST requests here, anything else gets code "405 - Method Not Allowed"
+                t.sendResponseHeaders(200 ,-1);
+                logger.info("Replied to OPTIONS request");
             } else {
                 // we only accept POST requests here, anything else gets code "405 - Method Not Allowed"
                 t.sendResponseHeaders(405 ,-1);
@@ -132,6 +144,7 @@ private static class GetResultHandler implements HttpHandler {
 
         @Override
         public void handle(HttpExchange t) throws IOException {
+            addCORSHeaders(t.getResponseHeaders());
             if (t.getRequestMethod().equals("GET")) {
                 Map<String, String> params = queryToMap(t.getRequestURI().getRawQuery());
                 if (params.containsKey(QUERY_PARAM_JOB_ID) && params.containsKey(QUERY_PARAM_RESULT_TYPE) &&
@@ -186,6 +199,11 @@ public void handle(HttpExchange t) throws IOException {
                     t.sendResponseHeaders(400 ,-1);
                     logger.info("Bad request: " + t.getRequestURI() + "\nPlease specify job_id and result_type query parameters!");
                 }
+
+            } else if (t.getRequestMethod().equals("OPTIONS")) {
+                // we only accept POST requests here, anything else gets code "405 - Method Not Allowed"
+                t.sendResponseHeaders(200 ,-1);
+                logger.info("Replied to OPTIONS request");
             } else {
                 // we only accept GET requests here, anything else gets code "405 - Method Not Allowed"
                 t.sendResponseHeaders(405 ,-1);
@@ -198,6 +216,7 @@ private static class GetStatusHandler implements HttpHandler {
 
         @Override
         public void handle(HttpExchange t) throws IOException {
+            addCORSHeaders(t.getResponseHeaders());
             if (t.getRequestMethod().equals("GET")) {
                 Map<String, String> params = queryToMap(t.getRequestURI().getRawQuery());
                 if (params.containsKey(QUERY_PARAM_JOB_ID)) {
@@ -226,6 +245,10 @@ public void handle(HttpExchange t) throws IOException {
                     t.sendResponseHeaders(400, -1);
                     logger.info("Bad request: " + t.getRequestURI() + "\nPlease specify job_id query parameters!");
                 }
+            } else if (t.getRequestMethod().equals("OPTIONS")) {
+                // we only accept POST requests here, anything else gets code "405 - Method Not Allowed"
+                t.sendResponseHeaders(200 ,-1);
+                logger.info("Replied to OPTIONS request");
             } else {
                 // we only accept GET requests here, anything else gets code "405 - Method Not Allowed"
                 t.sendResponseHeaders(405, -1);
@@ -234,24 +257,24 @@ public void handle(HttpExchange t) throws IOException {
         }
     }
 
-        public static Map<String, String> queryToMap(String query){
-            Map<String, String> result = new HashMap<>();
-            if (query == null)
-                return result;
-            for (String param : query.split("&")) {
-                try {
-                    param = java.net.URLDecoder.decode(param, "UTF-8");
-                    String pair[] = param.split("=");
-                    if (pair.length > 1) {
-                        result.put(pair[0], pair[1]);
-                    } else {
-                        result.put(pair[0], "");
-                    }
-                } catch (UnsupportedEncodingException e) {
-                    e.printStackTrace();
+    private static Map<String, String> queryToMap(String query){
+        Map<String, String> result = new HashMap<>();
+        if (query == null)
+            return result;
+        for (String param : query.split("&")) {
+            try {
+                param = java.net.URLDecoder.decode(param, "UTF-8");
+                String pair[] = param.split("=");
+                if (pair.length > 1) {
+                    result.put(pair[0], pair[1]);
+                } else {
+                    result.put(pair[0], "");
                 }
+            } catch (UnsupportedEncodingException e) {
+                e.printStackTrace();
             }
-            return result;
         }
-
+        return result;
     }
+
+}