DedupConf parsed using Jackson library

dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/ClusteringResolver.java

@@ -1,24 +0,0 @@
-package eu.dnetlib.pace.clustering;
-
-import java.io.Serializable;
-import java.lang.reflect.InvocationTargetException;
-import java.util.Map;
-import java.util.stream.Collectors;
-
-import org.reflections.Reflections;
-
-public class ClusteringResolver implements Serializable {
-    private final Map<String, Class<ClusteringFunction>> functionMap;
-
-    public ClusteringResolver() {
-
-        this.functionMap = new Reflections("eu.dnetlib").getTypesAnnotatedWith(ClusteringClass.class).stream()
-                .filter(ClusteringFunction.class::isAssignableFrom)
-                .collect(Collectors.toMap(cl -> cl.getAnnotation(ClusteringClass.class).value(), cl -> (Class<ClusteringFunction>)cl));
-    }
-
-    public ClusteringFunction resolve(String clusteringFunction, Map<String, Integer> params) throws IllegalAccessException, InstantiationException, NoSuchMethodException, InvocationTargetException {
-
-        return functionMap.get(clusteringFunction).getDeclaredConstructor(Map.class).newInstance(params);
-    }
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/condition/ConditionResolver.java

@@ -1,25 +0,0 @@
-package eu.dnetlib.pace.condition;
-
-import java.io.Serializable;
-import java.lang.reflect.InvocationTargetException;
-import java.util.List;
-import java.util.Map;
-import java.util.stream.Collectors;
-
-import eu.dnetlib.pace.model.FieldDef;
-import org.reflections.Reflections;
-
-public class ConditionResolver implements Serializable {
-    private final Map<String, Class<ConditionAlgo>> functionMap;
-
-    public ConditionResolver() {
-
-        this.functionMap = new Reflections("eu.dnetlib").getTypesAnnotatedWith(ConditionClass.class).stream()
-                .filter(ConditionAlgo.class::isAssignableFrom)
-                .collect(Collectors.toMap(cl -> cl.getAnnotation(ConditionClass.class).value(), cl -> (Class<ConditionAlgo>)cl));
-    }
-
-    public ConditionAlgo resolve(String name, List<FieldDef> fields) throws IllegalAccessException, InstantiationException, NoSuchMethodException, InvocationTargetException {
-        return functionMap.get(name).getDeclaredConstructor(String.class, List.class).newInstance(name, fields);
-    }
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/config/DedupConfig.java

@@ -7,12 +7,11 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import eu.dnetlib.pace.util.PaceException;
 import org.antlr.stringtemplate.StringTemplate;
 import org.apache.commons.io.IOUtils;
 
 import com.google.common.collect.Maps;
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
 
 import eu.dnetlib.pace.condition.ConditionAlgo;
 import eu.dnetlib.pace.model.ClusteringDef;
@@ -35,7 +34,7 @@ public class DedupConfig implements Config, Serializable {
 
 	static {
 		defaults.put("threshold", "0");
-		defaults.put("run", "001");
+		defaults.put("dedupRun", "001");
 		defaults.put("entityType", "result");
 		defaults.put("orderField", "title");
 		defaults.put("queueMaxSize", "2000");
@@ -49,11 +48,15 @@ public class DedupConfig implements Config, Serializable {
 
 	public static DedupConfig load(final String json) {
 
-		final DedupConfig config = new Gson().fromJson(json, DedupConfig.class);
+		final DedupConfig config;
-
+		try {
+			config = new ObjectMapper().readValue(json, DedupConfig.class);
 			config.getPace().initModel();
-
 			return config;
+		} catch (IOException e) {
+			throw new PaceException("Error in parsing configuration json", e);
+		}
+
 	}
 
 	public static DedupConfig loadDefault() throws IOException {

dnet-pace-core/src/main/java/eu/dnetlib/pace/config/PaceConfig.java

@@ -11,6 +11,7 @@ import eu.dnetlib.pace.condition.ConditionAlgo;
 import eu.dnetlib.pace.model.ClusteringDef;
 import eu.dnetlib.pace.model.CondDef;
 import eu.dnetlib.pace.model.FieldDef;
+import eu.dnetlib.pace.util.PaceResolver;
 import org.apache.commons.collections.CollectionUtils;
 
 public class PaceConfig implements Serializable {
@@ -23,6 +24,8 @@ public class PaceConfig implements Serializable {
 
 	private Map<String, FieldDef> modelMap;
 
+	public static PaceResolver paceResolver;
+
 	public PaceConfig() {}
 
 	public void initModel() {
@@ -30,6 +33,8 @@ public class PaceConfig implements Serializable {
 		for(FieldDef fd : getModel()) {
 			modelMap.put(fd.getName(), fd);
 		}
+
+		paceResolver = new PaceResolver();
 	}
 
 	public List<FieldDef> getModel() {

dnet-pace-core/src/main/java/eu/dnetlib/pace/distance/DistanceResolver.java

@@ -1,24 +0,0 @@
-package eu.dnetlib.pace.distance;
-
-import java.io.Serializable;
-import java.lang.reflect.InvocationTargetException;
-import java.util.Map;
-import java.util.stream.Collectors;
-
-import org.reflections.Reflections;
-
-public class DistanceResolver implements Serializable {
-    private final Map<String, Class<DistanceAlgo>> functionMap;
-
-    public DistanceResolver() {
-
-        this.functionMap = new Reflections("eu.dnetlib").getTypesAnnotatedWith(DistanceClass.class).stream()
-                .filter(DistanceAlgo.class::isAssignableFrom)
-                .collect(Collectors.toMap(cl -> cl.getAnnotation(DistanceClass.class).value(), cl -> (Class<DistanceAlgo>)cl));
-    }
-
-    public DistanceAlgo resolve(String algo, Map<String, Number> params) throws IllegalAccessException, InstantiationException, NoSuchMethodException, InvocationTargetException {
-
-        return functionMap.get(algo).getDeclaredConstructor(Map.class).newInstance(params);
-    }
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/ClusteringDef.java

@@ -1,12 +1,14 @@
 package eu.dnetlib.pace.model;
 
+import java.io.IOException;
 import java.io.Serializable;
-import java.lang.reflect.InvocationTargetException;
 import java.util.List;
 import java.util.Map;
 
-import com.google.gson.Gson;
 import eu.dnetlib.pace.clustering.*;
+import eu.dnetlib.pace.config.PaceConfig;
+import eu.dnetlib.pace.util.PaceException;
+import org.codehaus.jackson.map.ObjectMapper;
 
 public class ClusteringDef implements Serializable {
 
@@ -16,8 +18,6 @@ public class ClusteringDef implements Serializable {
 
 	private Map<String, Integer> params;
 
-	private ClusteringResolver clusteringResolver = new ClusteringResolver();
-
 	public ClusteringDef() {}
 
 	public String getName() {
@@ -29,12 +29,11 @@ public class ClusteringDef implements Serializable {
 	}
 
 	public ClusteringFunction getClusteringFunction() {
-
 		try {
-			return clusteringResolver.resolve(getName(), params);
+			return PaceConfig.paceResolver.getClusteringFunction(getName(), params);
-		} catch (IllegalAccessException | InstantiationException | NoSuchMethodException | InvocationTargetException e) {
+		} catch (PaceException e) {
 			e.printStackTrace();
-			return new RandomClusteringFunction(getParams());
+			return null;
 		}
 	}
 
@@ -56,7 +55,11 @@ public class ClusteringDef implements Serializable {
 
 	@Override
 	public String toString() {
-		return new Gson().toJson(this);
+		try {
+			return new ObjectMapper().writeValueAsString(this);
+		} catch (IOException e) {
+			return e.getStackTrace().toString();
+		}
 	}
 
 }

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/CondDef.java

@@ -1,11 +1,12 @@
 package eu.dnetlib.pace.model;
 
+import java.io.IOException;
 import java.io.Serializable;
-import java.lang.reflect.InvocationTargetException;
 import java.util.List;
 
-import com.google.gson.Gson;
 import eu.dnetlib.pace.condition.*;
+import eu.dnetlib.pace.config.PaceConfig;
+import org.codehaus.jackson.map.ObjectMapper;
 
 public class CondDef implements Serializable {
 
@@ -13,19 +14,10 @@ public class CondDef implements Serializable {
 
 	private List<String> fields;
 
-	private ConditionResolver conditionResolver = new ConditionResolver();
-
 	public CondDef() {}
 
-	public ConditionAlgo getConditionAlgo(final List<FieldDef> fields) {
+	public ConditionAlgo getConditionAlgo(final List<FieldDef> fields){
-
+		return PaceConfig.paceResolver.getConditionAlgo(getName(), fields);
-		try {
-			return conditionResolver.resolve(getName(), fields);
-		} catch (IllegalAccessException | InstantiationException | NoSuchMethodException | InvocationTargetException e) {
-			e.printStackTrace();
-			return new AlwaysTrueCondition(getName(), fields);
-		}
-
 	}
 
 	public String getName() {
@@ -46,7 +38,11 @@ public class CondDef implements Serializable {
 
 	@Override
 	public String toString() {
-		return new Gson().toJson(this);
+		try {
+			return new ObjectMapper().writeValueAsString(this);
+		} catch (IOException e) {
+			return e.getStackTrace().toString();
+		}
 	}
 
 }

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java

@@ -9,9 +9,11 @@ import java.util.Map;
 import com.google.common.base.Splitter;
 import com.google.common.collect.Lists;
 import com.google.gson.Gson;
+import eu.dnetlib.pace.config.PaceConfig;
 import eu.dnetlib.pace.config.Type;
 import eu.dnetlib.pace.distance.*;
 import eu.dnetlib.pace.distance.algo.*;
+import eu.dnetlib.pace.util.PaceException;
 
 /**
  * The schema is composed by field definitions (FieldDef). Each field has a type, a name, and an associated distance algorithm.
@@ -38,8 +40,6 @@ public class FieldDef implements Serializable {
 
 	private Map<String, Number> params;
 
-	private DistanceResolver distanceResolver = new DistanceResolver();
-
 	public FieldDef() {}
 
 	// def apply(s: String): Field[A]
@@ -70,18 +70,12 @@ public class FieldDef implements Serializable {
 
 	public DistanceAlgo getDistanceAlgo() {
 
-		try {
 		if (params == null) {
 			params = new HashMap<>();
 		}
 		params.put("limit", getLimit());
 		params.put("weight", getWeight());
-			return distanceResolver.resolve(getAlgo(), params);
+		return PaceConfig.paceResolver.getDistanceAlgo(getAlgo(), params);
-		} catch (IllegalAccessException | InstantiationException | NoSuchMethodException | InvocationTargetException e) {
-			e.printStackTrace();
-			return new NullDistanceAlgo(params);
-		}
-
 	}
 
 	public boolean isIgnoreMissing() {

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/GTAuthor.java

@@ -13,7 +13,6 @@ import com.google.common.collect.Maps;
 import com.google.common.collect.Ordering;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
-import eu.dnetlib.pace.model.adaptor.PidOafSerialiser;
 
 public class GTAuthor implements Comparable<GTAuthor> {
 

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/ScoredResult.java

@@ -1,6 +1,8 @@
 package eu.dnetlib.pace.model.gt;
 
-import com.google.gson.Gson;
+import org.codehaus.jackson.map.ObjectMapper;
+
+import java.io.IOException;
 
 public class ScoredResult extends Result {
 
@@ -20,7 +22,11 @@ public class ScoredResult extends Result {
 
 	@Override
 	public String toString() {
-		return new Gson().toJson(this);
+		try {
+			return new ObjectMapper().writeValueAsString(this);
+		} catch (IOException e) {
+			return e.getStackTrace().toString();
+		}
 	}
 
 }

dnet-pace-core/src/main/java/eu/dnetlib/pace/util/PaceException.java

@@ -0,0 +1,9 @@
+package eu.dnetlib.pace.util;
+
+public class PaceException extends RuntimeException {
+
+    public PaceException(String s, Throwable e){
+        super(s, e);
+    }
+
+}

dnet-pace-core/src/main/java/eu/dnetlib/pace/util/PaceResolver.java

@@ -0,0 +1,63 @@
+package eu.dnetlib.pace.util;
+
+import eu.dnetlib.pace.clustering.ClusteringClass;
+import eu.dnetlib.pace.clustering.ClusteringFunction;
+import eu.dnetlib.pace.condition.ConditionAlgo;
+import eu.dnetlib.pace.condition.ConditionClass;
+import eu.dnetlib.pace.distance.DistanceAlgo;
+import eu.dnetlib.pace.distance.DistanceClass;
+import eu.dnetlib.pace.model.FieldDef;
+import org.reflections.Reflections;
+
+import java.io.Serializable;
+import java.lang.reflect.InvocationTargetException;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+public class PaceResolver implements Serializable {
+
+    private final Map<String, Class<ClusteringFunction>> clusteringFunctions;
+    private final Map<String, Class<ConditionAlgo>> conditionAlgos;
+    private final Map<String, Class<DistanceAlgo>> distanceAlgos;
+
+    public PaceResolver() {
+
+        this.clusteringFunctions = new Reflections("eu.dnetlib").getTypesAnnotatedWith(ClusteringClass.class).stream()
+                .filter(ClusteringFunction.class::isAssignableFrom)
+                .collect(Collectors.toMap(cl -> cl.getAnnotation(ClusteringClass.class).value(), cl -> (Class<ClusteringFunction>)cl));
+
+        this.conditionAlgos = new Reflections("eu.dnetlib").getTypesAnnotatedWith(ConditionClass.class).stream()
+                .filter(ConditionAlgo.class::isAssignableFrom)
+                .collect(Collectors.toMap(cl -> cl.getAnnotation(ConditionClass.class).value(), cl -> (Class<ConditionAlgo>)cl));
+
+        this.distanceAlgos = new Reflections("eu.dnetlib").getTypesAnnotatedWith(DistanceClass.class).stream()
+                .filter(DistanceAlgo.class::isAssignableFrom)
+                .collect(Collectors.toMap(cl -> cl.getAnnotation(DistanceClass.class).value(), cl -> (Class<DistanceAlgo>)cl));
+    }
+
+    public ClusteringFunction getClusteringFunction(String name, Map<String, Integer> params) throws PaceException {
+        try {
+            return clusteringFunctions.get(name).getDeclaredConstructor(Map.class).newInstance(params);
+        } catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException e) {
+            throw new PaceException(name + "not found", e);
+        }
+    }
+
+    public DistanceAlgo getDistanceAlgo(String name, Map<String, Number> params) throws PaceException {
+        try {
+            return distanceAlgos.get(name).getDeclaredConstructor(Map.class).newInstance(params);
+        } catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException e) {
+            throw new PaceException(name + "not found", e);
+        }
+    }
+
+    public ConditionAlgo getConditionAlgo(String name, List<FieldDef> fields) throws PaceException {
+        try {
+            return conditionAlgos.get(name).getDeclaredConstructor(String.class, List.class).newInstance(name, fields);
+        } catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException e) {
+            throw new PaceException(name + "not found", e);
+        }
+    }
+
+}

dnet-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringResolverTest.java

@@ -1,30 +0,0 @@
-package eu.dnetlib.pace.clustering;
-
-import org.junit.Before;
-import org.junit.Test;
-
-import java.lang.reflect.InvocationTargetException;
-import java.util.HashMap;
-import java.util.Map;
-
-import static org.junit.Assert.assertEquals;
-
-public class ClusteringResolverTest {
-
-    private ClusteringResolver clusteringResolver;
-    private Map<String,Integer> params = new HashMap<String, Integer>();
-
-    @Before
-    public void setUp(){
-        clusteringResolver = new ClusteringResolver();
-    }
-
-    @Test
-    public void testResolve() throws InstantiationException, IllegalAccessException, NoSuchMethodException, InvocationTargetException {
-
-        ClusteringFunction ngrams = clusteringResolver.resolve("ngrams", params);
-
-        assertEquals(ngrams.getClass(), Ngrams.class);
-    }
-
-}

dnet-pace-core/src/test/java/eu/dnetlib/pace/condition/ConditionResolverTest.java

@@ -1,35 +0,0 @@
-package eu.dnetlib.pace.condition;
-
-import eu.dnetlib.pace.clustering.ClusteringFunction;
-import eu.dnetlib.pace.clustering.ClusteringResolver;
-import eu.dnetlib.pace.clustering.Ngrams;
-import eu.dnetlib.pace.model.FieldDef;
-import org.junit.Before;
-import org.junit.Test;
-
-import java.lang.reflect.InvocationTargetException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import static org.junit.Assert.assertEquals;
-
-public class ConditionResolverTest {
-
-    private ConditionResolver conditionResolver;
-    private List<FieldDef> fields;
-    private String name;
-
-    @Before
-    public void setUp(){
-        conditionResolver = new ConditionResolver();
-    }
-
-    @Test
-    public void testResolve() throws InstantiationException, IllegalAccessException, NoSuchMethodException, InvocationTargetException {
-
-        ConditionAlgo sizeMatch = conditionResolver.resolve("sizeMatch", fields);
-
-        assertEquals(sizeMatch.getClass(), SizeMatch.class);
-    }
-}

dnet-pace-core/src/test/java/eu/dnetlib/pace/config/ConfigTest.java

@@ -76,8 +76,16 @@ public class ConfigTest extends AbstractPaceTest {
 		final DedupConfig cfgFromSerialization = DedupConfig.load(cfgFromClasspath.toString());
 		String params = "\"params\":{\"limit\":-1,\"weight\":0.0}";
 		//verify if the serialization produces the same result of the input json
-//		assertEquals(cfgFromSerialization.toString().replaceAll("[\n\t\r ]", "").replaceAll("\"params\":null", params), cfgFromClasspath.toString().replaceAll("[\n\t\r ]", ""));
+		assertEquals(cfgFromSerialization.toString().replaceAll("[\n\t\r ]", "").replaceAll("\"params\":null", params), cfgFromClasspath.toString().replaceAll("[\n\t\r ]", ""));
 
 	}
 
+	@Test
+	public void dedupConfigTest() {
+
+		DedupConfig load = DedupConfig.load(readFromClasspath("result.pace.conf.json"));
+
+		System.out.println(load.toString());
+	}
+
 }

dnet-pace-core/src/test/resources/eu/dnetlib/pace/config/result.pace.conf.json

@@ -1,7 +1,7 @@
 { 
 	"wf" : { 
         "threshold" : "0.99", 
-        "run" : "001", 
+        "dedupRun" : "001",
         "entityType" : "result", 
         "orderField" : "title", 
         "queueMaxSize" : "2000",