General cleanup (#7)

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 bakdata
+Copyright (c) 2019 bakdata
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

build.gradle.kts

@@ -1,9 +1,8 @@
 plugins {
-    `java-library`
     // release
     id("net.researchgate.release") version "2.6.0"
-    id("com.bakdata.sonar") version "1.0.1"
-    id("com.bakdata.sonatype") version "1.0.1"
+    id("com.bakdata.sonar") version "1.1.2"
+    id("com.bakdata.sonatype") version "1.1.2"
     id("org.hildan.github.changelog") version "0.8.0"
 }
 
@@ -46,13 +45,13 @@ subprojects {
     }
 
     dependencies {
-        testImplementation("org.junit.jupiter:junit-jupiter-api:5.3.0")
-        testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine:5.3.0")
-        testImplementation(group= "org.assertj", name= "assertj-core", version= "3.11.1")
-
-        compileOnly("org.projectlombok:lombok:1.18.4")
-        annotationProcessor("org.projectlombok:lombok:1.18.4")
-        testCompileOnly("org.projectlombok:lombok:1.18.4")
-        testAnnotationProcessor("org.projectlombok:lombok:1.18.4")
+        "testImplementation"("org.junit.jupiter:junit-jupiter-api:5.3.0")
+        "testRuntimeOnly"("org.junit.jupiter:junit-jupiter-engine:5.3.0")
+        "testImplementation"(group = "org.assertj", name = "assertj-core", version = "3.11.1")
+
+        "compileOnly"("org.projectlombok:lombok:1.18.6")
+        "annotationProcessor"("org.projectlombok:lombok:1.18.6")
+        "testCompileOnly"("org.projectlombok:lombok:1.18.6")
+        "testAnnotationProcessor"("org.projectlombok:lombok:1.18.6")
     }
 }

common/build.gradle.kts

@@ -6,4 +6,4 @@ dependencies {
     "api"(group = "commons-codec", name = "commons-codec", version = "1.11")
 
     implementation(group = "com.google.guava", name = "guava", version = "26.0-jre")
-}
+}

common/src/main/java/com/bakdata/deduplication/candidate_selection/CompositeValue.java

@@ -1,7 +1,7 @@
 /*
- * The MIT License
+ * MIT License
  *
- * Copyright (c) 2018 bakdata GmbH
+ * Copyright (c) 2019 bakdata GmbH
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -20,7 +20,6 @@
  * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
- *
  */
 package com.bakdata.deduplication.candidate_selection;
 

common/src/main/java/com/bakdata/deduplication/candidate_selection/SortingKey.java

@@ -1,7 +1,7 @@
 /*
- * The MIT License
+ * MIT License
  *
- * Copyright (c) 2018 bakdata GmbH
+ * Copyright (c) 2019 bakdata GmbH
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -20,7 +20,6 @@
  * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
- *
  */
 package com.bakdata.deduplication.candidate_selection;
 

common/src/main/java/com/bakdata/deduplication/candidate_selection/online/OnlineSortedNeighborhoodMethod.java

@@ -1,7 +1,7 @@
 /*
- * The MIT License
+ * MIT License
  *
- * Copyright (c) 2018 bakdata GmbH
+ * Copyright (c) 2019 bakdata GmbH
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -20,7 +20,6 @@
  * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
- *
  */
 package com.bakdata.deduplication.candidate_selection.online;
 
@@ -46,7 +45,8 @@ public class OnlineSortedNeighborhoodMethod<T> implements OnlineCandidateSelecti
     int defaultWindowSize = 10;
 
     public List<Candidate<T>> getCandidates(final T newRecord) {
-        return this.passes.stream().flatMap(pass -> pass.getCandidates(newRecord).stream()).distinct().collect(Collectors.toList());
+        return this.passes.stream().flatMap(pass -> pass.getCandidates(newRecord).stream()).distinct()
+                .collect(Collectors.toList());
     }
 
     @Value
@@ -58,14 +58,14 @@ public static class Pass<T> {
 
         List<Candidate<T>> getCandidates(final T newRecord) {
             final Comparable<?> newKey = this.sortingKey.getKeyExtractor().apply(newRecord);
-            if(newKey == null) {
+            if (newKey == null) {
                 return List.of();
             }
             final Stream<T> largerRecords = this.index.tailMap(newKey).values().stream().flatMap(List::stream).limit(
-                this.windowSize / 2);
+                    this.windowSize / 2);
             final Stream<T> smallerRecords =
-                this.index.descendingMap().tailMap(newKey).values().stream().flatMap(List::stream).limit(
-                this.windowSize / 2);
+                    this.index.descendingMap().tailMap(newKey).values().stream().flatMap(List::stream).limit(
+                            this.windowSize / 2);
             final List<Candidate<T>> candidates = Stream.concat(smallerRecords, largerRecords)
                     .map(oldRecord -> new Candidate<>(newRecord, oldRecord))
                     .collect(Collectors.toList());
@@ -77,7 +77,8 @@ List<Candidate<T>> getCandidates(final T newRecord) {
     @SuppressWarnings({"WeakerAccess", "unused"})
     public static class OnlineSortedNeighborhoodMethodBuilder<T> {
 
-        public OnlineSortedNeighborhoodMethodBuilder<T> sortingKey(final SortingKey<T> sortingKey, final int windowSize) {
+        public OnlineSortedNeighborhoodMethodBuilder<T> sortingKey(final SortingKey<T> sortingKey,
+                final int windowSize) {
             return this.pass(new Pass<>(sortingKey, windowSize));
         }
 
@@ -90,7 +91,7 @@ public OnlineSortedNeighborhoodMethodBuilder<T> sortingKeys(final Collection<Sor
         }
 
         public OnlineSortedNeighborhoodMethodBuilder<T> sortingKeys(final Iterable<SortingKey<T>> sortingKeys,
-            final int windowSize) {
+                final int windowSize) {
             for (final SortingKey<T> sortingKey : sortingKeys) {
                 this.sortingKey(sortingKey, windowSize);
             }

common/src/main/java/com/bakdata/deduplication/classifier/OracleClassifier.java

@@ -1,3 +1,27 @@
+/*
+ * MIT License
+ *
+ * Copyright (c) 2019 bakdata GmbH
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
 package com.bakdata.deduplication.classifier;
 
 import com.bakdata.deduplication.candidate_selection.Candidate;
@@ -11,9 +35,9 @@
 @Value
 public class OracleClassifier<T> implements Classifier<T> {
     private static final Classification DUPLICATE =
-        Classification.builder().result(Classification.ClassificationResult.DUPLICATE).confidence(1).build();
+            Classification.builder().result(Classification.ClassificationResult.DUPLICATE).confidence(1).build();
     private static final Classification NON_DUPLICATE =
-        Classification.builder().result(Classification.ClassificationResult.NON_DUPLICATE).confidence(1).build();
+            Classification.builder().result(Classification.ClassificationResult.NON_DUPLICATE).confidence(1).build();
 
     @NonNull
     Set<Candidate<T>> goldDuplicates;
@@ -22,13 +46,13 @@ public class OracleClassifier<T> implements Classifier<T> {
 
     private Set<Candidate<T>> calculateSymmetricDuplicates() {
         return this.getGoldDuplicates().stream()
-            .flatMap(duplicate ->
-                Stream.of(duplicate, new Candidate<>(duplicate.getOldRecord(), duplicate.getNewRecord())))
-            .collect(Collectors.toSet());
+                .flatMap(duplicate ->
+                        Stream.of(duplicate, new Candidate<>(duplicate.getOldRecord(), duplicate.getNewRecord())))
+                .collect(Collectors.toSet());
     }
 
     @Override
     public Classification classify(final Candidate<T> candidate) {
         return this.getSymmetricDuplicates().contains(candidate) ? DUPLICATE : NON_DUPLICATE;
     }
-}
+}

common/src/main/java/com/bakdata/deduplication/classifier/RuleBasedClassifier.java

@@ -1,7 +1,7 @@
 /*
- * The MIT License
+ * MIT License
  *
- * Copyright (c) 2018 bakdata GmbH
+ * Copyright (c) 2019 bakdata GmbH
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -20,7 +20,6 @@
  * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
- *
  */
 package com.bakdata.deduplication.classifier;
 
@@ -36,16 +35,21 @@
 import lombok.Value;
 
 /**
- * Successively applies a list of rules to the record and returns the respective {@link Classification} with the following cases:
+ * Successively applies a list of rules to the record and returns the respective {@link Classification} with the
+ * following cases:
  * <ul>
- * <li>If any rule classifies the pair unambiguously as {@link Classification.ClassificationResult#DUPLICATE} or {@link Classification.ClassificationResult#NON_DUPLICATE}, the classification is immediately returned.</li>
- * <li>If some rule classifies the pair as {@link Classification.ClassificationResult#POSSIBLE_DUPLICATE}, the remaining rules with be evaluated to see if an unambiguous classification will be reached, in which case that classification is returned. If the results are only ambiguous, the last {@code POSSIBLE_DUPLICATE} classification will be returned.</li>
+ * <li>If any rule classifies the pair unambiguously as {@link Classification.ClassificationResult#DUPLICATE} or {@link
+ * Classification.ClassificationResult#NON_DUPLICATE}, the classification is immediately returned.</li>
+ * <li>If some rule classifies the pair as {@link Classification.ClassificationResult#POSSIBLE_DUPLICATE}, the
+ * remaining
+ * rules with be evaluated to see if an unambiguous classification will be reached, in which case that classification is
+ * returned. If the results are only ambiguous, the last {@code POSSIBLE_DUPLICATE} classification will be
+ * returned.</li>
  * <li>If no rule can be applied, the result is {@link #UNKNOWN}.</li>
  * </ul>
  * <br>
- * The {@code Classification} will contain a description naming the triggered rule and converts the rule score into a confidence score.
- *
- * @param <T>
+ * The {@code Classification} will contain a description naming the triggered rule and converts the rule score into a
+ * confidence score.
  */
 @Value
 @Builder
@@ -84,50 +88,56 @@ private SimilarityException createException(final Candidate<T> candidate, final
     }
 
     private Optional<Classification> evaluateRule(final Rule<? super T> rule, final Candidate<? extends T> candidate,
-        final SimilarityContext context) {
-        return context.safeExecute(() -> rule.evaluate(candidate.getNewRecord(), candidate.getOldRecord(), context)).map(score -> {
-            if (Float.isNaN(score)) {
-                return UNKNOWN;
-            }
-            if (score <= -0.0f) {
-                return Classification.builder()
-                        .result(Classification.ClassificationResult.NON_DUPLICATE)
-                        .confidence(-score)
-                        .explanation(rule.getName())
-                        .build();
-            } else {
-                return Classification.builder()
-                        .result(Classification.ClassificationResult.DUPLICATE)
-                        .confidence(score)
-                        .explanation(rule.getName())
-                        .build();
-            }
-        });
+            final SimilarityContext context) {
+        return context.safeExecute(() -> rule.evaluate(candidate.getNewRecord(), candidate.getOldRecord(), context))
+                .map(score -> {
+                    if (Float.isNaN(score)) {
+                        return UNKNOWN;
+                    }
+                    if (score <= -0.0f) {
+                        return Classification.builder()
+                                .result(Classification.ClassificationResult.NON_DUPLICATE)
+                                .confidence(-score)
+                                .explanation(rule.getName())
+                                .build();
+                    } else {
+                        return Classification.builder()
+                                .result(Classification.ClassificationResult.DUPLICATE)
+                                .confidence(score)
+                                .explanation(rule.getName())
+                                .build();
+                    }
+                });
     }
 
     @SuppressWarnings({"WeakerAccess", "UnusedReturnValue"})
     public static class RuleBasedClassifierBuilder<T> {
 
-        public RuleBasedClassifierBuilder<T> positiveRule(final String name, final BiPredicate<T, T> applicablePredicate,
-                                                          final SimilarityMeasure<T> similarityMeasure) {
+        public RuleBasedClassifierBuilder<T> positiveRule(final String name,
+                final BiPredicate<T, T> applicablePredicate,
+                final SimilarityMeasure<T> similarityMeasure) {
             return this.positiveRule(name, (left, right, context) ->
-                    applicablePredicate.test(left, right) ? similarityMeasure.getSimilarity(left, right, context) : DOES_NOT_APPLY);
+                    applicablePredicate.test(left, right) ? similarityMeasure.getSimilarity(left, right, context)
+                            : DOES_NOT_APPLY);
         }
 
-        public RuleBasedClassifierBuilder<T> positiveRule(final String name, final SimilarityMeasure<T> similarityMeasure) {
+        public RuleBasedClassifierBuilder<T> positiveRule(final String name,
+                final SimilarityMeasure<T> similarityMeasure) {
             return this.rule(new Rule<>(name, similarityMeasure.unknownIf(s -> s <= 0)));
         }
 
-        public RuleBasedClassifierBuilder<T> negativeRule(final String name, final BiPredicate<T, T> applicablePredicate,
-                                                          final SimilarityMeasure<T> similarityMeasure) {
+        public RuleBasedClassifierBuilder<T> negativeRule(final String name,
+                final BiPredicate<T, T> applicablePredicate,
+                final SimilarityMeasure<T> similarityMeasure) {
             return this.negativeRule(name, (left, right, context) ->
-                    applicablePredicate.test(left, right) ? similarityMeasure.getSimilarity(left, right, context) : DOES_NOT_APPLY);
+                    applicablePredicate.test(left, right) ? similarityMeasure.getSimilarity(left, right, context)
+                            : DOES_NOT_APPLY);
         }
 
         public RuleBasedClassifierBuilder<T> negativeRule(final String name,
-            final SimilarityMeasure<? super T> similarityMeasure) {
+                final SimilarityMeasure<? super T> similarityMeasure) {
             final SimilarityMeasure<T> negativeSim =
-                (left, right, context) -> -similarityMeasure.getSimilarity(left, right, context);
+                    (left, right, context) -> -similarityMeasure.getSimilarity(left, right, context);
             return this.rule(new Rule<>(name, negativeSim.unknownIf(s -> s >= 0)));
         }
 
@@ -150,4 +160,4 @@ float evaluate(final T left, final T right, final SimilarityContext context) {
             return this.measure.getSimilarity(left, right, context);
         }
     }
-}
+}

common/src/main/java/com/bakdata/deduplication/clustering/ConsistentClustering.java

@@ -1,7 +1,7 @@
 /*
- * The MIT License
+ * MIT License
  *
- * Copyright (c) 2018 bakdata GmbH
+ * Copyright (c) 2019 bakdata GmbH
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -20,7 +20,6 @@
  * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
- *
  */
 package com.bakdata.deduplication.clustering;
 
@@ -38,21 +37,23 @@
 import lombok.Value;
 
 /**
- * Wraps another clustering and keeps clusters together, when the wrapped clustering would split it.<br>
- * Example: consider a stable marriage-based clustering where A1-B have been previously matched and subsequently clustered.
- * If a strong A2-B would replace that pair and thus split the cluster, this consistent clustering returns a cluster [A1, A2, B] instead.<br>
+ * Wraps another clustering and keeps clusters together, when the wrapped clustering would split it.<br> Example:
+ * consider a stable marriage-based clustering where A1-B have been previously matched and subsequently clustered. If a
+ * strong A2-B would replace that pair and thus split the cluster, this consistent clustering returns a cluster [A1, A2,
+ * B] instead.<br>
  * <p>
- * This clustering is similar to {@link TransitiveClosure} but allows the wrapped clustering to split temporary (=not-returned) clusters. Thus, in the example above, we have the following two situations:
- * - If A1-B and A2-B would be passed in the same invocation of {@link #cluster(List)}, only cluster [A2, B] would be returned.
- * - If A-B is passed in a first invocation, this invocation returns [A1, B]. The following invocation with A2-B would then return [A1, A2, B].
+ * This clustering is similar to {@link TransitiveClosure} but allows the wrapped clustering to split temporary
+ * (=not-returned) clusters. Thus, in the example above, we have the following two situations: - If A1-B and A2-B would
+ * be passed in the same invocation of {@link #cluster(List)}, only cluster [A2, B] would be returned. - If A-B is
+ * passed in a first invocation, this invocation returns [A1, B]. The following invocation with A2-B would then return
+ * [A1, A2, B].
  * </p>
  * It thus trades off clustering accuracy to increase reliability of subsequent data processing.
- *
- * @param <T>
  */
 @Value
 @Builder
-public class ConsistentClustering<C extends Comparable<C>, T, I extends Comparable<? super I>> implements Clustering<C, T> {
+public class ConsistentClustering<C extends Comparable<C>, T, I extends Comparable<? super I>>
+        implements Clustering<C, T> {
     @NonNull
     Clustering<C, T> clustering;
     Function<T, I> idExtractor;