Merge pull request #6 from VIDA-NYU/trimmer

Refactor signature trimmer and robust signature blocks generator

pom.xml

@@ -71,10 +71,14 @@
                       <manifest>
                             <addClasspath>true</addClasspath>
                             <mainClass>org.opendata.curation.d4.D4</mainClass>
+                            <!--mainClass>org.opendata.curation.d4.signature.RobustSignatureGenerator</mainClass-->
                             <!--mainClass>org.opendata.db.tools.Dataset2ColumnsConverter</mainClass-->
                             <!--mainClass>org.opendata.db.tools.EQIndexGenerator</mainClass-->
                             <!--mainClass>org.opendata.db.tools.TermIndexGenerator</mainClass-->
-                            <!--mainClass>org.opendata.curation.d4.export.PrimaryDomainWriter</mainClass-->
+                            <!--mainClass>org.opendata.db.eq.EQColumnCountHistorgramWriter</mainClass-->
+                            <!--mainClass>org.opendata.curation.d4.experiments.SignatureDropStatsExperiment</mainClass-->
+                            <!--mainClass>org.opendata.curation.d4.explore.GTDisjointTermsPrinter</mainClass-->
+                            <!--mainClass>org.opendata.curation.d4.export.ExportStrongDomains</mainClass-->
                       </manifest>
                    </archive>
                 </configuration>

src/main/java/org/opendata/core/graph/UndirectedConnectedComponents.java

@@ -76,33 +76,10 @@ public synchronized boolean contains(int nodeId) {
         }
     }
 
-    /**
-     * Get the connected component that contains the node with the given
-     * identifier.
-     * 
-     * @param nodeId
-     * @return 
-     */
-    private int getComponentForNode(int nodeId) {
-
-        //if (!_nodes.contains(nodeId)) {
-        //    throw new RuntimeException("Unknown node identifier: " + nodeId);
-        //}
-
-        // If the nodeId is not contained in the component map then the node
-        // is in the component that has the same identifier as the nodeId
-        //if (_componentMap.containsKey(nodeId)) {
-        //    return _componentMap.get(nodeId);
-        //} else {
-        //    return nodeId;
-        //}
-        return _componentMap[nodeId];
-    }
-
     public synchronized void edge(int sourceId, int targetId) {	
 
-        int sourceCompId = this.getComponentForNode(sourceId);
-        int targetCompId = this.getComponentForNode(targetId);
+        int sourceCompId = _componentMap[sourceId];
+        int targetCompId = _componentMap[targetId];
 
         if (sourceCompId != targetCompId) {
             // The respective components may not have been instantiated yet.
@@ -165,6 +142,20 @@ public synchronized IdentifiableObjectSet<IdentifiableIDSet> getComponents() {
 
         return result;
     }
+
+    /**
+     * Test if all nodes belong to the same single component.
+     * 
+     * @return 
+     */
+    public boolean isComplete() {
+
+        if (_components.size() == 1) {
+            int compSize = _components.values().iterator().next().size();
+            return (compSize == _nodes.length());
+        }
+        return false;
+    }
 
     private void merge(
             HashSet<Integer> target,
@@ -180,11 +171,4 @@ private void merge(
 
         _components.remove(sourceCompId);
     }
-
-    public synchronized boolean nodesAreInSameComponent(int node1, int node2) {
-
-        int comp1 = this.getComponentForNode(node1);
-        int comp2 = this.getComponentForNode(node2);
-        return (comp1 == comp2);
-    }
 }

src/main/java/org/opendata/core/io/EntitySetReader.java

@@ -65,7 +65,7 @@ public void read(
 
     public void read(EntityConsumer consumer) throws java.io.IOException {
 
-        this.read(new AnyObjectFilter<Integer>(), consumer);
+        this.read(new AnyObjectFilter<>(), consumer);
     }
 
     public EntitySet readEntities(ObjectFilter<Integer> filter) throws java.io.IOException {

src/main/java/org/opendata/curation/d4/column/ExpandedColumnConsumerFactory.java → src/main/java/org/opendata/core/io/prov/DataCollection.java

@@ -15,17 +15,16 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package org.opendata.curation.d4.column;
-
-import java.util.HashMap;
-import org.opendata.core.set.HashIDSet;
+package org.opendata.core.io.prov;
 
 /**
- * Factory pattern for column consumers.
+ * Simple interface to manage the information source for different types of
+ * object collections. These collections may either be read from disk or
+ * generated in memory.
  * 
  * @author Heiko Mueller <[email protected]>
  */
-public interface ExpandedColumnConsumerFactory {
+public interface DataCollection {
 
-    public ExpandedColumnConsumer getConsumer(HashMap<Integer, HashIDSet> groups);
+    public String source();
 }

src/main/java/org/opendata/core/io/prov/DataSink.java

@@ -0,0 +1,28 @@
+/*
+ * This file is part of the Data-Driven Domain Discovery Tool (D4).
+ * 
+ * Copyright (c) 2018-2020 New York University.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.opendata.core.io.prov;
+
+/**
+ * Simple interface to manage the data sink name for data generators.
+ * 
+ * @author Heiko Mueller <[email protected]>
+ */
+public interface DataSink {
+
+    public String target();
+}