Initial cluestringCoefficient has been implemented

bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/CliOptionsParser.java

@@ -148,6 +148,9 @@ public class QueryCommandOptions {
         @Parameter(names = {"--betweenness"}, description = "", required = false, arity = 0)
         public boolean betweenness;
 
+        @Parameter(names = {"--clusteringCoeff"}, description = "", required = false, arity = 0)
+        public boolean clusteringCoeff;
+
         @Parameter(names = {"-o", "--output-file"}, description = "", required = false, arity = 1)
         public String outputFile;
 

bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/QueryCommandExecutor.java

@@ -30,6 +30,13 @@ public void execute() {
                 networkDBAdaptor.betweenness(query);
             }
 
+            if (queryCommandOptions.clusteringCoeff) {
+                Query query = new Query("id", queryCommandOptions.id);
+                query.put("nodeLabel", queryCommandOptions.nodeType);
+
+                networkDBAdaptor.clusteringCoefficient(query);
+            }
+
         } catch (Exception e) {
             e.printStackTrace();
         }

bionetdb-core/pom.xml

@@ -55,6 +55,10 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-math3</artifactId>
+        </dependency>
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JNetworkDBAdaptor.java

@@ -1,5 +1,6 @@
 package org.opencb.bionetdb.core.neo4j;
 
+import org.apache.commons.math3.util.CombinatoricsUtils;
 import org.neo4j.graphdb.*;
 import org.neo4j.graphdb.factory.GraphDatabaseFactory;
 import org.neo4j.graphdb.index.IndexManager;
@@ -12,6 +13,7 @@
 import org.opencb.datastore.core.QueryOptions;
 import org.opencb.datastore.core.QueryResult;
 
+import java.text.DecimalFormat;
 import java.util.*;
 
 /**
@@ -278,7 +280,7 @@ private void insertPhysicalEntities(List<PhysicalEntity> physicalEntityList, Que
                     addRelationship(n, ont, RelTypes.ONTOLOGY);
                 }
 
-                    /* Insert the cellular locations */
+                /* Insert the cellular locations */
                 for (CellularLocation c : p.getCellularLocation()) {
                     Node cel = getOrCreateCellularLocationNode(parseCellularLocation(c));
                     addRelationship(n, cel, RelTypes.CELLULARLOCATION);
@@ -847,6 +849,54 @@ public QueryResult betweenness(Query query) {
 
     @Override
     public QueryResult clusteringCoefficient(Query query) {
+        // The clustering coefficient of a node is defined as the probability that two randomly
+        // selected neighbors are connected to each other. With the number of neighbors as n and
+        // the number of mutual connections between the neighbors r the calculation is:
+        // clusteringCoefficient = r/NumberOfPossibleConnectionsBetweenTwoNeighbors. Where:
+        // NumberOfPossibleConnectionsBetweenTwoNeighbors: n!/(2!(n-2)!).
+
+        // TODO multiple ids
+        String id = query.getString("id");
+
+        StringBuilder cypherQuery = new StringBuilder();
+        cypherQuery.append("MATCH (a { name: \"" + id + "\" })--(:Interaction)--(b)");
+        cypherQuery.append(" WITH a, count(DISTINCT b) AS n");
+        cypherQuery.append(" MATCH (a)--(:Interaction)--(:PhysicalEntity)"
+                + "--(:Interaction)-[r]-(:PhysicalEntity)--(:Interaction)--(a)");
+        cypherQuery.append(" MATCH (a)-[:CELLULARLOCATION]-(c:CellularLocation)");
+        cypherQuery.append(" RETURN a.name, c.id, n, count(DISTINCT r) AS r");
+
+        Result execute = this.database.execute(cypherQuery.toString());
+
+        if (execute.hasNext()) {
+            String msg = "#ID\tLOCATION\tCLUSTERING_COEFFICIENT";
+            System.out.println(msg);
+            while (execute.hasNext()) {
+                Map<String, Object> result = execute.next();
+                Integer r = (int) (long) result.get("r");
+                Integer n = (int) (long) result.get("n");
+
+                // Computed value must fit into a double. The largest n for which n! < Double.MAX_VALUE is 170.
+                if (n > 170) {
+                    String msg2 = "\"" + result.get("a.name").toString() + "\"\t"
+                            + "\"" + result.get("c.id").toString() + "\"\t"
+                            + "\"NA\"";
+                    System.out.println(msg2);
+                } else if (n > 1) {
+                    double possibleConnexions = CombinatoricsUtils.factorialDouble(n)
+                            / (CombinatoricsUtils.factorialDouble(2) * (CombinatoricsUtils.factorialDouble(n - 2)));
+                    DecimalFormat df = new DecimalFormat("###.##");
+                    String msg3 = "\"" + result.get("a.name").toString() + "\"\t"
+                            + "\"" + result.get("c.id").toString() + "\"\t"
+                            + "\"" + df.format(r / possibleConnexions) + "\"";
+                    System.out.println(msg3);
+                } else {
+                    System.out.println(0.00);
+                }
+            }
+        } else {
+            System.out.println("Physical Entity not found");
+        }
         return null;
     }
 

bionetdb-core/src/test/java/org/opencb/bionetdb/core/neo4j/Neo4JNetworkDBAdaptorTest.java

@@ -217,6 +217,13 @@ public void testBetweenness() throws Exception {
 
     }
 
+    @Test
+    public void testClusteringCoefficient() throws Exception {
+        loadTestData();
+        networkDBAdaptor.clusteringCoefficient(new Query("id", "PEP"));
+
+    }
+
     private void loadTestData() throws URISyntaxException, IOException, NetworkDBException {
         BioPaxParser bioPaxParser = new BioPaxParser("L3");
         Path inputPath = Paths.get(getClass().getResource("/Saccharomyces_cerevisiae.owl.gz").toURI());

pom.xml

@@ -151,6 +151,11 @@
                 <artifactId>jersey-client</artifactId>
                 <version>${jersey.version}</version>
             </dependency>
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-math3</artifactId>
+                <version>3.5</version>
+            </dependency>
             <dependency>
                 <groupId>junit</groupId>
                 <artifactId>junit</artifactId>