diff --git a/java/src/main/java/org/softwareheritage/graph/algo/Traversal.java b/java/src/main/java/org/softwareheritage/graph/algo/Traversal.java
index df422f7..4c2a433 100644
--- a/java/src/main/java/org/softwareheritage/graph/algo/Traversal.java
+++ b/java/src/main/java/org/softwareheritage/graph/algo/Traversal.java
@@ -1,457 +1,449 @@
package org.softwareheritage.graph.algo;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.Map;
import java.util.Queue;
import java.util.Random;
import java.util.Stack;
import it.unimi.dsi.bits.LongArrayBitVector;
import org.softwareheritage.graph.AllowedEdges;
import org.softwareheritage.graph.Endpoint;
import org.softwareheritage.graph.Graph;
import org.softwareheritage.graph.Neighbors;
import org.softwareheritage.graph.Node;
/**
* Traversal algorithms on the compressed graph.
*
* Internal implementation of the traversal API endpoints. These methods only input/output internal
* long ids, which are converted in the {@link Endpoint} higher-level class to Software Heritage
* PID.
*
* @author The Software Heritage developers
* @see org.softwareheritage.graph.Endpoint
*/
public class Traversal {
/** Graph used in the traversal */
Graph graph;
/** Boolean to specify the use of the transposed graph */
boolean useTransposed;
/** Graph edge restriction */
AllowedEdges edges;
/** Hash set storing if we have visited a node */
HashSet visited;
/** Hash map storing parent node id for each nodes during a traversal */
Map parentNode;
/** Number of edges accessed during traversal */
long nbEdgesAccessed;
/** random number generator, for random walks */
Random rng;
/**
* Constructor.
*
* @param graph graph used in the traversal
* @param direction a string (either "forward" or "backward") specifying edge orientation
* @param edgesFmt a formatted string describing allowed edges
*/
public Traversal(Graph graph, String direction, String edgesFmt) {
if (!direction.matches("forward|backward")) {
throw new IllegalArgumentException("Unknown traversal direction: " + direction);
}
this.graph = graph;
this.useTransposed = (direction.equals("backward"));
this.edges = new AllowedEdges(graph, edgesFmt);
long nbNodes = graph.getNbNodes();
this.visited = new HashSet<>();
this.parentNode = new HashMap<>();
this.nbEdgesAccessed = 0;
this.rng = new Random();
}
/**
* Returns number of accessed edges during traversal.
*
* @return number of edges accessed in last traversal
*/
public long getNbEdgesAccessed() {
return nbEdgesAccessed;
}
/**
* Returns number of accessed nodes during traversal.
*
* @return number of nodes accessed in last traversal
*/
public long getNbNodesAccessed() {
return this.visited.size();
}
/**
* Push version of {@link leaves}: will fire passed callback for each leaf.
*/
public void leavesVisitor(long srcNodeId, NodeIdConsumer cb) {
Stack stack = new Stack();
this.nbEdgesAccessed = 0;
stack.push(srcNodeId);
visited.add(srcNodeId);
while (!stack.isEmpty()) {
long currentNodeId = stack.pop();
long neighborsCnt = 0;
nbEdgesAccessed += graph.degree(currentNodeId, useTransposed);
for (long neighborNodeId : new Neighbors(graph, useTransposed, edges, currentNodeId)) {
neighborsCnt++;
if (!visited.contains(neighborNodeId)) {
stack.push(neighborNodeId);
visited.add(neighborNodeId);
}
}
if (neighborsCnt == 0) {
cb.accept(currentNodeId);
}
}
}
/**
* Returns the leaves of a subgraph rooted at the specified source node.
*
* @param srcNodeId source node
* @return list of node ids corresponding to the leaves
*/
public ArrayList leaves(long srcNodeId) {
ArrayList nodeIds = new ArrayList();
leavesVisitor(srcNodeId, (nodeId) -> nodeIds.add(nodeId));
return nodeIds;
}
/**
* Push version of {@link neighbors}: will fire passed callback on each
* neighbor.
*/
public void neighborsVisitor(long srcNodeId, NodeIdConsumer cb) {
this.nbEdgesAccessed = graph.degree(srcNodeId, useTransposed);
for (long neighborNodeId : new Neighbors(graph, useTransposed, edges, srcNodeId)) {
cb.accept(neighborNodeId);
}
}
/**
* Returns node direct neighbors (linked with exactly one edge).
*
* @param srcNodeId source node
* @return list of node ids corresponding to the neighbors
*/
public ArrayList neighbors(long srcNodeId) {
ArrayList nodeIds = new ArrayList();
neighborsVisitor(srcNodeId, (nodeId) -> nodeIds.add(nodeId));
return nodeIds;
}
/**
* Push version of {@link visitNodes}: will fire passed callback on each
* visited node.
*/
public void visitNodesVisitor(long srcNodeId, NodeIdConsumer cb) {
Stack stack = new Stack();
this.nbEdgesAccessed = 0;
stack.push(srcNodeId);
visited.add(srcNodeId);
while (!stack.isEmpty()) {
long currentNodeId = stack.pop();
cb.accept(currentNodeId);
nbEdgesAccessed += graph.degree(currentNodeId, useTransposed);
for (long neighborNodeId : new Neighbors(graph, useTransposed, edges, currentNodeId)) {
if (!visited.contains(neighborNodeId)) {
stack.push(neighborNodeId);
visited.add(neighborNodeId);
}
}
}
}
/**
* Performs a graph traversal and returns explored nodes.
*
* @param srcNodeId source node
* @return list of explored node ids
*/
public ArrayList visitNodes(long srcNodeId) {
ArrayList nodeIds = new ArrayList();
visitNodesVisitor(srcNodeId, (nodeId) -> nodeIds.add(nodeId));
return nodeIds;
}
/**
* Push version of {@link visitPaths}: will fire passed callback on each
* discovered (complete) path.
*/
public void visitPathsVisitor(long srcNodeId, PathConsumer cb) {
Stack currentPath = new Stack();
this.nbEdgesAccessed = 0;
visitPathsInternalVisitor(srcNodeId, currentPath, cb);
}
/**
* Performs a graph traversal and returns explored paths.
*
* @param srcNodeId source node
* @return list of explored paths (represented as a list of node ids)
*/
public ArrayList> visitPaths(long srcNodeId) {
ArrayList> paths = new ArrayList<>();
visitPathsVisitor(srcNodeId, (path) -> paths.add(path));
return paths;
}
private void visitPathsInternalVisitor(long currentNodeId,
Stack currentPath,
PathConsumer cb) {
currentPath.push(currentNodeId);
long visitedNeighbors = 0;
nbEdgesAccessed += graph.degree(currentNodeId, useTransposed);
for (long neighborNodeId : new Neighbors(graph, useTransposed, edges, currentNodeId)) {
visitPathsInternalVisitor(neighborNodeId, currentPath, cb);
visitedNeighbors++;
}
if (visitedNeighbors == 0) {
ArrayList path = new ArrayList();
for (long nodeId : currentPath) {
path.add(nodeId);
}
cb.accept(path);
}
currentPath.pop();
}
/**
* Performs a graph traversal with backtracking, and returns the first
* found path from source to destination.
*
* @param srcNodeId source node
* @param dst destination (either a node or a node type)
* @return found path as a list of node ids
*/
public ArrayList walk(long srcNodeId, T dst, String visitOrder) {
long dstNodeId = -1;
if (visitOrder.equals("dfs")) {
dstNodeId = walkInternalDFS(srcNodeId, dst);
} else if (visitOrder.equals("bfs")) {
dstNodeId = walkInternalBFS(srcNodeId, dst);
} else {
throw new IllegalArgumentException("Unknown visit order: " + visitOrder);
}
if (dstNodeId == -1) {
throw new IllegalArgumentException("Cannot find destination: " + dst);
}
ArrayList nodeIds = backtracking(srcNodeId, dstNodeId);
return nodeIds;
}
/**
* Performs a random walk (picking a random successor at each step) from
* source to destination.
*
* @param srcNodeId source node
* @param dst destination (either a node or a node type)
* @return found path as a list of node ids or an empty path to indicate
* that no suitable path have been found
*/
public ArrayList randomWalk(long srcNodeId, T dst) {
return randomWalk(srcNodeId, dst, 0);
}
/**
* Performs a stubborn random walk (picking a random successor at each
* step) from source to destination. The walk is "stubborn" in the sense
* that it will not give up the first time if a satisfying target node is
* found, but it will retry up to a limited amount of times.
*
* @param srcNodeId source node
* @param dst destination (either a node or a node type)
* @param retries number of times to retry; 0 means no retries (single walk)
* @return found path as a list of node ids or an empty path to indicate
* that no suitable path have been found
*/
public ArrayList randomWalk(long srcNodeId, T dst, int retries) {
long curNodeId = srcNodeId;
ArrayList path = new ArrayList();
this.nbEdgesAccessed = 0;
boolean found;
if (retries < 0) {
throw new IllegalArgumentException("Negative number of retries given: " + retries);
}
while (true) {
path.add(curNodeId);
- long nbNeighbors = graph.degree(curNodeId, useTransposed);
- if (nbNeighbors == 0) {
+ Neighbors neighbors = new Neighbors(graph, useTransposed, edges, curNodeId);
+ curNodeId = randomPick(neighbors.iterator());
+ if (curNodeId < 0) {
found = false;
break;
}
- Neighbors neighbors = new Neighbors(graph, useTransposed, edges, curNodeId);
- Iterator successors = neighbors.iterator();
-
- curNodeId = randomPick(successors, nbNeighbors);
if (isDstNode(curNodeId, dst)) {
path.add(curNodeId);
found = true;
break;
}
}
if (found) {
return path;
} else if (retries > 0) { // try again
return randomWalk(srcNodeId, dst, retries - 1);
} else { // not found and no retries left
path.clear();
return path;
}
}
/**
- * Randomly choose an element from an iterator
+ * Randomly choose an element from an iterator over Longs using reservoir
+ * sampling
*
* @param elements iterator over selection domain
- * @param lenght total length of elements iterated upon
- * @return randomly chosen element
+ * @return randomly chosen element or -1 if no suitable element was found
*/
- private T randomPick(Iterator elements, long length) {
- long elementsToSkip = Math.round(rng.nextFloat() * (length - 1));
- long skippedElements = -1;
- T e;
+ private long randomPick(Iterator elements) {
+ long curPick = -1;
+ long seenCandidates = 0;
while (elements.hasNext()) {
- e = elements.next();
- skippedElements++;
- this.nbEdgesAccessed++;
- if (skippedElements < elementsToSkip) {
- continue;
- } else {
- return e;
+ seenCandidates++;
+ if (Math.round(rng.nextFloat() * (seenCandidates - 1)) == 0) {
+ curPick = elements.next();
}
}
- throw new IllegalStateException("Skipped past all available elements");
+ return curPick;
}
/**
* Internal DFS function of {@link #walk}.
*
* @param srcNodeId source node
* @param dst destination (either a node or a node type)
* @return final destination node or -1 if no path found
*/
private long walkInternalDFS(long srcNodeId, T dst) {
Stack stack = new Stack();
this.nbEdgesAccessed = 0;
stack.push(srcNodeId);
visited.add(srcNodeId);
while (!stack.isEmpty()) {
long currentNodeId = stack.pop();
if (isDstNode(currentNodeId, dst)) {
return currentNodeId;
}
nbEdgesAccessed += graph.degree(currentNodeId, useTransposed);
for (long neighborNodeId : new Neighbors(graph, useTransposed, edges, currentNodeId)) {
if (!visited.contains(neighborNodeId)) {
stack.push(neighborNodeId);
visited.add(neighborNodeId);
parentNode.put(neighborNodeId, currentNodeId);
}
}
}
return -1;
}
/**
* Internal BFS function of {@link #walk}.
*
* @param srcNodeId source node
* @param dst destination (either a node or a node type)
* @return final destination node or -1 if no path found
*/
private long walkInternalBFS(long srcNodeId, T dst) {
Queue queue = new LinkedList();
this.nbEdgesAccessed = 0;
queue.add(srcNodeId);
visited.add(srcNodeId);
while (!queue.isEmpty()) {
long currentNodeId = queue.poll();
if (isDstNode(currentNodeId, dst)) {
return currentNodeId;
}
nbEdgesAccessed += graph.degree(currentNodeId, useTransposed);
for (long neighborNodeId : new Neighbors(graph, useTransposed, edges, currentNodeId)) {
if (!visited.contains(neighborNodeId)) {
queue.add(neighborNodeId);
visited.add(neighborNodeId);
parentNode.put(neighborNodeId, currentNodeId);
}
}
}
return -1;
}
/**
* Internal function of {@link #walk} to check if a node corresponds to the destination.
*
* @param nodeId current node
* @param dst destination (either a node or a node type)
* @return true if the node is a destination, or false otherwise
*/
private boolean isDstNode(long nodeId, T dst) {
if (dst instanceof Long) {
long dstNodeId = (Long) dst;
return nodeId == dstNodeId;
} else if (dst instanceof Node.Type) {
Node.Type dstType = (Node.Type) dst;
return graph.getNodeType(nodeId) == dstType;
} else {
return false;
}
}
/**
* Internal backtracking function of {@link #walk}.
*
* @param srcNodeId source node
* @param dstNodeId destination node
* @return the found path, as a list of node ids
*/
private ArrayList backtracking(long srcNodeId, long dstNodeId) {
ArrayList path = new ArrayList();
long currentNodeId = dstNodeId;
while (currentNodeId != srcNodeId) {
path.add(currentNodeId);
currentNodeId = parentNode.get(currentNodeId);
}
path.add(srcNodeId);
Collections.reverse(path);
return path;
}
}