Using the Java API

While the HTTP API is useful for many common use-cases, it is often not sufficient to implement more complex algorithms. This section describes the low-level Java API that swh-graph provides on top of the WebGraph framework to manipulate the compressed graph of Software Heritage.

A cursory understanding of the WebGraph framework and its API is helpful to understand the notions detailed here.

Basics

In the WebGraph framework, graphs are generally subclasses of ImmutableGraph, the abstract class providing the core API to manipulate and iterate on graphs. Under the hood, compressed graphs are stored as the BVGraph class, which contains the actual codec used to compress and decompress adjacency lists.

Graphs nodes are mapped to a contiguous set of integers \([0, n - 1]\) where n is the total number of nodes in the graph. Each node has an associated adjacency list, i.e., a list of nodes going from that source node to a destination node. This list represents the edges (or arcs) of the graph.

Note: edges are always directed. Undirected graphs are internally stored as a pair of directed edges (src → dst, dst → src), and are called “symmetric” graphs.

On disk, a simple BVGraph with the basename graph would be represented as the following set of files:

  • graph.graph: contains the compressed adjacency lists of each node, which can be decompressed by the BVGraph codec.

  • graph.properties: contains metadata on the graph, such as the number of nodes and arcs, as well as additional loading information needed by the BVGraph codec.

  • graph.offsets: a list of offsets of where the adjacency list of each node is stored in the main graph file.

  • graph.obl: optionally, an “offset big-list file” which can be used to load graphs faster.

An ImmutableGraph can be loaded using different load methods, which have each different performance implications:

  • load(): the entire graph is loaded in RAM and supports random access.

  • loadMapped(): the graph is loaded by memory-mapping it from disk (see mmap(1)), at the cost of being potentially slower, especially when doing random access on slow storage.

  • loadOffline(): no data is actually loaded is memory, only sequential iteration is possible.

The following code loads a graph stored on disk under the compressed/graph basename, using the memory-mapped loading mode, and stores it as a generic ImmutableGraph:

ImmutableGraph graph = ImmutableGraph.loadMapped("compressed/graph");

Note that most of the time you will want to use the SWH-specific subclass SwhUnidirectionalGraph instead, which has the same API as an ImmutableGraph except it adds other SWH-specific methods. It is described later in the Node types and SWHIDs section.

Running the code

To run a piece of Java code written using the Java API, you need to run it with all the dependencies in your classpath (the WebGraph libraries and the swh-graph library). The easiest way to do it is to add the fat jar shipped in the swh-graph library on PyPI, which contains all the required dependencies.

$ java -cp venv/share/swh-graph/swh-graph-0.5.2.jar MyAlgo.java

Note that to load bigger graphs, the default heap size of the JVM is likely to be insufficient to load entire graphs in memory. It is advised to increase this heap size with the -Xmx flag:

$ java -Xmx300G -cp venv/share/swh-graph/swh-graph-0.5.2.jar MyAlgo.java

For more information on performance tuning and memory considerations, you should also read the Memory & Performance tuning page, in which we recommend additional JVM options for loading large graphs.

Simple traversal

The ImmutableGraph class provides primitives to iterate and traverse graphs. It contains the following methods:

  • graph.numNodes() returns the number of nodes in the graph (n).

  • graph.numArcs() returns the number of arcs in the graph.

And, given a node ID \(k \in [0, n - 1]\):

  • graph.successors(k) returns a LazyLongIterator on the nodes that are adjacent to k (i.e., its outgoing neighbors).

  • graph.outdegree(k) returns the number of outgoing neighbors of k.

Example: Average outdegree

The following code can be used to compute the average outdegree of a graph, which is a useful measure of its density:

public static long averageOutdegree(ImmutableGraph graph) {
    return ((long) graph.numArcs()) / graph.numNodes();
}

Example: Degree distributions

Using the outdegree() primitive, we can compute the outdegree distribution of the graph by iterating on all its nodes. The distribution will be returned as a map that associates to each degree d the number of nodes with outdegree d.

public static Map<Long, Long> outdegreeDistribution(ImmutableGraph graph) {
    HashMap<Long, Long> distribution = new HashMap<Long, Long>();
    for (long k = 0; k < graph.numNodes(); ++k) {
        distribution.merge(graph.outdegree(k), 1L, Long::sum);
    }
    return distribution;
}

Example: Depth-First Traversal

The successors primitive can be used to write a simple stack-based DFS traversal on the graph which starts from a given node and prints all the descendant nodes in its transitive closure:

 public static void visitNodesDFS(ImmutableGraph graph, long srcNodeId) {
     Stack<Long> stack = new Stack<>();
     HashSet<Long> visited = new HashSet<Long>();
     stack.push(srcNodeId);
     visited.add(srcNodeId);

     while (!stack.isEmpty()) {
         long currentNodeId = stack.pop();
         System.out.println(currentNodeId);

         LazyLongIterator it = graph.successors(currentNodeId);
         for (long neighborNodeId; (neighborNodeId = it.nextLong()) != -1;) {
             if (!visited.contains(neighborNodeId)) {
                 stack.push(neighborNodeId);
                 visited.add(neighborNodeId);
             }
         }
     }
 }

Example: Breadth-First Traversal

Swapping the stack for a queue changes the traversal order from depth-first to breadth-first:

 public static void visitNodesBFS(ImmutableGraph graph, long srcNodeId) {
     Queue<Long> queue = new ArrayDeque<>();
     HashSet<Long> visited = new HashSet<Long>();
     queue.add(srcNodeId);
     visited.add(srcNodeId);

     while (!queue.isEmpty()) {
         long currentNodeId = queue.poll();
         System.out.println(currentNodeId);

         LazyLongIterator it = graph.successors(currentNodeId);
         for (long neighborNodeId; (neighborNodeId = it.nextLong()) != -1;) {
             if (!visited.contains(neighborNodeId)) {
                 queue.add(neighborNodeId);
                 visited.add(neighborNodeId);
             }
         }
     }
 }

Node types and SWHIDs

In the Software Heritage archive, nodes are not represented by a simple integer, but by a SWHID, which contain both the type of the node (revision, directory, blob…) and its unique identifier. We use node mappings which allow us to translate between SWHIDs and the compact node IDs used in the compressed graph.

Most notably, we use a MPH (Minimal Perfect Hash) function implemented in the GOVMinimalPerfectHashFunction class of the Sux4J library, which maps N keys to N consecutive integers with no collisions.

The following files are used to store the mappings between the nodes and their types:

  • graph.mph: contains a serialized minimal perfect hash function computed on the list of all the SWHIDs in the graph.

  • graph.order: contains the permutation that associates with each output of the MPH the node ID to which it corresponds

  • graph.node2swhid.bin: contains a compact binary representation of all the SWHIDs in the graph, ordered by their rank in the graph file.

  • graph.node2type.bin: contains a LongBigArrayBitVector which stores the type of each node.

To use these mappings easily, we provide the class SwhUnidirectionalGraph, an ImmutableGraph which wraps the underlying graph and adds a few utility methods to obtain SWH-specific information on the graph.

A SwhUnidirectionalGraph can be loaded in a similar way to any ImmutableGraph, as long as the mapping files listed above are present:

SwhUnidirectionalGraph graph = SwhUnidirectionalGraph.load(basename);

This class exposes the same graph primitives as an ImmutableGraph, but it additionally contains the following methods:

  • SWHID getSWHID(long nodeId): returns the SWHID associated with a given node ID. This function does a lookup of the SWHID at offset i in the file graph.node2swhid.bin.

  • long getNodeID(SWHID swhid): returns the node ID associated with a given SWHID. It works by hashing the SWHID with the function stored in graph.mph, then permuting it using the permutation stored in graph.order. It does additional domain-checking by calling getSWHID() on its own result to check that the input SWHID was valid.

  • SwhType getNodeType(long nodeID): returns the type of a given node, as an enum of all the different object types in the Software Heritage data model. It does so by looking up the value at offset i in the bit vector stored in graph.node2type.bin.

Example: Find the target directory of a revision

As an example, we use the methods mentioned above to perform the following task: “given a revision, return its target directory”. To do so, we first look up the node ID of the given revision in the compressed graph. We iterate on the successors of that node, and return the SWHID of the first destination node that has the “directory” type.

 public SWHID findDirectoryOfRevision(SwhUnidirectionalGraph graph, SWHID revSwhid) {
     long src = graph.getNodeId(revSwhid);
     assert graph.getNodeType(src) == SwhType.REV;
     LazyLongIterator it = graph.successors(currentNodeId);
     for (long dst; (dst = it.nextLong()) != -1;) {
         if (graph.getNodeType(dst) == SwhType.DIR) {
             return graph.getSWHID(dst);
         }
     }
     throw new RuntimeError("Revision has no target directory");
 }

Node properties

The Software Heritage Graph is a property graph, which means it has various properties associated with its nodes and edges (e.g., commit timestamps, authors, messages, …). We compress these properties and store them in files alongside the compressed graph. This allows you to write traversal algorithms that depend on these properties.

By default, properties are not assumed to be present are are not loaded when the graph itself is loaded. If you want to use a property, you need to explicitly load it first. As an example, this is how you load the “content length” property to get the length of a given blob:

SwhUnidirectionalGraph graph = SwhUnidirectionalGraph.load(basename);
graph.loadContentLength();
long blobSize = graph.getContentLength(graph.getNodeID(swhid));

The documentation of the SwhGraphProperties class (TODO: link) lists all the different properties, their types, and the methods used to load them and to get their value for a specific node.

A few things of note:

  • A single loading call can load multiple properties at once; this is because they are stored in the same file to be more space efficient.

  • Persons (authors, committers etc) are exported as a single pseudonymized integer ID, that uniquely represents a full name + email.

  • Timestamps are stored as a long integer (for the timestamp itself) and a short integer (for the UTC offset).

Edge labels

While looking up graph properties on the nodes of the graph is relatively straightforward, doing so for labels on the arcs is comparatively more difficult. These include the names and permissions of directory entries, as well as the branch names of snapshots.

The ArcLabelledImmutableGraph class in WebGraph wraps an ImmutableGraph, but augments its iterators by making them labelled iterators, which essentially allow us to look up the label of the arcs while iterating on them.

This labelled graph is stored in the following files:

  • graph-labelled.properties: a property file describing the graph, notably containing the basename of the wrapped graph.

  • graph-labelled.labels: the compressed labels

  • graph-labelled.labeloffsets: the offsets used to access the labels in random order.

The SwhUnidirectionalGraph class contains labelled loading methods (loadLabelled(), loadLabelledMapped(), …). When these loading methods are used instead of the standard non-labelled ones, the graph is loaded as an ArcLabelledImmutableGraph instead of an ImmutableGraph. The following methods can then be used:

  • labelledSuccessors(k) returns a LabelledArcIterator which is used in the same way as a LazyLongIterator except it also contains a label() method to get the label of the currently traversed arc.

  • labelledNodeIterator() returns an ArcLabelledNodeIterator of all the nodes in the graph, which replaces the LazyLongIterator of the successor() function by a LabelledArcIterator similar to above.

Label format

The labels of each arc are returned as a DirEntry[] array. They encode both the name of a directory entry and its permissions. For snapshot branches, only the “name” field is useful.

Arc label names are encoded as an integer ID representing each unique entry/branch name present in the graph. To retrieve the actual name associated with a given label ID, one needs to load the reverse mapping similar to how you would do for a normal property:

SwhUnidirectionalGraph graph = SwhUnidirectionalGraph.loadLabelled(basename);
graph.loadLabelNames();

The byte array representing the actual label name can then be loaded with:

byte[] name = graph.getLabelName(label.filenameId);

Multiedges

The Software Heritage is not a simple graph, where at most one edge can exist between two vertices, but a multigraph, where multiple edges can be incident to the same two vertices. Consider for instance the case of a single directory test/ containing twice the same file blob (e.g., the empty file), under two different names (e.g., ISSUES.txt and TODO.txt, both completely empty). The simple graph view of this directory will represent it as a single edge testempty file, while the multigraph view will represent it as two edges between the same nodes.

Due to the copy-list model of compression, WebGraph only stores simple graphs, and thus stores multiedges as single edges, to which we cannot associate a single label name (in our example, we need to associate both names ISSUES.txt and TODO.txt). To represent this possibility of having multiple file names for a single arc, in the case of multiple relationships between two identical nodes, each arc label is stored as an array of DirEntry, each record representing one relationship between two nodes.

Example: Printing all the entries of a directory

The following code showcases how one can print all the entries (name, permission and target SWHID) of a given directory, using the labelled methods seen above.

public static void printEntries(ImmutableGraph g, long dirNode) {
    LabelledArcIterator s = g.labelledSuccessors(dirNode);
    for (long dst; (dst = it.nextLong()) >= 0;) {
        DirEntry[] labels = (DirEntry[]) s.label().get();
        for (DirEntry label : labels) {
            System.out.format(
                "%s %s %d\n",
                graph.getSWHID(dst);
                new String(graph.getLabelName(label.filenameId)),
                label.permission
            );
        }
    }
}

// Usage: $PROGRAM <GRAPH_BASENAME> <DIR_SWHID>
public static void main(String[] args) {
    SwhUnidirectionalGraph g = SwhUnidirectionalGraph.loadLabelledMapped(args[0]);
    g.loadLabelNames();
    long dirNode = g.getNodeID(new SWHID(args[1]));
    printEntries(g, dirNode);
}

Transposed graph

Up until now, we have only looked at how to traverse the forward graph, i.e., the directed graph whose edges are in the same direction as the Merkle DAG of the Software Heritage archive. For many purposes, especially that of finding the provenance of software artifacts, it is useful to query the backward (or transposed) graph instead, which is the same as the forward graph except all the edges are reversed.

The transposed graph has its own set of files, counterparts to the files needed for the forward graph:

  • graph-transposed.graph

  • graph-transposed.properties

  • graph-transposed.offsets

  • graph-transposed.obl

  • graph-transposed-labelled.labels

  • graph-transposed-labelled.labeloffsets

  • graph-transposed-labelled.properties

However, because node IDs are the same in the forward and the backward graph, all the files that pertain to mappings between the node IDs and various properties (SWHIDs, property data, node permutations etc) remain the same.

Example: Earliest revision containing a given blob

The following code loads all the committer timestamps of the revisions in the graph, then walks the transposed graph to return the earliest revision containing a given object.

public static long findEarliestRevisionContaining(SwhUnidirectionalGraph g, long src) {
    long oldestRev = -1;
    long oldestRevTs = Long.MAX_VALUE;

    Stack<Long> stack = new Stack<>();
    HashSet<Long> visited = new HashSet<Long>();
    stack.push(src);
    visited.add(src);
    while (!stack.isEmpty()) {
        long currentNodeId = stack.pop();
        LazyLongIterator it = graph.successors(currentNodeId);
        for (long neighborNodeId; (neighborNodeId = it.nextLong()) != -1;) {
            if (!visited.contains(neighborNodeId)) {
                stack.push(neighborNodeId);
                visited.add(neighborNodeId);
                if (g.getNodeType(neighborNodeId) == SwhType.REV) {
                    Long ts = g.getCommitterTimestamp(neighborNodeId);
                    if (ts != null && ts < oldestRevTs) {
                        oldestRev = neighborNodeId;
                        oldestRevTs = ts;
                    }
                }
            }
        }
    }
    return oldestRev;
}

// Usage: $PROGRAM <GRAPH_BASENAME> <BLOB_SWHID>
public static void main(String[] args) {
    // Load the backward (= transposed) graph as a SwhUnidirectionalGraph
    SwhUnidirectionalGraph g = SwhUnidirectionalGraph.loadMapped(args[0] + "-transposed");
    g.loadCommitterTimestamps();
    long node = g.getNodeID(new SWHID(args[1]));
    long oldestRev = findEarliestRevisionContaining(g, node);
    System.out.println(g.getSWHID(oldestRev));
}

Bidirectional Graph

BidirectionalImmutableGraph

While graph-transposed can be loaded as a simple SwhUnidirectionalGraph and then manipulated just like the forward graph, it is often convenient to have both the forward and the backward graph in memory. Some traversal algorithms require first going down in the forward graph to select some nodes, then going up to find their provenance.

To achieve that, we use the BidirectionalImmutableGraph class from WebGraph, which stores both a graph and its transpose. This class provides the following methods to iterate on the backward graph, shown here with their counterparts for the forward graph:

Forward graph operation

Backward graph operation

outdegree(k)

indegree(k)

successors(k)

predecessors(k)

In addition, the class offers a few convenience methods which are generally useful when you have both a graph and its transpose:

  • transpose() returns the transpose of the BidirectionalImmutableGraph by inverting the references to the forward and the backward graphs. Successors become predecessors, and vice-versa.

  • symmetrize() returns the symmetric (= undirected) version of the bidirectional graph. It is implemented by a union between the forward and the backward graph, which basically boils down to removing the directionality of the edges (the successors of a node are also its predecessors).

SwhBidirectionalGraph

Like for ImmutableGraph, we extend the BidirectionalImmutableGraph with SWH-specific methods, in the subclass SwhBidirectionalGraph. Notably, it contains the method labelledPredecessors(), the equivalent of labelledSuccessors() but on the backward graph.

Because SwhUnidirectionalGraph inherits from ImmutableGraph, and SwhBidirectionalGraph inherits from BidirectionalImmutableGraph, we put the common behavior between the two classes in a SwhGraph interface, which can represent either an unidirectional or a bidirectional graph.

To avoid loading the node properties two times (once for each direction), they are stored in a separate class called SwhGraphProperties. In a SwhBidirectionalGraph, the two SwhUnidirectionalGraph share their node properties in memory by storing references to the same SwhGraphProperty object.

               ┌──────────────┐
               │ImmutableGraph◄────────┐
               └────▲─────────┘        │extends
                    │                  │
                    │       ┌──────────┴────────────────┐
             extends│       │BidirectionalImmutableGraph│
                    │       └────────────▲──────────────┘
                    │                    │extends
     ┌──────────────┴───────┐     ┌──────┴──────────────┐
     │SwhUnidirectionalGraph│◄────┤SwhBidirectionalGraph│
     └──┬──────────────┬────┘     └────────┬───────────┬┘
        │              │    contains x2    │           │
        │              │                   │           │
        │    implements│                   │implements │
        │             ┌▼──────────┐        │           │
        │             │SwhGraph(I)◄────────┘           │
contains│             └───────────┘                    │contains
        │                                              │
        │            ┌──────────────────┐              │
        └────────────►SwhGraphProperties◄──────────────┘
                     └──────────────────┘

Example: Find all the shared-commit forks of a given origin

It is possible to define the forks of an origin as being the set of origins which share at least one revision with that origin.

The following code loads the graph in both directions using a SwhBidirectionalGraph. Given an origin SWHID, it first walks the forward graph to find all its root revisions. It then walks the backward graph to find all the origins containing these root revisions, i.e., its forks.

public static void findSharedCommitForks(SwhUnidirectionalGraph g, long srcOrigin) {
    Stack<Long> forwardStack = new Stack<>();
    HashSet<Long> forwardVisited = new HashSet<Long>();
    Stack<Long> backwardStack = new Stack<>();
    HashSet<Long> backwardVisited = new HashSet<Long>();

    // First traversal (forward graph): find all the root revisions of the
    // origin
    forwardStack.push(srcOrigin);
    forwardVisited.add(srcOrigin);
    while (!forwardStack.isEmpty()) {
        long curr = forwardStack.pop();
        LazyLongIterator it = graph.successors(curr);
        boolean isRootRevision = true;
        for (long succ; (succ = it.nextLong()) != -1;) {
            SwhType nt = g.getNodeType(succ);
            if (!forwardVisited.contains(succ)
                    && nt != SwhType.DIR && nt != SwhType.CNT) {
                forwardStack.push(succ);
                forwardVisited.add(succ);
                isRootRevision = false;
            }
        }
        if (g.getNodeType(curr) == SwhType.REV && isRootRevision) {
            // Found a root revision, add it to the second stack
            backwardStack.push(curr);
            backwardVisited.add(curr);
        }
    }

    // Second traversal (backward graph): find all the origins containing
    // any of these root revisions and print them
    while (!backwardStack.isEmpty()) {
        long curr = backwardStack.pop();
        LazyLongIterator it = graph.predecessors(curr);
        boolean isRootRevision = true;
        for (long succ; (succ = it.nextLong()) != -1;) {
            SwhType nt = g.getNodeType(succ);
            if (!backwardVisited.contains(succ)) {
                backwardStack.push(succ);
                backwardVisited.add(succ);
                if (nt == SwhType.ORI) {
                    // Found an origin, print it.
                    System.out.println(g.getSWHID(succ));
                }
            }
        }
    }
}

// Usage: $PROGRAM <GRAPH_BASENAME> <ORI_SWHID>
public static void main(String[] args) {
    // Load both forward and backward graphs as a SwhBidirectionalGraph
    SwhBidirectionalGraph g = SwhBidirectionalGraph.loadMapped(args[0]);
    long node = g.getNodeID(new SWHID(args[1]));
    findSharedCommitForks(g, node);
}

Large-scale processing

Multithreading

ImmutableGraph is not thread-safe. When writing multithreaded algorithms, calling successors() on the same graph from multiple threads will return garbage.

Instead, each thread should create its own “lightweight copy” of the graph by calling .copy(). This will not actually copy the entire graph data, which will remain shared across threads, but it will create new instances of the iterators so that each thread can independently iterate on the graph data.

Data structures for large traversals

When doing very large traversals, such as a BFS on the entire graph, the usual data structures (HashSet, Stack, ArrayDeque, etc.) will be quite inefficient. If you know you are going to traverse large parts of the graph, it’s better to use more appropriate data structures, a lot of which can be found in the dsiutils library. In particular:

  • LongArrayBitVector is an efficient bit-vector implementation, which can be used to store the nodes that have already been seen in the visit. Its memory footprint is too big to use for small traversals, but it is very efficient to traverse the full graph, as every node only takes a single bit.

  • ByteDiskQueue can be used to efficiently store the queue of nodes to visit on disk, when it is too large to fit in RAM.

Other types in dsiutils and fastutil can save significant memory: LongArrayList saves at least 8 bytes per entry over ArrayList<Long>, and Long2LongOpenHashMap saves at least 16 bytes for every entry over HashMap<Long, Long>. We strongly recommend reading the documentation of the unimi libraries and looking at the code for usage examples.

BigArrays

When working with the Software Heritage graph, is often necessary to store large arrays of values, with a size exceeding 2^32 items. Unfortunately, standard Java arrays do not support this.

To circumvent this, WebGraph uses the BigArrays scheme from the fastutil library: “big arrays” are stored as arrays of arrays, supporting quadrillions of records.

A BigArray long[][] a can be used with the following methods:

  • BigArrays.get(a, i) to get the value at index i

  • BigArrays.set(a, i, v) to set the value at index i to v.

  • BigArrays.length(a) to get the total length of the bigarray.