GraphML (Graph Markup Language) serialization support.
Provides functions to serialize and deserialize graphs in the GraphML format, an XML-based format widely supported by graph visualization and analysis tools like Gephi, yEd, Cytoscape, and NetworkX.
Format Overview
GraphML is an XML-based format that supports:
- Nodes with custom attributes
- Edges with custom attributes
- Directed and undirected graphs
- Hierarchical graphs (not yet supported)
Performance
For optimal performance with large GraphML files, add the optional saxy
dependency to your project:
{:saxy, "~> 1.5"}When available, saxy provides a fast streaming SAX parser that significantly
improves loading times:
- Without saxy: Uses Erlang's
:xmerl(DOM parser, slower for large files) - With saxy: Uses streaming parser (up to 3-4x faster for large files)
Examples
Basic Serialization and Deserialization
iex> graph = Yog.directed()
...> |> Yog.add_node(1, "Alice")
...> |> Yog.add_node(2, "Bob")
...> |> Yog.add_edge_ensure(from: 1, to: 2, with: "friend")
iex> xml = Yog.IO.GraphML.serialize(graph)
iex> String.contains?(xml, "Alice")
true
iex> String.contains?(xml, "Bob")
trueCustom Attributes with Type Information
iex> graph = Yog.directed()
...> |> Yog.add_node(1, %{name: "Alice", age: 30})
...> |> Yog.add_node(2, %{name: "Bob", age: 25})
...> |> Yog.add_edge_ensure(from: 1, to: 2, with: %{weight: 5, relation: "friend"})
iex> node_attr = fn data ->
...> %{"label" => data.name, "age" => Integer.to_string(data.age)}
...> end
iex> edge_attr = fn data ->
...> %{"weight" => Integer.to_string(data.weight), "type" => data.relation}
...> end
iex> xml = Yog.IO.GraphML.serialize_with(node_attr, edge_attr, graph)
iex> String.contains?(xml, "Alice")
trueReading from File
# Read a GraphML file from disk
{:ok, graph} = Yog.IO.GraphML.read("network.graphml")Writing to File
# Write with default string conversion
Yog.IO.GraphML.write("output.graphml", graph)Summary
Functions
Returns default GraphML serialization options.
Deserializes a GraphML string to a graph using default conversion.
Deserializes a GraphML string into a graph with custom data mappers.
Creates GraphML options with custom formatting.
Reads a graph from a GraphML file using default conversion.
Reads a graph from a GraphML file with custom data mappers.
Serializes a graph to GraphML string using default attribute conversion.
Serializes a graph to GraphML string with custom attribute mappers.
Serializes a graph to a GraphML string with custom options.
Serializes a graph to GraphML with typed attributes for Gephi compatibility.
Serializes a graph to GraphML with typed attributes and custom options.
Writes a graph to a GraphML file using default attribute conversion.
Writes a graph to a GraphML file with custom attribute mappers.
Writes a graph to a GraphML file with typed attributes for Gephi compatibility.
Functions
@spec default_options() :: tuple()
Returns default GraphML serialization options.
Time complexity: $\mathcal{O}(1)$
Deserializes a GraphML string to a graph using default conversion.
Raises ArgumentError if xml is not a binary string.
Time complexity: $\mathcal{O}(V + E)$
@spec deserialize_with((map() -> any()), (map() -> any()), String.t()) :: {:ok, Yog.graph()} | {:error, term()}
Deserializes a GraphML string into a graph with custom data mappers.
Raises ArgumentError if xml or data mappers are invalid.
Time complexity: $\mathcal{O}(V + E)$
@spec options_with(non_neg_integer(), boolean(), keyword()) :: tuple()
Creates GraphML options with custom formatting.
Raises ArgumentError if parameters are invalid.
Time complexity: $\mathcal{O}(1)$
Reads a graph from a GraphML file using default conversion.
Raises ArgumentError if path is not a binary string.
Time complexity: $\mathcal{O}(V + E)$ + file I/O
@spec read_with(String.t(), (map() -> any()), (map() -> any())) :: {:ok, Yog.graph()} | {:error, term()}
Reads a graph from a GraphML file with custom data mappers.
Raises ArgumentError if path is not a binary string or mappers are invalid.
Time complexity: $\mathcal{O}(V + E)$ + file I/O
Serializes a graph to GraphML string using default attribute conversion.
Raises ArgumentError if graph is invalid.
Time complexity: $\mathcal{O}(V + E)$
Serializes a graph to GraphML string with custom attribute mappers.
Raises ArgumentError if mappers or graph are invalid.
Time complexity: $\mathcal{O}(V + E)$
@spec serialize_with_options( (any() -> map()), (any() -> map()), tuple(), Yog.graph() | Yog.DAG.t() ) :: String.t()
Serializes a graph to a GraphML string with custom options.
Raises ArgumentError if arguments or options are invalid.
Time complexity: $\mathcal{O}(V + E)$
@spec serialize_with_types( (any() -> map()), (any() -> map()), Yog.graph() | Yog.DAG.t() ) :: String.t()
Serializes a graph to GraphML with typed attributes for Gephi compatibility.
Raises ArgumentError if mappers or graph are invalid.
Time complexity: $\mathcal{O}(V + E)$
@spec serialize_with_types_and_options( (any() -> map()), (any() -> map()), tuple(), Yog.graph() | Yog.DAG.t() ) :: String.t()
Serializes a graph to GraphML with typed attributes and custom options.
Raises ArgumentError if arguments or options are invalid.
Time complexity: $\mathcal{O}(V + E)$
Writes a graph to a GraphML file using default attribute conversion.
Raises ArgumentError if path is not a binary string or graph is invalid.
Time complexity: $\mathcal{O}(V + E)$ + file I/O
@spec write_with( String.t(), (any() -> map()), (any() -> map()), Yog.graph() | Yog.DAG.t() ) :: {:ok, nil} | {:error, atom()}
Writes a graph to a GraphML file with custom attribute mappers.
Raises ArgumentError if path is not a binary string or graph/mappers are invalid.
Time complexity: $\mathcal{O}(V + E)$ + file I/O
@spec write_with_types( String.t(), (any() -> map()), (any() -> map()), Yog.graph() | Yog.DAG.t() ) :: {:ok, nil} | {:error, atom()}
Writes a graph to a GraphML file with typed attributes for Gephi compatibility.
Raises ArgumentError if path is not a binary string or graph/mappers are invalid.
Time complexity: $\mathcal{O}(V + E)$ + file I/O