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From: Tiago de Paula Peixoto (tiago_at_[hidden])
Date: 2006-08-14 22:14:19
Hi.
I'm sending attached a new version of the reader with the following
modifications:
- separation into graphml.hpp and graphml.cpp, where all the expat stuff
is confined to the latter
- support for default attribute values (had forgotten about this one)
- the minor corrections you pointed out in the other email
I'm sending also a test program with a test file, and some documentation
(which I blatantly ripped off from read_graphviz and write_graphviz). I
didn't check if the generated html is OK, so it will probably need some
review.
On 08/14/2006 02:06 PM, Douglas Gregor wrote:
>>> I've been busy integrating this GraphML reader into the BGL
>>> Python bindings, and I have a few comments along the way:
>> Cool!
>
> And FWIW, everything has worked out very well. Great work!
That's excellent! I can't wait to use it myself...
> The only other issue I ran into is that I had to build expat
> carefully to get the C++ exceptions (e.g., undirected_graph_error)
> to propagate through expat properly. With GCC, this means compiler
> with -fexceptions; I'm not sure about other compilers. I think the
> "right" fix (which I've hacked up in the BGL-Python tree) is to build
> expat with a C++ compiler. We'll have to think about how to handle
> this in Boost.
Well, since this would be a problem with every C++ program that tried to
use expat, perhaps it could be considered just a problem with the
system's expat build, and not Boost's fault (but a note should be added
nevertheless to the documentation). In my system (gentoo GNU/linux), the
exceptions work OK, which probably means that the library was build like
you described (and thus whoever packaged it did the right thing).
If it is really necessary to accept the lack of exceptions from expat,
than perhaps the exceptions could be delayed and thrown only at the top
level function, outside expat. But that would make the code a lot uglier...
Take care.
-- Tiago de Paula Peixoto <tiago_at_[hidden]>
============================
|(logo)|__ ``read_graphml``
============================
.. |(logo)| image:: ../../../boost.png
:align: middle
:alt: Boost
__ ../../../index.htm
::
void read_graphml(std::istream& in, MutableGraph& graph,
dynamic_properties& dp);
The ``read_graphml`` function interprets a graph described using the
graphml_ format and builds a BGL graph that captures that
description. Using this function, you can initialize a graph using
data stored as text.
The graphml format can specify both directed and undirected graphs, and
``read_graphml`` differentiates between the two. One must pass
``read_graphml`` an undirected graph when reading an undirected graph;
the same is true for directed graphs. Furthermore, ``read_graphml``
will throw an exception if it encounters parallel edges and cannot add
them to the graph.
To handle attributes expressed in the graphml format, ``read_graphml``
takes a dynamic_properties_ object and operates on its collection of
property maps. The reader passes all the properties encountered to
this object, using the graphml attribute names as the property keys,
and with the appropriate C++ type based on the graphml attribute type
definition.
Requirements:
- The type of the graph must model the `Mutable Graph`_ concept.
- The type of the iterator must model the `Multi-Pass Iterator`_
concept.
- The property map value types must be default-constructible.
.. contents::
Where Defined
-------------
``<boost/graph/graphml.hpp>``
Exceptions
----------
::
struct graph_exception : public std::exception {
virtual ~graph_exception() throw();
virtual const char* what() const throw() = 0;
};
struct bad_parallel_edge : public graph_exception {
std::string from;
std::string to;
bad_parallel_edge(const std::string&, const std::string&);
virtual ~bad_parallel_edge() throw();
const char* what() const throw();
};
struct directed_graph_error : public graph_exception {
virtual ~directed_graph_error() throw();
virtual const char* what() const throw();
};
struct undirected_graph_error : public graph_exception {
virtual ~undirected_graph_error() throw();
virtual const char* what() const throw();
};
struct parse_error : public graph_exception {
parse_error(const std::string&);
virtual ~parse_error() throw() {}
virtual const char* what() const throw();
std::string statement;
};
Under certain circumstances, ``read_graphml`` will throw one of the
above exceptions. The three concrete exceptions can all be caught
using the general ``graph_exception`` moniker when greater precision
is not needed. In addition, all of the above exceptions derive from
the standard ``std::exception`` for even more generalized error
handling.
The ``bad_parallel_edge`` exception is thrown when an attempt to add a
parallel edge to the supplied MutableGraph fails. The graphml format
supports parallel edges, but some BGL-compatible graph types do not.
One example of such a graph is ``boost::adjacency_list<setS,vecS>``,
which allows at most one edge can between any two vertices.
The ``directed_graph_error`` exception occurs when an undirected graph
type is passed to ``read_graph`` but the textual representation of the
graph is directed, as indicated by the ``edgedefault="directed"``
graph attribute in the graphml format.
The ``undirected_graph_error`` exception occurs when a directed graph
type is passed to ``read_graph`` but the textual representation of the
graph is undirected, as indicated by the ``edgedefault="undirected"``
graph attribute in the graphml format.
Building the graphml reader
-----------------------------
To use the graphml reader, you will need to build and link against
the "bgl-graphml" library. The library can be built by following the
`Boost Jam Build Instructions`_ for the subdirectory ``libs/graph/build``.
Notes
-----
- On successful reading of a graph, every vertex and edge will have
an associated value for every respective edge and vertex property
encountered while interpreting the graph. These values will be set
using the ``dynamic_properties`` object. Some properties may be
``put`` multiple times during the course of reading in order to
ensure the graphml semantics. Those edges and vertices that are
not explicitly given a value for a property (and that property has
no default) will be given the default constructed value of the
value type. **Be sure that property map value types are default
constructible.**
- Nested graphs are supported as long as they are exactly of the same
type as the root graph, i.e., are also directed or undirected. Note
that since nested graphs are not directly supported by BGL, they
are in fact completely ignored when building the graph, and the
internal vertices or edges are interpreted as belonging to the root
graph.
- Hyperedges and Ports are not supported.
See Also
--------
write_graphml_
Future Work
-----------
- Better expat error detection.
.. _Graphml: http://graphml.graphdrawing.org/
.. _`Mutable Graph`: MutableGraph.html
.. _`Multi-Pass Iterator`: ../../iterator/index.html
.. _dynamic_properties: ../../property_map/doc/dynamic_property_map.html
.. _write_graphml: write_graphml.html
.. _Boost Jam Build Instructions: ../../../more/getting_started.html#Build_Install
============================
|(logo)|__ ``write_graphml``
============================
.. |(logo)| image:: ../../../boost.png
:align: middle
:alt: Boost
__ ../../../index.htm
::
template<typename Graph>
void
write_graphml(std::ostream& out, const Graph& g, const dynamic_properties& dp,
bool ordered_vertices=false);
template<typename Graph, typename VertexIndexMap>
void
write_graphml(std::ostream& out, const Graph& g, VertexIndexMap vertex_index,
const dynamic_properties& dp, bool ordered_vertices=false);
This is to write a BGL graph object into an output stream in the
graphml_ format. Both overloads of ``write_graphml`` will emit all of
the properties stored in the dynamic_properties_ object, thereby
retaining the properties that have been read in through the dual
function read_graphml_. The second overload must be used when the
graph doesn't have an internal vertex index map, which must then be
supplied with the appropriate parameter.
.. contents::
Where Defined
-------------
``<boost/graph/graphml.hpp>``
Parameters
----------
OUT: ``std::ostream& out``
A standard ``std::ostream11 object.
IN: ``VertexListGraph& g``
A directed or undirected graph. The
graph's type must be a model of VertexListGraph_. If the graph
doesn't have an internal ``vertex_index`` property map, one
must be supplied with the vertex_index parameter.
IN: ``VertexIndexMap vertex_index``>
A vertex property map containing the indexes in the range
[0,num_vertices(g)].
IN: ``dynamic_properties& dp``
Contains all of the vertex and edge properties that should be
emitted by the graphml writer.
IN: ``bool ordered_vertices``
This tells whether or not the order of the vertices from vertices(g)
matches the order of the indexes. If ``true``, the ``parse.nodeids``
graph attribute will be set to ``canonical``. Otherwise it will be
set to ``free``.
Example
-------
This example demonstrates using BGL-graphml interface to write
a BGL graph into a graphml format file.
::
enum files_e { dax_h, yow_h, boz_h, zow_h, foo_cpp,
foo_o, bar_cpp, bar_o, libfoobar_a,
zig_cpp, zig_o, zag_cpp, zag_o,
libzigzag_a, killerapp, N };
const char* name[] = { "dax.h", "yow.h", "boz.h", "zow.h", "foo.cpp",
"foo.o", "bar.cpp", "bar.o", "libfoobar.a",
"zig.cpp", "zig.o", "zag.cpp", "zag.o",
"libzigzag.a", "killerapp" };
int main(int,char*[])
{
typedef pair<int,int> Edge;
Edge used_by[] = {
Edge(dax_h, foo_cpp), Edge(dax_h, bar_cpp), Edge(dax_h, yow_h),
Edge(yow_h, bar_cpp), Edge(yow_h, zag_cpp),
Edge(boz_h, bar_cpp), Edge(boz_h, zig_cpp), Edge(boz_h, zag_cpp),
Edge(zow_h, foo_cpp),
Edge(foo_cpp, foo_o),
Edge(foo_o, libfoobar_a),
Edge(bar_cpp, bar_o),
Edge(bar_o, libfoobar_a),
Edge(libfoobar_a, libzigzag_a),
Edge(zig_cpp, zig_o),
Edge(zig_o, libzigzag_a),
Edge(zag_cpp, zag_o),
Edge(zag_o, libzigzag_a),
Edge(libzigzag_a, killerapp)
};
const int nedges = sizeof(used_by)/sizeof(Edge);
typedef adjacency_list< vecS, vecS, directedS,
property< vertex_color_t, string >,
property< edge_weight_t, int >
> Graph;
Graph g(used_by, used_by + nedges, N);
graph_traits<Graph>::vertex_iterator v, v_end;
for (tie(v,v_end) = vertices(g); v != v_end; ++v)
put(vertex_color_t(), g, *v, name[*v]);
graph_traits<Graph>::edge_iterator e, e_end;
for (tie(e,e_end) = edges(g); e != e_end; ++e)
put(edge_weight_t(), g, *e, 3);
dynamic_properties dp;
dp.property("name", get(vertex_color_t(), g));
dp.property("weight", get(edge_weight_t(), g));
write_graphml(std::cout, g, dp, true);
}
The output will be:
::
<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns/graphml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns/graphml http://graphml.graphdrawing.org/xmlns/graphml/graphml-attributes-1.0rc.xsd">
<key id="key0" for="node" attr.name="name" attr.type="string" />
<key id="key1" for="edge" attr.name="weight" attr.type="int" />
<graph id="G" edgedefault="directed" parse.nodeids="canonical" parse.edgeids="canonical" parse.order="nodesfirst">
<node id="n0">
<data key="key0">dax.h</data>
</node>
<node id="n1">
<data key="key0">yow.h</data>
</node>
<node id="n2">
<data key="key0">boz.h</data>
</node>
<node id="n3">
<data key="key0">zow.h</data>
</node>
<node id="n4">
<data key="key0">foo.cpp</data>
</node>
<node id="n5">
<data key="key0">foo.o</data>
</node>
<node id="n6">
<data key="key0">bar.cpp</data>
</node>
<node id="n7">
<data key="key0">bar.o</data>
</node>
<node id="n8">
<data key="key0">libfoobar.a</data>
</node>
<node id="n9">
<data key="key0">zig.cpp</data>
</node>
<node id="n10">
<data key="key0">zig.o</data>
</node>
<node id="n11">
<data key="key0">zag.cpp</data>
</node>
<node id="n12">
<data key="key0">zag.o</data>
</node>
<node id="n13">
<data key="key0">libzigzag.a</data>
</node>
<node id="n14">
<data key="key0">killerapp</data>
</node>
<edge id="e0" source="n0" target="n4">
<data key="key1">3</data>
</edge>
<edge id="e1" source="n0" target="n6">
<data key="key1">3</data>
</edge>
<edge id="e2" source="n0" target="n1">
<data key="key1">3</data>
</edge>
<edge id="e3" source="n1" target="n6">
<data key="key1">3</data>
</edge>
<edge id="e4" source="n1" target="n11">
<data key="key1">3</data>
</edge>
<edge id="e5" source="n2" target="n6">
<data key="key1">3</data>
</edge>
<edge id="e6" source="n2" target="n9">
<data key="key1">3</data>
</edge>
<edge id="e7" source="n2" target="n11">
<data key="key1">3</data>
</edge>
<edge id="e8" source="n3" target="n4">
<data key="key1">3</data>
</edge>
<edge id="e9" source="n4" target="n5">
<data key="key1">3</data>
</edge>
<edge id="e10" source="n5" target="n8">
<data key="key1">3</data>
</edge>
<edge id="e11" source="n6" target="n7">
<data key="key1">3</data>
</edge>
<edge id="e12" source="n7" target="n8">
<data key="key1">3</data>
</edge>
<edge id="e13" source="n8" target="n13">
<data key="key1">3</data>
</edge>
<edge id="e14" source="n9" target="n10">
<data key="key1">3</data>
</edge>
<edge id="e15" source="n10" target="n13">
<data key="key1">3</data>
</edge>
<edge id="e16" source="n11" target="n12">
<data key="key1">3</data>
</edge>
<edge id="e17" source="n12" target="n13">
<data key="key1">3</data>
</edge>
<edge id="e18" source="n13" target="n14">
<data key="key1">3</data>
</edge>
</graph>
</graphml>
See Also
--------
_read_graphml
Notes
-----
- Note that you can use graphml file write facilities without the
library ``libbglgraphml.a``.
.. _graphml: http://graphml.graphdrawing.org/
.. _dynamic_properties: ../../property_map/doc/dynamic_property_map.html
.. _read_graphml: read_graphml.html
.. _VertexListGraph: VertexListGraph.html
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