guppy_basecaller: env/lib/python3.7/site-packages/networkx/readwrite/graphml.py annotate

annotate env/lib/python3.7/site-packages/networkx/readwrite/graphml.py @ 2:6af9afd405e9 draft

"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"

author	shellac
date	Thu, 14 May 2020 14:56:58 -0400
parents	26e78fe6e8c4
children

rev	line source
0 26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1 # Copyright (C) 2008-2019 by
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	2 # Aric Hagberg <hagberg@lanl.gov>
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	3 # Dan Schult <dschult@colgate.edu>
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	4 # Pieter Swart <swart@lanl.gov>
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	5 # All rights reserved.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	6 # BSD license.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	7 #
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	8 # Authors: Salim Fadhley
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	9 # Aric Hagberg (hagberg@lanl.gov)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	10 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	11 *******
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	12 GraphML
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	13 *******
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	14 Read and write graphs in GraphML format.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	15
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	16 This implementation does not support mixed graphs (directed and unidirected
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	17 edges together), hyperedges, nested graphs, or ports.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	18
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	19 "GraphML is a comprehensive and easy-to-use file format for graphs. It
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	20 consists of a language core to describe the structural properties of a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	21 graph and a flexible extension mechanism to add application-specific
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	22 data. Its main features include support of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	23
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	24 * directed, undirected, and mixed graphs,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	25 * hypergraphs,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	26 * hierarchical graphs,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	27 * graphical representations,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	28 * references to external data,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	29 * application-specific attribute data, and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	30 * light-weight parsers.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	31
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	32 Unlike many other file formats for graphs, GraphML does not use a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	33 custom syntax. Instead, it is based on XML and hence ideally suited as
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	34 a common denominator for all kinds of services generating, archiving,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	35 or processing graphs."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	36
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	37 http://graphml.graphdrawing.org/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	38
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	39 Format
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	40 ------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	41 GraphML is an XML format. See
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	42 http://graphml.graphdrawing.org/specification.html for the specification and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	43 http://graphml.graphdrawing.org/primer/graphml-primer.html
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	44 for examples.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	45 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	46 import warnings
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	47 from collections import defaultdict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	48
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	49 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	50 from xml.etree.cElementTree import Element, ElementTree
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	51 from xml.etree.cElementTree import tostring, fromstring
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	52 except ImportError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	53 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	54 from xml.etree.ElementTree import Element, ElementTree
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	55 from xml.etree.ElementTree import tostring, fromstring
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	56 except ImportError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	57 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	58
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	59 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	60 import lxml.etree as lxmletree
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	61 except ImportError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	62 lxmletree = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	63
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	64 import networkx as nx
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	65 from networkx.utils import open_file, make_str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	66
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	67 __all__ = ['write_graphml', 'read_graphml', 'generate_graphml',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	68 'write_graphml_xml', 'write_graphml_lxml',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	69 'parse_graphml', 'GraphMLWriter', 'GraphMLReader']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	70
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	71
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	72 @open_file(1, mode='wb')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	73 def write_graphml_xml(G, path, encoding='utf-8', prettyprint=True,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	74 infer_numeric_types=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	75 """Write G in GraphML XML format to path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	76
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	77 Parameters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	78 ----------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	79 G : graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	80 A networkx graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	81 path : file or string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	82 File or filename to write.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	83 Filenames ending in .gz or .bz2 will be compressed.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	84 encoding : string (optional)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	85 Encoding for text data.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	86 prettyprint : bool (optional)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	87 If True use line breaks and indenting in output XML.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	88 infer_numeric_types : boolean
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	89 Determine if numeric types should be generalized.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	90 For example, if edges have both int and float 'weight' attributes,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	91 we infer in GraphML that both are floats.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	92
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	93 Examples
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	94 --------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	95 >>> G = nx.path_graph(4)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	96 >>> nx.write_graphml(G, "test.graphml")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	97
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	98 Notes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	99 -----
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	100 It may be a good idea in Python2 to convert strings to unicode
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	101 before giving the graph to write_gml. At least the strings with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	102 either many characters to escape.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	103
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	104 This implementation does not support mixed graphs (directed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	105 and unidirected edges together) hyperedges, nested graphs, or ports.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	106 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	107 writer = GraphMLWriter(encoding=encoding, prettyprint=prettyprint,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	108 infer_numeric_types=infer_numeric_types)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	109 writer.add_graph_element(G)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	110 writer.dump(path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	111
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	112
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	113 @open_file(1, mode='wb')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	114 def write_graphml_lxml(G, path, encoding='utf-8', prettyprint=True,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	115 infer_numeric_types=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	116 """Write G in GraphML XML format to path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	117
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	118 This function uses the LXML framework and should be faster than
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	119 the version using the xml library.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	120
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	121 Parameters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	122 ----------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	123 G : graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	124 A networkx graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	125 path : file or string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	126 File or filename to write.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	127 Filenames ending in .gz or .bz2 will be compressed.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	128 encoding : string (optional)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	129 Encoding for text data.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	130 prettyprint : bool (optional)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	131 If True use line breaks and indenting in output XML.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	132 infer_numeric_types : boolean
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	133 Determine if numeric types should be generalized.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	134 For example, if edges have both int and float 'weight' attributes,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	135 we infer in GraphML that both are floats.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	136
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	137 Examples
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	138 --------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	139 >>> G = nx.path_graph(4)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	140 >>> nx.write_graphml_lxml(G, "fourpath.graphml") # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	141
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	142 Notes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	143 -----
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	144 This implementation does not support mixed graphs (directed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	145 and unidirected edges together) hyperedges, nested graphs, or ports.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	146 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	147 writer = GraphMLWriterLxml(path, graph=G, encoding=encoding,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	148 prettyprint=prettyprint,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	149 infer_numeric_types=infer_numeric_types)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	150 writer.dump()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	151
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	152
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	153 def generate_graphml(G, encoding='utf-8', prettyprint=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	154 """Generate GraphML lines for G
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	155
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	156 Parameters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	157 ----------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	158 G : graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	159 A networkx graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	160 encoding : string (optional)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	161 Encoding for text data.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	162 prettyprint : bool (optional)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	163 If True use line breaks and indenting in output XML.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	164
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	165 Examples
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	166 --------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	167 >>> G = nx.path_graph(4)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	168 >>> linefeed = chr(10) # linefeed = \n
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	169 >>> s = linefeed.join(nx.generate_graphml(G)) # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	170 >>> for line in nx.generate_graphml(G): # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	171 ... print(line)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	172
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	173 Notes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	174 -----
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	175 This implementation does not support mixed graphs (directed and unidirected
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	176 edges together) hyperedges, nested graphs, or ports.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	177 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	178 writer = GraphMLWriter(encoding=encoding, prettyprint=prettyprint)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	179 writer.add_graph_element(G)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	180 for line in str(writer).splitlines():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	181 yield line
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	182
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	183
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	184 @open_file(0, mode='rb')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	185 def read_graphml(path, node_type=str, edge_key_type=int):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	186 """Read graph in GraphML format from path.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	187
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	188 Parameters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	189 ----------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	190 path : file or string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	191 File or filename to write.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	192 Filenames ending in .gz or .bz2 will be compressed.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	193
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	194 node_type: Python type (default: str)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	195 Convert node ids to this type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	196
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	197 edge_key_type: Python type (default: int)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	198 Convert graphml edge ids to this type as key of multi-edges
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	199
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	200
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	201 Returns
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	202 -------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	203 graph: NetworkX graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	204 If no parallel edges are found a Graph or DiGraph is returned.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	205 Otherwise a MultiGraph or MultiDiGraph is returned.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	206
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	207 Notes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	208 -----
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	209 Default node and edge attributes are not propagated to each node and edge.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	210 They can be obtained from `G.graph` and applied to node and edge attributes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	211 if desired using something like this:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	212
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	213 >>> default_color = G.graph['node_default']['color'] # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	214 >>> for node, data in G.nodes(data=True): # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	215 ... if 'color' not in data:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	216 ... data['color']=default_color
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	217 >>> default_color = G.graph['edge_default']['color'] # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	218 >>> for u, v, data in G.edges(data=True): # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	219 ... if 'color' not in data:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	220 ... data['color']=default_color
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	221
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	222 This implementation does not support mixed graphs (directed and unidirected
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	223 edges together), hypergraphs, nested graphs, or ports.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	224
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	225 For multigraphs the GraphML edge "id" will be used as the edge
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	226 key. If not specified then they "key" attribute will be used. If
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	227 there is no "key" attribute a default NetworkX multigraph edge key
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	228 will be provided.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	229
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	230 Files with the yEd "yfiles" extension will can be read but the graphics
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	231 information is discarded.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	232
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	233 yEd compressed files ("file.graphmlz" extension) can be read by renaming
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	234 the file to "file.graphml.gz".
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	235
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	236 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	237 reader = GraphMLReader(node_type=node_type, edge_key_type=edge_key_type)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	238 # need to check for multiple graphs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	239 glist = list(reader(path=path))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	240 if len(glist) == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	241 # If no graph comes back, try looking for an incomplete header
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	242 header = b'<graphml xmlns="http://graphml.graphdrawing.org/xmlns">'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	243 path.seek(0)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	244 old_bytes = path.read()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	245 new_bytes = old_bytes.replace(b'<graphml>', header)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	246 glist = list(reader(string=new_bytes))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	247 if len(glist) == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	248 raise nx.NetworkXError('file not successfully read as graphml')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	249 return glist[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	250
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	251
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	252 def parse_graphml(graphml_string, node_type=str):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	253 """Read graph in GraphML format from string.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	254
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	255 Parameters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	256 ----------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	257 graphml_string : string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	258 String containing graphml information
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	259 (e.g., contents of a graphml file).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	260
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	261 node_type: Python type (default: str)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	262 Convert node ids to this type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	263
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	264 Returns
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	265 -------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	266 graph: NetworkX graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	267 If no parallel edges are found a Graph or DiGraph is returned.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	268 Otherwise a MultiGraph or MultiDiGraph is returned.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	269
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	270 Examples
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	271 --------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	272 >>> G = nx.path_graph(4)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	273 >>> linefeed = chr(10) # linefeed = \n
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	274 >>> s = linefeed.join(nx.generate_graphml(G))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	275 >>> H = nx.parse_graphml(s)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	276
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	277 Notes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	278 -----
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	279 Default node and edge attributes are not propagated to each node and edge.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	280 They can be obtained from `G.graph` and applied to node and edge attributes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	281 if desired using something like this:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	282
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	283 >>> default_color = G.graph['node_default']['color'] # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	284 >>> for node, data in G.nodes(data=True): # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	285 ... if 'color' not in data:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	286 ... data['color']=default_color
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	287 >>> default_color = G.graph['edge_default']['color'] # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	288 >>> for u, v, data in G.edges(data=True): # doctest: +SKIP
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	289 ... if 'color' not in data:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	290 ... data['color']=default_color
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	291
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	292 This implementation does not support mixed graphs (directed and unidirected
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	293 edges together), hypergraphs, nested graphs, or ports.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	294
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	295 For multigraphs the GraphML edge "id" will be used as the edge
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	296 key. If not specified then they "key" attribute will be used. If
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	297 there is no "key" attribute a default NetworkX multigraph edge key
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	298 will be provided.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	299
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	300 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	301 reader = GraphMLReader(node_type=node_type)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	302 # need to check for multiple graphs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	303 glist = list(reader(string=graphml_string))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	304 if len(glist) == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	305 # If no graph comes back, try looking for an incomplete header
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	306 header = '<graphml xmlns="http://graphml.graphdrawing.org/xmlns">'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	307 new_string = graphml_string.replace('<graphml>', header)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	308 glist = list(reader(string=new_string))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	309 if len(glist) == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	310 raise nx.NetworkXError('file not successfully read as graphml')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	311 return glist[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	312
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	313
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	314 class GraphML(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	315 NS_GRAPHML = "http://graphml.graphdrawing.org/xmlns"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	316 NS_XSI = "http://www.w3.org/2001/XMLSchema-instance"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	317 # xmlns:y="http://www.yworks.com/xml/graphml"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	318 NS_Y = "http://www.yworks.com/xml/graphml"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	319 SCHEMALOCATION = \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	320 ' '.join(['http://graphml.graphdrawing.org/xmlns',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	321 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	322
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	323 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	324 chr(12345) # Fails on Py!=3.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	325 unicode = str # Py3k's str is our unicode type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	326 long = int # Py3K's int is our long type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	327 except ValueError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	328 # Python 2.x
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	329 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	330
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	331 types = [(int, "integer"), # for Gephi GraphML bug
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	332 (str, "yfiles"), (str, "string"), (unicode, "string"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	333 (int, "int"), (long, "long"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	334 (float, "float"), (float, "double"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	335 (bool, "boolean")]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	336
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	337 # These additions to types allow writing numpy types
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	338 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	339 import numpy as np
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	340 except:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	341 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	342 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	343 # prepend so that python types are created upon read (last entry wins)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	344 types = [(np.float64, "float"), (np.float32, "float"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	345 (np.float16, "float"), (np.float_, "float"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	346 (np.int, "int"), (np.int8, "int"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	347 (np.int16, "int"), (np.int32, "int"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	348 (np.int64, "int"), (np.uint8, "int"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	349 (np.uint16, "int"), (np.uint32, "int"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	350 (np.uint64, "int"), (np.int_, "int"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	351 (np.intc, "int"), (np.intp, "int"),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	352 ] + types
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	353
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	354 xml_type = dict(types)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	355 python_type = dict(reversed(a) for a in types)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	356
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	357 # This page says that data types in GraphML follow Java(TM).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	358 # http://graphml.graphdrawing.org/primer/graphml-primer.html#AttributesDefinition
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	359 # true and false are the only boolean literals:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	360 # http://en.wikibooks.org/wiki/Java_Programming/Literals#Boolean_Literals
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	361 convert_bool = {
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	362 # We use data.lower() in actual use.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	363 'true': True, 'false': False,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	364 # Include integer strings for convenience.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	365 '0': False, 0: False,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	366 '1': True, 1: True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	367 }
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	368
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	369
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	370 class GraphMLWriter(GraphML):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	371 def __init__(self, graph=None, encoding="utf-8", prettyprint=True,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	372 infer_numeric_types=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	373 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	374 import xml.etree.ElementTree
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	375 except ImportError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	376 msg = 'GraphML writer requires xml.elementtree.ElementTree'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	377 raise ImportError(msg)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	378 self.myElement = Element
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	379
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	380 self.infer_numeric_types = infer_numeric_types
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	381 self.prettyprint = prettyprint
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	382 self.encoding = encoding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	383 self.xml = self.myElement("graphml",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	384 {'xmlns': self.NS_GRAPHML,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	385 'xmlns:xsi': self.NS_XSI,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	386 'xsi:schemaLocation': self.SCHEMALOCATION})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	387 self.keys = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	388 self.attributes = defaultdict(list)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	389 self.attribute_types = defaultdict(set)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	390
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	391 if graph is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	392 self.add_graph_element(graph)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	393
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	394 def __str__(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	395 if self.prettyprint:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	396 self.indent(self.xml)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	397 s = tostring(self.xml).decode(self.encoding)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	398 return s
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	399
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	400 def attr_type(self, name, scope, value):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	401 """Infer the attribute type of data named name. Currently this only
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	402 supports inference of numeric types.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	403
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	404 If self.infer_numeric_types is false, type is used. Otherwise, pick the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	405 most general of types found across all values with name and scope. This
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	406 means edges with data named 'weight' are treated separately from nodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	407 with data named 'weight'.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	408 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	409 if self.infer_numeric_types:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	410 types = self.attribute_types[(name, scope)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	411
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	412 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	413 chr(12345) # Fails on Py<3.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	414 local_long = int # Py3's int is Py2's long type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	415 local_unicode = str # Py3's str is Py2's unicode type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	416 except ValueError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	417 # Python 2.x
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	418 local_long = long
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	419 local_unicode = unicode
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	420
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	421 if len(types) > 1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	422 if str in types:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	423 return str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	424 elif local_unicode in types:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	425 return local_unicode
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	426 elif float in types:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	427 return float
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	428 elif local_long in types:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	429 return local_long
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	430 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	431 return int
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	432 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	433 return list(types)[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	434 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	435 return type(value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	436
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	437 def get_key(self, name, attr_type, scope, default):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	438 keys_key = (name, attr_type, scope)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	439 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	440 return self.keys[keys_key]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	441 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	442 new_id = "d%i" % len(list(self.keys))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	443 self.keys[keys_key] = new_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	444 key_kwargs = {"id": new_id,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	445 "for": scope,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	446 "attr.name": name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	447 "attr.type": attr_type}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	448 key_element = self.myElement("key", **key_kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	449 # add subelement for data default value if present
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	450 if default is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	451 default_element = self.myElement("default")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	452 default_element.text = make_str(default)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	453 key_element.append(default_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	454 self.xml.insert(0, key_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	455 return new_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	456
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	457 def add_data(self, name, element_type, value,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	458 scope="all",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	459 default=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	460 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	461 Make a data element for an edge or a node. Keep a log of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	462 type in the keys table.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	463 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	464 if element_type not in self.xml_type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	465 msg = 'GraphML writer does not support %s as data values.'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	466 raise nx.NetworkXError(msg % element_type)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	467 keyid = self.get_key(name, self.xml_type[element_type], scope, default)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	468 data_element = self.myElement("data", key=keyid)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	469 data_element.text = make_str(value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	470 return data_element
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	471
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	472 def add_attributes(self, scope, xml_obj, data, default):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	473 """Appends attribute data to edges or nodes, and stores type information
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	474 to be added later. See add_graph_element.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	475 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	476 for k, v in data.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	477 self.attribute_types[(make_str(k), scope)].add(type(v))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	478 self.attributes[xml_obj].append([k, v, scope, default.get(k)])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	479
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	480 def add_nodes(self, G, graph_element):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	481 default = G.graph.get('node_default', {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	482 for node, data in G.nodes(data=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	483 node_element = self.myElement("node", id=make_str(node))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	484 self.add_attributes("node", node_element, data, default)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	485 graph_element.append(node_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	486
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	487 def add_edges(self, G, graph_element):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	488 if G.is_multigraph():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	489 for u, v, key, data in G.edges(data=True, keys=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	490 edge_element = self.myElement("edge", source=make_str(u),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	491 target=make_str(v),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	492 id=make_str(key))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	493 default = G.graph.get('edge_default', {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	494 self.add_attributes("edge", edge_element, data, default)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	495 graph_element.append(edge_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	496 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	497 for u, v, data in G.edges(data=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	498 edge_element = self.myElement("edge", source=make_str(u),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	499 target=make_str(v))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	500 default = G.graph.get('edge_default', {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	501 self.add_attributes("edge", edge_element, data, default)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	502 graph_element.append(edge_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	503
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	504 def add_graph_element(self, G):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	505 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	506 Serialize graph G in GraphML to the stream.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	507 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	508 if G.is_directed():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	509 default_edge_type = 'directed'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	510 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	511 default_edge_type = 'undirected'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	512
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	513 graphid = G.graph.pop('id', None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	514 if graphid is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	515 graph_element = self.myElement("graph",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	516 edgedefault=default_edge_type)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	517 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	518 graph_element = self.myElement("graph",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	519 edgedefault=default_edge_type,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	520 id=graphid)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	521 default = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	522 data = {k: v for (k, v) in G.graph.items()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	523 if k not in ['node_default', 'edge_default']}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	524 self.add_attributes("graph", graph_element, data, default)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	525 self.add_nodes(G, graph_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	526 self.add_edges(G, graph_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	527
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	528 # self.attributes contains a mapping from XML Objects to a list of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	529 # data that needs to be added to them.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	530 # We postpone processing in order to do type inference/generalization.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	531 # See self.attr_type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	532 for (xml_obj, data) in self.attributes.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	533 for (k, v, scope, default) in data:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	534 xml_obj.append(self.add_data(make_str(k),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	535 self.attr_type(k, scope, v),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	536 make_str(v), scope, default))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	537 self.xml.append(graph_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	538
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	539 def add_graphs(self, graph_list):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	540 """ Add many graphs to this GraphML document. """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	541 for G in graph_list:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	542 self.add_graph_element(G)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	543
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	544 def dump(self, stream):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	545 if self.prettyprint:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	546 self.indent(self.xml)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	547 document = ElementTree(self.xml)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	548 document.write(stream, encoding=self.encoding, xml_declaration=True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	549
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	550 def indent(self, elem, level=0):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	551 # in-place prettyprint formatter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	552 i = "\n" + level * " "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	553 if len(elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	554 if not elem.text or not elem.text.strip():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	555 elem.text = i + " "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	556 if not elem.tail or not elem.tail.strip():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	557 elem.tail = i
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	558 for elem in elem:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	559 self.indent(elem, level + 1)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	560 if not elem.tail or not elem.tail.strip():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	561 elem.tail = i
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	562 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	563 if level and (not elem.tail or not elem.tail.strip()):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	564 elem.tail = i
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	565
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	566
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	567 class IncrementalElement(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	568 """Wrapper for _IncrementalWriter providing an Element like interface.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	569
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	570 This wrapper does not intend to be a complete implementation but rather to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	571 deal with those calls used in GraphMLWriter.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	572 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	573
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	574 def __init__(self, xml, prettyprint):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	575 self.xml = xml
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	576 self.prettyprint = prettyprint
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	577
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	578 def append(self, element):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	579 self.xml.write(element, pretty_print=self.prettyprint)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	580
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	581
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	582 class GraphMLWriterLxml(GraphMLWriter):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	583 def __init__(self, path, graph=None, encoding='utf-8', prettyprint=True,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	584 infer_numeric_types=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	585 self.myElement = lxmletree.Element
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	586
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	587 self._encoding = encoding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	588 self._prettyprint = prettyprint
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	589 self.infer_numeric_types = infer_numeric_types
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	590
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	591 self._xml_base = lxmletree.xmlfile(path, encoding=encoding)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	592 self._xml = self._xml_base.__enter__()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	593 self._xml.write_declaration()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	594
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	595 # We need to have a xml variable that support insertion. This call is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	596 # used for adding the keys to the document.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	597 # We will store those keys in a plain list, and then after the graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	598 # element is closed we will add them to the main graphml element.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	599 self.xml = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	600 self._keys = self.xml
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	601 self._graphml = self._xml.element(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	602 'graphml',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	603 {
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	604 'xmlns': self.NS_GRAPHML,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	605 'xmlns:xsi': self.NS_XSI,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	606 'xsi:schemaLocation': self.SCHEMALOCATION
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	607 })
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	608 self._graphml.__enter__()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	609 self.keys = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	610 self.attribute_types = defaultdict(set)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	611
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	612 if graph is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	613 self.add_graph_element(graph)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	614
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	615 def add_graph_element(self, G):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	616 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	617 Serialize graph G in GraphML to the stream.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	618 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	619 if G.is_directed():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	620 default_edge_type = 'directed'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	621 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	622 default_edge_type = 'undirected'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	623
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	624 graphid = G.graph.pop('id', None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	625 if graphid is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	626 graph_element = self._xml.element('graph',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	627 edgedefault=default_edge_type)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	628 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	629 graph_element = self._xml.element('graph',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	630 edgedefault=default_edge_type,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	631 id=graphid)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	632
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	633 # gather attributes types for the whole graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	634 # to find the most general numeric format needed.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	635 # Then pass through attributes to create key_id for each.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	636 graphdata = {k: v for k, v in G.graph.items()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	637 if k not in ('node_default', 'edge_default')}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	638 node_default = G.graph.get('node_default', {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	639 edge_default = G.graph.get('edge_default', {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	640 # Graph attributes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	641 for k, v in graphdata.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	642 self.attribute_types[(make_str(k), "graph")].add(type(v))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	643 for k, v in graphdata.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	644 element_type = self.xml_type[self.attr_type(k, "graph", v)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	645 self.get_key(make_str(k), element_type, "graph", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	646 # Nodes and data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	647 for node, d in G.nodes(data=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	648 for k, v in d.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	649 self.attribute_types[(make_str(k), "node")].add(type(v))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	650 for node, d in G.nodes(data=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	651 for k, v in d.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	652 T = self.xml_type[self.attr_type(k, "node", v)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	653 self.get_key(make_str(k), T, "node", node_default.get(k))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	654 # Edges and data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	655 if G.is_multigraph():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	656 for u, v, ekey, d in G.edges(keys=True, data=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	657 for k, v in d.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	658 self.attribute_types[(make_str(k), "edge")].add(type(v))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	659 for u, v, ekey, d in G.edges(keys=True, data=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	660 for k, v in d.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	661 T = self.xml_type[self.attr_type(k, "edge", v)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	662 self.get_key(make_str(k), T, "edge", edge_default.get(k))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	663 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	664 for u, v, d in G.edges(data=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	665 for k, v in d.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	666 self.attribute_types[(make_str(k), "edge")].add(type(v))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	667 for u, v, d in G.edges(data=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	668 for k, v in d.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	669 T = self.xml_type[self.attr_type(k, "edge", v)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	670 self.get_key(make_str(k), T, "edge", edge_default.get(k))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	671
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	672 # Now add attribute keys to the xml file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	673 for key in self.xml:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	674 self._xml.write(key, pretty_print=self._prettyprint)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	675
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	676 # The incremental_writer writes each node/edge as it is created
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	677 incremental_writer = IncrementalElement(self._xml, self._prettyprint)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	678 with graph_element:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	679 self.add_attributes('graph', incremental_writer, graphdata, {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	680 self.add_nodes(G, incremental_writer) # adds attributes too
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	681 self.add_edges(G, incremental_writer) # adds attributes too
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	682
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	683 def add_attributes(self, scope, xml_obj, data, default):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	684 """Appends attribute data."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	685 for k, v in data.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	686 data_element = self.add_data(make_str(k),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	687 self.attr_type(make_str(k), scope, v),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	688 make_str(v), scope, default.get(k))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	689 xml_obj.append(data_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	690
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	691 def __str__(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	692 return object.__str__(self)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	693
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	694 def dump(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	695 self._graphml.__exit__(None, None, None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	696 self._xml_base.__exit__(None, None, None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	697
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	698
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	699 # Choose a writer function for default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	700 if lxmletree is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	701 write_graphml = write_graphml_xml
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	702 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	703 write_graphml = write_graphml_lxml
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	704
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	705
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	706 class GraphMLReader(GraphML):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	707 """Read a GraphML document. Produces NetworkX graph objects."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	708
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	709 def __init__(self, node_type=str, edge_key_type=int):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	710 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	711 import xml.etree.ElementTree
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	712 except ImportError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	713 msg = 'GraphML reader requires xml.elementtree.ElementTree'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	714 raise ImportError(msg)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	715 self.node_type = node_type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	716 self.edge_key_type = edge_key_type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	717 self.multigraph = False # assume multigraph and test for multiedges
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	718 self.edge_ids = {} # dict mapping (u,v) tuples to id edge attributes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	719
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	720 def __call__(self, path=None, string=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	721 if path is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	722 self.xml = ElementTree(file=path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	723 elif string is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	724 self.xml = fromstring(string)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	725 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	726 raise ValueError("Must specify either 'path' or 'string' as kwarg")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	727 (keys, defaults) = self.find_graphml_keys(self.xml)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	728 for g in self.xml.findall("{%s}graph" % self.NS_GRAPHML):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	729 yield self.make_graph(g, keys, defaults)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	730
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	731 def make_graph(self, graph_xml, graphml_keys, defaults, G=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	732 # set default graph type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	733 edgedefault = graph_xml.get("edgedefault", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	734 if G is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	735 if edgedefault == 'directed':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	736 G = nx.MultiDiGraph()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	737 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	738 G = nx.MultiGraph()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	739 # set defaults for graph attributes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	740 G.graph['node_default'] = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	741 G.graph['edge_default'] = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	742 for key_id, value in defaults.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	743 key_for = graphml_keys[key_id]['for']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	744 name = graphml_keys[key_id]['name']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	745 python_type = graphml_keys[key_id]['type']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	746 if key_for == 'node':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	747 G.graph['node_default'].update({name: python_type(value)})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	748 if key_for == 'edge':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	749 G.graph['edge_default'].update({name: python_type(value)})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	750 # hyperedges are not supported
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	751 hyperedge = graph_xml.find("{%s}hyperedge" % self.NS_GRAPHML)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	752 if hyperedge is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	753 raise nx.NetworkXError("GraphML reader doesn't support hyperedges")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	754 # add nodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	755 for node_xml in graph_xml.findall("{%s}node" % self.NS_GRAPHML):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	756 self.add_node(G, node_xml, graphml_keys, defaults)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	757 # add edges
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	758 for edge_xml in graph_xml.findall("{%s}edge" % self.NS_GRAPHML):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	759 self.add_edge(G, edge_xml, graphml_keys)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	760 # add graph data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	761 data = self.decode_data_elements(graphml_keys, graph_xml)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	762 G.graph.update(data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	763
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	764 # switch to Graph or DiGraph if no parallel edges were found.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	765 if not self.multigraph:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	766 if G.is_directed():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	767 G = nx.DiGraph(G)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	768 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	769 G = nx.Graph(G)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	770 nx.set_edge_attributes(G, values=self.edge_ids, name='id')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	771
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	772 return G
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	773
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	774 def add_node(self, G, node_xml, graphml_keys, defaults):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	775 """Add a node to the graph.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	776 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	777 # warn on finding unsupported ports tag
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	778 ports = node_xml.find("{%s}port" % self.NS_GRAPHML)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	779 if ports is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	780 warnings.warn("GraphML port tag not supported.")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	781 # find the node by id and cast it to the appropriate type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	782 node_id = self.node_type(node_xml.get("id"))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	783 # get data/attributes for node
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	784 data = self.decode_data_elements(graphml_keys, node_xml)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	785 G.add_node(node_id, **data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	786 # get child nodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	787 if node_xml.attrib.get('yfiles.foldertype') == 'group':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	788 graph_xml = node_xml.find("{%s}graph" % self.NS_GRAPHML)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	789 self.make_graph(graph_xml, graphml_keys, defaults, G)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	790
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	791 def add_edge(self, G, edge_element, graphml_keys):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	792 """Add an edge to the graph.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	793 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	794 # warn on finding unsupported ports tag
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	795 ports = edge_element.find("{%s}port" % self.NS_GRAPHML)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	796 if ports is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	797 warnings.warn("GraphML port tag not supported.")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	798
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	799 # raise error if we find mixed directed and undirected edges
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	800 directed = edge_element.get("directed")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	801 if G.is_directed() and directed == 'false':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	802 msg = "directed=false edge found in directed graph."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	803 raise nx.NetworkXError(msg)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	804 if (not G.is_directed()) and directed == 'true':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	805 msg = "directed=true edge found in undirected graph."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	806 raise nx.NetworkXError(msg)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	807
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	808 source = self.node_type(edge_element.get("source"))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	809 target = self.node_type(edge_element.get("target"))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	810 data = self.decode_data_elements(graphml_keys, edge_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	811 # GraphML stores edge ids as an attribute
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	812 # NetworkX uses them as keys in multigraphs too if no key
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	813 # attribute is specified
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	814 edge_id = edge_element.get("id")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	815 if edge_id:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	816 # self.edge_ids is used by `make_graph` method for non-multigraphs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	817 self.edge_ids[source, target] = edge_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	818 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	819 edge_id = self.edge_key_type(edge_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	820 except ValueError: # Could not convert.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	821 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	822 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	823 edge_id = data.get('key')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	824
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	825 if G.has_edge(source, target):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	826 # mark this as a multigraph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	827 self.multigraph = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	828
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	829 # Use add_edges_from to avoid error with add_edge when `'key' in data`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	830 G.add_edges_from([(source, target, edge_id, data)])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	831
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	832 def decode_data_elements(self, graphml_keys, obj_xml):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	833 """Use the key information to decode the data XML if present."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	834 data = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	835 for data_element in obj_xml.findall("{%s}data" % self.NS_GRAPHML):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	836 key = data_element.get("key")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	837 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	838 data_name = graphml_keys[key]['name']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	839 data_type = graphml_keys[key]['type']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	840 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	841 raise nx.NetworkXError("Bad GraphML data: no key %s" % key)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	842 text = data_element.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	843 # assume anything with subelements is a yfiles extension
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	844 if text is not None and len(list(data_element)) == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	845 if data_type == bool:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	846 # Ignore cases.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	847 # http://docs.oracle.com/javase/6/docs/api/java/lang/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	848 # Boolean.html#parseBoolean%28java.lang.String%29
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	849 data[data_name] = self.convert_bool[text.lower()]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	850 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	851 data[data_name] = data_type(text)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	852 elif len(list(data_element)) > 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	853 # Assume yfiles as subelements, try to extract node_label
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	854 node_label = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	855 for node_type in ['ShapeNode', 'SVGNode', 'ImageNode']:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	856 pref = "{%s}%s/{%s}" % (self.NS_Y, node_type, self.NS_Y)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	857 geometry = data_element.find("%sGeometry" % pref)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	858 if geometry is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	859 data['x'] = geometry.get('x')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	860 data['y'] = geometry.get('y')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	861 if node_label is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	862 node_label = data_element.find("%sNodeLabel" % pref)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	863 if node_label is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	864 data['label'] = node_label.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	865
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	866 # check all the different types of edges avaivable in yEd.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	867 for e in ['PolyLineEdge', 'SplineEdge', 'QuadCurveEdge',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	868 'BezierEdge', 'ArcEdge']:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	869 pref = "{%s}%s/{%s}" % (self.NS_Y, e, self.NS_Y)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	870 edge_label = data_element.find("%sEdgeLabel" % pref)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	871 if edge_label is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	872 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	873
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	874 if edge_label is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	875 data['label'] = edge_label.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	876 return data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	877
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	878 def find_graphml_keys(self, graph_element):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	879 """Extracts all the keys and key defaults from the xml.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	880 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	881 graphml_keys = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	882 graphml_key_defaults = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	883 for k in graph_element.findall("{%s}key" % self.NS_GRAPHML):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	884 attr_id = k.get("id")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	885 attr_type = k.get('attr.type')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	886 attr_name = k.get("attr.name")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	887 yfiles_type = k.get("yfiles.type")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	888 if yfiles_type is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	889 attr_name = yfiles_type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	890 attr_type = 'yfiles'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	891 if attr_type is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	892 attr_type = "string"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	893 warnings.warn("No key type for id %s. Using string" % attr_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	894 if attr_name is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	895 raise nx.NetworkXError("Unknown key for id %s." % attr_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	896 graphml_keys[attr_id] = {"name": attr_name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	897 "type": self.python_type[attr_type],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	898 "for": k.get("for")}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	899 # check for "default" subelement of key element
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	900 default = k.find("{%s}default" % self.NS_GRAPHML)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	901 if default is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	902 graphml_key_defaults[attr_id] = default.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	903 return graphml_keys, graphml_key_defaults
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	904
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	905
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	906 # fixture for pytest
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	907 def setup_module(module):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	908 import pytest
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	909 xml.etree.ElementTree = pytest.importorskip('xml.etree.ElementTree')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	910
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	911
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	912 # fixture for pytest
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	913 def teardown_module(module):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	914 import os
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	915 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	916 os.unlink('test.graphml')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	917 except:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	918 pass

Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/networkx/readwrite/graphml.py @ 2:6af9afd405e9 draft