graphkit-learn/gklearn/utils/graphfiles.py

""" Utilities function to manage graph files
"""
from os.path import dirname, splitext

def loadCT(filename):
	"""load data from a Chemical Table (.ct) file.

	Notes
	------
	a typical example of data in .ct is like this:

	3 2  <- number of nodes and edges

	0.0000	0.0000	0.0000 C <- each line describes a node (x,y,z + label)

	0.0000	0.0000	0.0000 C

	0.0000	0.0000	0.0000 O

	1  3  1  1 <- each line describes an edge : to, from, bond type, bond stereo

	2  3  1  1
	  
	Check `CTFile Formats file <https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=2ahUKEwivhaSdjsTlAhVhx4UKHczHA8gQFjAJegQIARAC&url=https%3A%2F%2Fwww.daylight.com%2Fmeetings%2Fmug05%2FKappler%2Fctfile.pdf&usg=AOvVaw1cDNrrmMClkFPqodlF2inS>`__
	for detailed format discription.
	"""
	import networkx as nx
	from os.path import basename
	g = nx.Graph()
	with open(filename) as f:
		content = f.read().splitlines()
		g = nx.Graph(
			name = str(content[0]),
			filename = basename(filename))  # set name of the graph
		tmp = content[1].split(" ")
		if tmp[0] == '':
			nb_nodes = int(tmp[1])  # number of the nodes
			nb_edges = int(tmp[2])  # number of the edges
		else:
			nb_nodes = int(tmp[0])
			nb_edges = int(tmp[1])
			# patch for compatibility : label will be removed later
		for i in range(0, nb_nodes):
			tmp = content[i + 2].split(" ")
			tmp = [x for x in tmp if x != '']
			g.add_node(i, atom=tmp[3].strip(), 
					   label=[item.strip() for item in tmp[3:]], 
					   attributes=[item.strip() for item in tmp[0:3]])
		for i in range(0, nb_edges):
			tmp = content[i + g.number_of_nodes() + 2].split(" ")
			tmp = [x for x in tmp if x != '']
			g.add_edge(int(tmp[0]) - 1, int(tmp[1]) - 1,
					   bond_type=tmp[2].strip(),
					   label=[item.strip() for item in tmp[2:]])
	return g


def loadGXL(filename):
	from os.path import basename
	import networkx as nx
	import xml.etree.ElementTree as ET

	tree = ET.parse(filename)
	root = tree.getroot()
	index = 0
	g = nx.Graph(filename=basename(filename), name=root[0].attrib['id'])
	dic = {}  # used to retrieve incident nodes of edges
	for node in root.iter('node'):
		dic[node.attrib['id']] = index
		labels = {}
		for attr in node.iter('attr'):
			labels[attr.attrib['name']] = attr[0].text
		if 'chem' in labels:
			labels['label'] = labels['chem']
			labels['atom'] = labels['chem']
		g.add_node(index, **labels)
		index += 1

	for edge in root.iter('edge'):
		labels = {}
		for attr in edge.iter('attr'):
			labels[attr.attrib['name']] = attr[0].text
		if 'valence' in labels:
			labels['label'] = labels['valence']
			labels['bond_type'] = labels['valence']
		g.add_edge(dic[edge.attrib['from']], dic[edge.attrib['to']], **labels)
	return g


def saveGXL(graph, filename, method='default', node_labels=[], edge_labels=[], node_attrs=[], edge_attrs=[]):
	if method == 'default':
		gxl_file = open(filename, 'w')
		gxl_file.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
		gxl_file.write("<!DOCTYPE gxl SYSTEM \"http://www.gupro.de/GXL/gxl-1.0.dtd\">\n")
		gxl_file.write("<gxl xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n")
		if 'name' in graph.graph:
			name = str(graph.graph['name'])
		else:
			name = 'dummy'
		gxl_file.write("<graph id=\"" + name + "\" edgeids=\"false\" edgemode=\"undirected\">\n")
		for v, attrs in graph.nodes(data=True):
			gxl_file.write("<node id=\"_" + str(v) + "\">")
			for l_name in node_labels:	
				gxl_file.write("<attr name=\"" + l_name + "\"><int>" + 
							   str(attrs[l_name]) + "</int></attr>")
			for a_name in node_attrs:	
				gxl_file.write("<attr name=\"" + a_name + "\"><float>" + 
							   str(attrs[a_name]) + "</float></attr>")
			gxl_file.write("</node>\n")
		for v1, v2, attrs in graph.edges(data=True):
			gxl_file.write("<edge from=\"_" + str(v1) + "\" to=\"_" + str(v2) + "\">")
			for l_name in edge_labels:	
				gxl_file.write("<attr name=\"" + l_name + "\"><int>" + 
							   str(attrs[l_name]) + "</int></attr>")
			for a_name in edge_attrs:	
				gxl_file.write("<attr name=\"" + a_name + "\"><float>" + 
							   str(attrs[a_name]) + "</float></attr>")
			gxl_file.write("</edge>\n")
		gxl_file.write("</graph>\n")
		gxl_file.write("</gxl>")
		gxl_file.close()
	elif method == 'benoit':
		import xml.etree.ElementTree as ET
		root_node = ET.Element('gxl')
		attr = dict()
		attr['id'] = str(graph.graph['name'])
		attr['edgeids'] = 'true'
		attr['edgemode'] = 'undirected'
		graph_node = ET.SubElement(root_node, 'graph', attrib=attr)
	
		for v in graph:
			current_node = ET.SubElement(graph_node, 'node', attrib={'id': str(v)})
			for attr in graph.nodes[v].keys():
				cur_attr = ET.SubElement(
					current_node, 'attr', attrib={'name': attr})
				cur_value = ET.SubElement(cur_attr,
										  graph.nodes[v][attr].__class__.__name__)
				cur_value.text = graph.nodes[v][attr]
	
		for v1 in graph:
			for v2 in graph[v1]:
				if (v1 < v2):  # Non oriented graphs
					cur_edge = ET.SubElement(
						graph_node,
						'edge',
						attrib={
							'from': str(v1),
							'to': str(v2)
						})
					for attr in graph[v1][v2].keys():
						cur_attr = ET.SubElement(
							cur_edge, 'attr', attrib={'name': attr})
						cur_value = ET.SubElement(
							cur_attr, graph[v1][v2][attr].__class__.__name__)
						cur_value.text = str(graph[v1][v2][attr])
	
		tree = ET.ElementTree(root_node)
		tree.write(filename)
	elif method == 'gedlib':
		# reference: https://github.com/dbblumenthal/gedlib/blob/master/data/generate_molecules.py#L22
#		pass
		gxl_file = open(filename, 'w')
		gxl_file.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
		gxl_file.write("<!DOCTYPE gxl SYSTEM \"http://www.gupro.de/GXL/gxl-1.0.dtd\">\n")
		gxl_file.write("<gxl xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n")
		gxl_file.write("<graph id=\"" + str(graph.graph['name']) + "\" edgeids=\"true\" edgemode=\"undirected\">\n")
		for v, attrs in graph.nodes(data=True):
			gxl_file.write("<node id=\"_" + str(v) + "\">")
			gxl_file.write("<attr name=\"" + "chem" + "\"><int>" + str(attrs['chem']) + "</int></attr>")
			gxl_file.write("</node>\n")
		for v1, v2, attrs in graph.edges(data=True):
			gxl_file.write("<edge from=\"_" + str(v1) + "\" to=\"_" + str(v2) + "\">")
			gxl_file.write("<attr name=\"valence\"><int>" + str(attrs['valence']) + "</int></attr>")
#			gxl_file.write("<attr name=\"valence\"><int>" + "1" + "</int></attr>")
			gxl_file.write("</edge>\n")
		gxl_file.write("</graph>\n")
		gxl_file.write("</gxl>")
		gxl_file.close()
	elif method == 'gedlib-letter':
		# reference: https://github.com/dbblumenthal/gedlib/blob/master/data/generate_molecules.py#L22
		# and https://github.com/dbblumenthal/gedlib/blob/master/data/datasets/Letter/HIGH/AP1_0000.gxl
		gxl_file = open(filename, 'w')
		gxl_file.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
		gxl_file.write("<!DOCTYPE gxl SYSTEM \"http://www.gupro.de/GXL/gxl-1.0.dtd\">\n")
		gxl_file.write("<gxl xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n")
		gxl_file.write("<graph id=\"" + str(graph.graph['name']) + "\" edgeids=\"false\" edgemode=\"undirected\">\n")
		for v, attrs in graph.nodes(data=True):
			gxl_file.write("<node id=\"_" + str(v) + "\">")
			gxl_file.write("<attr name=\"x\"><float>" + str(attrs['attributes'][0]) + "</float></attr>")
			gxl_file.write("<attr name=\"y\"><float>" + str(attrs['attributes'][1]) + "</float></attr>")
			gxl_file.write("</node>\n")
		for v1, v2, attrs in graph.edges(data=True):
			gxl_file.write("<edge from=\"_" + str(v1) + "\" to=\"_" + str(v2) + "\"/>\n")
		gxl_file.write("</graph>\n")
		gxl_file.write("</gxl>")
		gxl_file.close()


def loadSDF(filename):
	"""load data from structured data file (.sdf file).

	Notes
	------
	A SDF file contains a group of molecules, represented in the similar way as in MOL format.
	Check `here <http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx>`__ for detailed structure.
	"""
	import networkx as nx
	from os.path import basename
	from tqdm import tqdm
	import sys
	data = []
	with open(filename) as f:
		content = f.read().splitlines()
		index = 0
		pbar = tqdm(total=len(content) + 1, desc='load SDF', file=sys.stdout)
		while index < len(content):
			index_old = index

			g = nx.Graph(name=content[index].strip())  # set name of the graph

			tmp = content[index + 3]
			nb_nodes = int(tmp[:3])  # number of the nodes
			nb_edges = int(tmp[3:6])  # number of the edges

			for i in range(0, nb_nodes):
				tmp = content[i + index + 4]
				g.add_node(i, atom=tmp[31:34].strip())

			for i in range(0, nb_edges):
				tmp = content[i + index + g.number_of_nodes() + 4]
				tmp = [tmp[i:i + 3] for i in range(0, len(tmp), 3)]
				g.add_edge(
					int(tmp[0]) - 1, int(tmp[1]) - 1, bond_type=tmp[2].strip())

			data.append(g)

			index += 4 + g.number_of_nodes() + g.number_of_edges()
			while content[index].strip() != '$$$$':  # seperator
				index += 1
			index += 1

			pbar.update(index - index_old)
		pbar.update(1)
		pbar.close()

	return data


def loadMAT(filename, extra_params):
	"""Load graph data from a MATLAB (up to version 7.1) .mat file.

	Notes
	------
	A MAT file contains a struct array containing graphs, and a column vector lx containing a class label for each graph.
	Check README in `downloadable file <http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/>`__ for detailed structure.
	"""
	from scipy.io import loadmat
	import numpy as np
	import networkx as nx
	data = []
	content = loadmat(filename)
	order = extra_params['am_sp_al_nl_el']
	# print(content)
	# print('----')
	for key, value in content.items():
		if key[0] == 'l':  # class label
			y = np.transpose(value)[0].tolist()
			# print(y)
		elif key[0] != '_':
			# print(value[0][0][0])
			# print()
			# print(value[0][0][1])
			# print()
			# print(value[0][0][2])
			# print()
			# if len(value[0][0]) > 3:
			#	 print(value[0][0][3])
			# print('----')
			# if adjacency matrix is not compressed / edge label exists
			if order[1] == 0:
				for i, item in enumerate(value[0]):
					# print(item)
					# print('------')
					g = nx.Graph(name=i)  # set name of the graph
					nl = np.transpose(item[order[3]][0][0][0])  # node label
					# print(item[order[3]])
					# print()
					for index, label in enumerate(nl[0]):
						g.add_node(index, atom=str(label))
					el = item[order[4]][0][0][0]  # edge label
					for edge in el:
						g.add_edge(
							edge[0] - 1, edge[1] - 1, bond_type=str(edge[2]))
					data.append(g)
			else:
				from scipy.sparse import csc_matrix
				for i, item in enumerate(value[0]):
					# print(item)
					# print('------')
					g = nx.Graph(name=i)  # set name of the graph
					nl = np.transpose(item[order[3]][0][0][0])  # node label
					# print(nl)
					# print()
					for index, label in enumerate(nl[0]):
						g.add_node(index, atom=str(label))
					sam = item[order[0]]  # sparse adjacency matrix
					index_no0 = sam.nonzero()
					for col, row in zip(index_no0[0], index_no0[1]):
						# print(col)
						# print(row)
						g.add_edge(col, row)
					data.append(g)
					# print(g.edges(data=True))
	return data, y


def loadTXT(filename):
	"""Load graph data from a .txt file.

	Notes
	------
	The graph data is loaded from separate files.
	Check README in `downloadable file <http://tiny.cc/PK_MLJ_data>`__, 2018 for detailed structure.
	"""
#	import numpy as np
	import networkx as nx
	from os import listdir
	from os.path import dirname, basename
	
	
	def get_label_names(frm):
		"""Get label names from DS_label_readme.txt file.
		"""
		
		def get_names_from_line(line):
			"""Get names of labels/attributes from a line.
			"""
			str_names = line.split('[')[1].split(']')[0]
			names = str_names.split(',')
			names = [attr.strip() for attr in names]
			return names


		label_names = {'node_labels': [], 'node_attrs': [], 
					   'edge_labels': [], 'edge_attrs': []}
		content_rm = open(frm).read().splitlines()
		for line in content_rm:
			line = line.strip()
			if line.startswith('Node labels:'):
				label_names['node_labels'] = get_names_from_line(line)
			elif line.startswith('Node attributes:'):
				label_names['node_attrs'] = get_names_from_line(line)
			elif line.startswith('Edge labels:'):
				label_names['edge_labels'] = get_names_from_line(line)
			elif line.startswith('Edge attributes:'):
				label_names['edge_attrs'] = get_names_from_line(line)
		return label_names

	
	# get dataset name.
	dirname_dataset = dirname(filename)
	filename = basename(filename)
	fn_split = filename.split('_A')
	ds_name = fn_split[0].strip()
	
	# load data file names
	for name in listdir(dirname_dataset):
		if ds_name + '_A' in name:
			fam = dirname_dataset + '/' + name
		elif ds_name + '_graph_indicator' in name:
			fgi = dirname_dataset + '/' + name
		elif ds_name + '_graph_labels' in name:
			fgl = dirname_dataset + '/' + name
		elif ds_name + '_node_labels' in name:
			fnl = dirname_dataset + '/' + name
		elif ds_name + '_edge_labels' in name:
			fel = dirname_dataset + '/' + name
		elif ds_name + '_edge_attributes' in name:
			fea = dirname_dataset + '/' + name
		elif ds_name + '_node_attributes' in name:
			fna = dirname_dataset + '/' + name
		elif ds_name + '_graph_attributes' in name:
			fga = dirname_dataset + '/' + name
		elif ds_name + '_label_readme' in name:
			frm = dirname_dataset + '/' + name
		# this is supposed to be the node attrs, make sure to put this as the last 'elif'
		elif ds_name + '_attributes' in name:
			fna = dirname_dataset + '/' + name
			
	# get labels and attributes names.
	if 'frm' in locals():
		label_names = get_label_names(frm)
	else:
		label_names = {'node_labels': [], 'node_attrs': [], 
					   'edge_labels': [], 'edge_attrs': []}

	content_gi = open(fgi).read().splitlines()  # graph indicator
	content_am = open(fam).read().splitlines()  # adjacency matrix
	content_gl = open(fgl).read().splitlines()  # graph labels

	# create graphs and add nodes
	data = [nx.Graph(name=str(i), 
					 node_labels=label_names['node_labels'],
					 node_attrs=label_names['node_attrs'],
					 edge_labels=label_names['edge_labels'],
					 edge_attrs=label_names['edge_attrs']) for i in range(0, len(content_gl))]
	if 'fnl' in locals():
		content_nl = open(fnl).read().splitlines()  # node labels
		for idx, line in enumerate(content_gi):
			# transfer to int first in case of unexpected blanks
			data[int(line) - 1].add_node(idx)
			labels = [l.strip() for l in content_nl[idx].split(',')]
			data[int(line) - 1].nodes[idx]['atom'] = str(int(labels[0])) # @todo: this should be removed after.
			if data[int(line) - 1].graph['node_labels'] == []:
				for i, label in enumerate(labels):
					l_name = 'label_' + str(i)
					data[int(line) - 1].nodes[idx][l_name] = label
					data[int(line) - 1].graph['node_labels'].append(l_name)
			else:
				for i, l_name in enumerate(data[int(line) - 1].graph['node_labels']):
					data[int(line) - 1].nodes[idx][l_name] = labels[i]
	else:
		for i, line in enumerate(content_gi):
			data[int(line) - 1].add_node(i)
			
	# add edges
	for line in content_am:
		tmp = line.split(',')
		n1 = int(tmp[0]) - 1
		n2 = int(tmp[1]) - 1
		# ignore edge weight here.
		g = int(content_gi[n1]) - 1
		data[g].add_edge(n1, n2)

	# add edge labels
	if 'fel' in locals():
		content_el = open(fel).read().splitlines()
		for idx, line in enumerate(content_el):
			labels = [l.strip() for l in line.split(',')]
			n = [int(i) - 1 for i in content_am[idx].split(',')]
			g = int(content_gi[n[0]]) - 1
			data[g].edges[n[0], n[1]]['bond_type'] = labels[0] # @todo: this should be removed after.
			if data[g].graph['edge_labels'] == []:
				for i, label in enumerate(labels):
					l_name = 'label_' + str(i)
					data[g].edges[n[0], n[1]][l_name] = label
					data[g].graph['edge_labels'].append(l_name)
			else:
				for i, l_name in enumerate(data[g].graph['edge_labels']):
					data[g].edges[n[0], n[1]][l_name] = labels[i]

	# add node attributes
	if 'fna' in locals():
		content_na = open(fna).read().splitlines()
		for idx, line in enumerate(content_na):
			attrs = [a.strip() for a in line.split(',')]
			g = int(content_gi[idx]) - 1
			data[g].nodes[idx]['attributes'] = attrs # @todo: this should be removed after.
			if data[g].graph['node_attrs'] == []:
				for i, attr in enumerate(attrs):
					a_name = 'attr_' + str(i)
					data[g].nodes[idx][a_name] = attr
					data[g].graph['node_attrs'].append(a_name)
			else:
				for i, a_name in enumerate(data[g].graph['node_attrs']):
					data[g].nodes[idx][a_name] = attrs[i]

	# add edge attributes
	if 'fea' in locals():
		content_ea = open(fea).read().splitlines()
		for idx, line in enumerate(content_ea):
			attrs = [a.strip() for a in line.split(',')]
			n = [int(i) - 1 for i in content_am[idx].split(',')]
			g = int(content_gi[n[0]]) - 1
			data[g].edges[n[0], n[1]]['attributes'] = attrs # @todo: this should be removed after.
			if data[g].graph['edge_attrs'] == []:
				for i, attr in enumerate(attrs):
					a_name = 'attr_' + str(i)
					data[g].edges[n[0], n[1]][a_name] = attr
					data[g].graph['edge_attrs'].append(a_name)
			else:
				for i, a_name in enumerate(data[g].graph['edge_attrs']):
					data[g].edges[n[0], n[1]][a_name] = attrs[i]

	# load y
	y = [int(i) for i in content_gl]

	return data, y


def loadDataset(filename, filename_y=None, extra_params=None):
	"""Read graph data from filename and load them as NetworkX graphs.

	Parameters
	----------
	filename : string
		The name of the file from where the dataset is read.
	filename_y : string
		The name of file of the targets corresponding to graphs.
	extra_params : dict
		Extra parameters only designated to '.mat' format.

	Return
	------
	data : List of NetworkX graph.

	y : List

	Targets corresponding to graphs.
		
	Notes
	-----
	This function supports following graph dataset formats:

	'ds': load data from .ds file. See comments of function loadFromDS for a example.

	'cxl': load data from Graph eXchange Language file (.cxl file). See 
	`here <http://www.gupro.de/GXL/Introduction/background.html>`__ for detail.

	'sdf': load data from structured data file (.sdf file). See 
	`here <http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx>`__
	for details.

	'mat': Load graph data from a MATLAB (up to version 7.1) .mat file. See
	README in `downloadable file <http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/>`__
	for details.

	'txt': Load graph data from a special .txt file. See
	`here <https://ls11-www.cs.tu-dortmund.de/staff/morris/graphkerneldatasets>`__
	for details. Note here filename is the name of either .txt file in
	the dataset directory.
	"""
	extension = splitext(filename)[1][1:]
	if extension == "ds":
		data, y = loadFromDS(filename, filename_y)
	elif extension == "cxl":
		import xml.etree.ElementTree as ET
		
		dirname_dataset = dirname(filename)
		tree = ET.parse(filename)
		root = tree.getroot()
		data = []
		y = []
		for graph in root.iter('graph'):
			mol_filename = graph.attrib['file']
			mol_class = graph.attrib['class']
			data.append(loadGXL(dirname_dataset + '/' + mol_filename))
			y.append(mol_class)
	elif extension == 'xml':
		data, y = loadFromXML(filename, extra_params)
	elif extension == "sdf":
#		import numpy as np
		from tqdm import tqdm
		import sys

		data = loadSDF(filename)

		y_raw = open(filename_y).read().splitlines()
		y_raw.pop(0)
		tmp0 = []
		tmp1 = []
		for i in range(0, len(y_raw)):
			tmp = y_raw[i].split(',')
			tmp0.append(tmp[0])
			tmp1.append(tmp[1].strip())

		y = []
		for i in tqdm(range(0, len(data)), desc='ajust data', file=sys.stdout):
			try:
				y.append(tmp1[tmp0.index(data[i].name)].strip())
			except ValueError:  # if data[i].name not in tmp0
				data[i] = []
		data = list(filter(lambda a: a != [], data))
	elif extension == "mat":
		data, y = loadMAT(filename, extra_params)
	elif extension == 'txt':
		data, y = loadTXT(filename)
		# print(len(y))
		# print(y)
		# print(data[0].nodes(data=True))
		# print('----')
		# print(data[0].edges(data=True))
		# for g in data:
		#	 print(g.nodes(data=True))
		#	 print('----')
		#	 print(g.edges(data=True))

	return data, y


def loadFromXML(filename, extra_params):
	import xml.etree.ElementTree as ET
	
	if extra_params:
		dirname_dataset = extra_params
	else:
		dirname_dataset = dirname(filename)
	tree = ET.parse(filename)
	root = tree.getroot()
	data = []
	y = []
	for graph in root.iter('graph'):
		mol_filename = graph.attrib['file']
		mol_class = graph.attrib['class']
		data.append(loadGXL(dirname_dataset + '/' + mol_filename))
		y.append(mol_class)
		
	return data, y
			

def loadFromDS(filename, filename_y):
	"""Load data from .ds file.

	Possible graph formats include:

	'.ct': see function loadCT for detail.

	'.gxl': see dunction loadGXL for detail.

	Note these graph formats are checked automatically by the extensions of 
	graph files.
	"""
	dirname_dataset = dirname(filename)
	data = []
	y = []
	content = open(filename).read().splitlines()
	extension = splitext(content[0].split(' ')[0])[1][1:]
	if filename_y is None or filename_y == '':
		if extension == 'ct': 
			for i in range(0, len(content)):
				tmp = content[i].split(' ')
				# remove the '#'s in file names
				data.append(
					loadCT(dirname_dataset + '/' + tmp[0].replace('#', '', 1)))
				y.append(float(tmp[1]))
		elif extension == 'gxl':
			for i in range(0, len(content)):
				tmp = content[i].split(' ')
				# remove the '#'s in file names
				data.append(
					loadGXL(dirname_dataset + '/' + tmp[0].replace('#', '', 1)))
				y.append(float(tmp[1]))
	else:  # y in a seperate file
		if extension == 'ct':
			for i in range(0, len(content)):
				tmp = content[i]
				# remove the '#'s in file names
				data.append(
					loadCT(dirname_dataset + '/' + tmp.replace('#', '', 1)))
		elif extension == 'gxl':
			for i in range(0, len(content)):
				tmp = content[i]
				# remove the '#'s in file names
				data.append(
					loadGXL(dirname_dataset + '/' + tmp.replace('#', '', 1)))													   
															   
		content_y = open(filename_y).read().splitlines()
		# assume entries in filename and filename_y have the same order.
		for item in content_y:
			tmp = item.split(' ')
			# assume the 3rd entry in a line is y (for Alkane dataset)
			y.append(float(tmp[2]))
			
	return data, y
				

def saveDataset(Gn, y, gformat='gxl', group=None, filename='gfile', xparams=None):
	"""Save list of graphs.
	"""
	import os
	dirname_ds = os.path.dirname(filename)
	if dirname_ds != '':
		dirname_ds += '/'
		if not os.path.exists(dirname_ds) :
			os.makedirs(dirname_ds)
				
	if xparams is not None and 'graph_dir' in xparams:
		graph_dir = xparams['graph_dir'] + '/'
		if not os.path.exists(graph_dir):
			os.makedirs(graph_dir)
	else:
		graph_dir = dirname_ds 
			
	if group == 'xml' and gformat == 'gxl':
		kwargs = {'method': xparams['method']} if xparams is not None else {}
		with open(filename + '.xml', 'w') as fgroup:
			fgroup.write("<?xml version=\"1.0\"?>")
			fgroup.write("\n<!DOCTYPE GraphCollection SYSTEM \"http://www.inf.unibz.it/~blumenthal/dtd/GraphCollection.dtd\">")
			fgroup.write("\n<GraphCollection>")
			for idx, g in enumerate(Gn):
				fname_tmp = "graph" + str(idx) + ".gxl"
				saveGXL(g, graph_dir + fname_tmp, **kwargs)
				fgroup.write("\n\t<graph file=\"" + fname_tmp + "\" class=\"" + str(y[idx]) + "\"/>")
			fgroup.write("\n</GraphCollection>")
			fgroup.close()
			
			
if __name__ == '__main__':	
#	### Load dataset from .ds file.
#	# .ct files.
#	ds = {'name': 'Alkane', 'dataset': '../../datasets/Alkane/dataset.ds',
#		'dataset_y': '../../datasets/Alkane/dataset_boiling_point_names.txt'}
#	Gn, y = loadDataset(ds['dataset'], filename_y=ds['dataset_y'])
##	ds = {'name': 'Acyclic', 'dataset': '../../datasets/acyclic/dataset_bps.ds'}  # node symb
##	Gn, y = loadDataset(ds['dataset'])
##	ds = {'name': 'MAO', 'dataset': '../../datasets/MAO/dataset.ds'} # node/edge symb
##	Gn, y = loadDataset(ds['dataset'])
##	ds = {'name': 'PAH', 'dataset': '../../datasets/PAH/dataset.ds'} # unlabeled
##	Gn, y = loadDataset(ds['dataset'])
#	print(Gn[1].nodes(data=True))
#	print(Gn[1].edges(data=True))
#	print(y[1])
	
#	# .gxl file.
#	ds = {'name': 'monoterpenoides', 
#		  'dataset': '../../datasets/monoterpenoides/dataset_10+.ds'}  # node/edge symb
#	Gn, y = loadDataset(ds['dataset'])
#	print(Gn[1].nodes(data=True))
#	print(Gn[1].edges(data=True))
#	print(y[1])
	
#	### Convert graph from one format to another.
#	# .gxl file.
#	import networkx as nx
#	ds = {'name': 'monoterpenoides', 
#		  'dataset': '../../datasets/monoterpenoides/dataset_10+.ds'}  # node/edge symb
#	Gn, y = loadDataset(ds['dataset'])
#	y = [int(i) for i in y]
#	print(Gn[1].nodes(data=True))
#	print(Gn[1].edges(data=True))
#	print(y[1])
#	# Convert a graph to the proper NetworkX format that can be recognized by library gedlib.
#	Gn_new = []
#	for G in Gn:
#		G_new = nx.Graph()
#		for nd, attrs in G.nodes(data=True):
#			G_new.add_node(str(nd), chem=attrs['atom'])
#		for nd1, nd2, attrs in G.edges(data=True):
#			G_new.add_edge(str(nd1), str(nd2), valence=attrs['bond_type'])
##			G_new.add_edge(str(nd1), str(nd2))
#		Gn_new.append(G_new)
#	print(Gn_new[1].nodes(data=True))
#	print(Gn_new[1].edges(data=True))
#	print(Gn_new[1])
#	filename = '/media/ljia/DATA/research-repo/codes/others/gedlib/tests_linlin/generated_datsets/monoterpenoides/gxl/monoterpenoides'
#	xparams = {'method': 'gedlib'}
#	saveDataset(Gn, y, gformat='gxl', group='xml', filename=filename, xparams=xparams)
	
	# save dataset.
#	ds = {'name': 'MUTAG', 'dataset': '../../datasets/MUTAG/MUTAG.mat',
#		  'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}  # node/edge symb
#	Gn, y = loadDataset(ds['dataset'], extra_params=ds['extra_params'])
#	saveDataset(Gn, y, group='xml', filename='temp/temp')
	
	# test - new way to add labels and attributes.
#	dataset = '../../datasets/SYNTHETICnew/SYNTHETICnew_A.txt'
#	dataset = '../../datasets/Fingerprint/Fingerprint_A.txt'
#	dataset = '../../datasets/Letter-med/Letter-med_A.txt'
#	dataset = '../../datasets/AIDS/AIDS_A.txt'
#	dataset = '../../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'
#	Gn, y_all = loadDataset(dataset)
	pass