class TestPajek(unittest.TestCase):
def setUp(self):
self.output = io.StringIO()
self._node_stream = io.StringIO()
self.pjk = PajekFactory()
def test_stream_write(self):
self.pjk.add_edge("bob", "tim")
self.pjk.add_edge("bob", "rob")
self.pjk.add_edge("tim", "rob")
self.pjk.add_edge("tim", "bob")
self.pjk.write(self.output)
self.output.seek(0)
self.assertListEqual(self.output.readlines(), [
'*vertices 3\n', '1 "bob"\n', '2 "tim"\n', '3 "rob"\n',
'*edges 4\n', '1 2\n', '1 3\n', '2 3\n', '2 1\n'
])
def test_self_cite(self):
self.pjk.add_edge("bob", "bob")
self.pjk.write(self.output)
self.output.seek(0)
self.assertListEqual(
self.output.readlines(),
['*vertices 1\n', '1 "bob"\n', '*edges 1\n', '1 1\n'])
def pjk_writer(entries, output_file, bench_freq):
pjk = PajekFactory()
b = Benchmark()
for entry_list in iter(entries.get, 'STOP'):
for entry in entry_list:
for citation in entry["citations"]:
pjk.add_edge(entry["id"], citation)
b.increment()
entries.task_done()
b.print_freq()
with open_file(output_file, "w") as f:
pjk.write(f)
entries.task_done()
class TestPajek(unittest.TestCase):
def setUp(self):
self.output = io.StringIO()
self._node_stream = io.StringIO()
self.pjk = PajekFactory()
def test_stream_write(self):
self.pjk.add_edge("bob", "tim")
self.pjk.add_edge("bob", "rob")
self.pjk.add_edge("tim", "rob")
self.pjk.add_edge("tim", "bob")
self.pjk.write(self.output)
self.output.seek(0)
self.assertListEqual(self.output.readlines(), ['*vertices 3\n', '1 "bob"\n', '2 "tim"\n', '3 "rob"\n', '*edges 4\n', '1 2\n', '1 3\n', '2 3\n', '2 1\n'])
def test_self_cite(self):
self.pjk.add_edge("bob", "bob")
self.pjk.write(self.output)
self.output.seek(0)
self.assertListEqual(self.output.readlines(), ['*vertices 1\n', '1 "bob"\n', '*edges 1\n', '1 1\n'])
def pjk_writer(entries, output_file, bench_freq):
pjk = PajekFactory()
b = Benchmark()
for entry_list in iter(entries.get, 'STOP'):
for entry in entry_list:
for citation in entry["citations"]:
pjk.add_edge(entry["id"], citation)
b.increment()
entries.task_done()
b.print_freq()
with open_file(output_file, "w") as f:
pjk.write(f)
entries.task_done()
from util.PajekFactory import PajekFactory
from util.misc import open_file
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description="Creates Pajek (.net) files from an edge/link file")
parser.add_argument('outfile')
parser.add_argument('--delimiter', '-d', help="Field delimiter", default='\t')
parser.add_argument('--temp-dir', help="Directory to store temporary files in", default=None)
parser.add_argument('infile', nargs='+')
arguments = parser.parse_args()
pjk = PajekFactory(temp_dir=arguments.temp_dir)
for filename in arguments.infile:
with open_file(filename) as f:
for line in f:
v_from, v_to = line.split(arguments.delimiter)
pjk.add_edge(v_from, v_to.strip())
with open_file(arguments.outfile, 'w') as f:
pjk.write(f)
help="Directory to store temporary files in",
default=None)
parser.add_argument(
'--subject',
'-s',
help=
"For WoS, subject must include this. Can be a comma seperated list.")
parser.add_argument(
'--wos-only',
help="For WoS, exclude any citations or ids that contain a dot (.)",
action="store_true")
parser.add_argument('infile', nargs='+')
arguments = parser.parse_args()
b = Benchmark()
pjk = PajekFactory(temp_dir=arguments.temp_dir)
subjects = None
if arguments.subject:
subjects = set(arguments.subject.split(","))
for filename in arguments.infile:
with open_file(filename) as f:
for line in f:
entry = ujson.loads(line)
b.increment()
if arguments.wos_only and '.' in entry["id"]:
continue
if subjects:
def setUp(self):
self.output = io.StringIO()
self._node_stream = io.StringIO()
self.pjk = PajekFactory()
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description="Creates Pajek (.net) files from JSON")
parser.add_argument("outfile")
parser.add_argument("--temp-dir", help="Directory to store temporary files in", default=None)
parser.add_argument("--subject", "-s", help="For WoS, subject must include this. Can be a comma seperated list.")
parser.add_argument(
"--wos-only", help="For WoS, exclude any citations or ids that contain a dot (.)", action="store_true"
)
parser.add_argument("infile", nargs="+")
arguments = parser.parse_args()
b = Benchmark()
pjk = PajekFactory(temp_dir=arguments.temp_dir)
subjects = None
if arguments.subject:
subjects = set(arguments.subject.split(","))
for filename in arguments.infile:
with open_file(filename) as f:
for line in f:
entry = ujson.loads(line)
b.increment()
if arguments.wos_only and "." in entry["id"]:
continue
if subjects:
#!/usr/bin/env python
from util.misc import open_file, Benchmark
from util.PajekFactory import PajekFactory
import ujson
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description="Creates Pajek (.net) files from JSON")
parser.add_argument('outfile')
parser.add_argument('--temp-dir', help="Directory to store temporary files in", default=None)
parser.add_argument('infile', nargs='+')
arguments = parser.parse_args()
b = Benchmark()
pjk = PajekFactory(temp_dir=arguments.temp_dir)
for filename in arguments.infile:
with open_file(filename) as f:
for line in f:
entry = ujson.loads(line)
for citation in entry["citedBy"]:
pjk.add_edge(citation, entry["id"])
b.increment()
b.print_freq()
with open_file(arguments.outfile, "w") as f:
pjk.write(f)
from util.PajekFactory import PajekFactory
from util.misc import open_file
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(
description="Creates Pajek (.net) files from an edge/link file")
parser.add_argument('outfile')
parser.add_argument('--delimiter',
'-d',
help="Field delimiter",
default='\t')
parser.add_argument('--temp-dir',
help="Directory to store temporary files in",
default=None)
parser.add_argument('infile', nargs='+')
arguments = parser.parse_args()
pjk = PajekFactory(temp_dir=arguments.temp_dir)
for filename in arguments.infile:
with open_file(filename) as f:
for line in f:
v_from, v_to = line.split(arguments.delimiter)
pjk.add_edge(v_from, v_to.strip())
with open_file(arguments.outfile, 'w') as f:
pjk.write(f)
def setUp(self):
self.output = io.StringIO()
self._node_stream = io.StringIO()
self.pjk = PajekFactory()
