Skip to content
Permalink
master
Switch branches/tags
Go to file
 
 
Cannot retrieve contributors at this time
executable file 245 lines (205 sloc) 8.17 KB
#!/usr/bin/env python3
#!/usr/bin/env pypy3
"""Format ontology files using a uniform ttl serializer from rdflib
Usage:
ttlfmt [options]
ttlfmt [options] <file>...
Options:
-h --help print this
-v --verbose do something fun!
-a --vanilla use the regular rdflib turtle serializer
-y --subclass use the subClassOf turtle serializer
-c --compact use the compact turtle serializer
-u --uncompact use the uncompact turtle serializer
-r --racket use the racket turtle serializer
-j --jsonld use the rdflib-jsonld serializer
-f --format=FM specify the input format (used for pipes)
-t --outfmt=F specify the output format [default: nifttl]
-s --slow do not use a process pool
-n --nowrite parse the file and reserialize it but do not write changes
-o --output=FI serialize all input files to output file
-p --profile enable profiling on parsing and serialization
-d --debug launch debugger after parsing and before serialization
"""
import os
import sys
from io import StringIO, TextIOWrapper
from json.decoder import JSONDecodeError
from concurrent.futures import ProcessPoolExecutor
from docopt import docopt, parse_defaults
import rdflib
from rdflib.plugins.parsers.notation3 import BadSyntax
from ttlser.utils import regjsonld
defaults = {o.name:o.value if o.argcount else None for o in parse_defaults(__doc__)}
#GRAPHCLASS = rdflib.Graph
GRAPHCLASS = rdflib.ConjunctiveGraph
def getVersion():
ttlser = rdflib.plugin.get('nifttl', rdflib.serializer.Serializer)
ttlser_version = ttlser._CustomTurtleSerializer__version # FIXME
version = "ttlfmt v0.0.2\nttlser {}".format(ttlser_version)
return version
def prepare(filepath_or_stream, outpath=None, stream=False):
if stream:
infmt_guess = 'turtle'
if outpath is None:
outpath = sys.stdout
else:
filepath_or_stream = os.path.expanduser(filepath_or_stream)
_, ext = os.path.splitext(filepath_or_stream)
filetype = ext.strip('.')
if filetype == 'ttl':
infmt_guess = 'ttl'
elif filetype in ('json', 'jsonld'):
infmt_guess = 'json-ld'
regjsonld()
else:
infmt_guess = None
if outpath is None:
outpath = filepath_or_stream
print(filepath_or_stream)
return dict(source=filepath_or_stream,
format_guess=infmt_guess,
outpath=outpath)
formats = ('ttl', 'json-ld', None, 'xml', 'n3', 'nt', 'nquads', 'trix',
'trig', 'hturtle', 'rdfa', 'mdata', 'rdfa1.0', 'html')
def parse(source, format_guess, outpath, graph=None, infmt=None, graph_class=GRAPHCLASS):
graph = graph_class() if graph is None else graph
errors = []
if infmt:
format_guess = infmt
for format in (format_guess, *(f for f in formats if f != format_guess)):
# TODO we don't need to reset just saved parsed streams to the point where they fail?
if type(source) == TextIOWrapper: # stdin can't reset
src = source.read()
source = StringIO(src)
try:
graph.parse(source=source, format=format)
a = next(iter(graph))
return graph, outpath
except (StopIteration, BadSyntax, JSONDecodeError) as e:
print('PARSING FAILED', format, source)
if infmt: # or format_guess != None:
raise e
errors.append(e)
if type(source) == StringIO:
source.seek(0)
raise BadSyntax(str(errors)) from errors[0]
def serialize(graph, outpath, outfmt=defaults['--outfmt'],
debug=False, profile=False, nowrite=False):
if debug:
if type(outpath) == type(sys.stdout):
pipe_debug(graph=graph, outpath=outpath)
else:
breakpoint()
elif profile and type(outpath) != type(sys.stdout):
*_, _out = outpath.rsplit('/', 1)
print('triple count for {_out}:'.format(_out=_out), len(graph))
if outfmt == 'json-ld':
kwargs = {'auto_compact': True}
else:
kwargs = {}
out = graph.serialize(format=outfmt, encoding='utf-8', **kwargs)
if nowrite:
print('FILE NOT WRITTEN {}'.format(outpath))
return
if profile:
print('PARSING Success', outpath)
elif not isinstance(outpath, str): # FIXME not a good test that it is stdout
outpath.buffer.write(out)
else:
with open(outpath, 'wb') as f:
f.write(out)
def convert(file_or_list_or_stream, outpath=None, stream=False,
infmt=None, outfmt=defaults['--outfmt'],
debug=False, profile=False, nowrite=False, graph_class=GRAPHCLASS):
if stream or type(file_or_list_or_stream) == str:
file_or_stream = file_or_list_or_stream
serialize(*parse(**prepare(file_or_stream, outpath, stream),
infmt=infmt),
outfmt=outfmt, debug=debug, profile=profile, nowrite=nowrite)
else:
# file list is used here because this allows is to merge files
# without any additional code if we pass it more than one file
# in normal use a tuple with a single element is passed in
file_list = file_or_list_or_stream
if outpath is not None:
graph = graph_class()
[parse(**prepare(file, outpath), graph=graph, infmt=infmt) for file in file_list]
serialize(graph, outpath, outfmt=outfmt,
debug=debug, profile=profile, nowrite=nowrite)
else:
[convert(file, infmt=infmt, outfmt=outfmt,
debug=debug, profile=profile,
graph_class=graph_class) for file in file_list]
def pipe_debug(*args, source=None, graph=None, outpath=None, **kwargs):
fn = sys.stdout.fileno()
tty = os.ttyname(fn)
with open(tty) as sys.stdin:
breakpoint()
def main():
#global args # vastly preferable to classing everything since this way we can see
#global outfmt # in 2 lines what is actually shared instead of stuffed into self
args = docopt(__doc__, version=getVersion())
profile = args['--profile']
if profile:
try:
from desc.prof import profile_me
global parse
global serialize
parse = profile_me(parse)
serialize = profile_me(serialize)
except ImportError:
pass
nowrite = args['--nowrite']
infmt = args['--format']
debug = args['--debug']
if args['--subclass']:
outfmt = 'scottl'
elif args['--vanilla']:
outfmt = 'turtle'
elif args['--compact']:
outfmt = 'cmpttl'
elif args['--uncompact']:
outfmt = 'uncmpttl'
elif args['--jsonld']:
outfmt = 'json-ld'
elif args['--racket']:
outfmt = 'rktttl'
else:
outfmt = args['--outfmt']
if outfmt == 'json-ld' or infmt == 'json-ld':
regjsonld()
outpath = args['--output']
files = args['<file>']
if not files:
from ttlser.utils import readFromStdIn
stdin = readFromStdIn(sys.stdin)
if stdin is not None:
convert(stdin, outpath, stream=True,
infmt=infmt, outfmt=outfmt,
debug=debug, profile=profile,
nowrite=nowrite)
else:
print(__doc__)
else:
lenfiles = len(files)
if outpath or args['--slow'] or lenfiles == 1:
if lenfiles == 1:
files, = files
convert(files, outpath=outpath,
infmt=infmt, outfmt=outfmt,
debug=debug, profile=profile,
nowrite=nowrite)
else:
from joblib import Parallel, delayed
nj = 9
if lenfiles < nj:
nj = lenfiles
Parallel(n_jobs=nj, verbose=10)(delayed(convert)
(file,
infmt=infmt, outfmt=outfmt,
debug=debug, profile=profile,
nowrite=nowrite)
for file in files)
if __name__ == '__main__':
main()