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#!/usr/bin/env python3.6
#!/usr/bin/env pypy3
"""Format ontology files using a uniform ttl serializer from rdflib
Usage:
ttlfmt [options]
ttlfmt [options] <file>...
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 embed 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
import rdflib
from rdflib.plugins.parsers.notation3 import BadSyntax
from pyontutils.utils import readFromStdIn
profile_me = lambda f:f
def getVersion():
ttlser = rdflib.plugin.get('nifttl', rdflib.serializer.Serializer)
ttlser_version = ttlser._CustomTurtleSerializer__version # FIXME
version = f"ttlfmt v0.0.1\nttlser {ttlser_version}"
return version
if __name__ == '__main__':
args = docopt(__doc__, version=getVersion())
if args['--debug']:
from IPython import embed
if args['--profile']:
from desc.prof import profile_me
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 == 'json':
infmt_guess = 'json-ld'
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')
@profile_me
def parse(source, format_guess, outpath, graph=None):
graph = rdflib.Graph() if graph is None else graph
errors = []
if args['--format']:
format_guess = args['--format']
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 args['--format']: # or format_guess != None:
raise e
errors.append(e)
if type(source) == StringIO:
source.seek(0)
raise BadSyntax(str(errors)) from errors[0]
@profile_me
def serialize(graph, outpath):
if args['--debug']:
if type(outpath) == type(sys.stdout):
pipe_debug(graph=graph, outpath=outpath)
else:
from IPython import embed
embed()
out = graph.serialize(format=outfmt)
if args['--nowrite']:
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, outpath=None, stream=False):
if stream or type(file) == str:
file_or_stream = file
serialize(*parse(**prepare(file_or_stream, outpath, stream)))
else:
file_list = file
graph = rdflib.Graph()
[parse(**prepare(file, outpath), graph=graph) for file in file_list]
serialize(graph, outpath)
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:
from IPython import embed
embed()
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
if __name__ != '__main__':
args = docopt(__doc__, version=getVersion())
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']
outpath = args['--output']
files = args['<file>']
if not files:
stdin = readFromStdIn(sys.stdin)
if stdin is not None:
convert(stdin, outpath, stream=True)
else:
print(__doc__)
else:
from joblib import Parallel, delayed
if outpath or args['--slow'] or len(files) == 1:
if len(files) == 1:
files, = files
convert(files, outpath=outpath)
else:
Parallel(n_jobs=9)(delayed(convert)(f) for f in files)
if __name__ == '__main__':
main()