qnamefix.py

#!/usr/bin/env python3
#!/usr/bin/env pypy3
"""Set qnames based on the curies defined for a given ontology.

Usage:
    qnamefix [options]
    qnamefix [options] (-x <prefix>)...
    qnamefix [options] <file>...
    qnamefix [options] (-x <prefix>)... <file>...

Options:
    -h --help       print this
    -k --keep       keep only existing used prefixes
    -x --exclude=X  do not include the prefix when rewriting, ALL will strip
    -v --verbose    do something fun!
    -s --slow       do not use a process pool
    -n --nowrite    parse the file and reserialize it but do not write changes

    --noreord       do not reorder lists when serializing
    --id-swap       use consecutive integers for bnode ids

"""

import os
import sys
from glob import glob
import rdflib
from docopt import docopt
import ttlser.ttlfmt
from pyontutils.core import makeGraph, cull_prefixes
from ttlser.utils import readFromStdIn
from ttlser.ttlfmt import parse, prepare
from pyontutils.namespaces import PREFIXES as uPREFIXES

PREFIXES = {k:v for k, v in uPREFIXES.items() if k != 'NIFTTL'}

exclude = 'generated/swanson_hierarchies.ttl', 'generated/NIF-NIFSTD-mapping.ttl'

def serialize(graph, outpath):
    def prefix_cleanup(ps, graph):
        if 'parcellation/' in outpath:
            nsl = {p:n for p, n in graph.namespaces()}
            if '' in nsl:
                ps[''] = nsl['']
            elif 'hbaslim' in outpath:
                ps['HBA'] = nsl['HBA']
            elif 'mbaslim' in outpath:
                ps['MBA'] = nsl['MBA']
            elif 'cocomac' in outpath:
                ps['cocomac'] = nsl['cocomac']

        # special cases for NIFORG, NIFINV, NIFRET where there identifiers in
        # annotation properties that share the prefix, so we warn incase
        # at some point in the future for some reason want them again...
        if outpath == 'NIF-Organism.ttl':
            print('WARNING: special case for NIFORG')
            ps.pop('NIFORG')
        elif outpath == 'NIF-Investigation.ttl':
            print('WARNING: special case for NIFINV')
            ps.pop('NIFINV')
        elif outpath == 'unused/NIF-Retired.ttl':
            print('WARNING: special case for NIFRET')
            ps.pop('NIFGA')

    pc = prefix_cleanup if isinstance(outpath, str) else lambda a, b: None
    graph = cull_prefixes(graph, cleanup=pc, prefixes=PREFIXES)

    out = graph.g.serialize(format='nifttl', gen_prefix=bool(PREFIXES), encoding='utf-8')
    if 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_stream, stream=False, infmt=None):
    if file_or_stream in exclude:
        print('skipping', file)
        return file
    serialize(*parse(**prepare(file_or_stream, stream=stream), infmt=infmt))

def main():
    global PREFIXES
    args = docopt(__doc__, version = "qnamefix 0")
    infmt = args['--format'] = 'turtle'

    if args['--noreord'] or args['--id-swap']:
        from ttlser.serializers import CustomTurtleSerializer

    if args['--noreord']:
        class AllPredicates:
            def __contains__(self, other):
                return True

        CustomTurtleSerializer.no_reorder_list = AllPredicates()

    if args['--id-swap']:
        CustomTurtleSerializer._do_id_swap = True

    if args['--exclude'] == ['ALL']:
        for k in list(PREFIXES):
            PREFIXES.pop(k)
    else:
        for x in args['--exclude']:
            if x in PREFIXES:
                PREFIXES.pop(x)
    if not args['<file>']:
        stdin = readFromStdIn(sys.stdin)
        if stdin is not None:
            convert(stdin, stream=True, infmt=infmt)
        else:
            print(__doc__)
    else:
        if args['--slow'] or len(args['<file>']) == 1:
            [convert(f, infmt=infmt) for f in args['<file>']]
        else:
            from joblib import Parallel, delayed
            Parallel(n_jobs=9)(delayed(convert)(f, infmt=infmt) for f in args['<file>'])

if __name__ == '__main__':
    main()