def make_parser():
"""Create the argument parser, derived from the general scripts parser."""
parser = get_parser(
__doc__,
('A file containing a list of files/file paths to be read. These '
'should be nxml or txt files.'))
parser.add_argument(
dest='output_name',
help=('Results will be pickled in files '
'<output_name>_stmts.pkl and <output_name>_readings.pkl.'))
return parser
def make_parser():
"""Create the argument parser, derived from the general scripts parser."""
parser = get_parser(
__doc__,
('A file containing a list of files/file paths to be read. These '
'should be nxml or txt files.')
)
parser.add_argument(
dest='output_name',
help=('Results will be pickled in files '
'<output_name>_stmts.pkl and <output_name>_readings.pkl.')
)
return parser
"""Read a list of files located in your local directory."""
from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
import logging
import pickle
import random
logger = logging.getLogger('file_reader')
from indra.tools.reading.util.script_tools import get_parser, make_statements
if __name__ == '__main__':
parser = get_parser(
__doc__,
('A file containing a list of files/file paths to be read. These '
'should be nxml or txt files.'))
parser.add_argument(
dest='output_name',
help=('Results will be pickled in files '
'<output_name>_stmts.pkl and <output_name>_readings.pkl.'))
args = parser.parse_args()
if args.debug and not args.quiet:
logger.setLevel(logging.DEBUG)
from indra.tools.reading.readers import _get_dir, get_readers, Content
def read_files(files, readers, **kwargs):
"""Read the files in `files` with the reader objects in `readers`.
from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
import logging
import random
import pickle
from math import log10, floor, ceil
from datetime import datetime
from indra.tools.reading.util.script_tools import get_parser, make_statements,\
StatementData
logger = logging.getLogger('make_db_readings')
if __name__ == '__main__':
parser = get_parser(
'A tool to read and process content from the database.',
('A file containing a list of ids of the form <id_type>:<id>. '
'Note that besided the obvious id types (pmid, pmcid, doi, etc.), '
'you may use trid and tcid to indicate text ref and text content '
'ids, respectively. Note that these are specific to the database, '
'and should thus be used with care.'))
parser.add_argument(
'-m',
'--reading_mode',
choices=['all', 'unread', 'none'],
default='unread',
help=("Set the reading mode. If 'all', read everything, if "
"'unread', only read content that does not have pre-existing "
"readings of the same reader and version, if 'none', only "
"use pre-existing readings. Default is 'unread'."))
parser.add_argument(
'-S',
'--stmt_mode',