def reset(overwrite=False, ignore_initial=False):
# Automatically load presets
global _presets
_presets = {}
load_path = utils.get_write_path("presets")
if ignore_initial or not os.path.exists(
os.path.join(load_path, ".initial_complete")):
# Do initial population of presets from system install / cwd
if not os.path.exists(load_path):
os.makedirs(load_path)
# Write file to say we have done this
open(os.path.join(load_path, ".initial_complete"), "w").close()
# Copy actual files
search_paths = utils.get_search_paths()
if overwrite:
# Reverse search paths because things will get overwritten
search_paths = reversed(search_paths)
for path in search_paths:
full = os.path.join(path, "presets")
if full != load_path and os.path.exists(full):
for f in os.listdir(full):
# Do not overwrite existing files
if overwrite or not os.path.exists(
os.path.join(load_path, f)):
shutil.copy2(os.path.join(full, f), load_path)
load_directory(load_path)
def reset(overwrite=False, ignore_initial=False):
# Automatically load presets
global _presets
_presets = {}
load_path = utils.get_write_path("presets")
if ignore_initial or not os.path.exists(os.path.join(load_path, ".initial_complete")):
# Do initial population of presets from system install / cwd
if not os.path.exists(load_path):
os.makedirs(load_path)
# Write file to say we have done this
open(os.path.join(load_path, ".initial_complete"), "w").close()
# Copy actual files
for path in utils.get_search_paths():
full = os.path.join(path, "presets")
if full != load_path and os.path.exists(full):
for f in os.listdir(full):
# Do not overwrite existing files
if overwrite or not os.path.exists(os.path.join(load_path, f)):
shutil.copy2(os.path.join(full, f), load_path)
load_directory(load_path)
def reset(overwrite=False, ignore_initial=False):
# Automatically load presets
global _presets
_presets = {}
load_path = utils.get_write_path("presets")
if ignore_initial or not os.path.exists(os.path.join(load_path, ".initial_complete")):
# Do initial population of presets from system install / cwd
if not os.path.exists(load_path):
os.makedirs(load_path)
# Write file to say we have done this
open(os.path.join(load_path, ".initial_complete"), "w").close()
# Copy actual files
search_paths = utils.get_search_paths()
if overwrite:
# Reverse search paths because things will get overwritten
search_paths = reversed(search_paths)
print [path for path in search_paths]
"A tab separated file containing original terms before entity recognition."
)
parser.add_argument(
"-o",
"--output",
help=
"The optional path to which a file containing grounded terms in each sentence will be written.",
default="_")
args = parser.parse_args()
if any([i is None for i in [args.tags, args.input, args.dictionary]]):
parser.print_help()
sys.exit(1)
output_file = None
if args.output != "_" and utils.get_write_path(args.output):
output_file = utils.get_write_path(args.output)
tags = utils.read_tags(args.tags)
original = utils.parse_tsv(args.input)
dictionary = utils.parse_tsv(args.dictionary)
if len(original) != len(tags):
print("Error: mismatching original inputs and tags ({} and {}).".format(
len(original), len(tags)))
sys.exit(1)
if len(dictionary) == 0:
print("Error: read an empty dictionary, check the tsv.")
sys.exit(1)
help=
"A tab separated file containing original terms before entity recognition."
)
parser.add_argument(
"-o",
"--output",
help=
"The optional path to which a file containing grounded terms in each sentence will be written.",
default="_")
args = parser.parse_args()
if any([i is None for i in [args.tags, args.input, args.dictionary]]):
parser.print_help()
sys.exit(1)
output_file = utils.get_write_path(args.output)
out = open(output_file, 'w+')
# Build the disease and chemical dictionary choices separately.
dictionary = utils.parse_tsv(args.dictionary)
if len(dictionary) == 0:
print("Error: read an empty dictionary, check the tsv.")
sys.exit(1)
chemical_choices = {
i[2]: i[0]
for i in dictionary if i[1].lower() == "chemical"
}
disease_choices = {i[2]: i[0] for i in dictionary if i[1].lower() == "disease"}