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execute.py
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execute.py
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import argparse
from pathlib import Path
import json
import wget
from scripts.download_full_text import download_full_text, merge_full_text
from scripts.extract_tags import extract_annotations
from scripts.hetnet_id_extractor import filter_tags
from scripts.map_ids import map_ids
from scripts.pubtator_to_xml import convert_pubtator
parser = argparse.ArgumentParser(
description='Runs Pubtator/Pubtator Central Parser Pipeline'
)
parser.add_argument(
"--config", help="The config file for the extractor.",
default="config_files/pubtator_central_config.json"
)
args = parser.parse_args()
configuration = json.load(open(args.config, "r"))
if (
"repository_download" in configuration and
not configuration["repository_download"]["skip"]
):
print("Executing repository_download...")
wget.download(
configuration["repository_download"]['url'],
out=configuration["repository_download"]['download_folder']
)
del configuration["repository_download"]
if (
"pubtator_to_xml" in configuration and
not configuration["pubtator_to_xml"]["skip"]
):
print("Executing pubtator_to_xml...")
convert_pubtator(
configuration["pubtator_to_xml"]['documents'],
configuration["pubtator_to_xml"]['output']
)
del configuration["pubtator_to_xml"]
if (
"extract_tags" in configuration and
not configuration["extract_tags"]["skip"]
):
print("Executing extract_tags...")
extract_annotations(
configuration["extract_tags"]["input"],
configuration["extract_tags"]["output"]
)
del configuration["extract_tags"]
if (
"hetnet_id_extractor" in configuration and
not configuration["hetnet_id_extractor"]["skip"]
):
print("Executing hetnet_id_extractor...")
filter_tags(
configuration["hetnet_id_extractor"]["input"],
configuration["hetnet_id_extractor"]["output"]
)
del configuration["hetnet_id_extractor"]
if (
"map_pmids_to_pmcids" in configuration and
not configuration["map_pmids_to_pmcids"]["skip"]
):
print("Executing map_pmids_to_pmcids...")
map_ids(
configuration["map_pmids_to_pmcids"]["input"],
configuration["map_pmids_to_pmcids"]["output"],
configuration["map_pmids_to_pmcids"]["debug"]
)
del configuration["map_pmids_to_pmcids"]
if (
"download_full_text" in configuration and
not configuration["download_full_text"]["skip"]
):
print("Executing download_full_text...")
download_full_text(
configuration["download_full_text"]["input"],
configuration["download_full_text"]["document_batch"],
configuration["download_full_text"]["temp_dir"],
configuration["download_full_text"]["log_file"]
)
merge_full_text(
configuration["download_full_text"]["temp_dir"],
configuration["download_full_text"]["output"]
)
del configuration["download_full_text"]
if (
"extract_full_text_tags" in configuration and
not configuration["extract_full_text_tags"]["skip"]
):
print("Executing extract_full_text_tags...")
extract_annotations(
configuration["extract_full_text_tags"]["input"],
configuration["extract_full_text_tags"]["output"]
)
del configuration["extract_full_text_tags"]
if (
"hetnet_id_extractor_full_text" in configuration and
not configuration["hetnet_id_extractor_full_text"]["skip"]
):
print("Executing hetnet_id_extractor_full_text...")
filter_tags(
configuration["hetnet_id_extractor_full_text"]["input"],
configuration["hetnet_id_extractor_full_text"]["output"]
)
del configuration["hetnet_id_extractor_full_text"]
if len(configuration) > 0:
not_executed_commands = '\n'.join(configuration.keys())
print(
"\n"
"Commands not executed:\n"
f"{not_executed_commands}"
)