Mercurial > repos > iuc > data_manager_plant_tribes_scaffolds_downloader
diff data_manager/data_manager_plant_tribes_scaffolds_download.py @ 0:4c96b684f0fd draft
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author | iuc |
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date | Fri, 13 Jan 2017 10:34:15 -0500 |
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children | 80b0bd65cbfb |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_plant_tribes_scaffolds_download.py Fri Jan 13 10:34:15 2017 -0500 @@ -0,0 +1,104 @@ +#!/usr/bin/env python +# +# Data manager for downloading Plant Tribes scaffolds data. +import argparse +import json +import os +import shutil +import sys +import tarfile +import urllib2 +import zipfile + + +DEFAULT_DATA_TABLE_NAMES = ["plant_tribes_scaffolds"] + + +def add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): + data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) + data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, []) + data_manager_dict['data_tables'][data_table_name].append(data_table_entry) + return data_manager_dict + + +def make_directory(dir): + if not os.path.exists(dir): + os.makedirs(dir) + + +def remove_directory(dir): + if os.path.exists(dir): + shutil.rmtree(dir) + + +def url_download(target_directory, url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES): + work_directory = os.path.abspath(os.path.join(os.getcwd(), 'scaffolds')) + make_directory(work_directory) + file_path = os.path.join(work_directory, os.path.basename(url)) + src = None + dst = None + try: + req = urllib2.Request(url) + src = urllib2.urlopen(req) + dst = open(file_path, 'wb') + while True: + chunk = src.read(2**10) + if chunk: + dst.write(chunk) + else: + break + except Exception, e: + print >>sys.stderr, str(e) + finally: + if src: + src.close() + if dst: + dst.close() + if tarfile.is_tarfile(file_path): + fh = tarfile.open(file_path, 'r:*') + elif zipfile.is_zipfile(file_path): + fh = zipfile.ZipFile(file_path, 'r') + else: + return + fh.extractall(work_directory) + os.remove(file_path) + # Move the scaffolds data files into defined output directory. + for filename in os.listdir(work_directory): + shutil.move(os.path.join(work_directory, filename), target_directory) + remove_directory(work_directory) + data_manager_dict = {} + # Populate the data table, there should be a single entry in target_directory. + for file_path in os.listdir(target_directory): + full_path = os.path.abspath(os.path.join(target_directory, file_path)) + entry_name = "%s" % os.path.basename(file_path) + data_table_entry = dict(value=entry_name, name=entry_name, path=full_path, description=description) + for data_table_name in data_table_names: + data_manager_dict = add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) + return data_manager_dict + + +parser = argparse.ArgumentParser() +parser.add_argument('--description', dest='description', default=None, help='Description') +parser.add_argument('--name', dest='name', help='Data table entry unique ID') +parser.add_argument('--out_file', dest='out_file', help='JSON output file') +parser.add_argument('--web_url', dest='web_url', help='Web URL') + +args = parser.parse_args() + +# Some magic happens with tools of type "manage_data" in that the output +# file contains some JSON data that allows us to define the target directory. +params = json.loads(open(args.out_file).read()) +target_directory = params['output_data'][0]['extra_files_path'] +make_directory(target_directory) + +if args.description is None: + description = '' +else: + description = args.description.strip() + +# Get the scaffolds data. +data_manager_dict = url_download(target_directory, args.web_url, description) +# Write the JSON output dataset. +fh = open(args.out_file, 'wb') +fh.write(json.dumps(data_manager_dict)) +fh.close()