comparison data_manager/data_manager_plant_tribes_scaffolds_download.py @ 4:93253aebaf2e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"

3:5833ef61c1f8

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):

def url_download(url, 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 as e:
        print >>sys.stderr, str(e)
    finally:
        if src:
            src.close()
        if dst:
            dst.close()
    return file_path


def download(target_directory, web_url, config_web_url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES):
    data_manager_dict = {}

parser.add_argument('--web_url', dest='web_url', help='URL for downloading scaffolds')
parser.add_argument('--config_web_url', dest='config_web_url', help='URL for downloading default configs')

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 = ''

    description = args.description.strip()

# Get the scaffolds data.
data_manager_dict = download(target_directory, args.web_url, args.config_web_url, description)
# Write the JSON output dataset.
fh = open(args.out_file, 'wb')
fh.write(json.dumps(data_manager_dict))
fh.close()

4:93253aebaf2e

import json
import os
import shutil
import sys
import tarfile
import zipfile
from urllib.request import Request, urlopen

DEFAULT_DATA_TABLE_NAMES = ["plant_tribes_scaffolds"]


def add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):

def url_download(url, work_directory):
    file_path = os.path.join(work_directory, os.path.basename(url))
    src = None
    dst = None
    try:
        req = Request(url)
        src = urlopen(req)
        with open(file_path, 'wb') as dst:
            while True:
                chunk = src.read(2**10)
                if chunk:
                    dst.write(chunk)
                else:
                    break
    except Exception as e:
        sys.exit(str(e))
    finally:
        if src:
            src.close()
    return file_path


def download(target_directory, web_url, config_web_url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES):
    data_manager_dict = {}

parser.add_argument('--web_url', dest='web_url', help='URL for downloading scaffolds')
parser.add_argument('--config_web_url', dest='config_web_url', help='URL for downloading default configs')

args = parser.parse_args()

with open(args.out_file) as fh:
    params = json.loads(fh.read())
target_directory = params['output_data'][0]['extra_files_path']
make_directory(target_directory)

if args.description is None:
    description = ''

    description = args.description.strip()

# Get the scaffolds data.
data_manager_dict = download(target_directory, args.web_url, args.config_web_url, description)
# Write the JSON output dataset.
with open(args.out_file, 'w') as fh:
    fh.write(json.dumps(data_manager_dict, sort_keys=True))