comparison data_manager/data_manager.py @ 2:24c02af5fd77 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit 6a91765e86532f90dc2bdaae50d9d1a87cf62d9d-dirty

1:f7ad11d31098

import argparse
import datetime
import json
import os
import shutil
import tarfile
import zipfile
try:
    # For Python 3.0 and later
    from urllib.request import Request, urlopen
except ImportError:

    data_manager_entry = {}
    data_manager_entry['value'] = fname.split(".")[0]
    data_manager_entry['name'] = FILE2NAME[fname]
    data_manager_entry['type'] = FILE2TYPE[fname]
    data_manager_entry['path'] = path

    data_manager_json = dict(data_tables=dict(megan_tools=data_manager_entry))

    params = json.loads(open(outjson).read())
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    output_path = os.path.abspath(os.path.join(os.getcwd(), 'megan_tools'))
    for filename in os.listdir(workdir):
        shutil.move(os.path.join(output_path, filename), target_directory)
    file(outjson, 'w').write(json.dumps(data_manager_json))


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Create data manager json.')
    parser.add_argument('--out', action='store', help='JSON filename')

2:24c02af5fd77

import argparse
import json
import os
import shutil
import sys
import zipfile
try:
    # For Python 3.0 and later
    from urllib.request import Request, urlopen
except ImportError:

    data_manager_entry = {}
    data_manager_entry['value'] = fname.split(".")[0]
    data_manager_entry['name'] = FILE2NAME[fname]
    data_manager_entry['type'] = FILE2TYPE[fname]
    data_manager_entry['path'] = path
    
    data_manager_json = dict(data_tables=dict(megan_tools=data_manager_entry))

    params = json.loads(open(outjson).read())
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    output_path = os.path.abspath(os.path.join(os.getcwd(), 'megan_tools'))
    for filename in os.listdir(workdir):
        shutil.move(os.path.join(output_path, filename), target_directory)
    file(outjson, 'w').write(json.dumps(data_manager_json))
    sys.stderr.write("%s\n"%(json.dumps(data_manager_json, indent=4)))


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Create data manager json.')
    parser.add_argument('--out', action='store', help='JSON filename')