comparison alveo_item_list_importer.py @ 14:a38315ecf593 draft

planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty

13:be3fd14899a1

from __future__ import print_function
import json
import argparse
import pyalveo
import sys

API_URL = 'https://app.alveo.edu.au' # TODO: export constants to a separate module


def parser():
    parser = argparse.ArgumentParser(description="Retrieves Alveo Item Lists")
    parser.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key")
    parser.add_argument('--output', required=True, action="store", type=str, help="Path to output file")
    return parser.parse_args()

# TODO: export common function to helper module
def get_item_lists(api_key):
    client = pyalveo.Client(api_key=api_key, api_url=API_URL, use_cache=False)
    return client.get_item_lists()

def write_table(item_lists, filename):
    with open(filename, 'w') as outfile:
        for list_set in item_lists.values():
            for item_list in list_set:
                outfile.write("%s (%d)\t%s\n" % (item_list['name'], item_list['num_items'], item_list['item_list_url']))

def main():
    args = parser()
    try:
        api_key = open(args.api_key, 'r').read().strip()

14:a38315ecf593

from __future__ import print_function
import argparse
import sys
from util import get_item_lists


def parser():
    p = argparse.ArgumentParser(description="Retrieves Alveo Item Lists")
    p.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key")
    p.add_argument('--output', required=True, action="store", type=str, help="Path to output file")
    return p.parse_args()


def write_table(item_lists, filename):
    with open(filename, 'w') as outfile:
        for list_set in item_lists.values():
            for item_list in list_set:
                outfile.write("%s (%d)\t%s\n" % (item_list['name'], item_list['num_items'], item_list['item_list_url']))


def main():
    args = parser()
    try:
        api_key = open(args.api_key, 'r').read().strip()