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planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
author stevecassidy
date Mon, 15 Jan 2018 18:34:57 -0500
parents a38315ecf593
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1 """
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2 Utility functions and settings for API tools
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3 """
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4 import pyalveo
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5 import csv
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7 # this should be in a config file
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8 API_URL = 'https://app.alveo.edu.au'
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11 def write_key(api_key, output_path, client_module=pyalveo):
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12 """Tests whether an API key is valid and writes it to a file.
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14 :type api_key: String
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15 :param api_key: Alveo API key
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17 :type output_path: String
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18 :param output_path: Path to the file to store the API key in
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20 :type client_module: pyalveo.Client
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21 :param client_module: Module providing the client (used for testing purposes),
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22 defaults to pyalveo
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24 :raises: pyalveo.APIError if the API request is not successful
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26 """
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27 # validate the client key, raises an exception if it is not valid
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28 client_module.Client(api_key=api_key, api_url=API_URL, use_cache=False)
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29 outfile = open(output_path, 'w')
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30 outfile.write(api_key)
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31 outfile.close()
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34 def get_item_lists(api_key):
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35 client = pyalveo.Client(api_key=api_key, api_url=API_URL, use_cache=False)
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36 return client.get_item_lists()
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39 def read_item_list(filename, client):
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40 """Read an item list from a file
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41 which should be a tabular formatted file
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42 with one column header ItemURL.
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43 Return an instance of ItemGroup"""
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45 with open(filename) as fd:
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46 csvreader = csv.DictReader(fd, dialect='excel-tab')
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47 if 'ItemURL' not in csvreader.fieldnames:
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48 return None
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49 itemurls = []
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50 for row in csvreader:
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51 itemurls.append(row['ItemURL'])
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53 itemlist = pyalveo.ItemGroup(itemurls, client)
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55 return itemlist
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