Mercurial > repos > stevecassidy > alveoimport

annotate item_list_util.py @ 18:5e1b7d922ea3 draft default tip

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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
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5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
stevecassidy
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stevecassidy
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2 import json
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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4 API_URL = 'https://app.alveo.edu.au'
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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7 try:
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
stevecassidy
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8 from urllib.request import Request, build_opener, HTTPHandler, HTTPError
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
stevecassidy
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9 from urllib.parse import urlencode, unquote
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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10 except ImportError:
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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11 from urllib2 import Request, build_opener, HTTPHandler, HTTPError
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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12 from urllib import urlencode, unquote
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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15 def api_request(url, api_key):
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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16 """ Perform an API GET request to the given URL
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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17 """
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19 headers = {'X-API-KEY': api_key, 'Accept': 'application/json'}
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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21 req = Request(url, headers=headers)
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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23 try:
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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24 opener = build_opener(HTTPHandler())
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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25 response = opener.open(req)
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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26 except HTTPError as err:
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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27 raise APIError(err.code, err.reason, "Error accessing API (url: %s, method: %s)\nData: %s" % (url, req.get_method() or "GET", data or 'None'))
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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29 content = response.read()
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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31 return json.loads(content.decode('utf-8'))
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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34 def ds_item_lists_options(api_key):
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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35 """Return options for item lists for this user"""
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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37 fname = api_key.get_file_name()
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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38 with open(fname) as fd:
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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39 key = fd.read().strip()
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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41 url = API_URL + "/item_lists"
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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42 itemlists = api_request(url, key)
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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44 result = [(x['name'], x['item_list_url'], False) for x in itemlists['own']]
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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45 result.extend([(x['name'], x['item_list_url'], False) for x in itemlists['shared']])
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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47 return result
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50 if __name__=='__main__':
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52 class FakeHistObj:
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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54 def get_file_name(self):
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55 return "../../test-data/api-key.dat"
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57 fake = FakeHistObj()
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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59 il = ds_item_lists_options(fake)
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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61 import pprint
5e1b7d922ea3 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7
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63 pprint.pprint(il)