Mercurial > repos > iuc > ebi_metagenomics_run_downloader

annotate ebeye_urllib.py @ 2:6155fa39a899 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
author iuc
date Sat, 21 Jan 2017 14:40:54 -0500
parents e2e9fae080ad
children a1ef6c88ee37
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e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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1 #!/usr/bin/env python
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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2 # ======================================================================
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3 # Script derived from the EB-eye (REST) Python client available at
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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4 # http://www.ebi.ac.uk/Tools/webservices/services/eb-eye_rest
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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5 # and distributed under the Apache License
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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6 # ======================================================================
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7 # Load libraries
2
6155fa39a899 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
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8 import os
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9 import platform
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6155fa39a899 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
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10 import re
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e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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11 import urllib
2
6155fa39a899 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
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12 import urllib2
6155fa39a899 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
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13 from gzip import GzipFile
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e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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14 from optparse import OptionParser
2
6155fa39a899 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
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15 from StringIO import StringIO
6155fa39a899 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
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16
0
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17 from xmltramp2 import xmltramp
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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19 # Service base URL
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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20 baseUrl = 'http://www.ebi.ac.uk/ebisearch/ws/rest'
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22 # Debug level
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23 debugLevel = 0
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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26 # Debug print
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27 def printDebugMessage(functionName, message, level):
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28 if(level <= debugLevel):
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29 print ('[' + functionName + '] ' + message)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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30
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32 # User-agent for request.
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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33 def getUserAgent():
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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34 printDebugMessage('getUserAgent', 'Begin', 11)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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35 urllib_agent = 'Python-urllib/%s' % urllib2.__version__
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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36 clientRevision = '$Revision: 2468 $'
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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37 clientVersion = '0'
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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38 if len(clientRevision) > 11:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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39 clientVersion = clientRevision[11:-2]
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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40 user_agent = 'EBI-Sample-Client/%s (%s; Python %s; %s) %s' % (
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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41 clientVersion, os.path.basename(__file__),
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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42 platform.python_version(), platform.system(),
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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43 urllib_agent
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44 )
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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45 printDebugMessage('getUserAgent', 'user_agent: ' + user_agent, 12)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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46 printDebugMessage('getUserAgent', 'End', 11)
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47 return user_agent
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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48
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49
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50 # Wrapper for a REST (HTTP GET) request
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51 def restRequest(url):
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52 printDebugMessage('restRequest', 'Begin', 11)
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53 printDebugMessage('restRequest', 'url: ' + url, 11)
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54 # python 2
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55 url = urllib.quote(url, safe="%/:=&?~#+!$,;'@()*[]")
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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56 # python 3
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57 # url = urllib.request.quote(url, safe="%/:=&?~#+!$,;'@()*[]")
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58
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59 try:
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60 user_agent = getUserAgent()
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61 http_headers = {
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62 'User-Agent': user_agent,
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63 'Accept-Encoding': 'gzip'
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64 }
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65 req = urllib2.Request(url, None, http_headers)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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66 resp = urllib2.urlopen(req)
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67 # python2
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68 encoding = resp.info().getheader('Content-Encoding')
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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69 # python3
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70 # encoding = resp.info().__getitem__('Content-Encoding')
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71 result = None
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72 if encoding is None or encoding == 'identity':
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73 # python2
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74 result = resp.read()
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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75 # python3
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76 # result = str(resp.read(), 'utf-8')
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77 elif encoding == 'gzip':
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78 result = resp.read()
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79 printDebugMessage('restRequest', 'result: ' + str(result), 21)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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80 # python2
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81 gz = GzipFile(
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82 fileobj=StringIO(result),
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83 mode="r")
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84 result = gz.read()
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85 # python3
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86 # result = str(gzip.decompress(result), 'utf-8')
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diff changeset
87 else:
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parents:
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88 raise Exception('Unsupported Content-Encoding')
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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parents:
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89 resp.close()
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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parents:
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90 except urllib2.HTTPError as ex:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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91 raise ex
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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92 printDebugMessage('restRequest', 'result: ' + result, 11)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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93 printDebugMessage('restRequest', 'End', 11)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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parents:
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94 return result
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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95
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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96
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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97 def hasSubdomains(domainInfo):
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98 for dir in domainInfo._dir:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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99 if dir._name == 'subdomains':
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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parents:
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100 return True
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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101 return False
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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102
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103
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104 def extractUsefulFields(fieldInfos):
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105 searchable = []
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106 retrievable = []
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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107
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108 for fieldInfo in fieldInfos:
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109 if fieldInfo('id') == "$facets":
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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110 continue
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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111
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iuc
parents:
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112 options = fieldInfo['options']['option':]
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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113 for option in options:
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114 if option("name") == "searchable" and str(option) == "true":
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115 searchable.append(fieldInfo('id'))
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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116 if option("name") == "retrievable" and str(option) == "true":
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117 retrievable.append(fieldInfo('id'))
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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118 return searchable, retrievable
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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119
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120
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121 def extractLowerLevelDomains(domainInfo, domains):
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122 if hasSubdomains(domainInfo):
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iuc
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123 subdomains = domainInfo['subdomains']['domain':]
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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124 for subdomain in subdomains:
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iuc
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125 domains = extractLowerLevelDomains( subdomain, domains)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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126 else:
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127 searchable, retrievable = extractUsefulFields(
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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128 domainInfo['fieldInfos']['fieldInfo':])
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129
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130 domain_id = domainInfo('id')
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131 domains.setdefault(domain_id, {})
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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132 domains[domain_id]["name"] = domainInfo('name')
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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133 domains[domain_id]["searchable_fields"] = sorted(searchable)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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134 domains[domain_id]["retrievable_fields"] = sorted(retrievable)
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135 return domains
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136
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137
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138 # Get domain Hierarchy
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139 def getDomainHierarchy():
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140 requestUrl = baseUrl + '/allebi'
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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141 xmlDoc = restRequest(requestUrl)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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142 doc = xmltramp.parse(xmlDoc)
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143 allebi = doc['domains']['domain']
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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144 lower_level_domains = extractLowerLevelDomains(allebi, {})
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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145 printDebugMessage('getDomainHierarchy', 'End', 1)
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146 return lower_level_domains
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147
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148
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149 # Check if a databaseInfo matches a database name.
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150 def is_database(dbInfo, dbName):
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151 printDebugMessage('is_database', 'Begin', 11)
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152 retVal = False
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153 if str(dbInfo.name) == dbName:
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154 retVal = True
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155 else:
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156 for dbAlias in dbInfo.aliasList:
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157 if str(dbAlias) == dbName:
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158 retVal = True
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159 printDebugMessage('is_database', 'retVal: ' + str(retVal), 11)
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160 printDebugMessage('is_database', 'End', 11)
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parents:
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161 return retVal
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162
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163
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164 # Get number of results
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165 def getNumberOfResults(domain, query):
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166 printDebugMessage('getNumberOfResults', 'Begin', 1)
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parents:
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167 requestUrl = baseUrl + '/' + domain + '?query=' + query + '&size=0'
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168 printDebugMessage('getNumberOfResults', requestUrl, 2)
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169 xmlDoc = restRequest(requestUrl)
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170 doc = xmltramp.parse(xmlDoc)
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parents:
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171 numberOfResults = int(str(doc['hitCount']))
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parents:
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172 printDebugMessage('getNumberOfResults', 'End', 1)
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173 return numberOfResults
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174
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175
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176 def makeRequest(requestUrl):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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177 xmlDoc = restRequest(requestUrl)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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178 doc = xmltramp.parse(xmlDoc)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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179 entries = doc['entries']['entry':]
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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180 formatted_output = printEntries(entries)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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181 return formatted_output
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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182
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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183
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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184 # Get search results
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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185 def getResults(domain, query, fields):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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186 numberOfResults = getNumberOfResults(domain, query)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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187 maximum_size = 100
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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188 quotient = numberOfResults / maximum_size
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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189 start = 0
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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190
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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191 printDebugMessage('getResults', 'Begin', 1)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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192 request_output = "%s\tlink\n" % (fields.replace(",", "\t"))
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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193 for i in range(quotient):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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194 start = maximum_size * i
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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195 requestUrl = baseUrl + '/' + domain + '?query=' + query
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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196 requestUrl += '&fields=' + fields + '&size=' + str(maximum_size)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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197 requestUrl += '&start=' + str(start) + '&fieldurl=true'
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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198 request_output += makeRequest(requestUrl)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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199
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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200 if (numberOfResults % 100) > 0:
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iuc
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201 start = maximum_size * quotient
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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202 remainder = numberOfResults - start
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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203 requestUrl = baseUrl + '/' + domain + '?query=' + query
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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204 requestUrl += '&fields=' + fields + '&size=' + str(remainder)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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205 requestUrl += '&start=' + str(start) + '&fieldurl=true'
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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206 request_output += makeRequest(requestUrl)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
207
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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208 print(request_output)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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209
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
210
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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211 def printEntries(entries):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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212 output = ""
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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213 printDebugMessage('printEntries', 'Begin', 1)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
214 for entry in entries:
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iuc
parents:
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215 sep = ""
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
216 for field in entry['fields']['field':]:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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217 output += "%s" % (sep)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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218 fields = field['values']['value':]
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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219 if len(fields) > 0:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
220 sub_sep = ""
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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221 for value in field['values']['value':]:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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222 output += "%s%s" % (sub_sep, value)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
223 sub_sep = ","
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
224 sep = "\t"
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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225
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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226 if hasFieldUrls(entry):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
227 output += "%s" % (sep)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
228 sub_sep = ""
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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229 for fieldurl in entry['fieldURLs']['fieldURL':]:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
230 output += "%s%s" % (sub_sep, str(fieldurl))
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
231 sub_sep = ","
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
232 sep = "\t"
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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233 if hasViewUrls(entry):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
234 output += "%s" % (sep)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
235 sub_sep = ""
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
236 for viewurl in entry['viewURLs']['viewURL':]:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
237 output += "%s%s" % (sub_sep, str(viewurl))
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
238 sub_sep = ","
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
239 output += "\n"
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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240 printDebugMessage('printEntries', 'End', 1)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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parents:
diff changeset
241 return output
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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242
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243
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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244 def hasFieldUrls(entry):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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245 for dir in entry._dir:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
246 if dir._name == 'fieldURLs':
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
247 return True
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
248 return False
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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diff changeset
249
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
250
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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251 def hasViewUrls(entry):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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252 for dir in entry._dir:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
253 if dir._name == 'viewURLs':
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
254 return True
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
255 return False
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
256
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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parents:
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257
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iuc
parents:
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258 def getRunLink(run_id):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
259 printDebugMessage('getEntries', 'Begin', 1)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
260 requestUrl = baseUrl + '/metagenomics_runs/entry/' + run_id + '?fieldurl=true'
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
261 printDebugMessage('getEntries', requestUrl, 2)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
262 xmlDoc = restRequest(requestUrl)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
263 doc = xmltramp.parse(xmlDoc)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
264 entries = doc['entries']['entry':]
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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265 fieldURL = ''
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266 for entry in entries:
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267 for fieldurl in entry['fieldURLs']['fieldURL':]:
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268 fieldURL += str(fieldurl)
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269 printDebugMessage('getEntries', 'End', 1)
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270 p = re.compile('http')
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271 fieldURL = p.sub('https', fieldURL)
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272 print fieldURL
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273
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274
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275 if __name__ == '__main__':
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276 # Usage message
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277 usage = """
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278 %prog getDomainHierarchy
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279 %prog getResults <domain> <query> <fields>
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280 %prog getRunLink <runId>
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281 """
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282
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283 description = "Tools to query and download data from several EMBL-EBI databases"
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284 description += "The searching tools are using the EB-eye search engine. "
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285 description += "http://www.ebi.ac.uk/ebisearch/"
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286 # Process command-line options
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287 parser = OptionParser(
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288 usage=usage,
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289 description=description,
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290 version='1.0')
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291 (options, args) = parser.parse_args()
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292
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293 # No arguments, print usage
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294 if len(args) < 1:
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295 parser.print_help()
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296
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297 # Get domain hierarchy
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298 elif args[0] == 'getDomainHierarchy':
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299 getDomainHierarchy()
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300
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301 # Get search results
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302 elif args[0] == 'getResults':
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303 if len(args) < 4:
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304 print ('domain, query and fields should be given.')
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305 else:
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306 getResults(args[1], args[2], args[3])
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307
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308 # Get run link results
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309 elif args[0] == 'getRunLink':
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310 if len(args) < 2:
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311 print ('run id should be given.')
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312 else:
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313 getRunLink(args[1])
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314
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315 # Unknown argument combination, display usage
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316 else:
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317 print ('Error: unrecognised argument combination')
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318 parser.print_help()