Mercurial > repos > iuc > ebi_metagenomics_run_downloader

annotate ebeye_urllib.py @ 0:e2e9fae080ad draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
author iuc
date Thu, 01 Dec 2016 15:27:59 -0500
parents
children 6155fa39a899
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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
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
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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8 import platform
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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9 import os
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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10 import urllib
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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11 import re
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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12 from optparse import OptionParser
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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13 from gzip import GzipFile
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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14 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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15 # python2
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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16 from StringIO import StringIO
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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17 import urllib2
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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18 # python3
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19 # import urllib.request as urllib2
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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20
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21
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22 # Service base URL
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23 baseUrl = 'http://www.ebi.ac.uk/ebisearch/ws/rest'
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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24
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25 # Debug level
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26 debugLevel = 0
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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27
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29 # Debug print
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30 def printDebugMessage(functionName, message, level):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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31 if(level <= debugLevel):
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32 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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33
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34
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35 # 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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36 def getUserAgent():
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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37 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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38 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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39 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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40 clientVersion = '0'
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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41 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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42 clientVersion = clientRevision[11:-2]
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43 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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44 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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45 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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46 urllib_agent
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47 )
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48 printDebugMessage('getUserAgent', 'user_agent: ' + user_agent, 12)
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49 printDebugMessage('getUserAgent', 'End', 11)
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50 return user_agent
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51
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52
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53 # Wrapper for a REST (HTTP GET) request
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54 def restRequest(url):
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55 printDebugMessage('restRequest', 'Begin', 11)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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56 printDebugMessage('restRequest', 'url: ' + url, 11)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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57 # python 2
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58 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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59 # python 3
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60 # url = urllib.request.quote(url, safe="%/:=&?~#+!$,;'@()*[]")
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61
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62 try:
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63 user_agent = getUserAgent()
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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64 http_headers = {
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65 'User-Agent': user_agent,
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66 'Accept-Encoding': 'gzip'
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67 }
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68 req = urllib2.Request(url, None, http_headers)
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69 resp = urllib2.urlopen(req)
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70 # python2
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71 encoding = resp.info().getheader('Content-Encoding')
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72 # python3
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73 # encoding = resp.info().__getitem__('Content-Encoding')
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74 result = None
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75 if encoding is None or encoding == 'identity':
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76 # python2
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77 result = resp.read()
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78 # python3
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79 # result = str(resp.read(), 'utf-8')
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80 elif encoding == 'gzip':
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81 result = resp.read()
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82 printDebugMessage('restRequest', 'result: ' + str(result), 21)
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83 # python2
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84 gz = GzipFile(
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85 fileobj=StringIO(result),
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86 mode="r")
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87 result = gz.read()
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88 # python3
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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89 # result = str(gzip.decompress(result), 'utf-8')
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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90 else:
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91 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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92 resp.close()
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93 except urllib2.HTTPError as ex:
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94 raise ex
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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95 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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96 printDebugMessage('restRequest', 'End', 11)
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97 return result
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98
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99
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100 def hasSubdomains(domainInfo):
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101 for dir in domainInfo._dir:
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102 if dir._name == 'subdomains':
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103 return True
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104 return False
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105
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106
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107 def extractUsefulFields(fieldInfos):
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108 searchable = []
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109 retrievable = []
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110
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111 for fieldInfo in fieldInfos:
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112 if fieldInfo('id') == "$facets":
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113 continue
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114
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115 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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116 for option in options:
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117 if option("name") == "searchable" and str(option) == "true":
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118 searchable.append(fieldInfo('id'))
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119 if option("name") == "retrievable" and str(option) == "true":
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120 retrievable.append(fieldInfo('id'))
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121 return searchable, retrievable
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122
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123
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124 def extractLowerLevelDomains(domainInfo, domains):
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125 if hasSubdomains(domainInfo):
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126 subdomains = domainInfo['subdomains']['domain':]
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127 for subdomain in subdomains:
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128 domains = extractLowerLevelDomains( subdomain, domains)
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129 else:
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130 searchable, retrievable = extractUsefulFields(
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131 domainInfo['fieldInfos']['fieldInfo':])
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132
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133 domain_id = domainInfo('id')
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134 domains.setdefault(domain_id, {})
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135 domains[domain_id]["name"] = domainInfo('name')
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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136 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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137 domains[domain_id]["retrievable_fields"] = sorted(retrievable)
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138 return domains
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139
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140
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141 # Get domain Hierarchy
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142 def getDomainHierarchy():
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143 requestUrl = baseUrl + '/allebi'
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144 xmlDoc = restRequest(requestUrl)
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145 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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146 allebi = doc['domains']['domain']
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147 lower_level_domains = extractLowerLevelDomains(allebi, {})
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148 printDebugMessage('getDomainHierarchy', 'End', 1)
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149 return lower_level_domains
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150
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151
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152 # Check if a databaseInfo matches a database name.
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153 def is_database(dbInfo, dbName):
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154 printDebugMessage('is_database', 'Begin', 11)
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155 retVal = False
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156 if str(dbInfo.name) == dbName:
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157 retVal = True
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158 else:
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159 for dbAlias in dbInfo.aliasList:
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160 if str(dbAlias) == dbName:
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161 retVal = True
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162 printDebugMessage('is_database', 'retVal: ' + str(retVal), 11)
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163 printDebugMessage('is_database', 'End', 11)
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164 return retVal
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165
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166
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167 # Get number of results
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168 def getNumberOfResults(domain, query):
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169 printDebugMessage('getNumberOfResults', 'Begin', 1)
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170 requestUrl = baseUrl + '/' + domain + '?query=' + query + '&size=0'
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171 printDebugMessage('getNumberOfResults', requestUrl, 2)
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172 xmlDoc = restRequest(requestUrl)
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173 doc = xmltramp.parse(xmlDoc)
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174 numberOfResults = int(str(doc['hitCount']))
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175 printDebugMessage('getNumberOfResults', 'End', 1)
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parents:
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176 return numberOfResults
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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177
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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178
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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179 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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180 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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181 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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182 entries = doc['entries']['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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183 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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184 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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185
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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186
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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187 # Get search results
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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188 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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189 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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190 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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191 quotient = numberOfResults / maximum_size
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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192 start = 0
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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193
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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194 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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195 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
parents:
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196 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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197 start = maximum_size * i
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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198 requestUrl = baseUrl + '/' + domain + '?query=' + query
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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199 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
iuc
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200 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
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201 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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diff changeset
202
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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203 if (numberOfResults % 100) > 0:
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 start = maximum_size * quotient
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 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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206 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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207 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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208 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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209 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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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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diff changeset
211 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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diff changeset
212
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iuc
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diff changeset
213
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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214 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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215 output = ""
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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216 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
217 for entry in entries:
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iuc
parents:
diff changeset
218 sep = ""
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
219 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:
diff changeset
220 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
221 fields = field['values']['value':]
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
222 if len(fields) > 0:
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
223 sub_sep = ""
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
224 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:
diff changeset
225 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
parents:
diff changeset
226 sub_sep = ","
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
227 sep = "\t"
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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diff changeset
228
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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229 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
230 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
231 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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232 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
parents:
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233 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
parents:
diff changeset
234 sub_sep = ","
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
235 sep = "\t"
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
236 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
237 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
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 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
240 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
241 sub_sep = ","
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
242 output += "\n"
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
243 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
244 return output
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
245
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
246
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
247 def hasFieldUrls(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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248 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
249 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
250 return True
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
251 return False
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
252
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
253
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
254 def hasViewUrls(entry):
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
255 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
256 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
257 return True
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
258 return False
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
259
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff changeset
260
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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261 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
262 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
263 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
264 printDebugMessage('getEntries', requestUrl, 2)
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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265 xmlDoc = restRequest(requestUrl)
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266 doc = xmltramp.parse(xmlDoc)
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267 entries = doc['entries']['entry':]
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268 fieldURL = ''
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269 for entry in entries:
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270 for fieldurl in entry['fieldURLs']['fieldURL':]:
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271 fieldURL += str(fieldurl)
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272 printDebugMessage('getEntries', 'End', 1)
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273 p = re.compile('http')
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274 fieldURL = p.sub('https', fieldURL)
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275 print fieldURL
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276
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277
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278 if __name__ == '__main__':
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279 # Usage message
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280 usage = """
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281 %prog getDomainHierarchy
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282 %prog getResults <domain> <query> <fields>
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283 %prog getRunLink <runId>
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284 """
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285
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286 description = "Tools to query and download data from several EMBL-EBI databases"
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287 description += "The searching tools are using the EB-eye search engine. "
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288 description += "http://www.ebi.ac.uk/ebisearch/"
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289 # Process command-line options
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290 parser = OptionParser(
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291 usage=usage,
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292 description=description,
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293 version='1.0')
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294 (options, args) = parser.parse_args()
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295
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296 # No arguments, print usage
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297 if len(args) < 1:
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298 parser.print_help()
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299
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300 # Get domain hierarchy
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301 elif args[0] == 'getDomainHierarchy':
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302 getDomainHierarchy()
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303
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304 # Get search results
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305 elif args[0] == 'getResults':
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306 if len(args) < 4:
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307 print ('domain, query and fields should be given.')
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308 else:
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309 getResults(args[1], args[2], args[3])
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310
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311 # Get run link results
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312 elif args[0] == 'getRunLink':
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313 if len(args) < 2:
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314 print ('run id should be given.')
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315 else:
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316 getRunLink(args[1])
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317
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318 # Unknown argument combination, display usage
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319 else:
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320 print ('Error: unrecognised argument combination')
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321 parser.print_help()