Mercurial > repos > iuc > ncbi_eutils_efetch

annotate eutils.py @ 2:0977ec0f3ba8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
author iuc
date Wed, 11 Mar 2020 04:03:36 -0400
parents 0fc65a60436f
children c09fcbe4b16a
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1 import json
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2 import os
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0977ec0f3ba8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
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3 from io import StringIO
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4
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5 from Bio import Entrez
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7 Entrez.tool = "GalaxyEutils_1_0"
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8 BATCH_SIZE = 200
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11 class Client(object):
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13 def __init__(self, history_file=None, user_email=None, admin_email=None):
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14 self.using_history = False
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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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16 if user_email is not None and admin_email is not None:
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17 Entrez.email = ';'.join((admin_email, user_email))
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18 elif user_email is not None:
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19 Entrez.email = user_email
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20 elif admin_email is not None:
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21 Entrez.email = admin_email
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22 else:
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23 Entrez.email = os.environ.get('NCBI_EUTILS_CONTACT', None)
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25 if Entrez.email is None:
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26 raise Exception("Cannot continue without an email; please set "
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27 "administrator email in NCBI_EUTILS_CONTACT")
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29 if history_file is not None:
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30 with open(history_file, 'r') as handle:
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31 data = json.loads(handle.read())
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32 self.query_key = data['QueryKey']
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33 self.webenv = data['WebEnv']
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34 self.using_history = True
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36 def get_history(self):
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37 if not self.using_history:
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38 return {}
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39 else:
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40 return {
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41 'query_key': self.query_key,
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42 'WebEnv': self.webenv,
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43 }
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45 def post(self, database, **payload):
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46 return json.dumps(Entrez.read(Entrez.epost(database, **payload)), indent=4)
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47
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48 def fetch(self, db, ftype=None, **payload):
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49 os.makedirs("downloads")
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51 if 'id' in payload:
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52 summary = self.id_summary(db, payload['id'])
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53 else:
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54 summary = self.history_summary(db)
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56 count = len(summary)
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57 payload['retmax'] = BATCH_SIZE
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58
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59 # This may be bad. I'm not sure yet. I think it will be ... but UGH.
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60 for i in range(0, count, BATCH_SIZE):
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61 payload['retstart'] = i
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62 file_path = os.path.join('downloads', 'EFetch Results Chunk %s.%s' % (i, ftype))
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63 with open(file_path, 'w') as handle:
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64 handle.write(Entrez.efetch(db, **payload).read())
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65
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66 def id_summary(self, db, id_list):
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67 payload = {
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68 'db': db,
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69 'id': id_list,
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70 }
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71 return Entrez.read(Entrez.esummary(**payload))
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72
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73 def history_summary(self, db):
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74 if not self.using_history:
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75 raise Exception("History must be available for this method")
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76
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77 payload = {
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78 'db': db,
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79 'query_key': self.query_key,
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80 'WebEnv': self.webenv,
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81 }
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82 return Entrez.read(Entrez.esummary(**payload))
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83
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84 def summary(self, **payload):
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85 return Entrez.esummary(**payload).read()
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86
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87 def link(self, **payload):
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88 return Entrez.elink(**payload).read()
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89
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90 def extract_history(self, xml_data):
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91 parsed_data = Entrez.read(StringIO.StringIO(xml_data))
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92 history = {}
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93 for key in ('QueryKey', 'WebEnv'):
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94 if key in parsed_data:
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95 history[key] = parsed_data[key]
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96
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97 return history
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98
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99 def search(self, **payload):
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100 return Entrez.esearch(**payload).read()
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101
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102 def info(self, **kwargs):
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103 return Entrez.einfo(**kwargs).read()
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104
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105 def gquery(self, **kwargs):
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106 return Entrez.egquery(**kwargs).read()
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107
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108 def citmatch(self, **kwargs):
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109 return Entrez.ecitmatch(**kwargs).read()
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110
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111 @classmethod
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112 def parse_ids(cls, id_list, id, history_file):
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113 """Parse IDs passed on --cli or in a file passed to the cli
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114 """
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115 merged_ids = []
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116 if id is not None:
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117 for pid in id.replace('__cn__', ',').replace('\n', ',').split(','):
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118 if pid is not None and len(pid) > 0:
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119 merged_ids.append(pid)
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120
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121 if id_list is not None:
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122 with open(id_list, 'r') as handle:
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123 merged_ids += [x.strip() for x in handle.readlines()]
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124
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125 # Exception hanlded here for uniformity
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126 if len(merged_ids) == 0 and history_file is None:
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127 raise Exception("Must provide history file or IDs")
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128
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129 return merged_ids