Mercurial > repos > iuc > ncbi_eutils_ecitmatch

annotate eutils.py @ 0:68cd8d564e0a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author iuc
date Thu, 07 Jul 2016 02:39:21 -0400
parents
children 732a52c18758
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0
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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diff changeset
1 import os
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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2 import json
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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3 import StringIO
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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4 from Bio import Entrez
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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5 Entrez.tool = "GalaxyEutils_1_0"
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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6 BATCH_SIZE = 200
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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7
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8
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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9 class Client(object):
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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10
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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11 def __init__(self, history_file=None, user_email=None, admin_email=None):
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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12 self.using_history = False
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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13
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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14 if user_email is not None and admin_email is not None:
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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15 Entrez.email = ';'.join((admin_email, user_email))
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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16 elif user_email is not None:
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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17 Entrez.email = user_email
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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18 elif admin_email is not None:
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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19 Entrez.email = admin_email
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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20 else:
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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21 Entrez.email = os.environ.get('NCBI_EUTILS_CONTACT', None)
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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23 if Entrez.email is None:
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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24 raise Exception("Cannot continue without an email; please set "
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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25 "administrator email in NCBI_EUTILS_CONTACT")
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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27 if history_file is not None:
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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28 with open(history_file, 'r') as handle:
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29 data = json.loads(handle.read())
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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30 self.query_key = data['QueryKey']
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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31 self.webenv = data['WebEnv']
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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32 self.using_history = True
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33
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34 def get_history(self):
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35 if not self.using_history:
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36 return {}
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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37 else:
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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38 return {
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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39 'query_key': self.query_key,
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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40 'WebEnv': self.webenv,
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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41 }
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42
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43 def post(self, database, **payload):
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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44 return json.dumps(Entrez.read(Entrez.epost(database, **payload)), indent=4)
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45
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46 def fetch(self, db, ftype=None, **payload):
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47 os.makedirs("downloads")
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48
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49 if 'id' in payload:
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50 summary = self.id_summary(db, payload['id'])
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51 else:
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52 summary = self.history_summary(db)
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53
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54 count = len(summary)
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55 payload['retmax'] = BATCH_SIZE
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56
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57 # This may be bad. I'm not sure yet. I think it will be ... but UGH.
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58 for i in range(0, count, BATCH_SIZE):
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59 payload['retstart'] = i
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60 file_path = os.path.join('downloads', 'EFetch Results Chunk %s.%s' % (i, ftype))
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61 with open(file_path, 'w') as handle:
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62 handle.write(Entrez.efetch(db, **payload).read())
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63
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64 def id_summary(self, db, id_list):
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65 payload = {
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66 'db': db,
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67 'id': id_list,
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68 }
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69 return Entrez.read(Entrez.esummary(**payload))
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70
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71 def history_summary(self, db):
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72 if not self.using_history:
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73 raise Exception("History must be available for this method")
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74
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75 payload = {
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76 'db': db,
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77 'query_key': self.query_key,
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78 'WebEnv': self.webenv,
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79 }
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80 return Entrez.read(Entrez.esummary(**payload))
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81
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82 def summary(self, **payload):
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83 return Entrez.esummary(**payload).read()
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84
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85 def link(self, **payload):
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86 return Entrez.elink(**payload).read()
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87
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88 def extract_history(self, xml_data):
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89 parsed_data = Entrez.read(StringIO.StringIO(xml_data))
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90 history = {}
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91 for key in ('QueryKey', 'WebEnv'):
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92 if key in parsed_data:
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93 history[key] = parsed_data[key]
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94
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95 return history
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96
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97 def search(self, **payload):
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98 return Entrez.esearch(**payload).read()
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99
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100 def info(self, **kwargs):
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101 return Entrez.einfo(**kwargs).read()
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102
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103 def gquery(self, **kwargs):
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104 return Entrez.egquery(**kwargs).read()
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105
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106 def citmatch(self, **kwargs):
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107 return Entrez.ecitmatch(**kwargs).read()
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108
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109 @classmethod
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110 def parse_ids(cls, id_list, id, history_file):
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111 """Parse IDs passed on --cli or in a file passed to the cli
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112 """
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113 merged_ids = []
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114 if id is not None:
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115 for pid in id.replace('__cn__', ',').replace('\n', ',').split(','):
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116 if pid is not None and len(pid) > 0:
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117 merged_ids.append(pid)
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118
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119 if id_list is not None:
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120 with open(id_list, 'r') as handle:
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121 merged_ids += [x.strip() for x in handle.readlines()]
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122
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123 # Exception hanlded here for uniformity
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124 if len(merged_ids) == 0 and history_file is None:
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125 raise Exception("Must provide history file or IDs")
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126
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127 return merged_ids