Mercurial > repos > iuc > ncbi_eutils_efetch

annotate eutils.py @ 3:aa88712a7536 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
author iuc
date Fri, 10 Jun 2016 14:49:12 -0400
parents 1b4ac594d02a
children c26d1863f3f3
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1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
iuc
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1 import os
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
iuc
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2 import json
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
iuc
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3 import StringIO
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
iuc
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4 from Bio import Entrez
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
iuc
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5 Entrez.tool = "GalaxyEutils_1_0"
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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6 BATCH_SIZE = 200
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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9 class Client(object):
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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11 def __init__(self, history_file=None, user_email=None, admin_email=None):
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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12 self.using_history = False
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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14 if user_email is not None and admin_email is not None:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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15 Entrez.email = ';'.join((admin_email, user_email))
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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16 elif user_email is not None:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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17 Entrez.email = user_email
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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18 elif admin_email is not None:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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19 Entrez.email = admin_email
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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20 else:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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21 Entrez.email = os.environ.get('NCBI_EUTILS_CONTACT', None)
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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23 if Entrez.email is None:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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24 raise Exception("Cannot continue without an email; please set "
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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25 "administrator email in NCBI_EUTILS_CONTACT")
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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27 if history_file is not None:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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28 with open(history_file, 'r') as handle:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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29 data = json.loads(handle.read())
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aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
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30 print data
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1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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31 self.query_key = data['QueryKey']
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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32 self.webenv = data['WebEnv']
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33 self.using_history = True
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35 def get_history(self):
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36 if not self.using_history:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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37 return {}
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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38 else:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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39 return {
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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40 'query_key': self.query_key,
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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41 'WebEnv': self.webenv,
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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42 }
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44 def post(self, database, **payload):
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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45 return json.dumps(Entrez.read(Entrez.epost(database, **payload)), indent=4)
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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47 def fetch(self, db, whole=False, **payload):
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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48 if whole:
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49 if 'id' in payload:
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50 summary = self.id_summary(db, payload['id'])
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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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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56 payload['retmax'] = BATCH_SIZE
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57
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58 # Print the first one
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59 print Entrez.efetch(db, **payload).read()
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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60 # Then write subsequent to files for <discover datasets>
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61 for i in range(BATCH_SIZE, count, BATCH_SIZE):
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62 payload['retstart'] = i
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63 # TODO: output multiple files??? Collection?
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64 with open('%s.out' % i, 'w') as handle:
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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65 handle.write(Entrez.efetch(db, **payload).read())
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66 else:
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67 print Entrez.efetch(db, **payload).read()
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68
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69 def id_summary(self, db, id_list):
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70 payload = {
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71 'db': db,
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72 'id': id_list,
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73 }
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74 return Entrez.read(Entrez.esummary(**payload))
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75
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76 def history_summary(self, db):
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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77 if not self.using_history:
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78 raise Exception("History must be available for this method")
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79
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80 payload = {
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81 'db': db,
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82 'query_key': self.query_key,
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83 'WebEnv': self.webenv,
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84 }
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85 return Entrez.read(Entrez.esummary(**payload))
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86
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87 def summary(self, **payload):
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88 return Entrez.esummary(**payload).read()
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89
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90 def link(self, **payload):
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91 return Entrez.elink(**payload).read()
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92
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93 def extract_history(self, xml_data):
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94 parsed_data = Entrez.read(StringIO.StringIO(xml_data))
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95 history = {}
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96 for key in ('QueryKey', 'WebEnv'):
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97 if key in parsed_data:
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98 history[key] = parsed_data[key]
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99
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100 return history
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101
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102 def search(self, **payload):
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103 return Entrez.esearch(**payload).read()
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104
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105 def info(self, **kwargs):
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106 return Entrez.einfo(**kwargs).read()
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107
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108 def gquery(self, **kwargs):
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109 return Entrez.egquery(**kwargs).read()
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110
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111 def citmatch(self, **kwargs):
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112 return Entrez.ECitMatch(**kwargs).read()
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113
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114 @classmethod
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115 def parse_ids(cls, id_list, id, history_file):
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116 """Parse IDs passed on --cli or in a file passed to the cli
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117 """
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118 merged_ids = []
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119 if id is not None:
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120 for pid in id.replace('__cn__', ',').replace('\n', ',').split(','):
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121 if pid is not None and len(pid) > 0:
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122 merged_ids.append(pid)
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123
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124 if id_list is not None:
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125 with open(id_list, 'r') as handle:
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126 merged_ids += [x.strip() for x in handle.readlines()]
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127
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128 # Exception hanlded here for uniformity
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129 if len(merged_ids) == 0 and history_file is None:
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130 raise Exception("Must provide history file or IDs")
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131
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132 return merged_ids