Mercurial > repos > iuc > ncbi_eutils_esummary

annotate efetch.py @ 4:ff3a5e980fab draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 25545b698cffc9999cde0079b3be176f55e17803"
author iuc
date Mon, 04 Jan 2021 11:45:16 +0000
parents 254f40d3ae2b
children 7fe990069458
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92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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1 #!/usr/bin/env python
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254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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3 import argparse
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254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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4 import glob
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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5 import json
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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6 import logging
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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7 import os
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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c8d4ea6376a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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10 import eutils
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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13 logging.basicConfig(level=logging.INFO)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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16 def handleEfetchException(e, db, payload):
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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17 logging.error('No results returned. This could either be due to no records matching the supplied IDs for the query database or it could be an error due to invalid parameters. The reported exception was "%s".\n\nPayload used for the efetch query to database "%s"\n\n%s', e, db, json.dumps(payload, indent=4))
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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19 # Create a file in the downloads folder so that the user can access run information
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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20 current_directory = os.getcwd()
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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21 final_directory = os.path.join(current_directory, r'downloads')
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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22 if not os.path.exists(final_directory):
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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23 os.makedirs(final_directory)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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25 print('The following files were downloaded:')
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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26 print(os.listdir(final_directory))
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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28 file_path = os.path.join('downloads', 'no_results.txt')
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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29 with open(file_path, 'w') as handle:
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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30 handle.write('No results')
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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33 def localFetch(db, gformat, newname, **payload):
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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34 problem = None
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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35 try:
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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36 c.fetch(db, **payload)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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38 for chunk, file in enumerate(glob.glob('downloads/EFetch *')):
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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39 os.rename(file, '%s%s.%s' % (newname, chunk + 1, gformat))
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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41 except Exception as e:
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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42 problem = e
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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43 handleEfetchException(e, db, payload)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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44 else:
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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45 print('The following files were downloaded:')
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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46 print(os.listdir('downloads'))
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48 return problem
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50
0
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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51 if __name__ == '__main__':
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52 parser = argparse.ArgumentParser(description='EFetch', epilog='')
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53 parser.add_argument('db', help='Database to use')
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54 parser.add_argument('--user_email', help="User email")
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55 parser.add_argument('--admin_email', help="Admin email")
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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57 parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)')
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0
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59 # ID source
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60 parser.add_argument('--id_json', help='list of ids in a json file as returned by esearch or elink')
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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61 parser.add_argument('--id_xml', help='list of ids in an xml file as returned by esearch or elink')
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62 parser.add_argument('--id_list', help='list of ids')
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63 parser.add_argument('--id', help='Comma separated individual IDs')
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64 parser.add_argument('--history_file', help='Fetch results from previous query (JSON)')
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65 parser.add_argument('--history_xml', help='Fetch results from previous query (XML)')
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67 # Output
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68 parser.add_argument('--retmode', help='Retmode')
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69 parser.add_argument('--rettype', help='Rettype')
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70 parser.add_argument('--galaxy_format', help='Galaxy format')
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71 args = parser.parse_args()
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73 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
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75 payload = {}
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76 for attr in ('retmode', 'rettype'):
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77 if getattr(args, attr, None) is not None:
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78 payload[attr] = getattr(args, attr)
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79
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254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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80 if args.history_file is not None or args.history_xml is not None:
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81 if args.history_file is not None:
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82 input_histories = c.get_histories()
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83 else:
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84 input_histories = c.extract_histories_from_xml_file(args.history_xml)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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85
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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86 problem = None
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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87 for hist in input_histories:
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88 qkey = hist['query_key']
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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89 tmp_payload = payload
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90 tmp_payload.update(hist)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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91 newname = 'downloads/EFetch-%s-%s-querykey%s-chunk' % (args.rettype, args.retmode, qkey)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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92 problem = localFetch(args.db, args.galaxy_format, newname, **tmp_payload)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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93
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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94 if os.path.exists('downloads'):
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95 os.rename('downloads', 'downloads-qkey%s' % (qkey))
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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96
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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97 if not os.path.exists('downloads'):
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98 os.makedirs('downloads')
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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99
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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100 for relpath in glob.glob('downloads-qkey*/*'):
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101 file = os.path.basename(relpath)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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102 os.rename(relpath, 'downloads/%s' % (file))
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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103
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104 if problem is not None:
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105 raise(problem)
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106
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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107 else:
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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108 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file, args.id_xml, args.id_json)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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109 payload['id'] = ','.join(merged_ids)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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110 newname = 'downloads/EFetch-%s-%s-chunk' % (args.rettype, args.retmode)
254f40d3ae2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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111 localFetch(args.db, args.galaxy_format, newname, **payload)