Mercurial > repos > iuc > ncbi_eutils_ecitmatch

annotate efetch.py @ 8:ad1e5225bca4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 41f5eb8e0aee5b779d618b5178098c4be89a9ef1
author iuc
date Mon, 23 Jan 2023 10:36:54 +0000
parents b00212deaea7
children
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68cd8d564e0a 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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68cd8d564e0a 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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4 import glob
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5 import json
b00212deaea7 "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
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7 import os
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732a52c18758 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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68cd8d564e0a 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
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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13 logging.basicConfig(level=logging.INFO)
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16 def handleEfetchException(e, db, payload):
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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))
b00212deaea7 "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
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20 current_directory = os.getcwd()
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21 final_directory = os.path.join(current_directory, r'downloads')
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22 if not os.path.exists(final_directory):
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23 os.makedirs(final_directory)
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25 print('The following files were downloaded:')
b00212deaea7 "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))
b00212deaea7 "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')
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29 with open(file_path, 'w') as handle:
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30 handle.write('No results')
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33 def localFetch(db, gformat, newname, **payload):
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34 problem = None
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35 try:
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36 c.fetch(db, **payload)
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38 for chunk, file in enumerate(glob.glob('downloads/EFetch *')):
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39 os.rename(file, '%s%s.%s' % (newname, chunk + 1, gformat))
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41 except Exception as e:
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42 problem = e
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43 handleEfetchException(e, db, payload)
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44 else:
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45 print('The following files were downloaded:')
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46 print(os.listdir('downloads'))
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48 return problem
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50
0
68cd8d564e0a 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")
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57 parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)')
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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')
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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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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:
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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diff changeset
84 input_histories = c.extract_histories_from_xml_file(args.history_xml)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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85
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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86 problem = None
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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87 for hist in input_histories:
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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88 qkey = hist['query_key']
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
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89 tmp_payload = payload
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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90 tmp_payload.update(hist)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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91 newname = 'downloads/EFetch-%s-%s-querykey%s-chunk' % (args.rettype, args.retmode, qkey)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
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92 problem = localFetch(args.db, args.galaxy_format, newname, **tmp_payload)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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93
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
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94 if os.path.exists('downloads'):
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
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95 os.rename('downloads', 'downloads-qkey%s' % (qkey))
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
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96
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
97 if not os.path.exists('downloads'):
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
98 os.makedirs('downloads')
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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99
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
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100 for relpath in glob.glob('downloads-qkey*/*'):
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
101 file = os.path.basename(relpath)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
102 os.rename(relpath, 'downloads/%s' % (file))
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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103
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
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104 if problem is not None:
8
ad1e5225bca4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 41f5eb8e0aee5b779d618b5178098c4be89a9ef1
iuc
parents: 3
diff changeset
105 raise problem
3
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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106
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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107 else:
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
108 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file, args.id_xml, args.id_json)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
109 payload['id'] = ','.join(merged_ids)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
110 newname = 'downloads/EFetch-%s-%s-chunk' % (args.rettype, args.retmode)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
111 localFetch(args.db, args.galaxy_format, newname, **payload)