Mercurial > repos > iuc > ncbi_eutils_egquery

annotate efetch.py @ 13:e368e943b1d2 draft default tip

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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 10:35:23 +0000
parents f3f5ee550b17
children
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22fed2340d2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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1 #!/usr/bin/env python
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22fed2340d2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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3 import argparse
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4 import glob
f3f5ee550b17 "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
f3f5ee550b17 "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
f3f5ee550b17 "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
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22fed2340d2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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10 import eutils
22fed2340d2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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22fed2340d2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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13 logging.basicConfig(level=logging.INFO)
f3f5ee550b17 "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):
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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))
f3f5ee550b17 "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
f3f5ee550b17 "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()
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21 final_directory = os.path.join(current_directory, r'downloads')
f3f5ee550b17 "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):
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23 os.makedirs(final_directory)
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25 print('The following files were downloaded:')
f3f5ee550b17 "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))
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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
f3f5ee550b17 "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)
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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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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:
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84 input_histories = c.extract_histories_from_xml_file(args.history_xml)
f3f5ee550b17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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85
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86 problem = None
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iuc
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87 for hist in input_histories:
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iuc
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88 qkey = hist['query_key']
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iuc
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89 tmp_payload = payload
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90 tmp_payload.update(hist)
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91 newname = 'downloads/EFetch-%s-%s-querykey%s-chunk' % (args.rettype, args.retmode, qkey)
f3f5ee550b17 "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)
f3f5ee550b17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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93
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94 if os.path.exists('downloads'):
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iuc
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95 os.rename('downloads', 'downloads-qkey%s' % (qkey))
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96
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97 if not os.path.exists('downloads'):
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iuc
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98 os.makedirs('downloads')
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99
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100 for relpath in glob.glob('downloads-qkey*/*'):
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101 file = os.path.basename(relpath)
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102 os.rename(relpath, 'downloads/%s' % (file))
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103
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104 if problem is not None:
13
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105 raise problem
8
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106
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107 else:
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108 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file, args.id_xml, args.id_json)
f3f5ee550b17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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109 payload['id'] = ','.join(merged_ids)
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110 newname = 'downloads/EFetch-%s-%s-chunk' % (args.rettype, args.retmode)
f3f5ee550b17 "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)