4 from __future__ import print_function, unicode_literals
10 from htsworkflow.util import api
11 from htsworkflow.util.rdfhelp import \
16 from htsworkflow.submission.daf import get_submission_uri
17 from htsworkflow.submission.submission import list_submissions
18 from htsworkflow.submission.results import ResultMap
19 from htsworkflow.submission.condorfastq import CondorFastqExtract
20 from htsworkflow.submission.aws_submission import AWSSubmission
21 logger = logging.getLogger(__name__)
23 INDENTED = " " + os.linesep
26 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
27 os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings.local'
29 def main(cmdline=None):
30 parser = make_parser()
31 args = parser.parse_args(cmdline)
34 from django.conf import settings
37 settings.LOGGING['loggers']['htsworkflow']['level'] = 'DEBUG'
39 settings.LOGGING['loggers']['htsworkflow']['level'] = 'INFO'
43 model = get_model(args.model, args.db_path)
44 submission_names = list(list_submissions(model))
46 if len(submission_names) == 0 and args.name is None:
47 parser.error("Please name this submission")
48 elif args.name and submission_names and args.name not in submission_names:
49 parser.error("{} is not in this model. Choose from: {}{}".format(
52 INDENTED.join(submission_names)))
53 elif args.name is None and len(submission_names) > 1:
54 parser.error("Please choose submission name from: {}{}".format(
56 INDENTED.join(submission_names)))
57 elif len(submission_names) == 1:
58 name = submission_names[0]
61 submission_uri = get_submission_uri(name)
62 logger.info('Submission URI: %s', submission_uri)
64 mapper = AWSSubmission(name, model, encode_host=args.encoded, lims_host=args.host)
66 if args.load_rdf is not None:
67 if submission_uri is None:
68 parser.error("Please specify the submission name")
69 load_into_model(model, 'turtle', args.load_rdf, submission_uri)
72 for a in args.libraries:
74 results.add_results_from_file(a)
76 logger.warn("File %s doesn't exist.", a)
78 if args.make_link_tree_from is not None:
79 results.make_tree_from(args.make_link_tree_from, link=True)
81 if args.copy_tree_from is not None:
82 results.make_tree_from(args.copy_tree_from, link=False)
85 logger.info("Building fastq extraction scripts")
86 flowcells = os.path.join(args.sequence, 'flowcells')
87 extractor = CondorFastqExtract(args.host, flowcells,
89 compression=args.compression,
91 extractor.create_scripts(results)
93 if args.scan_submission:
95 parser.error("Please define a submission name")
96 mapper.scan_submission_dirs(results)
99 mapper.upload(results, args.dry_run)
101 if args.check_upload:
102 mapper.check_upload(results)
105 sparql_query(model, args.sparql)
108 writer = get_serializer()
109 print(writer.serialize_model_to_string(model))
113 parser = argparse.ArgumentParser()
115 model = parser.add_argument_group('model')
116 model.add_argument('--name', help="Set submission name")
117 model.add_argument('--db-path', default=None,
118 help="set rdf database path")
119 model.add_argument('--model', default=None,
120 help="Load model database")
121 model.add_argument('--load-rdf', default=None,
122 help="load rdf statements into model")
123 model.add_argument('--sparql', default=None, help="execute sparql query")
124 model.add_argument('--print-rdf', action="store_true", default=False,
125 help="print ending model state")
128 commands = parser.add_argument_group('commands')
129 commands.add_argument('--make-link-tree-from',
130 help="create directories & link data files",
132 commands.add_argument('--copy-tree-from',
133 help="create directories & copy data files",
135 commands.add_argument('--fastq', default=False, action="store_true",
136 help="generate scripts for making fastq files")
137 commands.add_argument('--scan-submission', default=False, action="store_true",
138 help="cache md5 sums")
139 commands.add_argument('--upload', default=False, action="store_true",
141 commands.add_argument('--check-upload', default=False, action='store_true',
142 help='check to see files are actually uploaded')
144 parser.add_argument('--force', default=False, action="store_true",
145 help="Force regenerating fastqs")
146 parser.add_argument('--compression', default=None,
148 help='select compression type for fastq files')
149 parser.add_argument('--library-url', default=None,
150 help="specify an alternate source for library information")
151 parser.add_argument('--encoded', default='www.encodeproject.org',
152 help='base url for talking to encode server')
153 parser.add_argument('--dry-run', default=False, action='store_true',
154 help='avoid making changes to encoded')
157 parser.add_argument('--verbose', default=False, action="store_true",
158 help='verbose logging')
159 parser.add_argument('--debug', default=False, action="store_true",
160 help='debug logging')
162 api.add_auth_options(parser)
164 parser.add_argument('libraries', nargs='+',
165 help='mapping of library id to directory to be processed')
169 if __name__ == "__main__":