2 from ConfigParser import SafeConfigParser
8 from optparse import OptionParser, OptionGroup
10 from pprint import pprint, pformat
12 from StringIO import StringIO
20 from zipfile import ZipFile
24 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
25 os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
28 from htsworkflow.util import api
29 from htsworkflow.util.rdfhelp import \
37 from htsworkflow.submission.daf import get_submission_uri
38 from htsworkflow.submission.results import ResultMap
39 from htsworkflow.submission.geo import GEOSubmission
40 from htsworkflow.submission.condorfastq import CondorFastqExtract
42 logger = logging.getLogger(__name__)
44 def main(cmdline=None):
45 parser = make_parser()
46 opts, args = parser.parse_args(cmdline)
50 logging.basicConfig(level = logging.DEBUG )
52 logging.basicConfig(level = logging.INFO )
54 logging.basicConfig(level = logging.WARNING )
56 apidata = api.make_auth_from_opts(opts, parser)
58 model = get_model(opts.model, opts.db_path)
61 mapper = GEOSubmission(opts.name, model, host=opts.host)
62 submission_uri = get_submission_uri(opts.name)
65 if opts.load_rdf is not None:
66 if submission_uri is None:
67 parser.error("Please specify the submission name")
68 load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
73 results.add_results_from_file(a)
75 logger.warn("File %s doesn't exist.", a)
77 if opts.make_tree_from is not None:
78 results.make_tree_from(opts.make_tree_from)
81 logger.info("Building fastq extraction scripts")
82 flowcells = os.path.join(opts.sequence, 'flowcells')
83 extractor = CondorFastqExtract(opts.host, flowcells,
86 extractor.create_scripts(results)
88 if opts.scan_submission:
90 parser.error("Please define a submission name")
91 mapper.scan_submission_dirs(results)
94 mapper.make_soft(results)
97 sparql_query(model, opts.sparql)
100 writer = get_serializer()
101 print writer.serialize_model_to_string(model)
105 parser = OptionParser()
107 model = OptionGroup(parser, 'model')
108 model.add_option('--name', help="Set submission name")
109 model.add_option('--db-path', default=None,
110 help="set rdf database path")
111 model.add_option('--model', default=None,
112 help="Load model database")
113 model.add_option('--load-rdf', default=None,
114 help="load rdf statements into model")
115 model.add_option('--sparql', default=None, help="execute sparql query")
116 model.add_option('--print-rdf', action="store_true", default=False,
117 help="print ending model state")
118 parser.add_option_group(model)
120 commands = OptionGroup(parser, 'commands')
121 commands.add_option('--make-tree-from',
122 help="create directories & link data files",
124 commands.add_option('--fastq', default=False, action="store_true",
125 help="generate scripts for making fastq files")
126 commands.add_option('--scan-submission', default=False, action="store_true",
127 help="Import metadata for submission into our model")
128 commands.add_option('--make-soft', help='make the soft file', default=False,
131 parser.add_option_group(commands)
133 parser.add_option('--force', default=False, action="store_true",
134 help="Force regenerating fastqs")
135 parser.add_option('--daf', default=None, help='specify daf name')
136 parser.add_option('--library-url', default=None,
137 help="specify an alternate source for library information")
139 parser.add_option('--verbose', default=False, action="store_true",
140 help='verbose logging')
141 parser.add_option('--debug', default=False, action="store_true",
142 help='debug logging')
144 api.add_auth_options(parser)
149 if __name__ == "__main__":