5 from ConfigParser import SafeConfigParser
11 from optparse import OptionParser, OptionGroup
13 from pprint import pprint, pformat
15 from StringIO import StringIO
23 from zipfile import ZipFile
27 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
28 os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
30 from htsworkflow.util import api
31 from htsworkflow.util.rdfhelp import \
39 from htsworkflow.submission.daf import get_submission_uri
40 from htsworkflow.submission.submission import list_submissions
41 from htsworkflow.submission.results import ResultMap
42 from htsworkflow.submission.trackhub_submission import TrackHubSubmission
43 from htsworkflow.submission.condorfastq import CondorFastqExtract
45 logger = logging.getLogger(__name__)
47 INDENTED = " " + os.linesep
49 def main(cmdline=None):
50 parser = make_parser()
51 opts, args = parser.parse_args(cmdline)
55 logging.basicConfig(level = logging.DEBUG )
57 logging.basicConfig(level = logging.INFO )
59 logging.basicConfig(level = logging.WARNING )
61 apidata = api.make_auth_from_opts(opts, parser)
63 model = get_model(opts.model, opts.db_path)
65 submission_names = list(list_submissions(model))
67 if len(submission_names) == 0 and opts.name is None:
68 parser.error("Please name this submission")
69 elif opts.name and submission_names and opts.name not in submission_names:
70 parser.error("{} is not in this model. Choose from: {}{}".format(
73 INDENTED.join(submission_names)))
74 elif opts.name is None and len(submission_names) > 1:
75 parser.error("Please choose submission name from: {}{}".format(
77 INDENTED.join(submission_names)))
78 elif len(submission_names) == 1:
79 name = submission_names[0]
82 if opts.make_track_hub:
83 mapper = TrackHubSubmission(name,
85 baseurl=opts.make_track_hub,
86 baseupload=opts.track_hub_upload,
88 submission_uri = get_submission_uri(name)
91 if opts.load_rdf is not None:
92 if submission_uri is None:
93 parser.error("Please specify the submission name")
94 load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
99 results.add_results_from_file(a)
101 logger.warn("File %s doesn't exist.", a)
103 if opts.make_link_tree_from is not None:
104 results.make_tree_from(opts.make_link_tree_from, link=True)
106 if opts.copy_tree_from is not None:
107 results.make_tree_from(opts.copy_tree_from, link=False)
110 logger.info("Building fastq extraction scripts")
111 flowcells = os.path.join(opts.sequence, 'flowcells')
112 extractor = CondorFastqExtract(opts.host, flowcells,
115 extractor.create_scripts(results)
117 if opts.scan_submission:
119 parser.error("Please define a submission name")
120 mapper.scan_submission_dirs(results)
122 if opts.make_track_hub:
123 trackdb = mapper.make_hub(results)
125 if opts.make_manifest:
126 make_manifest(mapper, results, opts.make_manifest)
129 sparql_query(model, opts.sparql)
132 writer = get_serializer()
133 print writer.serialize_model_to_string(model)
136 def make_manifest(mapper, results, filename=None):
137 manifest = mapper.make_manifest(results)
139 if filename is None or filename == '-':
140 sys.stdout.write(manifest)
142 with open(filename, 'w') as mainifeststream:
143 mainifeststream.write(manifest)
146 parser = OptionParser()
148 model = OptionGroup(parser, 'model')
149 model.add_option('--name', help="Set submission name")
150 model.add_option('--db-path', default=None,
151 help="set rdf database path")
152 model.add_option('--model', default=None,
153 help="Load model database")
154 model.add_option('--load-rdf', default=None,
155 help="load rdf statements into model")
156 model.add_option('--sparql', default=None, help="execute sparql query")
157 model.add_option('--print-rdf', action="store_true", default=False,
158 help="print ending model state")
159 parser.add_option_group(model)
161 commands = OptionGroup(parser, 'commands')
162 commands.add_option('--make-link-tree-from',
163 help="create directories & link data files",
165 commands.add_option('--copy-tree-from',
166 help="create directories & copy data files",
168 commands.add_option('--fastq', default=False, action="store_true",
169 help="generate scripts for making fastq files")
170 commands.add_option('--scan-submission', default=False, action="store_true",
171 help="Import metadata for submission into our model")
172 commands.add_option('--make-track-hub', default=None,
173 help='web root that will host the trackhub.')
174 commands.add_option('--track-hub-upload', default=None,
175 help='where to upload track hub <host>:<path>')
176 commands.add_option('--make-manifest',
177 help='name the manifest file name or - for stdout to create it',
181 parser.add_option_group(commands)
183 parser.add_option('--force', default=False, action="store_true",
184 help="Force regenerating fastqs")
185 parser.add_option('--daf', default=None, help='specify daf name')
186 parser.add_option('--library-url', default=None,
187 help="specify an alternate source for library information")
189 parser.add_option('--verbose', default=False, action="store_true",
190 help='verbose logging')
191 parser.add_option('--debug', default=False, action="store_true",
192 help='debug logging')
194 api.add_auth_options(parser)
198 if __name__ == "__main__":