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
50 def main(cmdline=None):
51 parser = make_parser()
52 opts, args = parser.parse_args(cmdline)
56 logging.basicConfig(level=logging.DEBUG)
58 logging.basicConfig(level=logging.INFO)
60 logging.basicConfig(level=logging.WARNING)
62 apidata = api.make_auth_from_opts(opts, parser)
64 model = get_model(opts.model, opts.db_path)
66 submission_names = list(list_submissions(model))
68 if len(submission_names) == 0 and opts.name is None:
69 parser.error("Please name this submission")
70 elif opts.name and submission_names and opts.name not in submission_names:
71 parser.error("{} is not in this model. Choose from: {}{}".format(
74 INDENTED.join(submission_names)))
75 elif opts.name is None and len(submission_names) > 1:
76 parser.error("Please choose submission name from: {}{}".format(
78 INDENTED.join(submission_names)))
79 elif len(submission_names) == 1:
80 name = submission_names[0]
83 submission_uri = get_submission_uri(name)
84 logger.info('Submission URI: %s', name)
86 logger.debug('No name, unable to create submission ur')
89 if opts.make_track_hub:
90 mapper = TrackHubSubmission(name,
92 baseurl=opts.make_track_hub,
93 baseupload=opts.track_hub_upload,
96 if opts.load_rdf is not None:
97 if submission_uri is None:
98 parser.error("Please specify the submission name")
99 load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
101 results = ResultMap()
103 if os.path.exists(a):
104 results.add_results_from_file(a)
106 logger.warn("File %s doesn't exist.", a)
108 if opts.make_link_tree_from is not None:
109 results.make_tree_from(opts.make_link_tree_from, link=True)
111 if opts.copy_tree_from is not None:
112 results.make_tree_from(opts.copy_tree_from, link=False)
115 logger.info("Building fastq extraction scripts")
116 flowcells = os.path.join(opts.sequence, 'flowcells')
117 extractor = CondorFastqExtract(opts.host, flowcells,
119 compression=opts.compression,
121 extractor.create_scripts(results)
123 if opts.scan_submission:
125 parser.error("Please define a submission name")
127 parser.error("Scan submission needs --make-track-hub=public-url")
128 mapper.scan_submission_dirs(results)
130 if opts.make_track_hub:
131 trackdb = mapper.make_hub(results)
133 if opts.make_manifest:
134 make_manifest(mapper, results, opts.make_manifest)
137 sparql_query(model, opts.sparql)
140 writer = get_serializer()
141 print writer.serialize_model_to_string(model)
144 def make_manifest(mapper, results, filename=None):
145 manifest = mapper.make_manifest(results)
147 if filename is None or filename == '-':
148 sys.stdout.write(manifest)
150 with open(filename, 'w') as mainifeststream:
151 mainifeststream.write(manifest)
155 parser = OptionParser()
157 model = OptionGroup(parser, 'model')
158 model.add_option('--name', help="Set submission name")
159 model.add_option('--db-path', default=None,
160 help="set rdf database path")
161 model.add_option('--model', default=None,
162 help="Load model database")
163 model.add_option('--load-rdf', default=None,
164 help="load rdf statements into model")
165 model.add_option('--sparql', default=None, help="execute sparql query")
166 model.add_option('--print-rdf', action="store_true", default=False,
167 help="print ending model state")
168 parser.add_option_group(model)
170 commands = OptionGroup(parser, 'commands')
171 commands.add_option('--make-link-tree-from',
172 help="create directories & link data files",
174 commands.add_option('--copy-tree-from',
175 help="create directories & copy data files",
177 commands.add_option('--fastq', default=False, action="store_true",
178 help="generate scripts for making fastq files")
179 commands.add_option('--scan-submission', default=False, action="store_true",
180 help="Import metadata for submission into our model")
181 commands.add_option('--make-track-hub', default=None,
182 help='web root that will host the trackhub.')
183 commands.add_option('--track-hub-upload', default=None,
184 help='where to upload track hub <host>:<path>')
185 commands.add_option('--make-manifest',
186 help='name the manifest file name or - for stdout to create it',
189 parser.add_option_group(commands)
191 parser.add_option('--force', default=False, action="store_true",
192 help="Force regenerating fastqs")
193 parser.add_option('--compression', default=None, type='choice',
195 help='select compression type for fastq files')
196 parser.add_option('--daf', default=None, help='specify daf name')
197 parser.add_option('--library-url', default=None,
198 help="specify an alternate source for library information")
200 parser.add_option('--verbose', default=False, action="store_true",
201 help='verbose logging')
202 parser.add_option('--debug', default=False, action="store_true",
203 help='debug logging')
205 api.add_auth_options(parser)
209 if __name__ == "__main__":