-"""Create a track hub
+"""Create a track hub
"""
#!/usr/bin/env python
import RDF
-if not 'DJANGO_SETTINGS_MODULE' in os.environ:
- os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
-
from htsworkflow.util import api
from htsworkflow.util.rdfhelp import \
- dafTermOntology, \
- fromTypedNode, \
- get_model, \
- get_serializer, \
- load_into_model, \
- sparql_query, \
- submissionOntology
+ dafTermOntology, \
+ fromTypedNode, \
+ get_model, \
+ get_serializer, \
+ load_into_model, \
+ sparql_query, \
+ submissionOntology
from htsworkflow.submission.daf import get_submission_uri
from htsworkflow.submission.submission import list_submissions
from htsworkflow.submission.results import ResultMap
INDENTED = " " + os.linesep
+import django
+if not 'DJANGO_SETTINGS_MODULE' in os.environ:
+ os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings.local'
+
def main(cmdline=None):
parser = make_parser()
opts, args = parser.parse_args(cmdline)
submission_uri = None
+ from django.conf import settings
+
if opts.debug:
- logging.basicConfig(level = logging.DEBUG )
+ settings.LOGGING['loggers']['htsworkflow']['level'] = 'DEBUG'
elif opts.verbose:
- logging.basicConfig(level = logging.INFO )
- else:
- logging.basicConfig(level = logging.WARNING )
+ settings.LOGGING['loggers']['htsworkflow']['level'] = 'INFO'
- apidata = api.make_auth_from_opts(opts, parser)
+ django.setup()
model = get_model(opts.model, opts.db_path)
-
submission_names = list(list_submissions(model))
name = opts.name
if len(submission_names) == 0 and opts.name is None:
INDENTED.join(submission_names)))
elif len(submission_names) == 1:
name = submission_names[0]
-
+
if name:
submission_uri = get_submission_uri(name)
logger.info('Submission URI: %s', name)
if opts.make_manifest:
make_manifest(mapper, results, opts.make_manifest)
-
+
if opts.sparql:
sparql_query(model, opts.sparql)
else:
with open(filename, 'w') as mainifeststream:
mainifeststream.write(manifest)
-
+
+
def make_parser():
parser = OptionParser()
model.add_option('--db-path', default=None,
help="set rdf database path")
model.add_option('--model', default=None,
- help="Load model database")
+ help="Load model database")
model.add_option('--load-rdf', default=None,
- help="load rdf statements into model")
+ help="load rdf statements into model")
model.add_option('--sparql', default=None, help="execute sparql query")
model.add_option('--print-rdf', action="store_true", default=False,
- help="print ending model state")
+ help="print ending model state")
parser.add_option_group(model)
# commands
commands = OptionGroup(parser, 'commands')
commands.add_option('--make-link-tree-from',
- help="create directories & link data files",
- default=None)
+ help="create directories & link data files",
+ default=None)
commands.add_option('--copy-tree-from',
- help="create directories & copy data files",
- default=None)
+ help="create directories & copy data files",
+ default=None)
commands.add_option('--fastq', default=False, action="store_true",
help="generate scripts for making fastq files")
commands.add_option('--scan-submission', default=False, action="store_true",
- help="Import metadata for submission into our model")
+ help="Import metadata for submission into our model")
commands.add_option('--make-track-hub', default=None,
help='web root that will host the trackhub.')
commands.add_option('--track-hub-upload', default=None,
help='where to upload track hub <host>:<path>')
- commands.add_option('--make-manifest',
- help='name the manifest file name or - for stdout to create it',
+ commands.add_option('--make-manifest',
+ help='name the manifest file name or - for stdout to create it',
default=None)
-
parser.add_option_group(commands)
parser.add_option('--force', default=False, action="store_true",