-"""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
-from htsworkflow.submission.trackhub_submission import TrackHubSubmission
from htsworkflow.submission.condorfastq import CondorFastqExtract
-
+from htsworkflow.submission.aws_submission import AWSSubmission
logger = logging.getLogger(__name__)
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:
elif len(submission_names) == 1:
name = submission_names[0]
- mapper = None
- if opts.make_track_hub:
- mapper = TrackHubSubmission(name,
- model,
- baseurl=opts.make_track_hub,
- baseupload=opts.track_hub_upload,
- host=opts.host)
+ if name:
submission_uri = get_submission_uri(name)
+ logger.info('Submission URI: %s', submission_uri)
+ mapper = AWSSubmission(name, model, encode_host=opts.encoded, lims_host=opts.host)
if opts.load_rdf is not None:
if submission_uri is None:
flowcells = os.path.join(opts.sequence, 'flowcells')
extractor = CondorFastqExtract(opts.host, flowcells,
model=opts.model,
+ compression=opts.compression,
force=opts.force)
extractor.create_scripts(results)
parser.error("Please define a submission name")
mapper.scan_submission_dirs(results)
- if opts.make_track_hub:
- trackdb = mapper.make_hub(results)
+ if opts.upload:
+ mapper.upload(results, opts.dry_run)
- if opts.make_manifest:
- make_manifest(mapper, results, opts.make_manifest)
-
if opts.sparql:
sparql_query(model, opts.sparql)
print writer.serialize_model_to_string(model)
-def make_manifest(mapper, results, filename=None):
- manifest = mapper.make_manifest(results)
-
- if filename is None or filename == '-':
- sys.stdout.write(manifest)
- 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")
- 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',
- default=None)
-
+ help="cache md5 sums")
+ commands.add_option('--upload', default=False, action="store_true",
+ help="Upload files")
parser.add_option_group(commands)
parser.add_option('--force', default=False, action="store_true",
help="Force regenerating fastqs")
- parser.add_option('--daf', default=None, help='specify daf name')
+ parser.add_option('--compression', default=None, type='choice',
+ choices=['gzip'],
+ help='select compression type for fastq files')
parser.add_option('--library-url', default=None,
help="specify an alternate source for library information")
+ parser.add_option('--encoded', default='www.encodeproject.org',
+ help='base url for talking to encode server')
+ parser.add_option('--dry-run', default=False, action='store_true',
+ help='avoid making changes to encoded')
# debugging
parser.add_option('--verbose', default=False, action="store_true",
help='verbose logging')
projects / htsworkflow.git / blobdiff