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
if name:
submission_uri = get_submission_uri(name)
- logger.info('Submission URI: %s', name)
- else:
- logger.debug('No name, unable to create submission ur')
-
- mapper = None
- if opts.make_track_hub:
- mapper = TrackHubSubmission(name,
- model,
- baseurl=opts.make_track_hub,
- baseupload=opts.track_hub_upload,
- host=opts.host)
+ 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:
if opts.scan_submission:
if name is None:
parser.error("Please define a submission name")
- if mapper is None:
- parser.error("Scan submission needs --make-track-hub=public-url")
mapper.scan_submission_dirs(results)
- if opts.make_track_hub:
- trackdb = mapper.make_hub(results)
-
- if opts.make_manifest:
- make_manifest(mapper, results, opts.make_manifest)
+ if opts.upload:
+ mapper.upload(results, opts.dry_run)
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()
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('--compression', default=None, type='choice',
choices=['gzip'],
help='select compression type for fastq files')
- parser.add_option('--daf', default=None, help='specify daf name')
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')