-"""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 import TrackHubSubmission
+from htsworkflow.submission.trackhub_submission import TrackHubSubmission
from htsworkflow.submission.condorfastq import CondorFastqExtract
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)
- mapper = None
- if opts.name:
- mapper = TrackHubSubmission(opts.name, model, host=opts.host)
- submission_uri = get_submission_uri(opts.name)
+ submission_names = list(list_submissions(model))
+ name = opts.name
+ if len(submission_names) == 0 and opts.name is None:
+ parser.error("Please name this submission")
+ elif opts.name and submission_names and opts.name not in submission_names:
+ parser.error("{} is not in this model. Choose from: {}{}".format(
+ opts.name,
+ os.linesep,
+ INDENTED.join(submission_names)))
+ elif opts.name is None and len(submission_names) > 1:
+ parser.error("Please choose submission name from: {}{}".format(
+ os.linesep,
+ 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)
+ 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)
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)
if opts.scan_submission:
- if opts.name is None:
+ 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_hub:
- make_hub(mapper, results, opts.make_hub)
+ if opts.make_track_hub:
+ trackdb = mapper.make_hub(results)
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_hub(mapper, results, filename=None):
- trackdb = mapper.make_hub(results)
-
- if filename is None or filename == '-':
- sys.stdout.write(trackdb)
- else:
- with open('trackDb.txt', 'w') as trackstream:
- trackstream.write(trackdb)
-
def make_manifest(mapper, results, filename=None):
manifest = mapper.make_manifest(results)
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-hub', default=None,
- help='name the hub file or - for stdout to create it')
- commands.add_option('--make-manifest',
- help='name the manifest file name or - for stdout to create it',
+ 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)
-
parser.add_option_group(commands)
parser.add_option('--force', default=False, action="store_true",
help="Force regenerating fastqs")
+ 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")
projects / htsworkflow.git / blobdiff