--- /dev/null
+"""Create a track hub
+"""
+
+#!/usr/bin/env python
+from ConfigParser import SafeConfigParser
+import fnmatch
+from glob import glob
+import json
+import logging
+import netrc
+from optparse import OptionParser, OptionGroup
+import os
+from pprint import pprint, pformat
+import shlex
+from StringIO import StringIO
+import stat
+import sys
+import time
+import types
+import urllib
+import urllib2
+import urlparse
+from zipfile import ZipFile
+
+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
+from htsworkflow.submission.daf import get_submission_uri
+from htsworkflow.submission.results import ResultMap
+from htsworkflow.submission.trackhub import TrackHubSubmission
+from htsworkflow.submission.condorfastq import CondorFastqExtract
+
+logger = logging.getLogger(__name__)
+
+def main(cmdline=None):
+ parser = make_parser()
+ opts, args = parser.parse_args(cmdline)
+ submission_uri = None
+
+ if opts.debug:
+ logging.basicConfig(level = logging.DEBUG )
+ elif opts.verbose:
+ logging.basicConfig(level = logging.INFO )
+ else:
+ logging.basicConfig(level = logging.WARNING )
+
+ apidata = api.make_auth_from_opts(opts, parser)
+
+ 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)
+
+
+ if opts.load_rdf is not None:
+ if submission_uri is None:
+ parser.error("Please specify the submission name")
+ load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
+
+ results = ResultMap()
+ for a in args:
+ if os.path.exists(a):
+ results.add_results_from_file(a)
+ else:
+ logger.warn("File %s doesn't exist.", a)
+
+ if opts.make_link_tree_from is not None:
+ results.make_tree_from(opts.make_link_tree_from, link=True)
+
+ if opts.copy_tree_from is not None:
+ results.make_tree_from(opts.copy_tree_from, link=False)
+
+ if opts.fastq:
+ logger.info("Building fastq extraction scripts")
+ flowcells = os.path.join(opts.sequence, 'flowcells')
+ extractor = CondorFastqExtract(opts.host, flowcells,
+ model=opts.model,
+ force=opts.force)
+ extractor.create_scripts(results)
+
+ if opts.scan_submission:
+ if opts.name is None:
+ parser.error("Please define a submission name")
+ mapper.scan_submission_dirs(results)
+
+ if opts.make_hub:
+ make_hub(mapper, results, opts.make_hub)
+
+ if opts.make_manifest:
+ make_manifest(mapper, results, opts.make_manifest)
+
+ if opts.sparql:
+ sparql_query(model, opts.sparql)
+
+ if opts.print_rdf:
+ writer = get_serializer()
+ 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)
+
+ 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 = OptionGroup(parser, 'model')
+ model.add_option('--name', help="Set submission name")
+ model.add_option('--db-path', default=None,
+ help="set rdf database path")
+ model.add_option('--model', default=None,
+ help="Load model database")
+ model.add_option('--load-rdf', default=None,
+ 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")
+ 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)
+ commands.add_option('--copy-tree-from',
+ 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',
+ default=None)
+
+
+ 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('--library-url', default=None,
+ help="specify an alternate source for library information")
+ # debugging
+ parser.add_option('--verbose', default=False, action="store_true",
+ help='verbose logging')
+ parser.add_option('--debug', default=False, action="store_true",
+ help='debug logging')
+
+ api.add_auth_options(parser)
+
+ return parser
+
+if __name__ == "__main__":
+ main()
projects / htsworkflow.git / blobdiff