encode_submission/trackhub.py

   1 """Create a track hub
   2 """
   3
   4 #!/usr/bin/env python
   5 from ConfigParser import SafeConfigParser
   6 import fnmatch
   7 from glob import glob
   8 import json
   9 import logging
  10 import netrc
  11 from optparse import OptionParser, OptionGroup
  12 import os
  13 from pprint import pprint, pformat
  14 import shlex
  15 from StringIO import StringIO
  16 import stat
  17 import sys
  18 import time
  19 import types
  20 import urllib
  21 import urllib2
  22 import urlparse
  23 from zipfile import ZipFile
  24
  25 import RDF
  26
  27 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
  28     os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
  29
  30 from htsworkflow.util import api
  31 from htsworkflow.util.rdfhelp import \
  32      dafTermOntology, \
  33      fromTypedNode, \
  34      get_model, \
  35      get_serializer, \
  36      load_into_model, \
  37      sparql_query, \
  38      submissionOntology
  39 from htsworkflow.submission.daf import get_submission_uri
  40 from htsworkflow.submission.results import ResultMap
  41 from htsworkflow.submission.trackhub import TrackHubSubmission
  42 from htsworkflow.submission.condorfastq import CondorFastqExtract
  43
  44 logger = logging.getLogger(__name__)
  45
  46 def main(cmdline=None):
  47     parser = make_parser()
  48     opts, args = parser.parse_args(cmdline)
  49     submission_uri = None
  50
  51     if opts.debug:
  52         logging.basicConfig(level = logging.DEBUG )
  53     elif opts.verbose:
  54         logging.basicConfig(level = logging.INFO )
  55     else:
  56         logging.basicConfig(level = logging.WARNING )
  57
  58     apidata = api.make_auth_from_opts(opts, parser)
  59
  60     model = get_model(opts.model, opts.db_path)
  61     mapper = None
  62     if opts.name:
  63         mapper = TrackHubSubmission(opts.name,  model, host=opts.host)
  64         submission_uri = get_submission_uri(opts.name)
  65
  66
  67     if opts.load_rdf is not None:
  68         if submission_uri is None:
  69             parser.error("Please specify the submission name")
  70         load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
  71
  72     results = ResultMap()
  73     for a in args:
  74         if os.path.exists(a):
  75             results.add_results_from_file(a)
  76         else:
  77             logger.warn("File %s doesn't exist.", a)
  78
  79     if opts.make_link_tree_from is not None:
  80         results.make_tree_from(opts.make_link_tree_from, link=True)
  81
  82     if opts.copy_tree_from is not None:
  83         results.make_tree_from(opts.copy_tree_from, link=False)
  84
  85     if opts.fastq:
  86         logger.info("Building fastq extraction scripts")
  87         flowcells = os.path.join(opts.sequence, 'flowcells')
  88         extractor = CondorFastqExtract(opts.host, flowcells,
  89                                        model=opts.model,
  90                                        force=opts.force)
  91         extractor.create_scripts(results)
  92
  93     if opts.scan_submission:
  94         if opts.name is None:
  95             parser.error("Please define a submission name")
  96         mapper.scan_submission_dirs(results)
  97
  98     if opts.make_hub:
  99         mapper.make_hub(results)
 100
 101     if opts.sparql:
 102         sparql_query(model, opts.sparql)
 103
 104     if opts.print_rdf:
 105         writer = get_serializer()
 106         print writer.serialize_model_to_string(model)
 107
 108
 109 def make_parser():
 110     parser = OptionParser()
 111
 112     model = OptionGroup(parser, 'model')
 113     model.add_option('--name', help="Set submission name")
 114     model.add_option('--db-path', default=None,
 115                      help="set rdf database path")
 116     model.add_option('--model', default=None,
 117       help="Load model database")
 118     model.add_option('--load-rdf', default=None,
 119       help="load rdf statements into model")
 120     model.add_option('--sparql', default=None, help="execute sparql query")
 121     model.add_option('--print-rdf', action="store_true", default=False,
 122       help="print ending model state")
 123     parser.add_option_group(model)
 124     # commands
 125     commands = OptionGroup(parser, 'commands')
 126     commands.add_option('--make-link-tree-from',
 127                       help="create directories & link data files",
 128                       default=None)
 129     commands.add_option('--copy-tree-from',
 130                       help="create directories & copy data files",
 131                       default=None)
 132     commands.add_option('--fastq', default=False, action="store_true",
 133                         help="generate scripts for making fastq files")
 134     commands.add_option('--scan-submission', default=False, action="store_true",
 135                       help="Import metadata for submission into our model")
 136     commands.add_option('--make-hub', help='make the hub file', default=False,
 137                       action="store_true")
 138
 139     parser.add_option_group(commands)
 140
 141     parser.add_option('--force', default=False, action="store_true",
 142                       help="Force regenerating fastqs")
 143     parser.add_option('--daf', default=None, help='specify daf name')
 144     parser.add_option('--library-url', default=None,
 145                       help="specify an alternate source for library information")
 146     # debugging
 147     parser.add_option('--verbose', default=False, action="store_true",
 148                       help='verbose logging')
 149     parser.add_option('--debug', default=False, action="store_true",
 150                       help='debug logging')
 151
 152     api.add_auth_options(parser)
 153
 154     return parser
 155
 156 if __name__ == "__main__":
 157     main()