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
  31 from htsworkflow.util import api
  32 from htsworkflow.util.rdfhelp import \
  33      dafTermOntology, \
  34      fromTypedNode, \
  35      get_model, \
  36      get_serializer, \
  37      load_into_model, \
  38      sparql_query, \
  39      submissionOntology
  40 from htsworkflow.submission.daf import get_submission_uri
  41 from htsworkflow.submission.results import ResultMap
  42 from htsworkflow.submission.trackhub import TrackHubSubmission
  43 from htsworkflow.submission.condorfastq import CondorFastqExtract
  44
  45 logger = logging.getLogger(__name__)
  46
  47 def main(cmdline=None):
  48     parser = make_parser()
  49     opts, args = parser.parse_args(cmdline)
  50     submission_uri = None
  51
  52     if opts.debug:
  53         logging.basicConfig(level = logging.DEBUG )
  54     elif opts.verbose:
  55         logging.basicConfig(level = logging.INFO )
  56     else:
  57         logging.basicConfig(level = logging.WARNING )
  58
  59     apidata = api.make_auth_from_opts(opts, parser)
  60
  61     model = get_model(opts.model, opts.db_path)
  62     mapper = None
  63     if opts.name:
  64         mapper = TrackHubSubmission(opts.name,  model, host=opts.host)
  65         submission_uri = get_submission_uri(opts.name)
  66
  67
  68     if opts.load_rdf is not None:
  69         if submission_uri is None:
  70             parser.error("Please specify the submission name")
  71         load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
  72
  73     results = ResultMap()
  74     for a in args:
  75         if os.path.exists(a):
  76             results.add_results_from_file(a)
  77         else:
  78             logger.warn("File %s doesn't exist.", a)
  79
  80     if opts.make_tree_from is not None:
  81         results.make_tree_from(opts.make_tree_from)
  82
  83     if opts.fastq:
  84         logger.info("Building fastq extraction scripts")
  85         flowcells = os.path.join(opts.sequence, 'flowcells')
  86         extractor = CondorFastqExtract(opts.host, flowcells,
  87                                        model=opts.model,
  88                                        force=opts.force)
  89         extractor.create_scripts(results)
  90
  91     if opts.scan_submission:
  92         if opts.name is None:
  93             parser.error("Please define a submission name")
  94         mapper.scan_submission_dirs(results)
  95
  96     if opts.make_hub:
  97         mapper.make_hub(results)
  98
  99     if opts.sparql:
 100         sparql_query(model, opts.sparql)
 101
 102     if opts.print_rdf:
 103         writer = get_serializer()
 104         print writer.serialize_model_to_string(model)
 105
 106
 107 def make_parser():
 108     parser = OptionParser()
 109
 110     model = OptionGroup(parser, 'model')
 111     model.add_option('--name', help="Set submission name")
 112     model.add_option('--db-path', default=None,
 113                      help="set rdf database path")
 114     model.add_option('--model', default=None,
 115       help="Load model database")
 116     model.add_option('--load-rdf', default=None,
 117       help="load rdf statements into model")
 118     model.add_option('--sparql', default=None, help="execute sparql query")
 119     model.add_option('--print-rdf', action="store_true", default=False,
 120       help="print ending model state")
 121     parser.add_option_group(model)
 122     # commands
 123     commands = OptionGroup(parser, 'commands')
 124     commands.add_option('--make-tree-from',
 125                       help="create directories & link data files",
 126                       default=None)
 127     commands.add_option('--fastq', default=False, action="store_true",
 128                         help="generate scripts for making fastq files")
 129     commands.add_option('--scan-submission', default=False, action="store_true",
 130                       help="Import metadata for submission into our model")
 131     commands.add_option('--make-hub', help='make the hub file', default=False,
 132                       action="store_true")
 133
 134     parser.add_option_group(commands)
 135
 136     parser.add_option('--force', default=False, action="store_true",
 137                       help="Force regenerating fastqs")
 138     parser.add_option('--daf', default=None, help='specify daf name')
 139     parser.add_option('--library-url', default=None,
 140                       help="specify an alternate source for library information")
 141     # debugging
 142     parser.add_option('--verbose', default=False, action="store_true",
 143                       help='verbose logging')
 144     parser.add_option('--debug', default=False, action="store_true",
 145                       help='debug logging')
 146
 147     api.add_auth_options(parser)
 148
 149     return parser
 150
 151 if __name__ == "__main__":
 152     main()