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_link_tree_from is not None:
  81         results.make_tree_from(opts.make_tree_from, link=True)
  82
  83     if opts.copy_tree_from is not None:
  84         results.make_tree_from(opts.make_tree_from, link=False)
  85
  86     if opts.fastq:
  87         logger.info("Building fastq extraction scripts")
  88         flowcells = os.path.join(opts.sequence, 'flowcells')
  89         extractor = CondorFastqExtract(opts.host, flowcells,
  90                                        model=opts.model,
  91                                        force=opts.force)
  92         extractor.create_scripts(results)
  93
  94     if opts.scan_submission:
  95         if opts.name is None:
  96             parser.error("Please define a submission name")
  97         mapper.scan_submission_dirs(results)
  98
  99     if opts.make_hub:
 100         mapper.make_hub(results)
 101
 102     if opts.sparql:
 103         sparql_query(model, opts.sparql)
 104
 105     if opts.print_rdf:
 106         writer = get_serializer()
 107         print writer.serialize_model_to_string(model)
 108
 109
 110 def make_parser():
 111     parser = OptionParser()
 112
 113     model = OptionGroup(parser, 'model')
 114     model.add_option('--name', help="Set submission name")
 115     model.add_option('--db-path', default=None,
 116                      help="set rdf database path")
 117     model.add_option('--model', default=None,
 118       help="Load model database")
 119     model.add_option('--load-rdf', default=None,
 120       help="load rdf statements into model")
 121     model.add_option('--sparql', default=None, help="execute sparql query")
 122     model.add_option('--print-rdf', action="store_true", default=False,
 123       help="print ending model state")
 124     parser.add_option_group(model)
 125     # commands
 126     commands = OptionGroup(parser, 'commands')
 127     commands.add_option('--make-link-tree-from',
 128                       help="create directories & link data files",
 129                       default=None)
 130     commands.add_option('--copy-tree-from',
 131                       help="create directories & copy data files",
 132                       default=None)
 133     commands.add_option('--fastq', default=False, action="store_true",
 134                         help="generate scripts for making fastq files")
 135     commands.add_option('--scan-submission', default=False, action="store_true",
 136                       help="Import metadata for submission into our model")
 137     commands.add_option('--make-hub', help='make the hub file', default=False,
 138                       action="store_true")
 139
 140     parser.add_option_group(commands)
 141
 142     parser.add_option('--force', default=False, action="store_true",
 143                       help="Force regenerating fastqs")
 144     parser.add_option('--daf', default=None, help='specify daf name')
 145     parser.add_option('--library-url', default=None,
 146                       help="specify an alternate source for library information")
 147     # debugging
 148     parser.add_option('--verbose', default=False, action="store_true",
 149                       help='verbose logging')
 150     parser.add_option('--debug', default=False, action="store_true",
 151                       help='debug logging')
 152
 153     api.add_auth_options(parser)
 154
 155     return parser
 156
 157 if __name__ == "__main__":
 158     main()