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         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_hub(results):
 111     trackdb = mapper.make_hub(results)
 112     manifest = mapper.make_manifest(results)
 113
 114     trackstream = sys.stdout
 115     #with open('trackDb.txt', 'w') as trackstream:
 116     trackstream.write(trackdb)
 117
 118     #with open('manifest.txt', 'w') as mainifeststream:
 119     manifeststream = sys.stdout
 120     mainifeststream.write(mainifest)
 121
 122 def make_parser():
 123     parser = OptionParser()
 124
 125     model = OptionGroup(parser, 'model')
 126     model.add_option('--name', help="Set submission name")
 127     model.add_option('--db-path', default=None,
 128                      help="set rdf database path")
 129     model.add_option('--model', default=None,
 130       help="Load model database")
 131     model.add_option('--load-rdf', default=None,
 132       help="load rdf statements into model")
 133     model.add_option('--sparql', default=None, help="execute sparql query")
 134     model.add_option('--print-rdf', action="store_true", default=False,
 135       help="print ending model state")
 136     parser.add_option_group(model)
 137     # commands
 138     commands = OptionGroup(parser, 'commands')
 139     commands.add_option('--make-link-tree-from',
 140                       help="create directories & link data files",
 141                       default=None)
 142     commands.add_option('--copy-tree-from',
 143                       help="create directories & copy data files",
 144                       default=None)
 145     commands.add_option('--fastq', default=False, action="store_true",
 146                         help="generate scripts for making fastq files")
 147     commands.add_option('--scan-submission', default=False, action="store_true",
 148                       help="Import metadata for submission into our model")
 149     commands.add_option('--make-hub', help='make the hub file', default=False,
 150                       action="store_true")
 151
 152     parser.add_option_group(commands)
 153
 154     parser.add_option('--force', default=False, action="store_true",
 155                       help="Force regenerating fastqs")
 156     parser.add_option('--daf', default=None, help='specify daf name')
 157     parser.add_option('--library-url', default=None,
 158                       help="specify an alternate source for library information")
 159     # debugging
 160     parser.add_option('--verbose', default=False, action="store_true",
 161                       help='verbose logging')
 162     parser.add_option('--debug', default=False, action="store_true",
 163                       help='debug logging')
 164
 165     api.add_auth_options(parser)
 166
 167     return parser
 168
 169 if __name__ == "__main__":
 170     main()