encode_submission/geo_gather.py

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