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, host=opts.host)
  62         submission_uri = get_submission_uri(opts.name)
  63
  64
  65     if opts.load_rdf is not None:
  66         if submission_uri is None:
  67             parser.error("Please specify the submission name")
  68         load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
  69
  70     results = ResultMap()
  71     for a in args:
  72         results.add_results_from_file(a)
  73
  74     if opts.make_tree_from is not None:
  75         results.make_tree_from(opts.make_tree_from)
  76
  77     if opts.fastq:
  78         logger.info("Building fastq extraction scripts")
  79         flowcells = os.path.join(opts.sequence, 'flowcells')
  80         extractor = CondorFastqExtract(opts.host, flowcells,
  81                                        model=opts.model,
  82                                        force=opts.force)
  83         extractor.create_scripts(results)
  84
  85     if opts.scan_submission:
  86         if opts.name is None:
  87             parser.error("Please define a submission name")
  88         mapper.scan_submission_dirs(results)
  89
  90     if opts.make_soft:
  91         mapper.make_soft(results)
  92
  93     if opts.sparql:
  94         sparql_query(model, opts.sparql)
  95
  96     if opts.print_rdf:
  97         writer = get_serializer()
  98         print writer.serialize_model_to_string(model)
  99
 100
 101 def make_parser():
 102     parser = OptionParser()
 103
 104     model = OptionGroup(parser, 'model')
 105     model.add_option('--name', help="Set submission name")
 106     model.add_option('--db-path', default=None,
 107                      help="set rdf database path")
 108     model.add_option('--model', default=None,
 109       help="Load model database")
 110     model.add_option('--load-rdf', default=None,
 111       help="load rdf statements into model")
 112     model.add_option('--sparql', default=None, help="execute sparql query")
 113     model.add_option('--print-rdf', action="store_true", default=False,
 114       help="print ending model state")
 115     parser.add_option_group(model)
 116     # commands
 117     commands = OptionGroup(parser, 'commands')
 118     commands.add_option('--make-tree-from',
 119                       help="create directories & link data files",
 120                       default=None)
 121     commands.add_option('--fastq', default=False, action="store_true",
 122                         help="generate scripts for making fastq files")
 123     commands.add_option('--scan-submission', default=False, action="store_true",
 124                       help="Import metadata for submission into our model")
 125     commands.add_option('--make-soft', help='make the soft file', default=False,
 126                       action="store_true")
 127
 128     parser.add_option_group(commands)
 129
 130     parser.add_option('--force', default=False, action="store_true",
 131                       help="Force regenerating fastqs")
 132     parser.add_option('--daf', default=None, help='specify daf name')
 133     parser.add_option('--library-url', default=None,
 134                       help="specify an alternate source for library information")
 135     # debugging
 136     parser.add_option('--verbose', default=False, action="store_true",
 137                       help='verbose logging')
 138     parser.add_option('--debug', default=False, action="store_true",
 139                       help='debug logging')
 140
 141     api.add_auth_options(parser)
 142
 143     return parser
 144
 145
 146 if __name__ == "__main__":
 147     main()