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         flowcells = os.path.join(opts.sequence, 'flowcells')
  81         extractor = CondorFastqExtract(opts.host, flowcells,
  82                                        model=opts.model,
  83                                        force=opts.force)
  84         extractor.create_scripts(results)
  85
  86     if opts.scan_submission:
  87         mapper.scan_submission_dirs(results)
  88
  89     if opts.make_soft:
  90         mapper.make_soft(results)
  91
  92     if opts.sparql:
  93         sparql_query(model, opts.sparql)
  94
  95     if opts.print_rdf:
  96         writer = get_serializer()
  97         print writer.serialize_model_to_string(model)
  98
  99
 100 def make_parser():
 101     parser = OptionParser()
 102
 103     model = OptionGroup(parser, 'model')
 104     model.add_option('--name', help="Set submission name")
 105     model.add_option('--db-path', default=None,
 106                      help="set rdf database path")
 107     model.add_option('--model', default=None,
 108       help="Load model database")
 109     model.add_option('--load-rdf', default=None,
 110       help="load rdf statements into model")
 111     model.add_option('--sparql', default=None, help="execute sparql query")
 112     model.add_option('--print-rdf', action="store_true", default=False,
 113       help="print ending model state")
 114     parser.add_option_group(model)
 115     # commands
 116     commands = OptionGroup(parser, 'commands')
 117     commands.add_option('--make-tree-from',
 118                       help="create directories & link data files",
 119                       default=None)
 120     commands.add_option('--fastq', default=False, action="store_true",
 121                         help="generate scripts for making fastq files")
 122     commands.add_option('--scan-submission', default=False, action="store_true",
 123                       help="Import metadata for submission into our model")
 124     commands.add_option('--make-soft', help='make the soft file', default=False,
 125                       action="store_true")
 126
 127     parser.add_option_group(commands)
 128
 129     parser.add_option('--force', default=False, action="store_true",
 130                       help="Force regenerating fastqs")
 131     parser.add_option('--daf', default=None, help='specify daf name')
 132     parser.add_option('--library-url', default=None,
 133                       help="specify an alternate source for library information")
 134     # debugging
 135     parser.add_option('--verbose', default=False, action="store_true",
 136                       help='verbose logging')
 137     parser.add_option('--debug', default=False, action="store_true",
 138                       help='debug logging')
 139
 140     api.add_auth_options(parser)
 141
 142     return parser
 143
 144
 145 if __name__ == "__main__":
 146     main()