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