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         if os.path.exists(a):
  73             results.add_results_from_file(a)
  74         else:
  75             logger.warn("File %s doesn't exist.", a)
  76
  77     if opts.make_tree_from is not None:
  78         results.make_tree_from(opts.make_tree_from)
  79
  80     if opts.fastq:
  81         logger.info("Building fastq extraction scripts")
  82         flowcells = os.path.join(opts.sequence, 'flowcells')
  83         extractor = CondorFastqExtract(opts.host, flowcells,
  84                                        model=opts.model,
  85                                        force=opts.force)
  86         extractor.create_scripts(results)
  87
  88     if opts.scan_submission:
  89         if opts.name is None:
  90             parser.error("Please define a submission name")
  91         mapper.scan_submission_dirs(results)
  92
  93     if opts.make_soft:
  94         mapper.make_soft(results)
  95
  96     if opts.sparql:
  97         sparql_query(model, opts.sparql)
  98
  99     if opts.print_rdf:
 100         writer = get_serializer()
 101         print writer.serialize_model_to_string(model)
 102
 103
 104 def make_parser():
 105     parser = OptionParser()
 106
 107     model = OptionGroup(parser, 'model')
 108     model.add_option('--name', help="Set submission name")
 109     model.add_option('--db-path', default=None,
 110                      help="set rdf database path")
 111     model.add_option('--model', default=None,
 112       help="Load model database")
 113     model.add_option('--load-rdf', default=None,
 114       help="load rdf statements into model")
 115     model.add_option('--sparql', default=None, help="execute sparql query")
 116     model.add_option('--print-rdf', action="store_true", default=False,
 117       help="print ending model state")
 118     parser.add_option_group(model)
 119     # commands
 120     commands = OptionGroup(parser, 'commands')
 121     commands.add_option('--make-tree-from',
 122                       help="create directories & link data files",
 123                       default=None)
 124     commands.add_option('--fastq', default=False, action="store_true",
 125                         help="generate scripts for making fastq files")
 126     commands.add_option('--scan-submission', default=False, action="store_true",
 127                       help="Import metadata for submission into our model")
 128     commands.add_option('--make-soft', help='make the soft file', default=False,
 129                       action="store_true")
 130
 131     parser.add_option_group(commands)
 132
 133     parser.add_option('--force', default=False, action="store_true",
 134                       help="Force regenerating fastqs")
 135     parser.add_option('--daf', default=None, help='specify daf name')
 136     parser.add_option('--library-url', default=None,
 137                       help="specify an alternate source for library information")
 138     # debugging
 139     parser.add_option('--verbose', default=False, action="store_true",
 140                       help='verbose logging')
 141     parser.add_option('--debug', default=False, action="store_true",
 142                       help='debug logging')
 143
 144     api.add_auth_options(parser)
 145
 146     return parser
 147
 148
 149 if __name__ == "__main__":
 150     main()