encode_submission/geo_gather.py

   1 #!/usr/bin/env python
   2 from __future__ import print_function, unicode_literals
   3
   4 from ConfigParser import SafeConfigParser
   5 import fnmatch
   6 from glob import glob
   7 import json
   8 import logging
   9 import netrc
  10 from optparse import OptionParser, OptionGroup
  11 import os
  12 from pprint import pprint, pformat
  13 import shlex
  14 from six.moves import StringIO
  15 import stat
  16 import sys
  17 import time
  18 import types
  19 from zipfile import ZipFile
  20
  21 import RDF
  22
  23 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
  24     os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
  25
  26
  27 from htsworkflow.util import api
  28 from htsworkflow.util.rdfhelp import \
  29      dafTermOntology, \
  30      fromTypedNode, \
  31      get_model, \
  32      get_serializer, \
  33      load_into_model, \
  34      sparql_query, \
  35      submissionOntology
  36 from htsworkflow.submission.daf import get_submission_uri
  37 from htsworkflow.submission.results import ResultMap
  38 from htsworkflow.submission.geo import GEOSubmission
  39 from htsworkflow.submission.condorfastq import CondorFastqExtract
  40
  41 logger = logging.getLogger(__name__)
  42
  43 def main(cmdline=None):
  44     parser = make_parser()
  45     opts, args = parser.parse_args(cmdline)
  46     submission_uri = None
  47
  48     if opts.debug:
  49         logging.basicConfig(level = logging.DEBUG )
  50     elif opts.verbose:
  51         logging.basicConfig(level = logging.INFO )
  52     else:
  53         logging.basicConfig(level = logging.WARNING )
  54
  55     apidata = api.make_auth_from_opts(opts, parser)
  56
  57     model = get_model(opts.model, opts.db_path)
  58     mapper = None
  59     if opts.name:
  60         mapper = GEOSubmission(opts.name,  model, host=opts.host)
  61         submission_uri = get_submission_uri(opts.name)
  62
  63
  64     if opts.load_rdf is not None:
  65         if submission_uri is None:
  66             parser.error("Please specify the submission name")
  67         load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
  68
  69     results = ResultMap()
  70     for a in args:
  71         if os.path.exists(a):
  72             results.add_results_from_file(a)
  73         else:
  74             logger.warn("File %s doesn't exist.", 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         logger.info("Building fastq extraction scripts")
  81         flowcells = os.path.join(opts.sequence, 'flowcells')
  82         extractor = CondorFastqExtract(opts.host, flowcells,
  83                                        model=opts.model,
  84                                        force=opts.force)
  85         extractor.create_scripts(results)
  86
  87     if opts.scan_submission:
  88         if opts.name is None:
  89             parser.error("Please define a submission name")
  90         mapper.scan_submission_dirs(results)
  91
  92     if opts.make_soft:
  93         mapper.make_soft(results)
  94
  95     if opts.sparql:
  96         sparql_query(model, opts.sparql)
  97
  98     if opts.print_rdf:
  99         writer = get_serializer()
 100         print(writer.serialize_model_to_string(model))
 101
 102
 103 def make_parser():
 104     parser = OptionParser()
 105
 106     model = OptionGroup(parser, 'model')
 107     model.add_option('--name', help="Set submission name")
 108     model.add_option('--db-path', default=None,
 109                      help="set rdf database path")
 110     model.add_option('--model', default=None,
 111       help="Load model database")
 112     model.add_option('--load-rdf', default=None,
 113       help="load rdf statements into model")
 114     model.add_option('--sparql', default=None, help="execute sparql query")
 115     model.add_option('--print-rdf', action="store_true", default=False,
 116       help="print ending model state")
 117     parser.add_option_group(model)
 118     # commands
 119     commands = OptionGroup(parser, 'commands')
 120     commands.add_option('--make-tree-from',
 121                       help="create directories & link data files",
 122                       default=None)
 123     commands.add_option('--fastq', default=False, action="store_true",
 124                         help="generate scripts for making fastq files")
 125     commands.add_option('--scan-submission', default=False, action="store_true",
 126                       help="Import metadata for submission into our model")
 127     commands.add_option('--make-soft', help='make the soft file', default=False,
 128                       action="store_true")
 129
 130     parser.add_option_group(commands)
 131
 132     parser.add_option('--force', default=False, action="store_true",
 133                       help="Force regenerating fastqs")
 134     parser.add_option('--daf', default=None, help='specify daf name')
 135     parser.add_option('--library-url', default=None,
 136                       help="specify an alternate source for library information")
 137     # debugging
 138     parser.add_option('--verbose', default=False, action="store_true",
 139                       help='verbose logging')
 140     parser.add_option('--debug', default=False, action="store_true",
 141                       help='debug logging')
 142
 143     api.add_auth_options(parser)
 144
 145     return parser
 146
 147
 148 if __name__ == "__main__":
 149     main()