encode_submission/encode3.py

   1 #!/usr/bin/env python
   2 """Create a track hub
   3 """
   4 from __future__ import print_function, unicode_literals
   5
   6 import argparse
   7 import logging
   8 import os
   9
  10 from htsworkflow.util import api
  11 from htsworkflow.util.rdfhelp import \
  12     get_model, \
  13     get_serializer, \
  14     load_into_model, \
  15     sparql_query
  16 from htsworkflow.submission.daf import get_submission_uri
  17 from htsworkflow.submission.submission import list_submissions
  18 from htsworkflow.submission.results import ResultMap
  19 from htsworkflow.submission.condorfastq import CondorFastqExtract
  20 from htsworkflow.submission.aws_submission import AWSSubmission
  21 logger = logging.getLogger(__name__)
  22
  23 INDENTED = "  " + os.linesep
  24
  25 import django
  26 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
  27     os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings.local'
  28
  29 def main(cmdline=None):
  30     parser = make_parser()
  31     args = parser.parse_args(cmdline)
  32     submission_uri = None
  33
  34     from django.conf import settings
  35
  36     if args.debug:
  37         settings.LOGGING['loggers']['htsworkflow']['level'] = 'DEBUG'
  38     elif args.verbose:
  39         settings.LOGGING['loggers']['htsworkflow']['level'] = 'INFO'
  40
  41     django.setup()
  42
  43     model = get_model(args.model, args.db_path)
  44     submission_names = list(list_submissions(model))
  45     name = args.name
  46     if len(submission_names) == 0 and args.name is None:
  47         parser.error("Please name this submission")
  48     elif args.name and submission_names and args.name not in submission_names:
  49         parser.error("{} is not in this model. Choose from: {}{}".format(
  50             args.name,
  51             os.linesep,
  52             INDENTED.join(submission_names)))
  53     elif args.name is None and len(submission_names) > 1:
  54         parser.error("Please choose submission name from: {}{}".format(
  55             os.linesep,
  56             INDENTED.join(submission_names)))
  57     elif len(submission_names) == 1:
  58         name = submission_names[0]
  59
  60     if name:
  61         submission_uri = get_submission_uri(name)
  62         logger.info('Submission URI: %s', submission_uri)
  63
  64     mapper = AWSSubmission(name, model, encode_host=args.encoded, lims_host=args.host)
  65
  66     if args.load_rdf is not None:
  67         if submission_uri is None:
  68             parser.error("Please specify the submission name")
  69         load_into_model(model, 'turtle', args.load_rdf, submission_uri)
  70
  71     results = ResultMap()
  72     for a in args.libraries:
  73         if os.path.exists(a):
  74             results.add_results_from_file(a)
  75         else:
  76             logger.warn("File %s doesn't exist.", a)
  77
  78     if args.make_link_tree_from is not None:
  79         results.make_tree_from(args.make_link_tree_from, link=True)
  80
  81     if args.copy_tree_from is not None:
  82         results.make_tree_from(args.copy_tree_from, link=False)
  83
  84     if args.fastq:
  85         logger.info("Building fastq extraction scripts")
  86         flowcells = os.path.join(args.sequence, 'flowcells')
  87         extractor = CondorFastqExtract(args.host, flowcells,
  88                                        model=args.model,
  89                                        compression=args.compression,
  90                                        force=args.force)
  91         extractor.create_scripts(results)
  92
  93     if args.scan_submission:
  94         if name is None:
  95             parser.error("Please define a submission name")
  96         mapper.scan_submission_dirs(results)
  97
  98     if args.upload:
  99         mapper.upload(results, args.dry_run)
 100
 101     if args.check_upload:
 102         mapper.check_upload(results)
 103
 104     if args.sparql:
 105         sparql_query(model, args.sparql)
 106
 107     if args.print_rdf:
 108         writer = get_serializer()
 109         print(writer.serialize_model_to_string(model))
 110
 111
 112 def make_parser():
 113     parser = argparse.ArgumentParser()
 114
 115     model = parser.add_argument_group('model')
 116     model.add_argument('--name', help="Set submission name")
 117     model.add_argument('--db-path', default=None,
 118                      help="set rdf database path")
 119     model.add_argument('--model', default=None,
 120                      help="Load model database")
 121     model.add_argument('--load-rdf', default=None,
 122                      help="load rdf statements into model")
 123     model.add_argument('--sparql', default=None, help="execute sparql query")
 124     model.add_argument('--print-rdf', action="store_true", default=False,
 125                      help="print ending model state")
 126
 127     # commands
 128     commands = parser.add_argument_group('commands')
 129     commands.add_argument('--make-link-tree-from',
 130                         help="create directories & link data files",
 131                         default=None)
 132     commands.add_argument('--copy-tree-from',
 133                         help="create directories & copy data files",
 134                         default=None)
 135     commands.add_argument('--fastq', default=False, action="store_true",
 136                         help="generate scripts for making fastq files")
 137     commands.add_argument('--scan-submission', default=False, action="store_true",
 138                         help="cache md5 sums")
 139     commands.add_argument('--upload', default=False, action="store_true",
 140                         help="Upload files")
 141     commands.add_argument('--check-upload', default=False, action='store_true',
 142                           help='check to see files are actually uploaded')
 143
 144     parser.add_argument('--force', default=False, action="store_true",
 145                       help="Force regenerating fastqs")
 146     parser.add_argument('--compression', default=None,
 147                       choices=['gzip'],
 148                       help='select compression type for fastq files')
 149     parser.add_argument('--library-url', default=None,
 150                       help="specify an alternate source for library information")
 151     parser.add_argument('--encoded', default='www.encodeproject.org',
 152                       help='base url for talking to encode server')
 153     parser.add_argument('--dry-run', default=False, action='store_true',
 154                       help='avoid making changes to encoded')
 155
 156     # debugging
 157     parser.add_argument('--verbose', default=False, action="store_true",
 158                       help='verbose logging')
 159     parser.add_argument('--debug', default=False, action="store_true",
 160                       help='debug logging')
 161
 162     api.add_auth_options(parser)
 163
 164     parser.add_argument('libraries', nargs='+',
 165                         help='mapping of library id to directory to be processed')
 166
 167     return parser
 168
 169 if __name__ == "__main__":
 170     main()