+++ /dev/null
-"""Create a track hub
-"""
-
-#!/usr/bin/env python
-from ConfigParser import SafeConfigParser
-import fnmatch
-from glob import glob
-import json
-import logging
-import netrc
-from optparse import OptionParser, OptionGroup
-import os
-from pprint import pprint, pformat
-import shlex
-from StringIO import StringIO
-import stat
-import sys
-import time
-import types
-import urllib
-import urllib2
-import urlparse
-from zipfile import ZipFile
-
-import RDF
-
-if not 'DJANGO_SETTINGS_MODULE' in os.environ:
- os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
-
-from htsworkflow.util import api
-from htsworkflow.util.rdfhelp import \
- dafTermOntology, \
- fromTypedNode, \
- get_model, \
- get_serializer, \
- load_into_model, \
- sparql_query, \
- submissionOntology
-from htsworkflow.submission.daf import get_submission_uri
-from htsworkflow.submission.results import ResultMap
-from htsworkflow.submission.trackhub import TrackHubSubmission
-from htsworkflow.submission.condorfastq import CondorFastqExtract
-
-logger = logging.getLogger(__name__)
-
-def main(cmdline=None):
- parser = make_parser()
- opts, args = parser.parse_args(cmdline)
- submission_uri = None
-
- if opts.debug:
- logging.basicConfig(level = logging.DEBUG )
- elif opts.verbose:
- logging.basicConfig(level = logging.INFO )
- else:
- logging.basicConfig(level = logging.WARNING )
-
- apidata = api.make_auth_from_opts(opts, parser)
-
- model = get_model(opts.model, opts.db_path)
- mapper = None
- if opts.name:
- mapper = TrackHubSubmission(opts.name, model, host=opts.host)
- submission_uri = get_submission_uri(opts.name)
-
-
- if opts.load_rdf is not None:
- if submission_uri is None:
- parser.error("Please specify the submission name")
- load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
-
- results = ResultMap()
- for a in args:
- if os.path.exists(a):
- results.add_results_from_file(a)
- else:
- logger.warn("File %s doesn't exist.", a)
-
- if opts.make_link_tree_from is not None:
- results.make_tree_from(opts.make_link_tree_from, link=True)
-
- if opts.copy_tree_from is not None:
- results.make_tree_from(opts.copy_tree_from, link=False)
-
- if opts.fastq:
- logger.info("Building fastq extraction scripts")
- flowcells = os.path.join(opts.sequence, 'flowcells')
- extractor = CondorFastqExtract(opts.host, flowcells,
- model=opts.model,
- force=opts.force)
- extractor.create_scripts(results)
-
- if opts.scan_submission:
- if opts.name is None:
- parser.error("Please define a submission name")
- mapper.scan_submission_dirs(results)
-
- if opts.make_hub:
- make_hub(mapper, results, opts.make_hub)
-
- if opts.make_manifest:
- make_manifest(mapper, results, opts.make_manifest)
-
- if opts.sparql:
- sparql_query(model, opts.sparql)
-
- if opts.print_rdf:
- writer = get_serializer()
- print writer.serialize_model_to_string(model)
-
-
-def make_hub(mapper, results, filename=None):
- trackdb = mapper.make_hub(results)
-
- if filename is None or filename == '-':
- sys.stdout.write(trackdb)
- else:
- with open('trackDb.txt', 'w') as trackstream:
- trackstream.write(trackdb)
-
-def make_manifest(mapper, results, filename=None):
- manifest = mapper.make_manifest(results)
-
- if filename is None or filename == '-':
- sys.stdout.write(manifest)
- else:
- with open(filename, 'w') as mainifeststream:
- mainifeststream.write(manifest)
-
-def make_parser():
- parser = OptionParser()
-
- model = OptionGroup(parser, 'model')
- model.add_option('--name', help="Set submission name")
- model.add_option('--db-path', default=None,
- help="set rdf database path")
- model.add_option('--model', default=None,
- help="Load model database")
- model.add_option('--load-rdf', default=None,
- help="load rdf statements into model")
- model.add_option('--sparql', default=None, help="execute sparql query")
- model.add_option('--print-rdf', action="store_true", default=False,
- help="print ending model state")
- parser.add_option_group(model)
- # commands
- commands = OptionGroup(parser, 'commands')
- commands.add_option('--make-link-tree-from',
- help="create directories & link data files",
- default=None)
- commands.add_option('--copy-tree-from',
- help="create directories & copy data files",
- default=None)
- commands.add_option('--fastq', default=False, action="store_true",
- help="generate scripts for making fastq files")
- commands.add_option('--scan-submission', default=False, action="store_true",
- help="Import metadata for submission into our model")
- commands.add_option('--make-hub', default=None,
- help='name the hub file or - for stdout to create it')
- commands.add_option('--make-manifest',
- help='name the manifest file name or - for stdout to create it',
- default=None)
-
-
- parser.add_option_group(commands)
-
- parser.add_option('--force', default=False, action="store_true",
- help="Force regenerating fastqs")
- parser.add_option('--daf', default=None, help='specify daf name')
- parser.add_option('--library-url', default=None,
- help="specify an alternate source for library information")
- # debugging
- parser.add_option('--verbose', default=False, action="store_true",
- help='verbose logging')
- parser.add_option('--debug', default=False, action="store_true",
- help='debug logging')
-
- api.add_auth_options(parser)
-
- return parser
-
-if __name__ == "__main__":
- main()
projects / htsworkflow.git / blobdiff