model = get_model(opts.model, opts.db_path)
mapper = None
if opts.name:
- mapper = GEOSubmission(opts.name, model)
- if opts.library_url is not None:
- mapper.library_url = opts.library_url
+ mapper = GEOSubmission(opts.name, model, host=opts.host)
submission_uri = get_submission_uri(opts.name)
results = ResultMap()
for a in args:
- results.add_results_from_file(a)
+ if os.path.exists(a):
+ results.add_results_from_file(a)
+ else:
+ logger.warn("File %s doesn't exist.", a)
if opts.make_tree_from is not None:
results.make_tree_from(opts.make_tree_from)
if opts.fastq:
+ logger.info("Building fastq extraction scripts")
flowcells = os.path.join(opts.sequence, 'flowcells')
extractor = CondorFastqExtract(opts.host, flowcells,
model=opts.model,