def test_is_process(self, mock_g, mock_s, mock_d, mock_get_sras_info):
mock_get_sras_info
mock_d.return_value = False
self.assertFalse(ppr.is_processed('some_gsm_dir'))
mock_d.return_value = True
mock_s.return_value = False
self.assertFalse(ppr.is_processed('some_gsm_dir'))
mock_d.return_value = True
mock_s.return_value = True
mock_g.return_value = False
self.assertFalse(ppr.is_processed('some_gsm_dir'))
mock_d.return_value = True
mock_s.return_value = True
mock_g.return_value = True
self.assertTrue(ppr.is_processed('some_gsm_dir'))
def select_gsms_to_transfer(samples, transferred_gsms,
l_top_outdir, r_free_to_use, fastq2rsem_ratio):
"""
select samples to transfer (different from select_samples_to_process in
utils_pre_pipeline.py, which are to process)
Walk through local top outdir, and for each GSMs, estimate its usage, and
if it fits free_to_use space on remote host, count it as an element
gsms_to_transfer
:param samples: a list of Sample instances representing both transferred
and non-transferred GSMs
:param transferred_gsms: a list of string with GSM ids. e.g. [GSM1, GSM2]
"""
# not yet transferred GSMs
non_tf_gsms = [_ for _ in samples if _.name not in transferred_gsms]
gsms_to_transfer = []
for gsm in non_tf_gsms:
gsm_id = os.path.relpath(gsm.outdir, l_top_outdir)
if not PPR.is_processed(gsm.outdir):
# debug info will be logged by PPR.processed
continue
rsem_usage = estimate_rsem_usage(gsm.outdir, fastq2rsem_ratio)
if rsem_usage > r_free_to_use:
logger.debug(
'{0} ({1}) doesn\'t fit current remote free_to_use ({2})'.format(
gsm_id, misc.pretty_usage(rsem_usage), misc.pretty_usage(r_free_to_use)))
continue
logger.info('{0} ({1}) fit remote free_to_use ({2})'.format(
gsm_id, misc.pretty_usage(rsem_usage), misc.pretty_usage(r_free_to_use)))
r_free_to_use -= rsem_usage
gsms_to_transfer.append(gsm)
return gsms_to_transfer
