def test_run_preprocessing_to_start(self, mock_demultiplex_run, mock_upload_to_statusdb, mock_get_run_status):
"""Run preprocessing start demux."""
run = self.completed
mock_get_run_status.return_value = 'TO_START'
an.run_preprocessing(run, force_trasfer=True, statusdb=True)
mock_upload_to_statusdb.assert_called_once()
mock_demultiplex_run.assert_called_once()
def test_run_preprocessing_in_progress(self, mock_check_run_status, mock_upload_to_statusdb, mock_get_run_status):
"""Run preprocessing demux in progress."""
run = self.completed
mock_get_run_status.return_value = 'IN_PROGRESS'
an.run_preprocessing(run, force_trasfer=True, statusdb=True)
mock_upload_to_statusdb.assert_called_once()
mock_check_run_status.assert_called_once()
def test_run_preprocessing_completed(self, mock_copy, mock_mkdir, mock_transfer_run, mock_send_mail, mock_upload_to_statusdb, mock_get_run_status):
"""Run preprocessing demux completed."""
run = self.completed
mock_get_run_status.return_value = 'COMPLETED'
an.run_preprocessing(run, force_trasfer=True, statusdb=True)
mock_upload_to_statusdb.assert_called_once()
message = 'The run 141124_ST-COMPLETED1_01_AFCIDXX has been demultiplexed.\n The Run will be transferred to Irma for further analysis.\n\n \
The run is available at : https://genomics-status.scilifelab.se/flowcells/141124_ST-COMPLETED1_01_AFCIDXX\n\n '
mock_send_mail.assert_called_once_with(message, rcp='some_user@some_email.com')
mock_transfer_run.assert_called_once_with('data/transfer.tsv', 'some_user@some_email.com')
def test_run_preprocessing_sequencing(self, mock_upload_to_statusdb, mock_get_run_status):
"""Run preprocess run still sequencing."""
run = self.completed
mock_get_run_status.return_value = 'SEQUENCING'
an.run_preprocessing(run, force_trasfer=True, statusdb=True)
mock_upload_to_statusdb.assert_called_once()
def demultiplex(run, force): """ Demultiplex all runs present in the data directories """ an.run_preprocessing(run, force_trasfer=force)
def demultiplex(run, force):
"""Demultiplex and transfer all runs present in the data directories."""
an.run_preprocessing(run, force_trasfer=force)
def demultiplex(run): """ Demultiplex all runs present in the data directories """ an.run_preprocessing(run)
def demultiplex(run):
""" Demultiplex all runs present in the data directories
"""
an.run_preprocessing(run)
