Пример #1
0
    def setUpClass(self):
        """ Creates the following directory tree for testing purposes:

        tmp/
        |__ 141124_ST-COMPLETED_01_AFCIDXX
        |   |__ RunInfo.xml
        |   |__ Demultiplexing
        |   |   |__ Stats
        |   |       |__ DemultiplexingStats.xml
        |   |__ RTAComplete.txt
        |__ 141124_ST-INPROGRESS_02_AFCIDXX
        |   |__ RunInfo.xml
        |   |__ Demultiplexing
        |   |__ RTAComplete.txt
        |__ 141124_ST-RUNNING_03_AFCIDXX
        |   |__ RunInfo.xml
        |__ 141124_ST-TOSTART_04_FCIDXXX
            |__ RunInfo.xml
            |__ RTAComplete.txt
        """
        self.tmp_dir = os.path.join(tempfile.mkdtemp(), 'tmp')
        self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv')

        running = os.path.join(self.tmp_dir, '141124_ST-RUNNING1_03_AFCIDXX')
        to_start = os.path.join(self.tmp_dir, '141124_ST-TOSTART1_04_FCIDXXX')
        in_progress = os.path.join(self.tmp_dir, '141124_ST-INPROGRESS1_02_AFCIDXX')
        completed = os.path.join(self.tmp_dir, '141124_ST-COMPLETED1_01_AFCIDXX')
        finished_runs = [to_start, in_progress, completed]

        # Create runs directory structure
        os.makedirs(self.tmp_dir)
        os.makedirs(running)
        os.makedirs(to_start)
        os.makedirs(os.path.join(in_progress, 'Demultiplexing'))
        os.makedirs(os.path.join(completed, 'Demultiplexing', 'Stats'))

        # Create files indicating that the run is finished
        for run in finished_runs:
            open(os.path.join(run, 'RTAComplete.txt'), 'w').close()

        # Create files indicating that the preprocessing is done
        open(os.path.join(completed, 'Demultiplexing', 'Stats', 'DemultiplexingStats.xml'), 'w').close()

        # Create transfer file and add the completed run
        with open(self.transfer_file, 'w') as f:
            tsv_writer = csv.writer(f, delimiter='\t')
            tsv_writer.writerow([os.path.basename(completed), str(datetime.now())])

        # Move sample RunInfo.xml file to every run directory
        for run in [running, to_start, in_progress, completed]:
            shutil.copy('data/RunInfo.xml', run)
            shutil.copy('data/runParameters.xml', run)
        
        # Create run objects
        # Jose : add tests for other sequencers
        self.running = HiSeqX_Run(os.path.join(self.tmp_dir, 
                                               '141124_ST-RUNNING1_03_AFCIDXX'), 
                                  CONFIG["analysis"]["HiSeqX"])
        self.to_start = Run(os.path.join(self.tmp_dir, 
                                         '141124_ST-TOSTART1_04_FCIDXXX'), 
                            CONFIG["analysis"]["HiSeqX"])
        self.in_progress = Run(os.path.join(self.tmp_dir, 
                                            '141124_ST-INPROGRESS1_02_AFCIDXX'), 
                               CONFIG["analysis"]["HiSeqX"])
        self.completed = Run(os.path.join(self.tmp_dir, 
                                          '141124_ST-COMPLETED1_01_AFCIDXX'), 
                             CONFIG["analysis"]["HiSeqX"])
        self.finished_runs = [self.to_start, self.in_progress, self.completed]
        self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv')
Пример #2
0
class TestTracker(unittest.TestCase):
    """ analysis.py script tests
    """
    @classmethod
    def setUpClass(self):
        """ Creates the following directory tree for testing purposes:

        tmp/
        |__ 141124_ST-COMPLETED_01_AFCIDXX
        |   |__ RunInfo.xml
        |   |__ Demultiplexing
        |   |   |__ Stats
        |   |       |__ DemultiplexingStats.xml
        |   |__ RTAComplete.txt
        |__ 141124_ST-INPROGRESS_02_AFCIDXX
        |   |__ RunInfo.xml
        |   |__ Demultiplexing
        |   |__ RTAComplete.txt
        |__ 141124_ST-RUNNING_03_AFCIDXX
        |   |__ RunInfo.xml
        |__ 141124_ST-TOSTART_04_FCIDXXX
            |__ RunInfo.xml
            |__ RTAComplete.txt
        """
        self.tmp_dir = os.path.join(tempfile.mkdtemp(), 'tmp')
        self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv')

        running = os.path.join(self.tmp_dir, '141124_ST-RUNNING1_03_AFCIDXX')
        to_start = os.path.join(self.tmp_dir, '141124_ST-TOSTART1_04_FCIDXXX')
        in_progress = os.path.join(self.tmp_dir, '141124_ST-INPROGRESS1_02_AFCIDXX')
        completed = os.path.join(self.tmp_dir, '141124_ST-COMPLETED1_01_AFCIDXX')
        finished_runs = [to_start, in_progress, completed]

        # Create runs directory structure
        os.makedirs(self.tmp_dir)
        os.makedirs(running)
        os.makedirs(to_start)
        os.makedirs(os.path.join(in_progress, 'Demultiplexing'))
        os.makedirs(os.path.join(completed, 'Demultiplexing', 'Stats'))

        # Create files indicating that the run is finished
        for run in finished_runs:
            open(os.path.join(run, 'RTAComplete.txt'), 'w').close()

        # Create files indicating that the preprocessing is done
        open(os.path.join(completed, 'Demultiplexing', 'Stats', 'DemultiplexingStats.xml'), 'w').close()

        # Create transfer file and add the completed run
        with open(self.transfer_file, 'w') as f:
            tsv_writer = csv.writer(f, delimiter='\t')
            tsv_writer.writerow([os.path.basename(completed), str(datetime.now())])

        # Move sample RunInfo.xml file to every run directory
        for run in [running, to_start, in_progress, completed]:
            shutil.copy('data/RunInfo.xml', run)
            shutil.copy('data/runParameters.xml', run)
        
        # Create run objects
        # Jose : add tests for other sequencers
        self.running = HiSeqX_Run(os.path.join(self.tmp_dir, 
                                               '141124_ST-RUNNING1_03_AFCIDXX'), 
                                  CONFIG["analysis"]["HiSeqX"])
        self.to_start = Run(os.path.join(self.tmp_dir, 
                                         '141124_ST-TOSTART1_04_FCIDXXX'), 
                            CONFIG["analysis"]["HiSeqX"])
        self.in_progress = Run(os.path.join(self.tmp_dir, 
                                            '141124_ST-INPROGRESS1_02_AFCIDXX'), 
                               CONFIG["analysis"]["HiSeqX"])
        self.completed = Run(os.path.join(self.tmp_dir, 
                                          '141124_ST-COMPLETED1_01_AFCIDXX'), 
                             CONFIG["analysis"]["HiSeqX"])
        self.finished_runs = [self.to_start, self.in_progress, self.completed]
        self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv')

    @classmethod
    def tearDownClass(self):
        shutil.rmtree(self.tmp_dir)

    def test_1_is_finished(self):
        """ Is finished should be True only if "RTAComplete.txt" file is present...
        """
        self.assertFalse(self.running._is_sequencing_done())
        self.assertTrue(all(map(lambda run: run._is_sequencing_done, self.finished_runs)))

    def test_2_processing_status(self):
        """ Status of the processing depends on the generated files
        """
        self.assertEqual('SEQUENCING', self.running.get_run_status())
        self.assertEqual('TO_START', self.to_start.get_run_status())
        self.assertEqual('IN_PROGRESS', self.in_progress.get_run_status())
        self.assertEqual('COMPLETED', self.completed.get_run_status())

    def test_3_is_transferred(self):
        """ is_transferred should rely on the info in transfer.tsv
        """
        self.assertTrue(self.completed.is_transferred(self.transfer_file))
        self.assertFalse(self.running.is_transferred(self.transfer_file))
        self.assertFalse(self.to_start.is_transferred(self.transfer_file))
        self.assertFalse(self.in_progress.is_transferred( self.transfer_file))