Exemplo n.º 1
0
 def test_send_notification(self):
     """Send an email notification"""
     
     rm = RunMonitor(self.config)
     exception = None
     try:
         rm.send_notification({'name': "test run"},"dummy value")
     except Exception, e: 
         exception = e
Exemplo n.º 2
0
    def test_parse_description(self):
        """Parse a description"""
        
        org_description = \
"""- extra comment
- project:J.Doe_11_02,J.Doe_12_01,J.Doe_13_01
- setup:2x101bp""".strip()
        
        rm = RunMonitor(self.config)
        org_metadata = rm.parse_description(org_description)
        exp_description = rm.create_description(org_metadata)
        exp_metadata = rm.parse_description(exp_description)
        
        self.assertEqual(org_description,
                         exp_description,
                         "The recreated card description does not match the original")
        
        self.assertDictEqual(org_metadata,
                             exp_metadata,
                             "The recreated card metadata does not match the original")
Exemplo n.º 3
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 def test_list_runs(self):
     """List run folders"""
     run_folders = ["120106_SN12345_0144_AABC123CXX",
                    "120521_M00123_0001_AFCGHY76-KTY500",
                    "130423_D00134_0011_AD1Y4UACXX"]
     invalid_run_folders = ["ABC_SN123_0123_BASDC34CXX",
                            "120106_SN12345_0144_CABC123CXX",
                            "120521_K00123_0001_AFCGHY76-KTY500"]
     for d in run_folders + invalid_run_folders:
         os.mkdir(os.path.join(self.dump_folder,d))
     
     rm = RunMonitor(self.config)
     rm.get_run_info = mock.Mock(return_value={})
     rm.get_run_parameters = mock.Mock(return_value={})
     runs = rm.list_runs()
     self.assertListEqual(sorted(run_folders),
                          sorted([r['name'] for r in runs]),
                          "Did not return expected list of runs")
     
     for d in run_folders + invalid_run_folders:
         shutil.rmtree(os.path.join(self.dump_folder,d))
Exemplo n.º 4
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 def test_get_status_list(self):
     """Get the status list to write card to"""
     
     run_folder = "120106_SN12345_0144_AABC123CXX"
     run_path = os.path.join(self.dump_folder,run_folder)
     os.mkdir(run_path)
     
     flags = ['initial_processing_started.txt', 'initial_processing_completed.txt', 'first_read_processing_started.txt']
     for f in flags:
         with open(os.path.join(run_path,f),"w") as fh:
             fh.write("{}Z".format(str(datetime.datetime.utcfromtimestamp(time.time() - 9*60*60))))
             
     run = {'name': run_folder,
            'path': run_path}
     
     rm = RunMonitor(self.config)
     rm.get_run_info = mock.Mock(return_value={'Reads': [{},{'IsIndexedRead': 'Y'},{'IsIndexedRead': 'Y'},{}]})
     self.assertEqual(rm.get_status_list(run),
                      "Check status",
                      "Expected status list 'Check status'")
     
     os.unlink(os.path.join(run_path,flags[-1]))
     
     self.assertEqual(rm.get_status_list(run),
                      "First read",
                      "Expected status list 'First read'")
     
     open(os.path.join(run_path,'Basecalling_Netcopy_complete_Read1.txt'),'w').close()
     self.assertEqual(rm.get_status_list(run),
                      "Index read",
                      "Expected status list 'Index read'")
     
     open(os.path.join(run_path,'Basecalling_Netcopy_complete_Read2.txt'),'w').close()
     self.assertEqual(rm.get_status_list(run),
                      "Index read",
                      "Expected status list 'Index read'")
     
     open(os.path.join(run_path,'Basecalling_Netcopy_complete_Read3.txt'),'w').close()
     self.assertEqual(rm.get_status_list(run),
                      "Second read",
                      "Expected status list 'Second read'")
     
     open(os.path.join(run_path,'Basecalling_Netcopy_complete_Read4.txt'),'w').close()
     self.assertEqual(rm.get_status_list(run),
                      "Processing",
                      "Expected status list 'Processing'")
     
     shutil.rmtree(run_path)
Exemplo n.º 5
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 def test_update_trello_board(self):
     """Update Trello list with runs"""
     
     run_folders = ["120106_SN12345_0144_AABC123CXX",
                    "120521_M00123_0001_AFCGHY76-KTY500"]
     for d in run_folders:
         os.mkdir(os.path.join(self.dump_folder,d))
     
     rm = RunMonitor(self.config)
     rm.get_run_projects = mock.Mock(return_value=['J.Doe_11_01','J.Moe_12_02'])
     rm.get_status_list = mock.Mock(return_value='First read')
     rm.get_run_info = mock.Mock(return_value={'Reads': [{'NumCycles': 50},{'IsIndexedRead': 'Y'},{'NumCycles': 50}]})
     rm.get_run_parameters = mock.Mock(return_value={})
     
     rm.update_trello_board()
     lst = rm.trello.get_list(rm.trello_board,'First read')
     for run in run_folders:
         card = rm.trello.get_card(lst,run)
         self.assertIsNotNone(card,
                              "Could not locate created card for run")
         self.assertEqual(run,
                          card.name,
                          "Created card name and run name are not equal")
         shutil.rmtree(os.path.join(self.dump_folder,run))
         
     # Move a card to another list
     run = {'name': run_folders[0]}
     rm.list_runs = mock.Mock(return_value=[run])
     rm.get_status_list.return_value = 'Index read'
     rm.update_trello_board()
     lst = rm.trello.get_list(rm.trello_board,'Index read')
     card = rm.trello.get_card(lst,run['name'])
     self.assertIsNotNone(card,
                          "Could not locate created card for run")
     self.assertEqual(run['name'],
                      card.name,
                      "Created card name and run name are not equal")
Exemplo n.º 6
0
 def update_run_status(self):
     """Update the status of runs on the run tracking board"""
     
     # Create a RunMonitor object to update the run tracking board
     from hugin.run_monitor import RunMonitor
     rm = RunMonitor(self.config)
     
     rm.run_folders = self.archive_folders
     rm.samplesheet_folders = []
     
     # Loop over the runs and check whether all samples and projects have been transferred to the 
     # analysis folder
     for run in rm.list_runs():
         print("Checking run {}".format(run['name']))
         if self.get_run_status(run):
             rm.set_run_completed(run)
             # Loop over the projects in the run and move them to the bcbb list
             # Note that this can cause the card to be moved back to sequencing by the run_monitor in case
             # the project is sequenced on multiple flowcells. Has no good solution at this moment.
             for project in run.get('projects',[]):
                  self.add_project_card(project,BCBB_ANALYSIS_IN_PROGRESS)
Exemplo n.º 7
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def monitor(config,check_descrip,check_finish):
	rm = RunMonitor(config)
	if check_descrip:
		rm.check_missing_description()
	elif check_finish:
		rm.check_finish_status()
	else:
		rm.update_trello_board()
		rm.update_trello_project_board()
		rm.archive_cards()
Exemplo n.º 8
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def monitor(config):
    rm = RunMonitor(config)
    rm.update_trello_board()
    rm.update_trello_project_board()
    rm.archive_cards()