def update_trello_project_board(self):
"""Update the project cards for projects in ongoing runs
"""
skip_list_ids = [self.trello.get_list_id(self.trello_board,COMPLETED),
self.trello.get_list_id(self.trello_board,ABORTED)]
from hugin.project_monitor import ProjectMonitor
pm = ProjectMonitor(self.config)
runs = self.list_runs()
for run in runs:
# check if the run has already been archived and if so, skip it
if self.trello_board_archive and self.trello.get_card_on_board(self.trello_board_archive,run['name']):
print("run {} is archived, skipping".format(run['name']))
continue
# check if the run is in a list that should be skipped
card = self.trello.get_card_on_board(self.trello_board,run['name'])
if card and card.list_id in skip_list_ids:
print("run {} is in list {}, skipping".format(run['name'],card.list_id))
continue
projects = self.get_run_projects(run)
for project in projects:
print("Adding run {} to project {}".format(run['name'],project))
pm.add_run_to_project(project,run)
def check_finish_status(self):
"""Get the runs in given list and check if the transfer is dont to UPPMAX"""
from hugin.project_monitor import ProjectMonitor
pm = ProjectMonitor(self.config)
pm.samplesheet_folders = []
uppmax_list = self.trello.get_list(self.trello_board,UPPMAX)
runs = []
# Gathering required keys for the purpose of this method
for card in uppmax_list.list_cards():
run_name = card.name
miseq = True if re.search(r'-',run_name.split('_')[-1]) else False
runs.append({
'name' : run_name,
'path' : os.path.join(self.config.get('archive_folders'),run_name),
'date' : run_name.split("_")[0],
'position' : run_name.split("_")[-1][0] if not miseq else '',
'flowcell_id' : run_name.split("_")[-1][1:] if not miseq else run_name.split("_")[-1]})
for run in runs:
if pm.get_run_status(run):
self.set_run_completed(run)
def test_add_project_card(self):
"""Add a project card to project board"""
pm = ProjectMonitor(self.config)
project = "J.Doe_11_01"
card = pm.add_project_card(project)
card.fetch()
self.assertIs(type(card),
trello.Card,
"Did not get a Card object back")
self.assertFalse(card.closed,
"The added card is closed")
lst = pm.trello.get_list(pm.trello_board, "Sequencing")
self.assertEqual(card.list_id,
lst.id,
"Card was not added to the expected list")
run = {'name': "Test run 001"}
pm.add_run_to_project(project, run)
run = {'name': "Test run 002"}
pm.add_run_to_project(project, run)
def monitor(config):
pm = ProjectMonitor(config)
pm.update_run_status()
pm.update_trello_board()
pm.archive_cards()