def print_statuses(self, uptodate_msg='All tasks up-to-date!',
outofdate_msg='Some tasks out of date!'):
'''Print the up-to-date status of all tasks.
Args:
uptodate_msg (str): The message to print if all tasks are up to
date.
Returns:
tuple: A bool (True if all up to date) and a dictionary of statuses.
'''
uptodate, statuses = self.check_uptodate()
if uptodate:
print(ui.paragraph(uptodate_msg))
else:
print(ui.paragraph(outofdate_msg))
uptodate_list = [t for t,s in statuses.items() if s is True]
outofdate_list = [t for t,s in statuses.items() if s is False]
if uptodate_list:
print('\nUp-to-date tasks:')
print(ui.listing(uptodate_list))
if outofdate_list:
print('\nOut-of-date tasks:')
print(ui.listing(outofdate_list))
return uptodate, statuses
def test_listing(self):
d = {'a': 2, 'b': 5, 'c': 10}
exp_d = '* a: 2\n* b: 5\n* c: 10\n'
exp_l = '* a\n* b\n* c\n'
assert listing(d) == exp_d
assert listing(d.keys()) == exp_l
def print_meta(handler):
'''Print metadata about the database pipeline.
Args:
handler (handler.TaskHandler): The database task handler.
'''
print(ui.header('Info', level=4))
info = {'Doit Database': handler.dep_file,
'Database Directory': handler.directory}
print(ui.listing(info))
def run_annotation(handler):
'''Run the annotation pipeline from the given handler.
Prints the appropriate output and exits of the pipeline is alredy completed.
Args:
handler (handler.TaskHandler): Handler with tasks for the pipeline.
'''
print(ui.header('Annotation', level=3))
print(ui.header('Info', level=4))
info = {'Doit Database': handler.dep_file,
'Input Transcriptome': handler.files['transcriptome']}
print(ui.listing(info))
msg = '*All annotation tasks up-to-date.*'
uptodate, statuses = handler.print_statuses(uptodate_msg=msg)
if not uptodate:
return handler.run()
else:
print('**Pipeline is already completed!**')
sys.exit(0)