def run(self):
print(ui.header('dammit'))
print(ui.header(__description__, level=2))
about = '\nby {0}\n\n**v{1}**, {2}\n'.format(', '.join(__authors__),
__version__, __date__)
print(about)
return self.args.func()
def run(self, doit_args=None, verbose=True):
'''Run the pipeline. Movees to the directory, loads the tasks into doit,
and executes that tasks that are not up-to-date.
Args:
doit_args (list): Args that would be passed to the doit shell
command. By default, just run.
verbose (bool): If True, print UI stuff.
Returns:
int: Exit status of the doit command.
'''
if verbose:
print(ui.header('Run Tasks', level=4))
if doit_args is None:
doit_args = ['run']
if self.n_threads > 1:
doit_args.extend(['-n', str(self.n_threads)])
runner = DoitMain(self)
with Move(self.directory):
if self.profile is True:
profile_fn = path.join(self.directory, 'profile.csv')
with StartProfiler(filename=profile_fn):
return runner.run(doit_args)
else:
return runner.run(doit_args)
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)
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 install(handler):
'''Run the database prep pipeline from the given handler.
'''
print(ui.header('Database Install', level=3))
print_meta(handler)
msg = '*All database tasks up-to-date.*'
uptodate, statuses = handler.print_statuses(uptodate_msg=msg)
if not uptodate:
print('Installing...')
return handler.run()
else:
print('Nothing to install!')
return 0
def check_or_fail(handler):
'''Check that the handler's tasks are complete, and if not, exit
with status 2.
'''
print(ui.header('Database Check', level=3))
print_meta(handler)
msg = '*All database tasks up-to-date.*'
uptodate, statuses = handler.print_statuses(uptodate_msg=msg)
if not uptodate:
print(ui.paragraph('Must install databases to continue. To do so,'
' run `dammit databases --install`. If you have'
' already installed them, make sure you\'ve given'
' the correct location to `--database-dir` or have'
' exported the $DAMMIT_DB_DIR environment'
' variable.'))
sys.exit(2)
def handle_databases(self):
log.start_logging()
print(ui.header('submodule: databases', level=2))
handler = databases.get_handler(self.config_d)
if self.args.quick:
databases.build_quick_pipeline(handler, self.config_d,
self.databases_d)
else:
databases.build_default_pipeline(handler,
self.config_d,
self.databases_d,
with_uniref=self.args.full,
with_nr=self.args.nr)
if self.args.install:
return databases.install(handler)
else:
databases.check_or_fail(handler)
def handle_annotate(self):
log.start_logging()
print(ui.header('submodule: annotate', level=2))
db_handler = databases.get_handler(self.config_d)
if self.args.quick:
databases.build_quick_pipeline(db_handler, self.config_d,
self.databases_d)
else:
databases.build_default_pipeline(db_handler,
self.config_d,
self.databases_d,
with_uniref=self.args.full,
with_nr=self.args.nr)
if self.config_d['force'] is True:
utd_msg = '*All database tasks up-to-date.*'
ood_msg = '*Some database tasks out-of-date; '\
'FORCE is True, ignoring!'
uptodate, statuses = db_handler.print_statuses(
uptodate_msg=utd_msg, outofdate_msg=ood_msg)
else:
databases.check_or_fail(db_handler)
annotate_handler = annotate.get_handler(self.config_d,
db_handler.files)
if self.args.quick:
build_quick_pipeline(annotate_handler, self.config_d,
db_handler.files)
elif self.args.full:
build_full_pipeline(annotate_handler, self.config_d,
db_handler.files)
elif self.args.nr:
build_nr_pipeline(annotate_handler, self.config_d,
db_handler.files)
else:
build_default_pipeline(annotate_handler, self.config_d,
db_handler.files)
return annotate.run_annotation(annotate_handler)
def description(self):
return ui.header('dammit: ' + __description__)
def test_header(self):
assert header('test') == '# test'
assert header('test', level=0) == '# test'
assert header('test', level=2) == '## test'
