def _targets_to_remove(self):
outs = []
# original data
# TODO: check if data is local, we don't want to delete that
download_task = DownloadExperiment(self.experiment_id, source='gemma')
outs.extend(flatten_output(download_task))
# any data resulting from trimming raw reads
trim_task = TrimExperiment(self.experiment_id, source='gemma')
outs.extend(flatten_output(trim_task))
return outs
def infer_bulk_complete_from_fs(task_cls, finite_datehours):
"""
Efficiently determines missing datehours by filesystem listing.
The current implementation works for the common case of a task writing
output to a FileSystemTarget whose path is built using strftime with format
like '...%Y...%m...%d...%H...', without custom complete() or exists().
(Eventually Luigi could have ranges of completion as first-class citizens.
Then this listing business could be factored away/be provided for
explicitly in target API or some kind of a history server.)
TODO support RangeDaily
"""
filesystems_and_globs_by_location = _get_filesystems_and_globs(task_cls)
paths_by_datehour = [[o.path for o in flatten_output(task_cls(d))]
for d in finite_datehours]
listing = set()
for (f, g), p in zip(
filesystems_and_globs_by_location, zip(*paths_by_datehour)
): # transposed, so here we're iterating over logical outputs, not datehours
listing |= _list_existing(f, g, p)
# quickly learn everything that's missing
missing_datehours = []
for d, p in zip(finite_datehours, paths_by_datehour):
if not set(p) <= listing:
missing_datehours.append(d)
return missing_datehours
def infer_bulk_complete_from_fs(datetimes, datetime_to_task, datetime_to_re):
"""
Efficiently determines missing datetimes by filesystem listing.
The current implementation works for the common case of a task writing
output to a FileSystemTarget whose path is built using strftime with format
like '...%Y...%m...%d...%H...', without custom complete() or exists().
(Eventually Luigi could have ranges of completion as first-class citizens.
Then this listing business could be factored away/be provided for
explicitly in target API or some kind of a history server.)
"""
filesystems_and_globs_by_location = _get_filesystems_and_globs(datetime_to_task, datetime_to_re)
paths_by_datetime = [[o.path for o in flatten_output(datetime_to_task(d))] for d in datetimes]
listing = set()
for (f, g), p in zip(
filesystems_and_globs_by_location, zip(*paths_by_datetime)
): # transposed, so here we're iterating over logical outputs, not datetimes
listing |= _list_existing(f, g, p)
# quickly learn everything that's missing
missing_datetimes = []
for d, p in zip(datetimes, paths_by_datetime):
if not set(p) <= listing:
missing_datetimes.append(d)
return missing_datetimes
def _get_filesystems_and_globs(datetime_to_task, datetime_to_re):
"""
Yields a (filesystem, glob) tuple per every output location of task.
The task can have one or several FileSystemTarget outputs.
For convenience, the task can be a luigi.WrapperTask,
in which case outputs of all its dependencies are considered.
"""
# probe some scattered datetimes unlikely to all occur in paths, other than by being sincere datetime parameter's representations
# TODO limit to [self.start, self.stop) so messages are less confusing? Done trivially it can kill correctness
sample_datetimes = [datetime(y, m, d, h) for y in range(2000, 2050, 10) for m in range(1, 4) for d in range(5, 8) for h in range(21, 24)]
regexes = [re.compile(datetime_to_re(d)) for d in sample_datetimes]
sample_tasks = [datetime_to_task(d) for d in sample_datetimes]
sample_outputs = [flatten_output(t) for t in sample_tasks]
for o, t in zip(sample_outputs, sample_tasks):
if len(o) != len(sample_outputs[0]):
raise NotImplementedError("Outputs must be consistent over time, sorry; was %r for %r and %r for %r" % (o, t, sample_outputs[0], sample_tasks[0]))
# TODO fall back on requiring last couple of days? to avoid astonishing blocking when changes like that are deployed
# erm, actually it's not hard to test entire hours_back..hours_forward and split into consistent subranges FIXME?
for target in o:
if not isinstance(target, FileSystemTarget):
raise NotImplementedError("Output targets must be instances of FileSystemTarget; was %r for %r" % (target, t))
for o in zip(*sample_outputs): # transposed, so here we're iterating over logical outputs, not datetimes
glob = _get_per_location_glob(sample_tasks, o, regexes)
yield o[0].fs, glob
def _get_filesystems_and_globs(task_cls):
"""
Yields a (filesystem, glob) tuple per every output location of task_cls.
task_cls can have one or several FileSystemTarget outputs.
For convenience, task_cls can be a wrapper task,
in which case outputs of all its dependencies are considered.
"""
# probe some scattered datehours unlikely to all occur in paths, other than by being sincere datehour parameter's representations
# TODO limit to [self.start, self.stop) so messages are less confusing? Done trivially it can kill correctness
sample_datehours = [datetime(y, m, d, h) for y in range(2000, 2050, 10) for m in range(1, 4) for d in range(5, 8) for h in range(21, 24)]
regexes = [re.compile('(%04d).*(%02d).*(%02d).*(%02d)' % (d.year, d.month, d.day, d.hour)) for d in sample_datehours]
sample_tasks = [task_cls(d) for d in sample_datehours]
sample_outputs = [flatten_output(t) for t in sample_tasks]
for o, t in zip(sample_outputs, sample_tasks):
if len(o) != len(sample_outputs[0]):
raise NotImplementedError("Outputs must be consistent over time, sorry; was %r for %r and %r for %r" % (o, t, sample_outputs[0], sample_tasks[0]))
# TODO fall back on requiring last couple of days? to avoid astonishing blocking when changes like that are deployed
# erm, actually it's not hard to test entire hours_back..hours_forward and split into consistent subranges FIXME?
for target in o:
if not isinstance(target, FileSystemTarget):
raise NotImplementedError("Output targets must be instances of FileSystemTarget; was %r for %r" % (target, t))
for o in zip(*sample_outputs): # transposed, so here we're iterating over logical outputs, not datehours
glob = _get_per_location_glob(sample_tasks, o, regexes)
yield o[0].fs, glob
def remove_task_output(task):
logger.info('Cleaning up %s...', repr(task))
for out in flatten_output(task):
if hasattr(out, 'remove') and out.exists():
try:
out.remove()
logger.info('Removed %s.', repr(out))
except:
logger.exception('Failed to remove %s.', repr(out))
def on_failure(self, err):
logger.info('Removing task output of %s due to failure.', repr(self))
for out in flatten_output(self):
if out.exists() and hasattr(out, 'remove'):
try:
out.remove()
except:
logger.exception('Failed to remove output %s while cleaning up %s.', repr(out), repr(self))
return super(RemoveTaskOutputOnFailureMixin, self).on_failure(err)
def missing_datehours(self, task_cls, finite_datehours):
"""Infers them by listing the task output target(s) filesystem.
"""
filesystems_and_globs_by_location = self._get_filesystems_and_globs(task_cls)
paths_by_datehour = [[o.path for o in flatten_output(task_cls(d))] for d in finite_datehours]
listing = set()
for (f, g), p in zip(filesystems_and_globs_by_location, zip(*paths_by_datehour)): # transposed, so here we're iterating over logical outputs, not datehours
listing |= self._list_existing(f, g, p)
# quickly learn everything that's missing
missing_datehours = []
for d, p in zip(finite_datehours, paths_by_datehour):
if not set(p) <= listing:
missing_datehours.append(d)
return missing_datehours
def missing_datehours(self, task_cls, finite_datehours):
"""Infers them by listing the task output target(s) filesystem.
"""
filesystems_and_globs_by_location = self._get_filesystems_and_globs(
task_cls)
paths_by_datehour = [[o.path for o in flatten_output(task_cls(d))]
for d in finite_datehours]
listing = set()
for (f, g), p in zip(
filesystems_and_globs_by_location, zip(*paths_by_datehour)
): # transposed, so here we're iterating over logical outputs, not datehours
listing |= self._list_existing(f, g, p)
# quickly learn everything that's missing
missing_datehours = []
for d, p in zip(finite_datehours, paths_by_datehour):
if not set(p) <= listing:
missing_datehours.append(d)
return missing_datehours
def run(self):
for out in flatten_output(self):
out.makedirs()
return super(CreateTaskOutputDirectoriesBeforeRunMixin, self).run()