def _load(self):
filename = self._filename
if local.path(self._filename).exists():
try:
d = pickle_load(filename)
del d["_filename"]
self.update(d)
except Exception:
info(f"Store {self._filename} was unloadable")
def _write_runs(self, job_folder, run_descs, props=[]):
"""
Convert the munch run_descs into folders
"""
if not job_folder.exists():
job_folder.mkdir()
found_run_names = {}
for i, run in enumerate(run_descs):
# FIND or OVERRIDE run_name
run_name = run.get("run_name")
assert run_name not in found_run_names
found_run_names[run_name] = True
# SETUP _erisyon block
if "_erisyon" not in run:
run._erisyon = Munch()
run._erisyon.run_i = i
run._erisyon.run_i_of = len(run_descs)
run._erisyon.run_name = run_name
# OVERRIDE with props
for prop in props:
k, v, t = prop.split("=")
if t == "bool":
v = True if v == "true" else False
elif t == "int":
v = int(v)
elif t == "float":
v = float(v)
elif t == "int_list":
v = [int(i) for i in v.split(",")]
elif t == "int_dict":
v = v.split(",")
v = {v[i]: int(v[i + 1]) for i in range(0, len(v), 2)}
else:
raise TypeError(f"Unknown type in prop coversion '{t}")
utils.block_update(run, k, v)
# Keep the run_name out
run.pop("run_name", None)
folder = job_folder / run_name
folder.mkdir()
RunExecutor(folder, tasks=run).save()
info(f"Wrote run to {folder}")
def _do_work_orders_process_mode(zap):
with ProcessPoolExecutor(max_workers=zap.max_workers) as executor:
try:
return _do_zap_with_executor(executor, zap)
except KeyboardInterrupt:
# If I do not os.kill the processes then it seems
# that will gracefully send kill signals and wait
# for the children. I typically want to just abandon
# anything that the process is doing and have it end instantly.
# Thus, I just reach in to get the child pids and kill -9 them.
debug()
for k, v in executor._processes.items():
try:
debug(k, v.pid)
os.kill(v.pid, signal.SIGKILL)
except ProcessLookupError:
info(f"{v.pid} had already died")
raise
def progress(self, n_complete, n_total, retry):
if retry:
info(f"\nRetry {n_complete}")
if self.progress_fn is not None:
self.progress_fn(self.task_name, self.start_time, n_complete,
n_total, self.phase)
def _info(msg):
"""mock point"""
info(msg)
def _show_work_order_exception(e):
"""Mock-point"""
error("\nAn exception was thrown by a work_order ------")
info("".join(e.exception_lines))
error("----------------------------------------------")
def counter(iterable):
list_ = list(iterable)
count = len(list_)
for i, val in enumerate(list_):
info(f"{i+1} of {count}")
yield val
def main(self):
if self.construct_fail:
return
with local.cwd("/erisyon"):
assert local.path("erisyon_root").exists()
job_folder = self.validate_job_name_and_folder()
schema = self.generator_klass.schema
defaults = self.generator_klass.defaults
requirements = schema.requirements()
# APPLY defaults and then ask user for any elements that are not declared
generator_args = {}
switches = self._switches_by_name
if self.protein_random is not None:
info(
f"Sampling {self.protein_random} random proteins from imported set"
)
n = len(self.derived_vals.protein)
assert n >= self.protein_random
self.derived_vals.protein = data.subsample(
self.derived_vals.protein, self.protein_random
)
assert len(self.derived_vals.protein) == self.protein_random
for arg_name, arg_type, arg_help, arg_userdata in requirements:
if (
arg_name in self.derived_vals
and self.derived_vals.get(arg_name) is not None
):
# Load from a derived switch (eg: protein)
generator_args[arg_name] = self.derived_vals[arg_name]
elif arg_name in switches and switches.get(arg_name) is not None:
# Load from a switch
generator_args[arg_name] = getattr(self, arg_name)
else:
# If the schema allows the user to enter manually
if arg_userdata.get("allowed_to_be_entered_manually"):
generator_args[arg_name] = self._request_field_from_user(
arg_name, arg_type, default=defaults.get(arg_name)
)
# Intentionally run the generate before the job folder is written
# so that if generate fails it doesn't leave around a partial job.
try:
generator_args["force_run_name"] = self.run_name
generator = self.generator_klass(**generator_args)
run_descs = generator.generate()
except (SchemaValidationFailed, ValidationError) as e:
# Emit clean failure and exit 1
error(str(e))
return 1
# WRITE the job & copy any file sources
self._write_runs(job_folder, run_descs, props=self.prop)
(job_folder / "_gen_sources").delete()
self.local_sources_tmp_folder.move(job_folder / "_gen_sources")
if not self.skip_report:
report = generator.report_assemble()
utils.json_save(job_folder / "report.ipynb", report)
utils.yaml_write(
job_folder / "job_manifest.yaml",
uuid=self.job_uuid,
localtime=time.strftime("%Y-%m-%d, %H:%M:%S", time.localtime()),
# Note: it seems localtime inside our container is UTC
who=local.env.get("RUN_USER", "Unknown"),
cmdline_args=sys.argv,
)