def parse_tsv(tsv):
kvs = {}
for line in tsv.split("\\n"):
parts = line.split("\\t")
if len(parts) == 2:
# These are in the form:
# ("part1/part2/part3", "some value")
# The "channel" is special because it is a LIST so that
# has to be treated separately.
k, v = parts
k = k.replace("/", ".")
# If v can be converted into a float, great, otherwise leave it alone
try:
v = float(v)
except ValueError:
pass
try:
# Remember if "channel" was present before the exception
had_channel = "channel" in kvs
utils.block_update(kvs, k, v)
except ValueError:
# This is probably because the "channel" key has
# not been yet been constructed; add "channel" and try again
n_channels = int(kvs.get("n_channels", 0))
if not had_channel and n_channels > 0:
kvs["channel"] = [dict() for c in range(n_channels)]
# RETRY
utils.block_update(kvs, k, v)
return kvs
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")
if run_name in found_run_names:
raise Exception(
f"More than one run with name {run_name} found")
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()
tell(f"Wrote run to {folder}")
def it_adds_blocks_that_do_not_exist():
a = {"sim": {"parameters": {"donotkill": 1}}}
utils.block_update(a, "sim.parameters.peptides", [1, 2])
assert a["sim"]["parameters"]["donotkill"] == 1
assert a["sim"]["parameters"]["peptides"][0] == 1
assert a["sim"]["parameters"]["peptides"][1] == 2
def it_adds_blocks_overwriting_scalar():
a = {"a": [{"b": 1}, {"c": 2}]}
utils.block_update(a, "a.0.b.d.f", 10)
assert a["a"][0]["b"]["d"]["f"] == 10
def it_overwrites_existing_dict_block():
a = {"a": [{"b": 1}, {"c": 2}]}
utils.block_update(a, "a", 3)
assert a["a"] == 3
def it_overwrites_existing_scalar():
a = {"a": [{"b": 1}, {"c": 2}]}
utils.block_update(a, "a.1.c", 3)
assert a["a"][1]["c"] == 3