def wait(args):
config = config_m.load(Path(args.working_dir, args.config_file_name))
state_filename = Path(args.working_dir, "state.json")
working_dir = Path(args.working_dir).resolve()
working_dir_short = str(working_dir).replace("/syn/eu/ac/results", "")
if state_filename.exists():
state = json_m.read_json(state_filename)
else:
state = {
"state": "init",
"working_dir": str(working_dir)
}
json_m.write_json(path=state_filename, data=state, indent=2, compact=True)
runner = create_runner(config=config, state=state)
try:
while state["state"] != "completed":
runner.step()
json_m.write_json(path=state_filename, data=state, indent=2, compact=True)
if args.email and config.get("email"):
body = "{} completed in\n{}\n\nBest tree: scp i19:{}/tree.json.xz\nhttps://notebooks.antigenic-cartography.org/eu/results{}/tree.pdf\n\n{}\n".format(
sys.argv[0], working_dir, working_dir, working_dir_short, working_dir.joinpath("result.all.txt").open().read())
email.send(to=config["email"], subject="{} completed in {}".format(sys.argv[0], working_dir_short), body=body)
except Exception as err:
if args.email and config.get("email"):
email.send(to=config["email"], subject="{} FAILED in {}".format(sys.argv[0], working_dir_short), body="{} FAILED in\n{}\n\n{}\n\n{}".format(sys.argv[0], working_dir, err, traceback.format_exc()))
raise
def step(args):
config = config_m.load(Path(args.working_dir, args.config_file_name))
state_filename = Path(args.working_dir, "state.json")
if state_filename.exists():
state = json_m.read_json(state_filename)
else:
state = {
"state": "init",
"working_dir": str(Path(args.working_dir).resolve())
}
json_m.write_json(path=state_filename, data=state, indent=2, compact=True)
new_state = create_runner(config=config, state=state).step().state
json_m.write_json(path=state_filename, data=new_state, indent=2, compact=True)
def make_results(self):
from .maker_base import Result
overall_time = self.state["raxmlng"]["overall_time"] + self.state["garli"]["overall_time"]
overall_time_s = Result.time_str(overall_time)
module_logger.info('Overall time: ' + overall_time_s)
from .garli import GarliResults
garli_results = GarliResults.from_json(config=self.config, state=self.state, filepath=Path(self.state["working_dir"], "result.garli.json"))
r_best = vars(garli_results.results[0])
r_best["overall_time"] = overall_time
r_best["overall_time_s"] = overall_time_s
json_m.write_json(Path(self.state["working_dir"], "result.best.json"), r_best, indent=2, compact=False)
with Path(self.state["working_dir"], "result.all.txt").open("w") as f:
f.write("Overall time: " + overall_time_s + "\n")
f.write("GARLI score : " + str(r_best["score"]) + "\n")
f.write("Tree : " + str(r_best["tree"]) + "\n")
self.convert_tree_to_json(r_best["tree"])
def make_results(self):
from .maker_base import Result
overall_time = self.state["raxml"]["overall_time"] + self.state["garli"]["overall_time"]
overall_time_s = Result.time_str(overall_time)
module_logger.info('Overall time: ' + overall_time_s)
from .garli import GarliResults
garli_results = GarliResults.from_json(config=self.config, state=self.state, filepath=Path(self.state["working_dir"], "result.garli.json"))
r_best = vars(garli_results.results[0])
r_best["overall_time"] = overall_time
r_best["overall_time_s"] = overall_time_s
json_m.write_json(Path(self.state["working_dir"], "result.best.json"), r_best, indent=2, compact=False)
with Path(self.state["working_dir"], "result.all.txt").open("w") as f:
f.write("Overall time: " + overall_time_s + "\n")
f.write("GARLI score : " + str(r_best["score"]) + "\n")
f.write("Tree : " + str(r_best["tree"]) + "\n")
# from .raxml import RaxmlResults
# raxml_results = RaxmlResults.from_json(config=self.config, state=self.state, filepath=Path(self.state["working_dir"], "result.raxml.json"))
# results = {
# " total": {
# "longest_time": longest_time,
# "longest_time_s": longest_time_s,
# "overall_time": overall_time,
# "overall_time_s": overall_time_s,
# "tree": str(garli_results.results[0].tree),
# "garli_score": garli_results.results[0].score,
# },
# "garli": [vars(r) for r in garli_results.results],
# "raxml": [r if isinstance(r, dict) else vars(r) for r in raxml_results.results],
# }
# json_m.write_json(Path(self.state["working_dir"], "result.all.json"), results, indent=2, compact=True)
# convert best tree from newick to json
import tree_newick_to_json
tree = tree_newick_to_json.Tree()
tree_newick_to_json.import_newick(open(r_best["tree"]).read(), tree)
j = tree_newick_to_json.json(tree)
files.write_binary(Path(self.state["working_dir"], "tree.json.xz"), j)
def save(filename: Path, config):
json.write_json(path=filename, data=config, indent=2, compact=True)