def parse_arguments() -> argparse.ArgumentParser:
parser = argparse.ArgumentParser()
msg = "The corresponding attribute to be passed to the job scheduler."
parser.add_argument("--mem", dest="mem", default="48G", help=msg)
parser.add_argument("--cores", dest="cores", default=4, help=msg)
parser.add_argument("--time", dest="time", default="02:00:00", help=msg)
parser.add_argument("--partition", dest="partition", default="panda", help=msg)
choices = divvy.ComputingConfiguration().list_compute_packages()
msg = "`Divvy` compute configuration to be used when submitting the jobs."
parser.add_argument("--divvy-configuration", dest="compute", choices=choices, help=msg)
msg = "Whether to do all steps except job submission."
parser.add_argument(
"-d", "--dry-run", dest="dry_run", action="store_true", default=False, help=msg,
)
msg = "Attribute in sample annotation containing the path to the input files."
parser.add_argument(
"--attribute", dest="sample_file_attribute", default="sample_name", help=msg,
)
msg = "The parent directory of containting the input data."
parser.add_argument("--input-dir", dest="input_dir", default="data", help=msg)
msg = "Parent directory for output files."
parser.add_argument("--output-dir", dest="output_dir", default="processed", help=msg)
msg = "CSV file with metadata for all samples."
parser.add_argument(dest="metadata", help=msg)
msg = (
"Whether all samples or only samples marked with a positive value in the `toggle`"
"column should be processed."
)
parser.add_argument("--toggle", dest="toggle", action="store_true", default=False, help=msg)
return parser
def set_comp_env():
global active_settings
if globs.compute_config is None:
globs.compute_config = divvy.ComputingConfiguration()
selected_package = request.args.get('compute', type=str)
globs.status_check_interval = int(request.args.get('interval', type=int)
or globs.status_check_interval
or POLL_INTERVAL)
if globs.compute_package is None:
globs.compute_package = "default"
if selected_package is not None:
success = globs.compute_config.clean_start(selected_package)
if not success:
msg = "Compute package '{}' cannot be activated".format(selected_package)
app.logger.warning(msg)
return jsonify(active_settings=render_template('compute_info.html', active_settings=None, msg=msg))
globs.compute_package = selected_package
active_settings = globs.compute_config.get_active_package()
write_preferences({"status_check_interval": globs.status_check_interval,
"compute_package": globs.compute_package})
return jsonify(active_settings=render_template('compute_info.html', active_settings=active_settings))
active_settings = globs.compute_config.get_active_package()
notify_not_set = COMPUTE_SETTINGS_VARNAME[0] if \
globs.compute_config.default_config_file == globs.compute_config.config_file else None
write_preferences({"status_check_interval": globs.status_check_interval,
"compute_package": globs.compute_package})
return render_template('preferences.html', env_conf_file=globs.compute_config.config_file,
compute_packages=globs.compute_config.list_compute_packages(), active_settings=active_settings,
compute_package=globs.compute_package, notify_not_set=notify_not_set,
default_interval=globs.status_check_interval)
def set_comp_env():
global active_settings
if globs.compute_config is None:
globs.compute_config = divvy.ComputingConfiguration()
selected_package = request.args.get('compute', type=str)
if globs.currently_selected_package is None:
globs.currently_selected_package = "default"
if selected_package is not None:
success = globs.compute_config.clean_start(selected_package)
if not success:
msg = "Compute package '{}' cannot be activated".format(
selected_package)
app.logger.warning(msg)
return jsonify(active_settings=render_template(
'compute_info.html', active_settings=None, msg=msg))
globs.currently_selected_package = selected_package
active_settings = globs.compute_config.get_active_package()
return jsonify(active_settings=render_template(
'compute_info.html', active_settings=active_settings))
active_settings = globs.compute_config.get_active_package()
notify_not_set = COMPUTE_SETTINGS_VARNAME[0] if globs.compute_config.default_config_file == globs.compute_config.config_file\
else None
return render_template(
'set_comp_env.html',
env_conf_file=globs.compute_config.config_file,
compute_packages=globs.compute_config.list_compute_packages(),
active_settings=active_settings,
currently_selected_package=globs.currently_selected_package,
notify_not_set=notify_not_set)
def main(cli=None) -> int:
log.info("IMCpipeline runner")
parser = parse_arguments()
args, unknown = parser.parse_known_args(cli)
# the extra arguments will be passed to the pipeline and
# compounded arguments (mostly the --cellprofiler-exec argument)
# should be quoted again
args.cli = ["'" + x + "'" if " " in x else x for x in unknown]
log.info("Generating project from given CSV annotation.")
annot = pd.read_csv(args.metadata).set_index(args.sample_file_attribute)
if args.toggle:
log.info("Subsampling samples based on the `toggle` column.")
annot = annot.loc[annot["toggle"].isin([1, "1", True, "TRUE", "True"]), :]
log.info("Setting compute settings using divvy.")
compute = divvy.ComputingConfiguration()
compute.activate_package(args.compute)
# Now prepare job submission
jobs = list()
cli_args = " ".join(args.cli)
# the '--' is to separate the nargs from the positional in case there aren't more args
if cli_args == "":
cli_args = "--"
for sample, _ in annot.iterrows():
log.info("Processing sample %s", sample)
input_dir = pjoin(args.input_dir, sample)
output_dir = pjoin(args.output_dir, sample)
cmd = f"imcpipeline {cli_args} -i {input_dir} -o {output_dir}"
job_name = f"imcpipeline_{sample}"
output_prefix = pjoin("submission", job_name)
job_file = output_prefix + ".sh"
data = {
"jobname": job_name,
"logfile": output_prefix + ".log",
"mem": args.mem,
"cores": args.cores,
"time": args.time,
"partition": args.partition,
"code": cmd,
}
compute.write_script(job_file, data)
jobs.append(job_file)
log.info("Submitting jobs.")
cmd = compute.get_active_package()["submission_command"]
if not args.dry_run:
for job in jobs:
print(cmd, job)
subprocess.call([cmd, job])
log.info("Finished with all samples.")
return 0
def test_activate_package(self):
dcc = divvy.ComputingConfiguration()
dcc.activate_package("default")
t = dcc.compute.submission_template
t2 = dcc["compute"]["submission_template"]
assert t == t2
dcc.activate_package("slurm")
t = dcc.compute.submission_template
t2 = dcc["compute"]["submission_template"]
assert t == t2
def test_write_script_adapters(self, compute, package):
"""Test successful adapter sourcing from various Mapping types"""
dcc = divvy.ComputingConfiguration()
dcc.activate_package(package)
extra_vars = {"compute": compute}
dcc.write_script("test.sub", extra_vars)
with open("test.sub", "r") as f:
contents = f.read()
assert contents.find("1000") > 0
os.remove("test.sub")
def test_adapters_overwitten_by_others(self):
dcc = divvy.ComputingConfiguration()
dcc.activate_package("singularity_slurm")
compute = YacAttMap({"mem": 1000})
extra_vars = [{"compute": compute}, {"MEM": 333}]
dcc.write_script("test1.sub", extra_vars)
with open("test1.sub", "r") as f:
contents = f.read()
assert not (contents.find("1000") > 0)
assert contents.find("333") > 0
os.remove("test1.sub")
def test_write_script(self):
dcc = divvy.ComputingConfiguration()
dcc
dcc.activate_package("singularity_slurm")
extra_vars = {
"singularity_image": "simg",
"jobname": "jbname",
"code": "mycode",
}
dcc.write_script("test.sub", extra_vars)
with open("test.sub", "r") as f:
contents = f.read()
assert contents.find("mycode") > 0
assert contents.find("{SINGULARITY_ARGS}") < 0
os.remove("test.sub")
return path
def _req_input_to_args(req_input):
"""
Given a list of the required inputs for the build command, create an args
string
:param list[str] req_input: input names
:return str: args string
"""
return ["--" + x + " <arg_here>" for x in req_input]
subdir_path = _make_sub_dir(args.path, args.genome)
dcc = divvy.ComputingConfiguration()
dcc.activate_package("slurm")
cmd_template = "refgenie build -g {g} -a {a} {req_input_str}"
genome = args.genome
to_remove = ["genome", "path"]
data = vars(args)
for i in to_remove:
data.pop(i)
for asset in asset_build_packages:
sub_script = os.path.join(subdir_path, asset + ".sub")
req_input = asset_build_packages[asset]["required_inputs"]
if req_input:
print(
"{} asset requires additional input in the command ({}), so '{}'"
def dcc(request):
"""Provide ComputingConfiguration objects for all files in divcfg repository"""
return divvy.ComputingConfiguration(filepath=request.param)
def empty_dcc():
"""Provide the empty/default ComputingConfiguration object"""
return divvy.ComputingConfiguration()
import os
import glob
import divvy
import pytest
THIS_DIR = os.path.dirname(os.path.abspath(__file__))
DATA_DIR = os.path.join(THIS_DIR, "data/divcfg-master")
FILES = glob.glob(DATA_DIR + "/*.yaml")
DCC_ATTRIBUTES = divvy.ComputingConfiguration().keys()
@pytest.fixture
def empty_dcc():
"""Provide the empty/default ComputingConfiguration object"""
return divvy.ComputingConfiguration()
@pytest.fixture(params=FILES)
def dcc(request):
"""Provide ComputingConfiguration objects for all files in divcfg repository"""
return divvy.ComputingConfiguration(filepath=request.param)
@pytest.fixture
def mock_env_missing(monkeypatch):
[
monkeypatch.delenv(env_var, raising=False)
for env_var in divvy.const.COMPUTE_SETTINGS_VARNAME
]
def submit_job(
code,
job_file,
log_file=None,
computing_configuration=None,
dry_run=False,
limited_number=False,
total_job_lim=500,
refresh_time=10,
in_between_time=5,
**kwargs
):
"""
Submit a job to be run.
Uses divvy to allow running on a local computer or distributed computing resources.
Parameters
----------
code : :obj:`str`
String of command(s) to be run.
job_file : :obj:`str`
File to write job ``code`` to.
log_file : :obj:`str`
Log file to write job output to.
Defaults to ``job_file`` with ".log" ending.
computing_configuration : :obj:`str`
Name of :class:`divvy` computing configuration to use.
Defaults to 'default' which is to run job in localhost.
dry_run: :obj:`bool`
Whether not to actually run job.
Defaults to :obj:`False`.
limited_number: :obj:`bool`
Whether to restrict jobs to a maximum number.
Currently only possible if using "slurm".
Defaults to :obj:`False`.
total_job_lim : :obj:`int`
Maximum number of jobs to restrict to.
Defaults to 500.
refresh_time : :obj:`int`
Time in between checking number of jobs in seconds.
Defaults to 10.
in_between_time : :obj:`int`
Time in between job submission in seconds.
Defaults to 5.
**kwargs : :obj:`dict`
Additional keyword arguments will be passed to the chosen submission template according to `computing_configuration`.
Pass for example: jobname="job", cores=2, mem=8000, partition="longq".
"""
import time
import subprocess
import divvy
from ngs_toolkit import _CONFIG, _LOGGER
# reduce level of logging from divvy
# only for divvy <=0.
if "logging" in divvy.__dict__.keys():
divvy.logging.getLogger("divvy").setLevel("ERROR")
def count_jobs_running(check_cmd="squeue", sep="\n"):
"""
Count running jobs on a cluster by invoquing a command that lists the jobs.
"""
return subprocess.check_output(check_cmd).split(sep).__len__()
def submit_job_if_possible(
cmd, check_cmd="squeue", total_job_lim=800, refresh_time=10, in_between_time=5
):
submit = count_jobs_running(check_cmd) < total_job_lim
while not submit:
time.sleep(refresh_time)
submit = count_jobs_running(check_cmd) < total_job_lim
subprocess.call(cmd)
time.sleep(in_between_time)
if log_file is None:
log_file = ".".join(job_file.split(".")[:-1]) + ".log"
# Get computing configuration from config
if computing_configuration is None:
try:
computing_configuration = _CONFIG["preferences"]["computing_configuration"]
except KeyError:
msg = "'computing_configuration' was not given"
msg += " and default could not be get from config."
hint = " Pass a value or add one to the section"
hint += " preferences:computing_configuration'"
hint += " in the ngs_toolkit config file."
_LOGGER.error(msg + hint)
raise
dcc = divvy.ComputingConfiguration()
if computing_configuration is not None:
dcc.activate_package(computing_configuration)
# Generate job script
d = {"code": code, "logfile": log_file}
d.update(kwargs)
dcc.write_script(job_file, d)
# Submit job
if not dry_run:
scmd = dcc["compute"]["submission_command"]
cmd = scmd.split(" ") + [job_file]
# simply submit if not limiting submission to the number of already running jobs
if not limited_number:
subprocess.call(cmd)
else:
# otherwise, submit only after `total_job_lim` is less than number of runnning jobs
# this is only possible for slurm now though
if scmd != "slurm":
subprocess.call(cmd)
else:
submit_job_if_possible(cmd, check_cmd="slurm")