def crds(authenticated_user):
get_local_bucket(empty=True)
creds = StorageCreds(user=authenticated_user, service_url="storage")
drive = Drive(creds=creds, name="test_drive")
filepath = os.path.join(
os.path.dirname(__file__),
"../../../tests/data/proc_test_data/CRDS/bsd.picarro.1minute.248m.dat",
)
filemeta = drive.upload(filepath)
par = PAR(location=filemeta.location(), user=authenticated_user)
hugs = Service(service_url="hugs")
par_secret = hugs.encrypt_data(par.secret())
auth = Authorisation(resource="process", user=authenticated_user)
args = {
"authorisation": auth.to_data(),
"par": {
"data": par.to_data()
},
"par_secret": {
"data": par_secret
},
"data_type": "CRDS",
"source_name": "bsd.picarro.1minute.248m",
}
hugs.call_function(function="process", args=args)
def process(args):
""" Take a PAR from an uploaded file and process the data
Args:
args (dict): Dictionary of JSON serialised objects to be
used by processing functions
Returns:
dict: Dictionary of results of processing
"""
data_type = args["data_type"]
data_par = PAR.from_data(args["par"]["data"])
data_secret = args["par_secret"]["data"]
auth = args["authorisation"]
authorisation = Authorisation.from_data(auth)
# Verify that this process had authorisation to be called
authorisation.verify("process")
hugs = get_this_service(need_private_access=True)
data_secret = hugs.decrypt_data(data_secret)
data_filename = data_par.resolve(secret=data_secret)
# Here we're downloading the data to the tmp directory
# Be good if we could load it directly from the object store
data_file = data_filename.download(dir="/tmp")
if data_type == "GC":
precision_par = PAR.from_data(args["par"]["precision"])
precision_secret = args["par_secret"]["precision"]
precision_secret = hugs.decrypt_data(precision_secret)
precision_filename = precision_par.resolve(precision_secret)
precision_file = precision_filename.download(dir="/tmp")
site = args["site"]
instrument = args["instrument"]
data_file = data_file, precision_file
else:
site = None
instrument = None
if "overwrite" in args:
overwrite = args["overwrite"]
else:
overwrite = False
source_name = args["source_name"]
results = process_data(
data_file=data_file,
source_name=source_name,
data_type=data_type,
site=site,
instrument_name=instrument,
overwrite=overwrite,
)
return {"results": results}
def load(self, par_uid, secret=None):
"""Load and return the PAR and identifiers associated with
the passed UID, locked with the passed secret
"""
# validate that the UID actually looks like a UID. This
# should prevent attacks that try weird UIDs
from Acquire.ObjectStore import validate_is_uid \
as _validate_is_uid
_validate_is_uid(par_uid)
from Acquire.ObjectStore import ObjectStore as _ObjectStore
from Acquire.Service import get_service_account_bucket \
as _get_service_account_bucket
try:
key = "%s/%s" % (_par_root, par_uid)
bucket = _get_service_account_bucket()
data = _ObjectStore.get_object_from_json(bucket, key)
from Acquire.Client import PAR as _PAR
import json as _json
par = _PAR.from_data(data["par"])
identifiers = _json.loads(data["identifiers"])
if secret != data["secret"]:
raise PermissionError()
except:
raise PermissionError("There is no valid PAR at ID '%s'" % par_uid)
if par.expired():
raise PermissionError(
"There is no valid PAR at ID '%s' as it has expired" % par_uid)
return (par, identifiers)
def test_process_CRDS(authenticated_user, tempdir):
creds = StorageCreds(user=authenticated_user, service_url="storage")
drive = Drive(creds=creds, name="test_drive")
filepath = os.path.join(
os.path.dirname(__file__),
"../../../tests/data/proc_test_data/CRDS/bsd.picarro.1minute.248m.dat",
)
filemeta = drive.upload(filepath)
Path("/tmp/bsd.picarro.1minute.248m.dat").unlink(missing_ok=True)
par = PAR(location=filemeta.location(), user=authenticated_user)
hugs = Service(service_url="hugs")
par_secret = hugs.encrypt_data(par.secret())
auth = Authorisation(resource="process", user=authenticated_user)
args = {
"authorisation": auth.to_data(),
"par": {
"data": par.to_data()
},
"par_secret": {
"data": par_secret
},
"data_type": "CRDS",
"source_name": "bsd.picarro.1minute.248m",
}
response = hugs.call_function(function="process", args=args)
expected_keys = [
"bsd.picarro.1minute.248m_ch4",
"bsd.picarro.1minute.248m_co",
"bsd.picarro.1minute.248m_co2",
]
results = response["results"]["bsd.picarro.1minute.248m.dat"]
return False
assert sorted(results.keys()) == expected_keys
def run():
parser = argparse.ArgumentParser(
description="Run and watch a job on a HPC resource")
parser.add_argument("j", help="JSON data filename")
args = parser.parse_args()
json_filename = args.j
with open(json_filename, "r") as f:
job_data = json.load(f)
par_data = job_data["par"]
par_secret = job_data["par_secret"]
try:
compilation_command = job_data["compilation_command"]
except KeyError:
compilation_command = None
run_command = job_data["run_command"]
# Make the output folder
fpath = Path(__file__).resolve().parent.joinpath("output")
fpath.mkdir(parents=True)
par = PAR.from_data(data=par_data)
drive = par.resolve(secret=par_secret)
# Download any data files and moved them to the input folders
files = drive.list_files()
for f in files:
filename = f.filename()
drive.download(filename=filename)
# Split the compilation command
if compilation_command is not None:
cmd_list = compilation_command.split()
# Run the compilation command and set the current working directory
# to our application code location in "app"
res = subprocess.run(cmd_list, stderr=True)
if res.returncode != 0:
raise subprocess.CalledProcessError("Compilation error : ",
res.stderr)
run_command = run_command.split()
# Run the actual code
runcmd_res = subprocess.run(run_command, stderr=True)
if runcmd_res.returncode != 0:
raise subprocess.CalledProcessError("Error running application : ",
runcmd_res.stderr)
# Upload everything in the output directory to the cloud drive
drive.upload("output")
def run(args):
"""Create a new PAR based on the information supplied
in the passed half-created PAR, and the supplied
Authorisation. This will return the URL that will
need to be used by the PAR to access the required
data. This will be encrypted using the supplied
PublicKey
"""
auth = Authorisation.from_data(args["authorisation"])
par = PAR.from_data(args["par"])
secret = args["secret"]
registry = PARRegistry()
par_uid = registry.register(par=par, authorisation=auth, secret=secret)
result = {"par_uid": par_uid}
return result
def run(args):
"""This function receives the request to submit a job on the
compute service. It processes the request and performs
everything needed to actually submit the job. This
returns confirmation the job has been submitted, as
well as some metadata about the job
"""
worksheet_uid = str(args["worksheet_uid"])
request = RunRequest.from_data(args["request"])
par = PAR.from_data(args["par"])
secret = args["secret"]
cheque = Cheque.from_data(args["cheque"])
job = ComputeJob.submit(worksheet_uid=worksheet_uid,
request=request,
par=par,
secret=secret,
cheque=cheque)
return {"uid": job.uid()}
def from_data(data):
"""Return a ComputeJob constructed from a json-deserialised
dictionary
"""
if data is None or len(data) == 0:
return ComputeJob()
from Acquire.ObjectStore import string_to_list as _string_to_list
from Acquire.Access import RunRequest as _RunRequest
from Acquire.Client import PAR as _PAR
from Acquire.Accounting import CreditNote as _CreditNote
job = ComputeJob()
job._uid = str(data["uid"])
job._credit_notes = _string_to_list(data["credit_notes"], _CreditNote)
job._par = _PAR.from_data(data["par"])
job._secret = str(data["secret"])
job._request = _RunRequest.from_data(data["request"])
return job
def test_process_GC(authenticated_user, tempdir):
creds = StorageCreds(user=authenticated_user, service_url="storage")
drive = Drive(creds=creds, name="test_drive")
data_filepath = os.path.join(
os.path.dirname(__file__),
"../../../tests/data/proc_test_data/GC/capegrim-medusa.18.C",
)
precision_filepath = os.path.join(
os.path.dirname(__file__),
"../../../tests/data/proc_test_data/GC/capegrim-medusa.18.precisions.C",
)
Path("/tmp/capegrim-medusa.18.C").unlink(missing_ok=True)
Path("/tmp/capegrim-medusa.18.precisions.C").unlink(missing_ok=True)
data_meta = drive.upload(data_filepath)
precision_meta = drive.upload(precision_filepath)
data_par = PAR(location=data_meta.location(), user=authenticated_user)
precision_par = PAR(location=precision_meta.location(),
user=authenticated_user)
hugs = Service(service_url="hugs")
data_secret = hugs.encrypt_data(data_par.secret())
precision_secret = hugs.encrypt_data(precision_par.secret())
auth = Authorisation(resource="process", user=authenticated_user)
args = {
"authorisation": auth.to_data(),
"par": {
"data": data_par.to_data(),
"precision": precision_par.to_data()
},
"par_secret": {
"data": data_secret,
"precision": precision_secret
},
"data_type": "GCWERKS",
"source_name": "capegrim-medusa",
"site": "CGO",
"instrument": "medusa",
}
response = hugs.call_function(function="process", args=args)
result_keys = (sorted(
response["results"]["capegrim-medusa.18.C"].keys()))[:8]
expected_keys = [
"capegrim-medusa.18_C4F10",
"capegrim-medusa.18_C6F14",
"capegrim-medusa.18_CCl4",
"capegrim-medusa.18_CF4",
"capegrim-medusa.18_CFC-11",
"capegrim-medusa.18_CFC-112",
"capegrim-medusa.18_CFC-113",
"capegrim-medusa.18_CFC-114",
]
assert result_keys == expected_keys
def create_job(
self,
auth_user,
requirements,
key_password,
data_files,
hugs_url=None,
storage_url=None,
):
""" Create a job
Args:
auth_user (Acquire.User): Authenticated Acquire user
The following keys are required:
"hostname", "username", "name", "run_command", "partition", "n_nodes", "n_tasks_per_node",
"n_cpus_per_task", "memory_req", "job_duration"
where partition must be one of:
"cpu_test", "dcv", "gpu", "gpu_veryshort", "hmem", "serial", "test", "veryshort"
Example:
requirements = {"hostname": hostname, "username": username, "name": "test_job,
"n_nodes": 2,"n_tasks_per_node": 2,
"n_cpus_per_task": 2, "memory": "128G", ...}
requirements (dict): Dictionary containing job details and requested resources
key_password (str): Password for private key used to access the HPC
data_files (dict): Data file(s) to be uploaded to the cloud drive to
run the simulation. Simulation code files should be given in the "app" key and data
files in the "data" key
TODO - having to pass in a password and get it through to Paramiko seems
long winded, is there a better way to do this?
hugs_url (str): URL of HUGS service
storage_url (str): URL of storage service
Returns:
dict: Dictionary containing information regarding job running on resource
This will contain the PAR for access for data upload and download.
"""
from Acquire.Client import (
Drive,
Service,
PAR,
Authorisation,
StorageCreds,
Location,
ACLRule,
)
from Acquire.ObjectStore import create_uuid
import datetime
import os
if self._service is None:
raise PermissionError("Cannot use a null service")
if storage_url is None:
storage_url = self._service_url + "/storage"
if hugs_url is None:
hugs_url = self._service_url + "/hugs"
if not isinstance(data_files["app"], list):
data_files["app"] = [data_files["app"]]
try:
if not isinstance(data_files["data"], list):
data_files["data"] = [data_files["data"]]
except KeyError:
pass
# Get an authorisaton to pass to the service
hugs = Service(service_url=hugs_url)
# Credentials to create the cloud storage drive
creds = StorageCreds(user=auth_user, service_url=storage_url)
# Append a shortened UUID to the job name to ensure we don't multiple drives with the same name
short_uuid = create_uuid(short_uid=True)
job_name = requirements["name"]
job_name = f"{job_name.lower()}_{short_uuid}"
# Create a cloud drive for the input and output data to be written to
drive = Drive(creds=creds, name=job_name)
# Check the size of the files and if we want to use the chunk uploader
# Now we want to upload the files to the cloud drive we've created for this job
chunk_limit = 50 * 1024 * 1024
# Store the metadata for the uploaded files
uploaded_files = {"app": {}, "data": {}}
# These probably won't be very big so don't check their size
for f in data_files["app"]:
file_meta = drive.upload(f, dir="app")
uploaded_files["app"][f] = file_meta
# We might not have any data files to upload
try:
for f in data_files["data"]:
filesize = os.path.getsize(f)
if filesize < chunk_limit:
file_meta = drive.upload(f, dir="data")
else:
file_meta = drive.chunk_upload(f, dir="data")
uploaded_files["data"][f] = file_meta
except KeyError:
pass
auth = Authorisation(resource="job_runner", user=auth_user)
# Create a PAR with a long lifetime here and return a version to the user
# and another to the server to allow writing of result data
drive_guid = drive.metadata().guid()
location = Location(drive_guid=drive_guid)
# Read the duration from the requirements dictionary
# TODO - add in some reading of the duration
# try:
# duration = requirements["duration"]
# par_expiry = datetime.datetime
par_lifetime = datetime.datetime.now() + datetime.timedelta(days=1)
# Create an ACL rule for this PAR so we can read and write to it
aclrule = ACLRule.owner()
par = PAR(
location=location,
user=auth_user,
aclrule=aclrule,
expires_datetime=par_lifetime,
)
par_secret = par.secret()
encryped_par_secret = hugs.encrypt_data(par_secret)
# Encrypt the password we use to decrypt the private key used to access the HPC cluster
# TODO - is this a sensible way of doing this?
encrypted_password = hugs.encrypt_data(key_password)
par_data = par.to_data()
args = {}
args["authorisation"] = auth.to_data()
args["par"] = par_data
args["par_secret"] = encryped_par_secret
args["requirements"] = requirements
args["key_password"] = encrypted_password
function_response = self._service.call_function(function="job_runner",
args=args)
response = {}
response["function_response"] = function_response
response["par"] = par_data
response["par_secret"] = par_secret
response["upload_data"] = uploaded_files
return response
def test_drive_par(authenticated_user, tempdir):
drive_name = "test å∫ç∂ pars"
creds = StorageCreds(user=authenticated_user, service_url="storage")
drive = Drive(name=drive_name, creds=creds)
drive.upload(filename=__file__, uploaded_name="tmp_test.py")
downloaded_name = drive.download(filename="tmp_test.py", dir=tempdir)
assert (_same_file(__file__, downloaded_name))
drive_guid = drive.metadata().guid()
location = Location(drive_guid=drive_guid)
par = PAR(location=location,
user=authenticated_user,
aclrule=ACLRule.reader())
par_drive = par.resolve()
assert (par_drive.metadata().acl() == ACLRule.reader())
assert (par_drive.metadata().uid() == drive.metadata().uid())
files = par_drive.list_files()
assert (len(files) == 1)
assert (files[0].filename() == "tmp_test.py")
downloaded_name = files[0].open().download(dir=tempdir, force_par=True)
assert (_same_file(__file__, downloaded_name))
par2 = PAR(location=location,
user=authenticated_user,
aclrule=ACLRule.writer())
par_drive = par2.resolve()
assert (par_drive.metadata().acl() == ACLRule.writer())
assert (par_drive.metadata().uid() == drive.metadata().uid())
files = par_drive.list_files()
assert (len(files) == 1)
assert (files[0].filename() == "tmp_test.py")
par_drive.upload(filename=__file__, uploaded_name="tmp_test2.py")
files = par_drive.list_files()
assert (len(files) == 2)
f = {}
f[files[0].filename()] = files[0]
f[files[1].filename()] = files[1]
files = f
assert ("tmp_test.py" in files)
assert ("tmp_test2.py" in files)
downloaded_name = files["tmp_test2.py"].open().download(dir=tempdir)
assert (_same_file(__file__, downloaded_name))
par = PAR(location=files["tmp_test.py"].location(),
user=authenticated_user,
aclrule=ACLRule.reader())
par_file = par.resolve()
assert (par_file.metadata().acl() == ACLRule.reader())
downloaded_name = par_file.download(dir=tempdir)
assert (_same_file(__file__, downloaded_name))
with pytest.raises(PermissionError):
par_file.upload(__file__)
par = PAR(location=files["tmp_test.py"].location(),
user=authenticated_user,
aclrule=ACLRule.writer())
par_file = par.resolve()
assert (par_file.metadata().acl() == ACLRule.writer())
par_file.upload(__file__)
def process_files(
self,
user,
files,
data_type,
source_name=None,
overwrite=False,
hugs_url=None,
storage_url=None,
datasource=None,
site=None,
instrument=None,
):
""" Process the passed file(s)
Args:
user (User): Authenticated Acquire User
files (str, list): Path of files to be processed
data_type (str): Type of data to be processed (CRDS, GC etc)
hugs_url (str): URL of HUGS service. Currently used for testing
datasource (str): Datasource name or UUID
This may be removed in the future.
storage_url (str): URL of storage service. Currently used for testing
This may be removed in the future.
site (str, default=None): Name of site, three letter code or long name
instrument (str, default=None): If no instrument name is passed we will attempt
to find it from the filename.
Returns:
dict: UUIDs of Datasources storing data of processed files keyed by filename
"""
data_type = data_type.upper()
if self._service is None:
raise PermissionError("Cannot use a null service")
if not isinstance(files, list):
files = [files]
if data_type.upper() == "GC":
if not all(isinstance(item, tuple) for item in files):
return TypeError(
"If data type is GC, a list of tuples for data and precision filenames must be passed"
)
files = [(Path(f), Path(p)) for f, p in files]
else:
files = [Path(f) for f in files]
if storage_url is None:
storage_url = self._service_url + "/storage"
if hugs_url is None:
hugs_url = self._service_url + "/hugs"
# # Take the filename without the file extension
# source_name = [os.path.splitext((filepath.name).split("/")[-1])[0] for filepath in files]
hugs = Service(service_url=hugs_url)
creds = StorageCreds(user=user, service_url=storage_url)
drive = Drive(creds=creds, name="test_drive")
auth = Authorisation(resource="process", user=user)
# Here we'll need special cases for different data types. As GC requires
# both the data file and precision data and they need to be kept together
# for use in processing.
# We can maybe reconsider the way this is done if there ends up being a lot of test
# cases and this gets a bit clunky
results = {}
for file in files:
if data_type == "GC":
if source_name is None:
source_name = file[0].stem
if site is None:
site = source_name.split(".")[0]
if "-" in site and data_type == "GC":
site = site.split("-")[0]
filemeta = drive.upload(file[0])
par = PAR(location=filemeta.location(), user=user)
par_secret = hugs.encrypt_data(par.secret())
prec_meta = drive.upload(file[1])
prec_par = PAR(location=prec_meta.location(), user=user)
prec_par_secret = hugs.encrypt_data(prec_par.secret())
args = {
"authorisation": auth.to_data(),
"par": {"data": par.to_data(), "precision": prec_par.to_data()},
"par_secret": {"data": par_secret, "precision": prec_par_secret},
"data_type": data_type,
"datasource": datasource,
"source_name": source_name,
"overwrite": overwrite,
"site": site,
"instrument": instrument,
}
else:
filemeta = drive.upload(file)
par = PAR(location=filemeta.location(), user=user)
par_secret = hugs.encrypt_data(par.secret())
args = {
"authorisation": auth.to_data(),
"par": {"data": par.to_data()},
"par_secret": {"data": par_secret},
"data_type": data_type,
"datasource": datasource,
"source_name": source_name,
"overwrite": overwrite,
}
# If we try to upload many files we don't want it to fail if a single
# file contains overlapping data
try:
response = self._service.call_function(function="process", args=args)
results.update(response["results"])
except ValueError as err:
results[file.name] = err
return results