def wrapper(*args,**kwargs):
# If view_func is a class view, args=[self, request, machine_name , ... ]
# If view_func is a regular function args=[request, machine_name , ...]
if isinstance(args[0], HttpRequest):
request = args[0]
machine_name = args[1]
elif isinstance(args[1], HttpRequest):
request = args[1]
machine_name = args[2]
else:
return json_response(status="ERROR",
status_code=500,
error="Missing request object")
hostname = None
conf = settings.NEWT_CONFIG
if not isinstance(machine_name , str) :
return json_response(status="ERROR",
status_code=500,
error="Missing machine name")
for s in conf['SYSTEMS']:
if machine_name==s['NAME']:
hostname = s['HOSTNAME']
break
if hostname is None:
return json_response(status="ERROR",
status_code=404,
error="Unrecognized system: %s" % machine_name)
return view_func(*args, **kwargs)
def get_user_info(user_name, uid):
"""Returns information about the user
Keyword arguments:
user_name -- username
uid -- user id
"""
try:
if uid:
user = User.objects.get(pk=uid)
elif user_name:
user = User.objects.get(username=user_name)
else:
raise Exception()
user_dict = model_to_dict(user)
del user_dict["password"]
return user_dict
except Exception:
logger.debug("No user found matching query: %s" % (user_name if user_name else uid))
if user_name:
return json_response(status="ERROR",
status_code=404,
error="User not found: No user has the username %s" % user_name)
else:
return json_response(status="ERROR",
status_code=404,
error="User not found: No user has the id %s" % uid)
def put_file(request, machine, path, local=False):
content_length = int(request.META.get('CONTENT_LENGTH', 0))
#print("content_length:" , content_length )
if content_length > 1048000:
return json_response(
status="ERROR",
status_code=500,
error="The file is too big ,please use other ways to upload!")
data = request.read()
if path.startswith('/~'):
path = path[1:]
tmp_file = tempfile.NamedTemporaryFile(prefix="newt_",
dir=tempdir,
delete=False)
tmp_file.write(data)
tmp_file.file.flush()
tmp_file.close()
if not local:
src = tmp_file.name
dest = path #
temphost = socket.gethostname()
taskenv = {"user": request.user.username, "machine": machine}
rest = put_file_task.delay(taskenv, temphost, os.path.basename(src),
dest)
cache.set("async-" + rest.id, "AsyncJob", 3600)
return json_response(status="ACCEPT",
status_code=201,
error="",
content=rest.id)
else:
os.rename(tmp_file.name, os.path.join(tempdir, os.path.basename(path)))
return {'location': tmp_file.name}
def get_dir(request, machine_name, path):
try:
command = 'ls -la %s' % path
(output, error, retcode) = run_command(command)
if retcode != 0:
return json_response(content=output, status="ERROR", status_code=500, error=error)
# import pdb; pdb.set_trace()
# Split the lines
output = map(lambda i: i.strip(), output.split('\n'))
# "awesome" regular expression that captures ls output of the form:
# drwxrwxr-x 4 shreyas newt 32768 Apr 15 10:59 home
patt=re.compile(r'(?P<perms>[\+\w@-]{10,})\s+(?P<hardlinks>\d+)\s+(?P<user>\S+)\s+(?P<group>\S+)\s+(?P<size>\d+)\s+(?P<date>\w{3}\s+\d+\s+[\d\:]+)\s+(?P<name>.+)$')
# filter out stuff that doesn't match pattern
output = filter(lambda line: patt.match(line), output)
# Convert output into dict from group names
output = map(lambda x: patt.match(x).groupdict(), output)
for line in output:
if line['perms'].startswith('l'):
name, symlink = line['name'].split(' -> ')
line['name'] = name
line['symlink'] = symlink
else:
line['symlink'] = ""
return output
except Exception as e:
logger.error("Could not get directory %s" % str(e))
return json_response(status="ERROR", status_code=500, error="Could not get directory: %s" % str(e))
def get_user_info(user_name, uid):
"""Returns information about the user
Keyword arguments:
user_name -- username
uid -- user id
"""
try:
if uid:
user = User.objects.get(pk=uid)
elif user_name:
user = User.objects.get(username=user_name)
else:
raise Exception()
user_dict = model_to_dict(user)
del user_dict["password"]
return user_dict
except Exception:
logger.debug("No user found matching query: %s" %
(user_name if user_name else uid))
if user_name:
return json_response(
status="ERROR",
status_code=404,
error="User not found: No user has the username %s" %
user_name)
else:
return json_response(
status="ERROR",
status_code=404,
error="User not found: No user has the id %s" % uid)
def patch(self, user, pk):
data = request.json
data.pop("user", "")
if not data:
return json_response({"message": "Cannot update obj without data"},
400)
if not pk:
return json_response(
{"message": "Cannot update obj pk is invalid"}, 400)
fields = data.keys()
obj = self.Meta.model.get(self.Meta.model.id == pk,
self.Meta.model.user == user)
for key in fields:
if key in self.Meta.model._meta.fields.keys():
setattr(obj, key, data[key])
setattr(obj, "id", pk)
obj.save()
json_obj = model_to_dict(obj)
json_obj["user"] = user.id
if self.Meta.fields:
for field in self.Meta.fields:
json_obj[field] = getattr(obj, field)
if self.Meta.replace_fields:
for field in self.Meta.replace_fields:
json_obj[field["field"]] = deepgetattr(obj, field["attr"])
self.pos_patch(obj)
return json_response(json_obj, 200)
def get_group_info(group_name, gid):
"""Returns information about the group
Keyword arguments:
group_name -- group name
gid -- group id
"""
try:
if gid:
group = Group.objects.get(pk=gid)
elif group_name:
group = Group.objects.get(name=group_name)
else:
raise Exception()
group_dict = model_to_dict(group)
group_dict['users'] = [{
"id": u.id,
"username": u.username
} for u in group.user_set.all()]
return group_dict
except Exception:
if group_name:
return json_response(
status="ERROR",
status_code=404,
error="Group not found: No group matches the name %s" %
group_name)
else:
return json_response(
status="ERROR",
status_code=404,
error="Group not found: No group matches the id %s" % gid)
def store_update(request, store_name, obj_id, data):
"""Updates the contents of a given document; Returns the oid of the
document.
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
obj_id -- ID of the document in the store
data -- Updated data of the document
"""
try:
store = Store.objects.get(name=store_name)
except ObjectDoesNotExist:
return json_response(status="ERROR",
status_code=404,
error="Store does not exist: %s" % store_name)
if not data:
return json_response(status="ERROR",
status_code=400,
error="No data received.")
doc = store.documents.get(oid=obj_id)
doc.data = data
doc.save()
return str(doc.oid)
def get_info(request, machine_name, job_id):
"""Gets the information of a job, given the id
Keyword arguments:
machine_name -- name of the machine
job_id -- the job id
"""
pass
machine = slurmutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR",
status_code=400,
error="Invalid machine name: %s" % machine_name)
env = slurmutil.get_cred_env(request.user)
mycmd = "ssh " + machine["hostname"] + " ' " + ' sacct -j ' + job_id + " '"
(output, error, retcode) = run_command(mycmd)
if retcode != 0:
return json_response(status="ERROR",
status_code=500,
error="Unable to get queue: %s" % error)
patt = re.compile(
r'(?P<jobid>[^\s]+)\s+(?P<jobname>[^\s]+)\s+(?P<partition>[^\s]+)\s+(?P<account>[^\s]+)\s+(?P<alloccpus>[^\s]+)\s+(?P<state>[^\s]+)\s+(?P<exitcode>.*)$'
)
output = output.splitlines()
output = [x.strip() for x in output]
output = filter(lambda line: patt.match(line), output)
output = list(map(lambda x: patt.match(x).groupdict(), output))[2:]
#print( output )
return (output)
def delete_job(request, machine_name, job_id):
"""Gets the information of a job, given the id
Keyword arguments:
machine_name -- name of the machine
job_id -- the job id
"""
machine = gridutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR", status_code=400, error="Invalid machine name: %s" % machine_name)
flags = ""
jobmanager = machine['jobmanagers']['fork']['url']
qdel = machine['qdel']['bin']
scheduler = machine['qdel']['scheduler']
cmd = "%s %s" % (qdel, job_id)
# Set environment flags for qsub
if scheduler == "sge":
sge_env_str = "-env SGE_ROOT=%s -env SGE_QMASTER_PORT=%s -env SGE_EXECD_PORT=%s" % (gridutil.SGE_ROOT, gridutil.SGE_QMASTER_PORT, gridutil.SGE_EXECD_PORT)
flags += " " + sge_env_str
if scheduler != "sge":
cmd = '/bin/bash -l -c "%s"' % cmd
try:
runner = GlobusHelper(request.user)
(output, error, retcode) = runner.run_job(cmd, jobmanager, flags)
except Exception, ex:
return json_response(status="ERROR",
status_code=500,
error="qsub failed with error: %s" % str(ex))
def view_queue(request, machine_name):
"""Returns the current state of the queue in a list
Keyword arguments:
request -- Django HttpRequest
machine_name -- name of the machine
"""
machine = gridutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR", status_code=400, error="Invalid machine name: %s" % machine_name)
env = gridutil.get_cred_env(request.user)
(output, error, retcode) = run_command(gridutil.GLOBUS_CONF['LOCATION'] + "bin/globus-job-run %s /project/projectdirs/osp/newt_tools/qs_moab.sh" % (machine['hostname']), env=env)
patt = re.compile(r'(?P<jobid>[^\s]+)\s+(?P<status>[^\s]+)\s+(?P<user>[^\s]+)\s+(?P<job_name>[^\s]+)\s+(?P<nodes>\d+)\s+(?P<walltime>[^\s]+)\s+(?P<time_use>[^\s]+)\s+(?P<time_submit>\w{3}\s\d{1,2}\s[\d\:]+)\s+(?P<rank>[^\s]+)\s+(?P<queue>[^\s]+)\s+(?P<q_state>[^\s]+)\s+(?P<processors>[^\s]+)\s*(?P<details>.*)$')
if retcode != 0:
return json_response(status="ERROR", status_code=500, error="Unable to get queue: %s" % error)
# filter out stuff that doesn't match pattern
output = output.splitlines()
output = [x.strip() for x in output]
output = filter(lambda line: patt.match(line), output)
# Convert output into dict from group names
output = map(lambda x: patt.match(x).groupdict(), output)
return output
def execute(request, machine_name, command):
"""Returns a the result of running command on machine_name
Keyword arguments:
machine_name -- name of the machine
command -- command to run
"""
machine = gridutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR",
status_code=400,
error="Invalid machine name: %s" % machine_name)
# Get the grid credentials for the user
env = gridutil.get_cred_env(request.user)
try:
# Run the command using globus-job-run
(output, error, retcode) = run_command(
gridutil.GLOBUS_CONF['LOCATION'] + "bin/globus-job-run %s %s" %
(machine['hostname'], command),
env=env)
response = {"output": output, "error": error, "retcode": retcode}
return response
except Exception as e:
logger.error("Could not run command: %s" % str(e))
return json_response(error="Could not run command: %s" % str(e),
status="ERROR",
status_code=500)
def _wrapper(*args, **kwargs):
try:
verify_jwt_in_request()
except NoAuthorizationError as e:
_ = e
return json_response(message="not authorization", status=401)
user = get_current_user()
if not user:
return json_response(message="account is disabled", status=403)
second_permission_alias = aliased(Permission,
name="second_permission")
third_permission_alias = aliased(Permission,
name="third_permission")
permission = db.session.query(Permission.id) \
.outerjoin(second_permission_alias, Permission.id == second_permission_alias.parent_id) \
.outerjoin(third_permission_alias, second_permission_alias.id == third_permission_alias.parent_id) \
.join(RolePermission, or_(RolePermission.permission_id == Permission.id,
RolePermission.permission_id == second_permission_alias.id,
RolePermission.permission_id == third_permission_alias.id)) \
.join(Role, and_(RolePermission.role_id == Role.id)) \
.join(UserRole, and_(Role.id == UserRole.role_id, UserRole.user_id == user.id)) \
.filter(Permission.parent_id.is_(None), or_(Permission.description == description,
second_permission_alias.description == description,
third_permission_alias.description == description))\
.order_by(Permission.id, second_permission_alias.id, third_permission_alias.id) \
.first()
if permission:
return fn(user, *args, **kwargs)
else:
return json_response(message='permission denied', status=401)
def wrapper(*args,**kwargs):
#return( args , kwargs )
if not isinstance(args[1] , dict) :
return json_response(status="ERROR",
status_code=500,
error="not a safty task: no taskenv")
if ( "user" not in args[1].keys() ) or ( "machine" not in args[1].keys() ) :
return json_response(status="ERROR",
status_code=500,
error="not a safty task: no taskenv")
# chuid :
username = args[1]["user"]
ngid = getpwnam( username ).pw_gid
nuid = getpwnam( username ).pw_uid
if nuid == 0 :
return json_response(status="ERROR",
status_code=500,
error="dangerous action ! ")
if nuid != os.getuid():
os.setgroups([])
os.setgid(ngid)
os.setuid(nuid)
os.putenv( "HOME" , getpwnam( username ).pw_dir )
os.chdir( getpwnam( username ).pw_dir )
old_umask = os.umask( 0o077 )
#os.seteuid(nuid)
#os.setegid(nuid)
return [ username , task_func( *args,**kwargs ) ]
def get_group_info(group_name, gid):
"""Returns information about the group
Keyword arguments:
group_name -- group name
gid -- group id
"""
try:
if gid:
group = Group.objects.get(pk=gid)
elif group_name:
group = Group.objects.get(name=group_name)
else:
raise Exception()
group_dict = model_to_dict(group)
group_dict['users'] = [{"id": u.id, "username": u.username} for u in group.user_set.all()]
return group_dict
except Exception:
if group_name:
return json_response(status="ERROR",
status_code=404,
error="Group not found: No group matches the name %s" % group_name)
else:
return json_response(status="ERROR",
status_code=404,
error="Group not found: No group matches the id %s" % gid)
def view_queue(request, machine_name):
"""Returns the current state of the queue in a list
Keyword arguments:
request -- Django HttpRequest
machine_name -- name of the machine
"""
pass
machine = slurmutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR",
status_code=400,
error="Invalid machine name: %s" % machine_name)
env = slurmutil.get_cred_env(request.user)
mycmd = "ssh " + machine["hostname"] + " ' " + machine["qstat"][
"bin"] + " '"
(output, error, retcode) = run_command(mycmd)
if retcode != 0:
return json_response(status="ERROR",
status_code=500,
error="Unable to get queue: %s" % error)
patt = re.compile(
r'(?P<jobid>[^\s]+)\s+(?P<partition>[^\s]+)\s+(?P<job_name>[^\s]+)\s+(?P<user>[^\s]+)\s+(?P<state>[^\s]+)\s+(?P<time>[^\s]+)\s+(?P<nodes>\d+)\s+(?P<nodelist>.*)$'
)
output = output.splitlines()
output = [x.strip() for x in output]
output = filter(lambda line: patt.match(line), output)
output = map(lambda x: patt.match(x).groupdict(), output)
#print( list(output) )
return list(output)
def execute(request, machine_name, command):
conf = settings.NEWT_CONFIG
try:
hostname = None
for s in conf['SYSTEMS']:
if machine_name == s['NAME']:
hostname = s['HOSTNAME']
break
if hostname is None:
return json_response(status="ERROR",
status_code=404,
error="Unrecognized system: %s" %
machine_name)
#user = request.POST.get('sudo_user')
logger.debug("Running command(ssh): %s (@ %s)" %
(command, machine_name))
#command = "sudo -u %s %s " % (user, command)
command = 'ssh %s " %s " ' % (hostname, command)
(output, error, retcode) = run_command(command)
response = {'output': output, 'error': error, 'retcode': retcode}
return response
except Exception as e:
logger.error("Could not run command: %s" % str(e))
return json_response(error="Could not run command: %s" % str(e),
status="ERROR",
status_code=500)
def store_insert(request, store_name, initial_data):
"""Creates a new document in the store with initial_data; Returns the oid
of the new document.
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
initial_data -- document data
"""
try:
store = Store.objects.get(name=store_name)
except ObjectDoesNotExist:
return json_response(status="ERROR",
status_code=404,
error="Store does not exist: %s" % store_name)
data = initial_data
if not data:
return json_response(status="ERROR",
status_code=400,
error="No data received.")
oid = store.documents.count()
new_doc = Document(oid=oid, data=data, store=store)
new_doc.save()
return str(oid)
def execute(request, machine_name, command):
"""Returns a the result of running command on machine_name
Keyword arguments:
machine_name -- name of the machine
command -- command to run
"""
machine = gridutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR", status_code=400, error="Invalid machine name: %s" % machine_name)
# Get the grid credentials for the user
env = gridutil.get_cred_env(request.user)
try:
# Run the command using globus-job-run
(output, error, retcode) = run_command(gridutil.GLOBUS_CONF['LOCATION'] + "bin/globus-job-run %s %s" % (machine['hostname'], command), env=env)
response = {
"output": output,
"error": error,
"retcode": retcode
}
return response
except Exception as e:
logger.error("Could not run command: %s" % str(e))
return json_response(error="Could not run command: %s" % str(e), status="ERROR", status_code=500)
def post(self, phone, password):
user = db.session.query(User).filter(
User.phone == phone, User.password == password).first()
if not user:
return json_response(message='username or password error',
status=403)
return json_response(data={"access_token": get_access_token(user)})
def submit_job(request, machine_name):
"""Submits a job to the queue
Keyword arguments:
request -- Django HttpRequest
machine_name -- name of the machine
"""
machine = gridutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR",
status_code=400,
error="Invalid machine name: %s" % machine_name)
flags = ""
jobmanager = machine['jobmanagers']['fork']['url']
qsub = machine['qsub']['bin']
scheduler = machine['qsub']['scheduler']
# Set environment flags for qsub
if scheduler == "sge":
sge_env_str = "-env SGE_ROOT=%s -env SGE_QMASTER_PORT=%s -env SGE_EXECD_PORT=%s" % (
gridutil.SGE_ROOT, gridutil.SGE_QMASTER_PORT,
gridutil.SGE_EXECD_PORT)
flags += " " + sge_env_str
if request.POST.get("jobfile", False):
# Create command for qsub on an existing pbs file
job_file_path = request.POST.get("jobfile")
cmd = "%s %s" % (qsub, job_file_path)
elif request.POST.get("jobscript", False):
# Create command for qsub from stdin data
job_script = request.POST.get("jobscript")
# Creates a temporary job file
tmp_job_file = tempfile.NamedTemporaryFile(prefix="newt_")
tmp_job_file.write(job_script)
tmp_job_file.flush()
# Stages the temporary job file and pass it as to stdin to qsub
flags += " -stdin -s %s" % tmp_job_file.name
cmd = qsub
else:
return json_response(status="ERROR",
status_code=400,
error="No data received")
if scheduler != "sge":
cmd = '/bin/bash -l -c "%s"' % cmd
try:
runner = GlobusHelper(request.user)
(output, error, retcode) = runner.run_job(cmd, jobmanager, flags)
except Exception, ex:
return json_response(status="ERROR",
status_code=500,
error="qsub failed with error: %s" % str(ex))
def post(self, **kwargs):
exist_user = db.session.query(
User.id).filter_by(phone=kwargs["phone"]).first()
if exist_user:
return json_response(message="user exists")
user = User(**kwargs)
db.session.add(user)
db.session.commit()
return json_response(message="user create success",
data={"access_token": get_access_token(user)})
def wrapper(*args, **kwargs):
try:
verify_jwt_in_request()
except NoAuthorizationError as e:
_ = e
return json_response(message="not authorization", status=401)
user = get_current_user()
if not user:
return json_response(message="account is disabled", status=403)
return fn(user=user, *args, **kwargs)
def submit_job(request, machine_name):
"""Submits a job to the queue
Keyword arguments:
request -- Django HttpRequest
machine_name -- name of the machine
"""
pass
machine = slurmutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR",
status_code=400,
error="Invalid machine name: %s" % machine_name)
qsub = machine['qsub']['bin']
env = slurmutil.get_cred_env(request.user)
user = request.user # User.objects.get(username=username)
if request.POST.get("jobfile", False):
# Create command for sbatch on an existing slurm file
job_file_path = request.POST.get("jobfile")
jobfile = job_file_path
cmd = "%s %s" % (qsub, job_file_path)
elif request.POST.get("jobscript", False):
# Create command for qsub from stdin data
job_script = request.POST.get("jobscript").encode()
# Creates a temporary job file
tmp_job_file = tempfile.NamedTemporaryFile(
prefix="newt_", dir='/HOME/nscc-gz_jiangli/tmp', delete=False)
print(job_script)
tmp_job_file.write(job_script)
tmp_job_file.flush()
jobfile = tmp_job_file.name
cmd = "%s %s" % (qsub, tmp_job_file.name)
else:
return json_response(status="ERROR",
status_code=400,
error="No data received")
job = HPCJob(user=user, jobfile=jobfile, machine=machine_name)
job.save()
try:
#runner = GlobusHelper(request.user)
cmd_str = "ssh " + machine["hostname"] + ' " ' + cmd + ' " '
print(cmd_str)
(output, error, retcode) = run_command(cmd_str, env=env)
except Exception as ex:
return json_response(status="ERROR",
status_code=500,
error="qsub failed with error: %s" % str(ex))
if retcode != 0:
return json_response(status="ERROR",
status_code=500,
error="qsub failed with error: %s" % error)
job.jobid = output.strip().split(' ')[-1]
job.save()
return {"jobid": job.jobid}
def submit_job(request, machine_name):
"""Submits a job to the queue
Keyword arguments:
request -- Django HttpRequest
machine_name -- name of the machine
"""
pass
user = request.user # User.objects.get(username=username)
job = HPCJob(user=user, jobfile='', machine=machine_name)
jobfilepath = request.POST.get("jobfilepath", None)
if request.POST.get("jobfile", False):
# Create command for sbatch on an existing slurm file
job_file_path = request.POST.get("jobfile")
job.jobfile = job_file_path
job.state = "unsubmit"
elif request.POST.get("jobscript", False):
# Create command for qsub from stdin data
job_script = request.POST.get("jobscript").encode()
# Creates a temporary job file
tmp_job_file = tempfile.NamedTemporaryFile(prefix="newt_",
dir=tempdir,
delete=False)
tmp_job_file.write(job_script)
tmp_job_file.flush()
tmp_job_file.close()
job.jobfile = tmp_job_file.name
job.state = "tempfile"
username = user.username #taskenv["user"]
else:
return json_response(status="ERROR",
status_code=400,
error="No data received")
#job = HPCJob( user = user,jobfile = jobfile , machine = machine_name )
if request.POST.get("jobconf", False):
try:
print(request.POST.get("jobconf"))
#job.configure( request.POST.get("jobconf") )
job.configure(json.loads(request.POST.get("jobconf")))
except Exception as ex:
return json_response(status="ERROR",
status_code=403,
error="Error jobconf : %s" % ex)
job.save()
taskenv = {"user": request.user.username, "machine": machine_name}
if job.state == "tempfile":
pass
taskenv["host"] = socket.gethostname()
rest = submit_job_task.delay(taskenv, job.id, jobfilepath)
cache.set("async-" + rest.id, "AsyncJob", 3600)
return json_response(status="ACCEPT",
status_code=201,
error="",
content=rest.id)
def download_path(request, machine_name, path):
#return json_response(status="ERROR",
# status_code=500,
# error="This API is forbidden yet. ")
try:
if path.startswith('/~'):
path = path[1:]
taskenv = {
"user": request.user.username,
"machine": machine_name,
"host": settings.TASKENV_HOST
}
#if not os.path.isfile( path ) :
# return json_response(status="ERROR",
# status_code=500,
# error=" no such file ")
#if not is_readable( path , request.user.username ):
# return json_response(status="ERROR",
# status_code=403,
# error="file not readable ")
if not os.path.isdir(tempdir):
os.makedirs(tempdir)
os.chmod(tempdir, stat.S_IWOTH + stat.S_IXOTH + stat.S_IROTH)
if os.path.dirname(path) == '/':
tmpfile = os.path.join(tempdir, os.path.basename(path))
logger.error("tempfile %s" % tmpfile)
#if not is_readable( tmpfile , request.user.username ):
# return json_response(status="ERROR",
# status_code=403,
# error="file not readable ")
# could download tmpfile ^ ^
file_handle = open(tmpfile, 'r')
content_type = get_mime_type(machine_name, tmpfile, file_handle)
logger.debug("File download requested: %s" % path)
if content_type is None:
content_type = "application/octet-stream"
return StreamingHttpResponse(file_handle,
content_type=content_type)
#file_handle = open(path, 'r')
#content_type = get_mime_type(machine_name, path, file_handle)
#logger.debug("File download requested: %s" % path)
#if content_type is None:
# content_type = "application/octet-stream"
#return StreamingHttpResponse(file_handle, content_type=content_type)
rest = download_path_task.delay(taskenv, path)
cache.set("async-" + rest.id, "AsyncJob", 3600)
return json_response(status="ACCEPT",
status_code=201,
error="",
content=rest.id)
except Exception as e:
logger.error("Could not get file %s" % str(e))
return json_response(status="ERROR", status_code=500, error=str(e))
def submit_job(request, machine_name):
"""Submits a job to the queue
Keyword arguments:
request -- Django HttpRequest
machine_name -- name of the machine
"""
machine = gridutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR", status_code=400, error="Invalid machine name: %s" % machine_name)
flags = ""
jobmanager = machine['jobmanagers']['fork']['url']
qsub = machine['qsub']['bin']
scheduler = machine['qsub']['scheduler']
# Set environment flags for qsub
if scheduler == "sge":
sge_env_str = "-env SGE_ROOT=%s -env SGE_QMASTER_PORT=%s -env SGE_EXECD_PORT=%s" % (gridutil.SGE_ROOT, gridutil.SGE_QMASTER_PORT, gridutil.SGE_EXECD_PORT)
flags += " " + sge_env_str
if request.POST.get("jobfile", False):
# Create command for qsub on an existing pbs file
job_file_path = request.POST.get("jobfile")
cmd = "%s %s" % (qsub, job_file_path)
elif request.POST.get("jobscript", False):
# Create command for qsub from stdin data
job_script = request.POST.get("jobscript")
# Creates a temporary job file
tmp_job_file = tempfile.NamedTemporaryFile(prefix="newt_")
tmp_job_file.write(job_script)
tmp_job_file.flush()
# Stages the temporary job file and pass it as to stdin to qsub
flags += " -stdin -s %s" % tmp_job_file.name
cmd = qsub
else:
return json_response(status="ERROR",
status_code=400,
error="No data received")
if scheduler != "sge":
cmd = '/bin/bash -l -c "%s"' % cmd
try:
runner = GlobusHelper(request.user)
(output, error, retcode) = runner.run_job(cmd, jobmanager, flags)
except Exception, ex:
return json_response(status="ERROR",
status_code=500,
error="qsub failed with error: %s" % str(ex))
def delete_job(request, machine_name, job_id):
machine = slurmutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR",
status_code=400,
error="Invalid machine name: %s" % machine_name)
taskenv = {"user": request.user.username, "machine": machine_name}
rest = delete_job_task.delay(taskenv, job_id)
cache.set("async-" + rest.id, "AsyncJob", 3600)
return json_response(status="ACCEPT",
status_code=201,
error="",
content=rest.id)
def delete_job(request, machine_name, job_id):
machine = slurmutil.GRID_RESOURCE_TABLE.get(machine_name, None)
if not machine:
return json_response(status="ERROR",
status_code=400,
error="Invalid machine name: %s" % machine_name)
env = slurmutil.get_cred_env(request.user)
mycmd = "ssh " + machine["hostname"] + " ' " + ' scancel ' + job_id + " '"
(output, error, retcode) = run_command(mycmd)
if retcode != 0:
return json_response(status="ERROR",
status_code=500,
error="Unable to get queue: %s" % error)
return (output)
def get_image(query):
import re
r = requests.get(nim_base_url + "/info/json/image/" + query)
if r.status_code == 200:
if re.search(r'\/photo\/?$', query):
return HttpResponse(r.content, content_type=r.headers['content-type'])
return r.json()['items']
elif r.status_code == 404:
return json_response(status="ERROR",
status_code=404,
error="Image not found at: " + path)
else:
return json_response(status="ERROR",
status_code=500,
error="Invalid image location: " + query)
def update_store_perms(request, store_name, perms):
"""Updates the permissions of the given store with perms; Returns the id of
the store.
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
perms -- list of the new permissions in the form of:
[
{
"user": <user_to_be_updated>,
"perms": <updated_perms>,
},
...
]
"""
try:
store = Store.objects.get(name=store_name)
except ObjectDoesNotExist:
return json_response(status="ERROR",
status_code=404,
error="Store does not exist: %s" % store_name)
for new_perm in perms:
try:
perm = Permission.objects.get(user__username=new_perm['name'], store=store)
except ObjectDoesNotExist:
u = User.objects.get(username=new_perm['name'])
perm = Permission(store=store, user=u)
perm.type = ",".join(new_perm['perms'])
perm.save()
return store_name
def get_store_perms(request, store_name):
"""Returns a dictionary of permissions of the store in the form of:
{
"name": <store_name>,
"perms": [
{
"user": <associated_user>,
"perms": <permissions_of_user>,
},
...
],
}
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
"""
storedb = redis.Redis(host=HOST, db=STOREDB)
if store_name not in get_store(request):
return json_response(status="ERROR", status_code=404, error="Store does not exist.")
all_perm_entries = storedb.lrange(store_name+":perms", 0, -1)
perms_list = []
for entry in all_perm_entries:
perms_list.append({
"name": entry[len(store_name) + 7:],
"perms": storedb.lrange(entry,0,-1)
})
return {"name": store_name, "perms": perms_list,}
def update_store_perms(request, store_name, perms):
"""Updates the permissions of the given store with perms; Returns the id of
the store.
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
perms -- list of the new permissions in the form of:
[
{
"user": <user_to_be_updated>,
"perms": <updated_perms>,
},
...
]
"""
storedb = redis.Redis(host=HOST, db=STOREDB)
if store_name not in get_store(request):
return json_response(status="ERROR", status_code=404, error="Store does not exist.")
new_perms = []
for new_perm in perms:
dbname = store_name + ":perms:" + new_perm['name']
if storedb.lrange(dbname, 0, -1):
storedb.delete(dbname)
for perm in new_perm['perms']:
storedb.rpush(dbname, perm)
new_perms.append({
"user": new_perm['name'],
"perms": storedb.lrange(dbname,0,-1),
})
return new_perms
def get_store_contents(request, store_name):
"""Returns a list containing all the contents of the store in the form of:
[
{
"oid": <document_id>,
"data": <document_data>,
},
...
]
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
"""
storedb = redis.Redis(host=HOST, db=STOREDB)
if store_name not in get_store(request):
return json_response(status="ERROR", status_code=404, error="Store does not exist.")
store_docs = storedb.lrange(store_name + ":docs",0,-1)
store_contents = []
for doc in store_docs:
store_contents.append({
"oid":doc[len(store_name)+1:],
"data":storedb.get(doc),
})
return store_contents
def get_store_contents(request, store_name):
"""Returns a list containing all the contents of the store in the form of:
[
{
"oid": <document_id>,
"data": <document_data>,
},
...
]
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
"""
try:
store = Store.objects.get(name=store_name)
except ObjectDoesNotExist:
return json_response(status="ERROR",
status_code=404,
error="Store does not exist: %s" % store_name)
documents = [{
"oid": str(doc.oid),
"data": doc.data
} for doc in store.documents.all()]
return documents
def store_insert(request, store_name, initial_data):
"""Creates a new document in the store with initial_data; Returns the oid
of the new document.
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
initial_data -- document data
"""
storedb = redis.Redis(host=HOST, db=STOREDB)
# Creating next docname
index_num = len(storedb.lrange(store_name + ":docs", 0, -1))
docname = store_name + ":" + str(index_num)
# Getting data
data = request.POST.get("data", None)
if not data:
return json_response(status="ERROR",
status_code=400,
error="No data received.")
storedb.set(docname, data)
storedb.rpush(store_name + ":docs", docname)
return str(index_num)
def update_store_perms(request, store_name, perms):
"""Updates the permissions of the given store with perms; Returns the id of
the store.
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
perms -- list of the new permissions in the form of:
[
{
"user": <user_to_be_updated>,
"perms": <updated_perms>,
},
...
]
"""
try:
store = Store.objects.get(name=store_name)
except ObjectDoesNotExist:
return json_response(status="ERROR",
status_code=404,
error="Store does not exist: %s" % store_name)
for new_perm in perms:
try:
perm = Permission.objects.get(user__username=new_perm['name'], store=store)
except ObjectDoesNotExist:
u = User.objects.get(username=new_perm['name'])
perm = Permission(store=store, user=u)
perm.type = ",".join(new_perm['perms'])
perm.save()
return store_name
def get_store_perms(request, store_name):
"""Returns a dictionary of permissions of the store in the form of:
{
"name": <store_name>,
"perms": [
{
"user": <associated_user>,
"perms": <permissions_of_user>,
},
...
],
}
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
"""
# Return the permissions of the store
db = MongoClient()['stores']
store = db["permissions"]
res = store.find_one({"name":store_name}, {"_id":0})
if res:
return res
else:
return json_response(status="ERROR", status_code="404", error="Store not found")
def get_store_contents(request, store_name):
"""Returns a list containing all the contents of the store in the form of:
[
{
"oid": <document_id>,
"data": <document_data>,
},
...
]
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
"""
# Check existance of the store
if store_name not in get_stores(request):
return json_response(status="ERROR",
status_code=404,
error="Store does not exist: %s" % store_name)
# Check privlages of user attempting to access store
# Get and return contents of the store
db = MongoClient()['stores']
store = db[store_name]
return [{
"oid": x["oid"],
"data": x['data']
} for x in store.find({}, {
"_id": 0,
"data": 1,
"oid": 1
})]
def get_store_perms(request, store_name):
"""Returns a dictionary of permissions of the store in the form of:
{
"name": <store_name>,
"perms": [
{
"user": <associated_user>,
"perms": <permissions_of_user>,
},
...
],
}
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
"""
# Return the permissions of the store
db = MongoClient()['stores']
store = db["permissions"]
res = store.find_one({"name": store_name}, {"_id": 0})
if res:
return res
else:
return json_response(status="ERROR",
status_code="404",
error="Store not found")
def get_store_contents(request, store_name):
"""Returns a list containing all the contents of the store in the form of:
[
{
"oid": <document_id>,
"data": <document_data>,
},
...
]
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
"""
# Check existance of the store
if store_name not in get_stores(request):
return json_response(status="ERROR",
status_code=404,
error="Store does not exist: %s" % store_name)
# Check privlages of user attempting to access store
# Get and return contents of the store
db = MongoClient()['stores']
store = db[store_name]
return [{"oid": x["oid"], "data": x['data']} for x in store.find({}, {"_id":0, "data":1, "oid":1})]
def get_store_contents(request, store_name):
"""Returns a list containing all the contents of the store in the form of:
[
{
"oid": <document_id>,
"data": <document_data>,
},
...
]
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
"""
storedb = redis.Redis(host=HOST, db=STOREDB)
if store_name not in get_store(request):
return json_response(status="ERROR",
status_code=404,
error="Store does not exist.")
store_docs = storedb.lrange(store_name + ":docs", 0, -1)
store_contents = []
for doc in store_docs:
store_contents.append({
"oid": doc[len(store_name) + 1:],
"data": storedb.get(doc),
})
return store_contents
def put_file(request, machine, path):
"""Writes the uploaded file to path and returns the path
Keyword arguments:
request -- HttpRequest containing the data
machine_name -- name of the machine
path -- path to file
"""
# Get data from request body
data = request.read()
# Write data to temporary location
# TODO: Get temporary path from settings.py
tmp_file = tempfile.NamedTemporaryFile(prefix="newt_")
tmp_file.write(data)
tmp_file.file.flush()
src = "file:///%s" % tmp_file.name
env = gridutil.get_cred_env(request.user)
dest = gridutil.get_grid_path(machine, path)
logger.debug("Putting file to location: %s" % dest)
(output, error, retcode) = run_command(gridutil.GLOBUS_CONF['LOCATION'] + "bin/globus-url-copy %s %s" % (src, dest), env=env)
if retcode != 0:
return json_response(content=output, status="ERROR", status_code=500, error=error)
tmp_file.close()
return {'location': path}
def get_usage(path):
r = requests.get(nim_base_url + "/usage/" + path + "/json/")
if r.status_code == 200:
return r.json()['items']
else:
return json_response(status="ERROR",
status_code=500,
error="Invalid resource location: " + path)
def post(self, request, machine_name):
logger.debug("Entering %s:%s" % (self.__class__.__name__, __name__))
command = urllib.unquote(request.POST['command'])
if not command:
return json_response(status="ERROR",
status_code=400,
error="No command received.")
return command_adapter.execute(request, machine_name, command)
def get_user_info(user_name=None, uid=None):
if uid:
return get_resource("user/id/%d/" % uid)
elif user_name:
return get_resource("user/%s/" % user_name)
else:
return json_response(status=ERROR,
status_code=400,
error="No data received.")
def wrapper(*args, **kwargs):
request = args[1]
if request.user.is_authenticated():
return view_func(*args, **kwargs)
else:
return json_response(status="ERROR",
status_code=403,
error="You must be logged in to access this.",
content=json.dumps({"login_url": "/api/auth/"}))
def query_store(request, store_name, query):
"""Queries the store; Returns the result of the query in the form of:
[
{
"oid": <document_id>,
"data": <document_data>,
},
...
]
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
query -- a query string
"""
if store_name not in get_store(request):
return json_response(status="ERROR", status_code=404, error="Store does not exist.")
return json_response(status="ERROR", status_code=501, error="Method not implemented.")
def execute(request, machine_name, command):
try:
logger.debug("Running command: %s" % command)
(output, error, retcode) = run_command(command)
response = {"output": output, "error": error, "retcode": retcode}
return response
except Exception as e:
logger.error("Could not run command: %s" % str(e))
return json_response(error="Could not run command: %s" % str(e), status="ERROR", status_code=500)
def wrapper(*args, **kwargs):
# If view_func is a class view, args=[self, request, ... ]
# If view_func is a regular function args=[request, ...]
if isinstance(args[0], HttpRequest):
request = args[0]
elif isinstance(args[1], HttpRequest):
request = args[1]
else:
return json_response(status="ERROR",
status_code=500,
error="Missing request object")
if request.user.is_authenticated():
return view_func(*args, **kwargs)
else:
return json_response(status="ERROR",
status_code=403,
error="You must be logged in to access this.",
content=json.dumps({"login_url": "/api/auth/"}))
def download_path(request, machine_name, path):
try:
file_handle = open(path, 'r')
content_type = get_mime_type(machine_name, path, file_handle)
logger.debug("File download requested: %s" % path)
return StreamingHttpResponse(file_handle, content_type=content_type)
except Exception as e:
logger.error("Could not get file %s" % str(e))
return json_response(status="ERROR",
status_code=500,
error=str(e))
def execute(request, machine_name, command):
try:
user = request.POST.get("sudo_user")
logger.debug("Running command: %s as %s" % (command, user))
command = "sudo -u %s %s " % (user, command)
(output, error, retcode) = run_command(command)
response = {"output": output, "error": error, "retcode": retcode}
return response
except Exception as e:
logger.error("Could not run command: %s" % str(e))
return json_response(error="Could not run command: %s" % str(e), status="ERROR", status_code=500)
def dispatch(self, request, *args, **kwargs):
"""
Override the dispatch method of the class view
"""
# Wrap the dispatch method, so that we autoencode JSON
response = super(JSONRestView, self).dispatch(request, *args, **kwargs)
# If this is not an HTTPResponseBase object (Base class for responses)
if not isinstance(response, HttpResponseBase):
response = json_response(response)
return response
def extras_router(request, query):
for pattern, func, req in patterns:
match = pattern.match(query)
if match and req:
return func(request, **match.groupdict())
elif match:
return func(**match.groupdict())
return json_response(status="Unimplemented",
status_code=501,
error="",
content="query: %s" % query)
def get_dir(request, machine_name, path):
"""Returns a directory listing of path (as an array)
Keyword arguments:
machine_name -- name of the machine
path -- path to file
"""
try:
env = gridutil.get_cred_env(request.user)
path = gridutil.get_grid_path(machine_name, path)
output, error, retcode = run_command(gridutil.GLOBUS_CONF['LOCATION'] + "bin/uberftp -ls %s" % path,
env=env)
if retcode != 0:
return json_response(content=output, status="ERROR", status_code=500, error=error)
# Split the lines
output = map(lambda i: i.strip(), output.splitlines())
# regular expression that captures ls output of the form:
# drwxrwxr-x 4 shreyas newt 32768 Apr 15 10:59 home
patt=re.compile(r'(?P<perms>[\+\w@-]{10,})\s+(?P<hardlinks>\d+)\s+(?P<user>\S+)\s+(?P<group>\S+)\s+(?P<size>\d+)\s+(?P<date>\w{3}\s+\d+\s+[\d\:]+)\s+(?P<name>.+)$')
# filter out stuff that doesn't match pattern
output = filter(lambda line: patt.match(line), output)
# break up line into tuple: (perms, hl, user, group, size, date, filename)
output = map(lambda x: patt.match(x).groupdict(), output)
for line in output:
if line['perms'].startswith('l'):
name, symlink = line['name'].split(' -> ')
line['name'] = name
line['symlink'] = symlink
else:
line['symlink'] = ""
return output
except Exception as e:
logger.error("Could not get directory %s" % str(e))
return json_response(status="ERROR", status_code=500, error="Could not get directory: %s" % str(e))
def submit_job(request, machine_name):
"""Submits a job to the queue
Keyword arguments:
request -- Django HttpRequest
machine_name -- name of the machine
"""
# Get data from POST
if request.POST.get("jobfile", False):
try:
f = open(request.POST.get("jobfile"), 'r')
data = f.read()
except Exception as e:
return json_response(status="ERROR",
status_code=400,
error="Unable to open job file. Be sure you gave an absolute path.")
finally:
f.close()
elif request.POST.get("jobscript", False):
data = request.POST.get("jobscript")
else:
return json_response(status="ERROR",
status_code=400,
error="No data received")
# Generate unique outfile name
tmp_job_name = str(ObjectId())
# Get job emulator path
job_emu = settings.PROJECT_DIR + "/job/adapters/emulate_job_run.sh"
# Run job with the commands in data
job = Popen([job_emu, tmp_job_name, request.user.username, data], stdout=PIPE)
# Get/return the job_id from stdout
job_id = job.stdout.readline().rstrip()
logger.debug("Spawned process: %s" % job_id)
return {"jobid": job_id}
def store_update(request, store_name, obj_id, data):
"""Updates the contents of a given document; Returns the oid of the
document.
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
obj_id -- ID of the document in the store
data -- Updated data of the document
"""
try:
store = Store.objects.get(name=store_name)
except ObjectDoesNotExist:
return json_response(status="ERROR",
status_code=404,
error="Store does not exist: %s" % store_name)
if not data:
return json_response(status="ERROR", status_code=400, error="No data received.")
doc = store.documents.get(oid=obj_id)
doc.data = data
doc.save()
return str(doc.oid)
def store_insert(request, store_name, initial_data):
"""Creates a new document in the store with initial_data; Returns the oid
of the new document.
Keyword arguments:
request -- Django HttpRequest object
store_name -- the name of the store
initial_data -- document data
"""
try:
store = Store.objects.get(name=store_name)
except ObjectDoesNotExist:
return json_response(status="ERROR",
status_code=404,
error="Store does not exist: %s" % store_name)
data = initial_data
if not data:
return json_response(status="ERROR", status_code=400, error="No data received.")
oid = store.documents.count()
new_doc = Document(oid=oid, data=data, store=store)
new_doc.save()
return str(oid)