def link_file(container_guid, lfn):
"""
GET: /pilot/file/<container_guid>/<lfn>/link
Returns ftp link to file
:param container_guid: Guid of container
:type container_guid: str
:param lfn: Local FileName
:type lfn: str
:return: id/guid/ftp
:rtype: json
"""
if ':' in container_guid:
container_guid = container_guid.split(':')[-1]
container = conts_.first(guid=container_guid)
site = sites_.first(se=current_app.config['DEFAULT_SE'])
cc = container.files
for c in cc:
f = c.file
if f.lfn == lfn:
replicas = f.replicas
for r in replicas:
if r.se == site.se and r.status == 'ready':
data = {}
data['lfn'] = f.lfn
data['guid'] = f.guid
data['ftp'] = getFtpLink(r.lfn)
return make_response(jsonify(data), 200)
raise WebpandaError('File not found')
def file_info(container_guid, lfn):
"""
GET: /pilot/file/<container_guid>/<lfn>/info
Returns file metadata
:param container_guid: Guid of container
:type container_guid: str
:param lfn: Local FileName
:type lfn: str
:return: lfn/guid/modtime/fsize/adler32/md5sum
:rtype: json
"""
if ':' in container_guid:
container_guid = container_guid.split(':')[-1]
container = conts_.first(guid=container_guid)
cc = container.files
for c in cc:
f = c.file
if f.lfn == lfn:
data = {}
data['lfn'] = f.lfn
data['guid'] = f.guid
data['modification_time'] = str(f.modification_time)
data['fsize'] = f.fsize
data['adler32'] = f.checksum
data['md5sum'] = f.md5sum
return make_response(jsonify(data), 200)
raise WebpandaError('File not found')
def get_token_by_code(code):
url = current_app.config["AUTH_TOKEN_ENDPOINT"]
redirect_uri = current_app.config["AUTH_REDIRECT_URI"]
client = current_app.config["AUTH_CLIENT"]
secret = current_app.config["AUTH_SECRET"]
headers = dict()
headers["Authorization"] = "Basic {code}".format(code=encode_cred(client, secret))
params = dict()
params['grant_type'] = "authorization_code"
params["code"] = code
params["redirect_uri"] = redirect_uri
rv = requests.post(url, data=params, headers=headers, verify=False)
data = rv.json()
if "error" not in data.keys():
access_token = data["access_token"]
token_type = data["token_type"]
refresh_token = data["refresh_token"]
expires_in = data["expires_in"]
id_token = data["id_token"]
return access_token
raise WebpandaError("Bad get_token response: " + str(data))
def send_job_(task, container, script):
"""
Prepares a job for task with container and trf script
:param task: Task obj to append a job
:param container: Container obj for job
:param script: str Trf script
:return: True
"""
# Get default ComputingElement
site = sites_.first(ce=current_app.config['DEFAULT_CE'])
if site is None:
raise WebpandaError("ComputingElement not found")
# Get distributive
distr = task.task_type.distr
# Define jobs
job = Job()
job.pandaid = None
job.status = 'pending'
job.owner = users_.get(task.owner_id)
job.params = b64encode(script)
job.distr = distr
job.container = container
job.creation_time = datetime.utcnow()
job.modification_time = datetime.utcnow()
#job.ninputfiles = 0
#job.noutputfiles = 0
job.corecount = 1
job.tags = task.tag
jobs_.save(job)
# Async sendjob
async_send_job.delay(jobid=job.id, siteid=site.id)
return True
def new_replica(container_guid, lfn, se):
"""
POST: /pilot/file/<container_guid>/<lfn>/makereplica/<se>
Creates task to make new file replica
:param container_guid: Guid of container
:type container_guid: str
:param lfn: Local FileName
:type lfn: str
:param se: SE codename
:type se: str
:return: Id of task
:rtype: json
"""
nsite = sites_.find(se=se).count()
if nsite == 0:
return make_response(jsonify({'error': 'SE not found'}), 400)
if ':' in container_guid:
container_guid = container_guid.split(':')[-1]
container = conts_.first(guid=container_guid)
cc = container.files
for c in cc:
f = c.file
if f.lfn == lfn:
rep_num = f.replicas.count()
replicas = f.replicas
if rep_num == 0:
raise WebpandaError('No replicas available')
ready_replica = None
for r in replicas:
if r.se == se:
return {'status': r.status}
if r.se == current_app.config[
'DEFAULT_SE']: # and r.status == 'ready'
ready_replica = r
if ready_replica is None:
ready_replica = replicas[0]
task = async_cloneReplica.delay(ready_replica.id, se)
return {'task_id': task.id}
raise WebpandaError('File not found')
def sso_get_user(token):
url = current_app.config["AUTH_USERINFO_ENDPOINT"]
headers = dict()
headers["Authorization"] = "Bearer {code}".format(code=token)
rv = requests.get(url, headers=headers, verify=False)
data = rv.json()
if "error" not in data.keys():
return data['sub'].split(":")[-1]
raise WebpandaError("Bad sso_get_user response: " + str(data))
def rm(self, lfn, rel=True):
if rel:
lfn = self.datadir + lfn
_logger.debug('HPC: Try to rm file %s' % lfn)
try:
proc = subprocess.Popen(['/bin/bash'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
out = proc.communicate("ssh -i %s %s@%s 'rm %s'" %
(self.key, self.user, self.host, lfn))
return True
except:
raise WebpandaError('Unable to rm:%s' % lfn)
def stage_in(container_guid, lfn):
"""
POST: /pilot/file/<container_guid>/<lfn>/copy
Creates task to copy file in path on se
:param container_guid: Guid of container
:type container_guid: str
:param lfn: Local FileName
:type lfn: str
:return: Id of task
:rtype: json
"""
args = request.form
if not ('to_se' in args.keys() and 'to_path' in args.keys()):
raise WebpandaError('Please specify correct request params')
to_se = args.get('to_se', type=str)
to_path = args.get('to_path', type=str)
if ':' in container_guid:
container_guid = container_guid.split(':')[-1]
container = conts_.first(guid=container_guid)
cc = container.files
for c in cc:
f = c.file
if f.lfn == lfn:
replicas = f.replicas
for r in replicas:
if r.status == 'ready':
task = async_copyReplica.delay(r.id, to_se, to_path)
return {'task_id': task.id}
raise WebpandaError('No replicas available')
raise WebpandaError('File not found')
def link(self, lfn, d, rel=True):
if rel:
lfn = self.datadir + lfn
d = self.datadir + d
_logger.debug('HPC: Try to link file from %s to %s' % (lfn, d))
try:
proc = subprocess.Popen(['/bin/bash'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
out = proc.communicate(
"ssh -i %s %s@%s 'mkdir -p %s && ln -s %s %s'" %
(self.key, self.user, self.host, d, lfn, d))
return True
except:
raise WebpandaError('Unable to link:%s to %s' % (lfn, d))
def cont_open(guid):
"""
POST: /pilot/container/<guid>/open
Changes container status to 'open'.
:param guid: Container guid
:type guid: str
"""
cont = conts_.first(guid=guid)
if cont is None:
raise WebpandaError("Container not found")
cont.status = 'open'
conts_.save(cont)
return {'response': 'Container status: open'}
def mv(self, lfn, lfn2, rel=True):
if rel:
lfn = self.datadir + lfn
lfn2 = self.datadir + lfn2
lfn2dir = "/".join(lfn2.split("/")[:-1])
_logger.debug('HPC: Try to link file from %s to %s' % (lfn, lfn2))
try:
proc = subprocess.Popen(['/bin/bash'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
out = proc.communicate(
"ssh -i %s %s@%s 'mkdir -p %s && mv %s %s'" %
(self.key, self.user, self.host, lfn2dir, lfn, lfn2))
return True
except:
raise WebpandaError('Unable to mv:%s to %s' % (lfn, lfn2))
def ls(self, path, rel=True):
if rel:
path = self.datadir + path
_logger.debug('HPC: Try to list files in path %s' % (path))
try:
proc = subprocess.Popen(['/bin/bash'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
out = proc.communicate(
"ssh -i {key} {user}@{host} 'ls -p {path} | grep -v /'".format(
key=self.key, user=self.user, host=self.host, path=path))
_logger.debug(out[0])
return out[0].split('\n')
except OSError:
raise WebpandaError('Unable to list files in: %s' % (path))
def adler32(self, path, rel=True):
if rel:
path = self.datadir + path
_logger.debug('HPC: Trying to get adler32 of file: %s' % (path))
cmd = "TODO:add script"
_logger.debug(cmd)
try:
# proc = subprocess.Popen(['/bin/bash'], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
# out = proc.communicate("ssh -i {key} {user}@{host} 'ls -p {path} | grep -v /'".format(key=self.key, user=self.user, host=self.host, path=path))
#_logger.debug(out[0])
#_logger.debug(out[1])
# return out[0].split('\n')
return "testtest"
except OSError:
raise WebpandaError('Unable to calculate adler32: %s' % (path))
def md5sum(self, path, rel=True):
if rel:
path = self.datadir + path
_logger.debug('HPC: Trying to get md5sum of file: %s' % (path))
cmd = "ssh -i {key} {user}@{host} 'md5sum {path}'".format(
key=self.key, user=self.user, host=self.host, path=path)
_logger.debug(cmd)
try:
proc = subprocess.Popen(['/bin/bash'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
out = proc.communicate(cmd)
_logger.debug(out[0])
_logger.debug(out[1])
return out[0].split(' ')[0]
except OSError:
raise WebpandaError('Unable to calculate md5: %s' % (path))
def cont_info(guid):
"""
POST: /pilot/container/<guid>/info
Returns container metadata
:param guid: Container guid
:type guid: str
:return: id/guid/status/nfiles
:rtype: json
"""
cont = conts_.first(guid=guid)
if cont is None:
raise WebpandaError("Container not found")
data = dict()
data['id'] = cont.id
data['guid'] = cont.guid
data['status'] = cont.status
data['nfiles'] = len(cont.files)
return data
def cont_close(guid):
"""
POST: /pilot/container/<guid>/close
Changes container status to 'close'
:param guid: Container guid
:type guid: str
"""
cont = conts_.first(guid=guid)
if cont is None:
raise WebpandaError("Container not found")
path = os.path.join(current_app.config['UPLOAD_FOLDER'],
getScope(g.user.username), cont.guid)
os.path.walk(path, registerLocalFile, cont.guid)
cont.status = 'close'
conts_.save(cont)
return {'response': 'Container status: close'}
def prepareInputFiles(cont_id, se):
_logger.debug('prepareInputFiles')
container = conts_.get(cont_id)
cc = container.files
tasks = []
for c in cc:
f = c.file
replicas_len = f.replicas.count()
if not replicas_len:
raise WebpandaError("No available replicas for file %s" % f.guid)
replicas = f.replicas
hasReplica = False
_logger.debug('prepareInputFiles: file.lfn={}'.format(f.lfn))
for replica in replicas:
if replica.se == se and replica.status == 'ready':
hasReplica = True
_logger.debug(
'prepareInputFiles: replica.se={} replica.status={} hasReplica={}'.
format(replica.se, replica.status, hasReplica))
if not hasReplica:
tasks.append(async_cloneReplica.s(replicas[0].id, se))
return tasks
def run(task):
try:
method = task.task_type.method
if task.status != 'sent':
return False
# raise WebpandaError('Illegal task status to start')
# Change task state to 'running'
task.status = 'preparing'
task.modification_time = datetime.utcnow()
tasks_.save(task)
# Custom payload
if method == 'init_task':
payload1(task)
elif method == 'split_task':
payload2(task)
elif method == 'run1_task':
payload3(task)
elif method == 'merge_task':
payload4(task)
else:
raise WebpandaError("Task payload error: method not found")
# Change task state to 'finished'
task.status = 'running'
task.modification_time = datetime.utcnow()
tasks_.save(task)
return True
except WebpandaError as e:
# Change task state to 'finished'
task.status = 'failed'
task.modification_time = datetime.utcnow()
task.comment = e.msg
tasks_.save(task)
return False
def new_pipeline_from_cont():
form = RunForm(request.form)
if request.method == 'POST':
icont = conts_.first(guid=form.guid.data)
if icont is None:
raise WebpandaError("Container not found")
current_user = g.user
# Prepare pipeline
pp = Pipeline()
pp.status = 'running'
pp.type_id = pipeline_types_.get(1).id
pp.owner_id = current_user.id
pipelines_.save(pp)
# Prepare container
pp_cont = Container()
pp_cont.guid = 'pipeline.' + commands.getoutput('uuidgen')
conts_.save(pp_cont)
# Add guids to container
for item in icont.files:
f = item.file
# Register file in catalog
fc.reg_file_in_cont(f, pp_cont, 'input')
# Set current task
start_task = pclient.get_start_task(pp)
start_task.input = pp_cont.id
start_task.output = pp_cont.id
tasks_.save(start_task)
return redirect(url_for('pipelines.list_all'))
return render_template('dashboard/pp/new.html', form=form)
def file_fetch(container_guid, lfn):
"""
GET: /pilot/file/<container_guid>/<lfn>/fetch
Returns file in response
:param container_guid: Guid of container
:type container_guid: str
:param lfn: Local FileName
:type lfn: str
:return: File
:rtype: application/octet-stream
"""
if ':' in container_guid:
container_guid = container_guid.split(':')[-1]
container = conts_.first(guid=container_guid)
cc = container.files
for c in cc:
f = c.file
if f.lfn == lfn:
replicas = f.replicas
for replica in replicas:
if replica.se == current_app.config['DEFAULT_SE']:
fullpath = current_app.config['DATA_PATH'] + replica.lfn
f = open(fullpath, 'r')
rr = Response(f.read(),
status=200,
content_type='application/octet-stream')
rr.headers[
'Content-Disposition'] = 'inline; filename="%s"' % f.lfn
rr.headers['Content-MD5'] = f.md5sum
f.downloaded += 1
files_.save(f)
return rr
raise WebpandaError('File not found')
def new_job():
"""Creates new job
"""
g.user = request.oauth.user
scope = getScope(request.oauth.user.username)
js = request.json
data = js['data']
distr_id = data['sw_id']
params = data['script']
corecount = data['cores']
site = sites_.first(ce=current_app.config['DEFAULT_CE'])
distr = distrs_.get(id)
container = Container()
guid = 'job.' + commands.getoutput('uuidgen')
container.guid = guid
container.status = 'open'
conts_.save(container)
# Process ftp files
if 'ftp_dir' in data.keys():
ftp_dir = data['ftp_dir']
register_ftp_files(ftp_dir, scope, container.guid)
# Process guid list
if 'guids' in data.keys():
guids = data['guids']
for f in guids:
if f != '':
file_ = files_.first(guid=f)
if file_ is not None:
# Register file in catalog
fc.reg_file_in_cont(file_, container, 'input')
else:
raise WebpandaError('File with guid %s not found' % f)
ofiles = ['results.tgz']
# Starts cloneReplica tasks
ftasks = prepareInputFiles(container.id, site.se)
# Saves output files meta
for lfn in ofiles:
file = File()
file.scope = scope
file.guid = getGUID(scope, lfn)
file.lfn = lfn
file.status = 'defined'
files_.save(file)
# Register file in catalog
fc.reg_file_in_cont(file, container, 'output')
# Counts files
allfiles = container.files
nifiles = 0
nofiles = 0
for f in allfiles:
if f.type == 'input':
nifiles += 1
if f.type == 'output':
nofiles += 1
# Defines job meta
job = Job()
job.pandaid = None
job.status = 'pending'
job.owner = request.oauth.user
job.params = params
job.distr = distr
job.container = container
job.creation_time = datetime.utcnow()
job.modification_time = datetime.utcnow()
job.ninputfiles = nifiles
job.noutputfiles = nofiles
job.corecount = corecount
job.tags = data['tags'] if 'tags' in data.keys() else ""
jobs_.save(job)
# Async sendjob
res = chord(ftasks)(async_send_job.s(jobid=job.id, siteid=site.id))
return {'id': job.id, 'container_id': guid}
def mv(self, lfn, lfn2, rel=True):
raise WebpandaError("SEPlugin.mv not implemented")
def payload2(task):
"""
split_task
Split input *.1.fastq and *.2.fastq into 'rn' pieces=
run panda /bin/bash split.sh
:param task:
:return:
"""
logger.debug("payload2: Start")
#### Prepare
# Check type of task
task_type = task.task_type
if task_type.id != 1:
raise WebpandaError("Illegal task_type.id")
logger.debug("payload2: tasktype " + str(task_type.id))
# Get user
user = users_.get(task.owner_id)
logger.debug("payload2: user " + str(user.id))
# Get containers
input_cont = conts_.get(task.input)
#TODO do smth with output container?
output_cont = conts_.get(task.output)
task.tag = "task." + commands.getoutput('uuidgen')
tasks_.save(task)
logger.debug("payload2: tag " + task.tag)
# Get container
container = Container()
container.guid = task.tag + ".0"
conts_.save(container)
logger.debug("payload2: cont " + container.guid)
script_add = ""
rn = 0
# Add input files to container
files_template_list = task_type.ifiles_template.split(',')
for item in input_cont.files:
f = item.file
if rn == 0:
if f.lfn.endswith('fastq'):
rn = getn(f.fsize)
elif f.lfn.endswith('fastq.bz2'):
rn = getn2(f.fsize)
for file_template in files_template_list:
# TODO: Change file template here
m = re.match(file_template, f.lfn)
if m is not None:
# Register file in container
fc.reg_file_in_cont(f, container, 'input')
if f.lfn.endswith('.fastq'):
for fi in gen_sfx(f.lfn[:-5]+'a', rn, '.fastq'):
fc.reg_file_in_cont_byname(user, fi, container, 'output')
if f.lfn.endswith('.fastq.bz2'):
for fi in gen_sfx(f.lfn[:-9]+'a', rn, '.fastq'):
fc.reg_file_in_cont_byname(user, fi, container, 'output')
if f.lfn.endswith('.fasta'):
fn=f.lfn+'.'
fc.reg_file_in_cont_byname(user, fn[:-6]+'dict', container, 'output')
# itert: validated file has null size
#for sfx in ('amb','ann','bwt','fai','pac','sa','validated'):
for sfx in ('amb','ann','bwt','fai','pac','sa', 'validated'):
fc.reg_file_in_cont_byname(user, fn+sfx, container, 'output')
script_add += "; echo 123 > ../{fname}".format(fname=fn+"validated")
logger.debug("payload2: reg Makefile")
#reg additional output
for fi in gen_sfx('Makefile.a', rn, '.yaml'):
fc.reg_file_in_cont_byname(user, fi, container, 'output')
#guids = ["web.it_4b7d4757-9ba4-4ed7-8bc0-6edb8bcc68d2",
# "web.it_3bc78e60-241b-418a-a631-2461d4ba1977",
# "web.it_1b88049e-463b-4b4f-8454-9587301a53e5",
# "web.it_a02271ea-8a9b-42f3-add2-ed6d0f9ff07e",
# "web.it_61bb7c80-e53c-4641-88b0-fbd16b0f3d56",
# "web.it_3930f596-25ea-49b0-8943-7a83c84c7940",
# "web.it_aa7b77a3-c765-464e-a4fa-29ce6dd50346",
# "web.it_211f2187-41f2-489f-ba63-73f004f21c66"
# ]
#for guid in guids:
# fc.reg_file_in_cont(files_.first(guid=guid), container, 'input')
# Prepare trf script
script = task.task_type.trf_template
# TO_DO just for test add "1" - script1.sh- only emulate, not real jobs
pipeline_path_name = 'paleomix_bam'
swdir='/s/ls2/users/poyda/swp/' + pipeline_path_name +'/'
script = "/bin/bash " + swdir + "genref.sh && /bin/bash " + swdir + "runtmplgen.sh -t 1>bam.out 2>bam.err & ;"
script += "/bin/bash " + swdir + "split.sh -t " + str(rn)
script += script_add
# Save rn as task param
task.params = str(rn)
tasks_.save(task)
logger.debug("payload2: script " + script)
logger.debug("payload2: send_job " + container.guid)
send_job_(task, container, script)
return True
def rm(self, lfn, rel=True):
raise WebpandaError("SEPlugin.rm not implemented")
def ls(self, path, rel=True):
raise WebpandaError("SEPlugin.ls not implemented")
def fsize(self, path, rel=True):
raise WebpandaError("SEPlugin.fsize not implemented")
def file_save(container_guid, lfn):
"""
POST: /pilot/file/<container_guid>/<lfn>/save
Saves file from request, returns file guid
:param container_guid: Guid of container
:type container_guid: str
:param lfn: Local FileName
:type lfn: str
:return: guid
:rtype: json
"""
site = sites_.first(se=current_app.config['DEFAULT_SE'])
if ':' in container_guid:
container_guid = container_guid.split(':')[-1]
container = conts_.first(guid=container_guid)
if container.status != 'open':
raise WebpandaError('Unable to upload: Container is not open')
cc = container.files
ff = None
for c in cc:
f = c.file
if f.lfn == lfn:
ff = f
if not ff:
ff = File()
ff.scope = getScope(g.user.username)
ff.lfn = lfn
ff.guid = getGUID(ff.scope, ff.lfn)
ff.status = 'defined'
files_.save(ff)
# Register file in container
fc.reg_file_in_cont(ff, container, 'input')
path = os.path.join(site.datadir, getScope(g.user.username),
container.guid)
replfn = '/' + os.path.join(getScope(g.user.username), container.guid,
ff.lfn)
destination = os.path.join(path, ff.lfn)
for r in ff.replicas:
if r.se == site.se:
destination = site.datadir + r.lfn
file_dir = '/'.join(destination.split('/')[:-1])
if r.status == 'ready':
if os.path.isfile(destination): # Check fsize, md5 or adler
raise WebpandaError('Replica exists')
else:
r.status = 'broken'
replicas_.save(r)
raise WebpandaError('Broken replica')
elif r.status == 'defined':
try:
os.makedirs(file_dir)
except (Exception):
pass
f = open(destination, 'wb')
f.write(request.data)
f.close()
# Update file info
setFileMeta(ff.id, destination)
r.status = 'ready'
replicas_.save(r)
return {'guid': ff.guid}
else:
raise WebpandaError('Replica status: %s' % r.status)
replica = Replica()
if os.path.isfile(destination):
raise WebpandaError('Unable to upload: File exists')
try:
os.makedirs(path)
except (Exception):
_logger.debug('Path exists: %s' % path)
f = open(destination, 'wb')
f.write(request.data)
f.close()
# Update file info
setFileMeta(ff.id, destination)
# Create/change replica
replica.se = site.se
replica.status = 'ready'
replica.lfn = replfn
replica.token = ''
replica.original = ff
replicas_.save(replica)
return {'guid': ff.guid}
def md5sum(self, path, rel=True):
raise WebpandaError("SEPlugin.md5sum not implemented")
def adler32(self, path, rel=True):
raise WebpandaError("SEPlugin.adler32 not implemented")
def run():
"""
Starts current defined task
:return:
"""
print "main started"
# Fetch pipelines (init state)
#TODO add SQL filter on status if possible
pipelines = pipelines_.all()
for pipeline in pipelines:
# Check if finished
if pipeline.status in ['finished', 'failed', 'cancelled']:
continue
# Fetch task object
current_task = pclient.get_current_task(pipeline)
if current_task is None:
return WebpandaError('Illegal task ID')
if current_task.status == 'failed':
#TODO: What to do if failed?
pipeline.status = 'failed'
current_task.modification_time = datetime.utcnow()
pipelines_.save(pipeline)
continue
if current_task.status == 'cancelled':
#TODO: What to do if cancelled? Who or by whom? If by system - resubmit, if by user -nothing?
pipeline.status = 'cancelled'
current_task.modification_time = datetime.utcnow()
pipelines_.save(pipeline)
continue
if current_task.status == 'finished':
# Get next_task
current_task = pclient.get_next_task(pipeline)
if current_task.status == 'defined':
if current_task.task_type.method == 'start':
# Do some general pipeline checks
current_task.status = 'finished'
current_task.modification_time = datetime.utcnow()
tasks_.save(current_task)
continue
elif current_task.task_type.method == 'finish':
current_task.status = 'finished'
current_task.modification_time = datetime.utcnow()
tasks_.save(current_task)
# Process system finish task
pipeline.status = 'finished'
pipeline.modification_time = datetime.utcnow()
pipelines_.save(pipeline)
continue
else:
# Process system start task
# Do some checks if it usefull - or we have all files already, or there would be never enough of them.
if not paleomix.has_input(current_task):
current_task.status = "failed"
current_task.modification_time = datetime.utcnow()
current_task.comment = "Input files check failed"
tasks_.save(current_task)
pipeline.status = 'failed'
pipeline.modification_time = datetime.utcnow()
pipelines_.save(pipeline)
continue
# Run task if defined
current_task.status = 'sent'
tasks_.save(current_task)
#TO_DO: Run async regime
paleomix.run(
current_task
) #, current_task.task_type.method) - we already get task from id. Not need to obtain again, is it?
# if we use async run, all params must be serializable (BaseQuery is not)
continue
