def payload4(task):
"""
run merge from N inputs
input: Makefile.all, *.fasta.{sfx list}, *1.{N}.fastq, *2.{N}.fastq, {N}reads.tgz, {N}maps.tgz
output: bam file + results.tgz?
:param task:
:return:
"""
logger.debug("payload4: Start")
#### Prepare
# Check type of task
task_type = task.task_type
# Get user
user = users_.get(task.owner_id)
task.tag = "task." + commands.getoutput('uuidgen')
tasks_.save(task)
n = 10
if task.params is not None:
n = int(task.params)
if n == 0:
n = 10
# Get containers
input_cont = conts_.get(task.input)
#TO_DO do smth with output container?
output_cont = conts_.get(task.output)
# Get container
container = Container()
container.guid = task.tag
conts_.save(container)
# Add input files to container
files_template_list = task_type.ifiles_template.split(',')
for item in input_cont.files:
f = item.file
for file_template in files_template_list:
# TO_DO: 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')
# reg additional output
fc.reg_file_in_cont_byname(user, 'output.bam', container, 'output')
fc.reg_file_in_cont_byname(user, 'myresults.bz2', container, 'output')
# Prepare trf script
script = task.task_type.trf_template
# TO_DO just for test - only emulate, not real jobs
pipeline_path_name = 'paleomix_bam'
swdir = '/s/ls2/users/poyda/swp/' + pipeline_path_name + '/'
script = "/bin/bash " + swdir + "runmerge.sh -t " + str(n)
send_job_(task, container, script)
return True
def container():
"""
New container form view
:return: Response obj
"""
form = NewContainerForm()
if request.method == 'POST':
user = g.user
scope = getScope(user.username)
ftpdir = form.ftpdir.data
#Create a unique container quid for this particular batch of uploads.
cguid = 'job.' + commands.getoutput('uuidgen')
# Create new container
container = Container()
container.guid = cguid
container.status = 'open'
conts_.save(container)
# Check if ftpdir empty
if ftpdir and len(ftpdir) > 0:
async_uploadContainer.delay(ftpdir, scope, container.guid)
return redirect(url_for('conts.cont_info', guid=container.guid))
return render_template("dashboard/cont/cont_new.html", form=form)
def new_cont():
"""
Creates new Container object
:return: New container
:rtype: Container
"""
# Prepare Container obj
f = Container()
f.guid = 'cont.' + commands.getoutput('uuidgen')
f.status = "open"
# Save to fc
conts_.save(f)
return f
def new_pipeline():
form = NewPipelineForm(request.form)
if request.method == 'POST':
ifiles = request.form.getlist('iguids[]')
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 ifiles:
if item != '':
f = files_.first(guid=item)
if f is not None:
# Register file in catalog
fc.reg_file_in_cont(f, pp_cont, 'input')
else:
pp_cont.status = 'broken'
conts_.save(pp_cont)
return make_response(jsonify({'error': "GUID {} not found".format(f)}))
# 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 new_cont():
"""
POST: /pilot/container
Saves new container
:return: ftp/guid
:rtype: json
"""
cont = Container()
guid = 'job.' + commands.getoutput('uuidgen')
cont.guid = guid
cont.status = 'open'
conts_.save(cont)
url = '%s/%s' % (current_app.config['FTP'], guid)
os.makedirs(
os.path.join(current_app.config['UPLOAD_FOLDER'],
getScope(g.user.username), cont.guid))
return {'ftp': url, 'guid': cont.guid}
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 payload3(task):
"""
run1 - N parallel jobs. {N} = sequence 0..01,0..02,...,N, not less than 2 placeholders
#TODO deal with {N}.fastq.bz2 ??
input: Makefile.{N}, *.fasta.{sfx list}, *1.{N}.fastq, *2.{N}.fastq
output: likely reads{N}.tgz, maps{N}.tgz
:param task:
:return:
"""
logger.debug("payload3: Start")
#### Prepare
# Check type of task
task_type = task.task_type
# if task_type.id != 3or6?:
# raise WebpandaError("Illegal task_type.id")
# Get user
user = users_.get(task.owner_id)
n=10
if task.params is not None:
n=int(task.params)
if n==0:
n=10
task.tag = "task." + commands.getoutput('uuidgen')
tasks_.save(task)
# Get containers
input_cont = conts_.get(task.input)
#TO_DO do smth with output container?
output_cont = conts_.get(task.output)
for jobname in gen_sfx("a",n):
# Get container
container = Container()
container.guid = task.tag + "."+jobname
conts_.save(container)
# Add input files to container
files_template_list = task_type.ifiles_template.split(',')
for item in input_cont.files:
f = item.file
for file_template in files_template_list:
# TO_DO: 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')
# reg additional output
fc.reg_file_in_cont_byname(user, jobname+'.reads.bz2', container, 'output')
fc.reg_file_in_cont_byname(user, jobname + '.maps.bz2', container, 'output')
# Prepare trf script
script = task.task_type.trf_template
# TO_DO just for test - only emulate, not real jobs
pipeline_path_name = 'paleomix_bam'
swdir = '/s/ls2/users/poyda/swp/' + pipeline_path_name +'/'
script = "/bin/bash "+swdir+"run11.sh -t " +jobname
send_job_(task, container, script)
return True
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 upload():
form = request.form
# Create a unique container quid for this particular batch of uploads.
cguid = 'job.' + commands.getoutput('uuidgen')
# Is the upload using Ajax, or a direct POST by the form?
is_ajax = False
if form.get("__ajax", None) == "true":
is_ajax = True
# Create new container
container = Container()
container.guid = cguid
container.status = 'open'
conts_.save(container)
# Process files in request
for upload in request.files.getlist("file"):
# Define file params
lfn = upload.filename.rsplit("/")[0]
scope = getScope(g.user.username)
guid = getGUID(scope, lfn)
site = sites_.first(se=current_app.config['DEFAULT_SE'])
# Target folder for these uploads.
dir = '/' + os.path.join('system', scope, guid)
target = site.datadir + dir
try:
os.makedirs(target)
except:
if is_ajax:
return ajax_response(
False, "Couldn't create upload directory: %s" % target)
else:
return "Couldn't create upload directory: %s" % target
replfn = os.path.join(dir, lfn)
destination = os.path.join(target, lfn)
upload.save(destination)
if os.path.isfile(destination):
# Check file existence in catalog
adler = adler32(destination)
md5 = md5sum(destination)
size = fsize(destination)
file_id = ddm_checkifexists(lfn, size, adler, md5)
if file_id:
# If file exists
file = files_.get(file_id)
else:
# Otherwise create new
file = File()
file.scope = scope
file.guid = guid
file.type = 'input'
file.lfn = lfn
file.token = ''
file.status = 'defined'
files_.save(file)
setFileMeta(file.id, destination)
replica = Replica()
replica.se = site.se
replica.status = 'ready'
replica.lfn = replfn
replica.original = file
replicas_.save(replica)
# Register file in container
fc.reg_file_in_cont(file, container, 'input')
else:
return ajax_response(False, "Couldn't save file: %s" % target)
if is_ajax:
return ajax_response(True, cguid)
else:
return redirect(url_for("jobs.jobs"))
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}