-from django.core.paginator import Paginator
-from django.db import transaction
-from django.utils.timezone import now
-from pyqcg.service import Registry
-from pyqcg.utils import Credential, TimePeriod
+# coding=utf-8
+
+from functools import wraps
+
+import os
+import string
+import random
+from django.contrib.auth.decorators import login_required
+from django.core.paginator import Paginator
+from django.utils.formats import date_format
+from django.utils.timezone import localtime
+from django.views.decorators.cache import cache_control
+from pyqcg import QCG
+from pyqcg.utils import Credential
+from pyqcg.description import JobDescription
+
+from filex.ftp import FTPOperation
from qcg import constants
+from django.utils import encoding
def get_attributes(obj, attrs):
return {name: getattr(obj, name) for name in attrs if getattr(obj, name) is not None}
return username
-@transaction.atomic
-def update_user_data(user, proxy):
- from qcg.models import User, Job, Task, Allocation, NodeInfo
-
- credential = Credential(proxy)
- registry = Registry(credential)
-
- # put lock on user record (hopefully..?)
- user = User.objects.select_for_update().get(pk=user.pk)
-
- changed_filter = {'changed': TimePeriod(after=user.last_update)}
-
- ###################################
- # Jobs
- ###################################
- for qcg_job in registry.jobs(**changed_filter):
- params = Job.qcg_map(qcg_job, user)
- job_id = params.pop('job_id')
-
- Job.objects.update_or_create(job_id=job_id, defaults=params)
-
- ###################################
- # Tasks
- ###################################
- jobs_cache = {j.job_id: j for j in Job.objects.filter(owner=user)}
- for qcg_task in registry.tasks(**changed_filter):
- params = Task.qcg_map(qcg_task, jobs_cache)
- task_id = params.pop('task_id')
-
- task, created = Task.objects.update_or_create(job__job_id=qcg_task.job_id, task_id=task_id, defaults=params)
-
- if not created:
- task.allocations.all().delete()
-
- for qcg_alloc in qcg_task.allocations:
- alloc = task.allocations.create(**Allocation.qcg_map(qcg_alloc))
-
- for qcg_node in qcg_alloc.nodes:
- alloc.nodes.create(**NodeInfo.qcg_map(qcg_node))
-
- # release user lock
- user.last_update = now()
- user.save()
-
-
def try_parse_int(s, default=None, base=10):
try:
return int(s, base)
min(max(page_num + 2, 5), paginator.num_pages) + 1)
return {'page': paginator.page(page_num), 'num_pages': paginator.num_pages, 'pages_range': pages_range}
+
+
+def localtime_str(datetime):
+ return date_format(localtime(datetime), 'DATETIME_FORMAT')
+
+
+def random_id(size=8, chars=string.ascii_uppercase + string.digits):
+ return ''.join(random.choice(chars) for _ in range(size))
+
+
+def chunks(seq, size):
+ return (seq[pos:pos + size] for pos in xrange(0, len(seq), size))
+
+def generate_md_inputfile(params):
+ md_input = list()
+ # Opis pliku wyjsciowego
+ opis=params['note'][:80]
+ md_input.append(encoding.smart_str(opis, encoding='ascii', errors='ignore'))
+ # Dane kontrolne obliczen
+ md_input.append('SEED=-3059743 PDBREF ONE_LETTER MD EXTCONF RESCALE_MODE=2')
+ ctl_data='nstep='+str(params['nstep'])+' ntwe='+str(params['ntwe'])
+ ctl_data+=' ntwx='+str(params['ntwx'])+' dt='+str(params['dt'])+' damax='+str(params['damax'])+'lang=0 tbf'
+ md_input.append('{:<79}&'.format(ctl_data))
+ md_input.append('tau_bath=1.0 t_bath=300 reset_vel=10000 respa ntime_split=1 maxtime_split=512')
+ # Paramatry pól siłowych
+ if params['force_field'] == 'GAB':
+ # Wagi pola GAB
+ md_input.append('WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &')
+ md_input.append('WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &')
+ md_input.append('WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &')
+ md_input.append('WVDWPP=0.11371 WHPB=1.00000 &')
+ md_input.append('CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0')
+ else:
+ # Wagi pola E0LLY
+ md_input.append('WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &')
+ md_input.append('WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &')
+ md_input.append('WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &')
+ md_input.append('WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &')
+ md_input.append('CUTOFF=7.00000 WCORR4=0.00000')
+ # Plik PDB
+ md_input.append(params['pdb_file'].split('/')[-1])
+ # Sekwencja aminokwasów
+ md_input.append(len(params['sequence']))
+ seq_str=params['sequence']
+ while seq_str:
+ md_input.append(seq_str[:80])
+ seq_str=seq_str[80:]
+ md_input.append(' 0')
+ md_input.append(' 0')
+
+ return md_input
+
+
+def to_job_desc(params, proxy):
+ QCG.start()
+ desc = JobDescription(Credential(proxy))
+
+ direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs',
+ 'wall_time', 'memory', 'memory_per_slot', 'modules', 'input', 'stage_in', 'native', 'notify',
+ 'preprocess', 'postprocess', 'persistent')
+
+ for name in direct_map:
+ if params[name]:
+ setattr(desc, name, params[name])
+
+ if params['application']:
+ desc.set_application(*params['application'])
+ desc.stage_in += [params['master_file']]
+ desc.arguments.insert(0, os.path.basename(params['master_file']))
+ if params['script']:
+ ftp = FTPOperation(proxy)
+
+ ftp.mkdir(constants.QCG_DATA_URL, parents=True)
+ url = os.path.join(constants.QCG_DATA_URL, 'script.{}.sh'.format(random_id()))
+ ftp.put(url)
+
+ for chunk in chunks(params['script'], 4096):
+ ftp.stream.put(chunk)
+ ftp.stream.put(None)
+ ftp.wait()
+
+ desc.executable = url
+ if params['nodes']:
+ desc.set_nodes(*params['nodes'])
+ if params['reservation']:
+ desc.set_reservation(params['reservation'])
+ if params['watch_output']:
+ desc.set_watch_output(params['watch_output'], params['watch_output_pattern'])
+
+ # TODO monitoring
+
+ return desc
+
+
+def to_form_data(xml):
+ # prevent circular import errors
+ from forms import JobDescriptionForm
+
+ QCG.start()
+ desc = JobDescription()
+ desc.xml_description = xml
+
+ direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs',
+ 'wall_time', 'memory', 'memory_per_slot', 'modules', 'input', 'stage_in', 'native', 'persistent')
+
+ params = {}
+ for name in direct_map:
+ attr = getattr(desc, name)
+ if isinstance(attr, bool) or attr:
+ params[name] = attr
+
+ if desc.application is not None:
+ app_name, app_ver = desc.application
+ params['application'] = app_name if app_ver is None else app_name + '/' + app_name
+ stage_in = params['stage_in']
+ params['stage_in'], params['master_file'] = stage_in[:-1], stage_in[-1]
+ params['arguments'] = params['arguments'][1:]
+ if desc.nodes is not None:
+ params['nodes'] = ':'.join(map(str, desc.nodes))
+ if desc.reservation is not None:
+ res_id, res_type = desc.reservation
+ params['reservation'] = res_id
+ if desc.notify is not None:
+ params['notify_type'], params['notify_address'] = desc.notify.split(':')
+ if desc.watch_output is not None:
+ watch_output, params['watch_output_pattern'] = desc.watch_output
+ params['watch_output_type'], params['watch_output_address'] = watch_output.split(':')
+ if desc.preprocess is not None:
+ if desc.preprocess.startswith('gsiftp://'):
+ params['preprocess_type'] = JobDescriptionForm.Process.SCRIPT
+ params['preprocess_script'] = desc.preprocess
+ else:
+ params['preprocess_type'] = JobDescriptionForm.Process.CMD
+ params['preprocess_cmd'] = desc.preprocess
+ if desc.postprocess is not None:
+ if desc.postprocess.startswith('gsiftp://'):
+ params['postprocess_type'] = JobDescriptionForm.Process.SCRIPT
+ params['postprocess_script'] = desc.postprocess
+ else:
+ params['postprocess_type'] = JobDescriptionForm.Process.CMD
+ params['postprocess_cmd'] = desc.postprocess
+
+ return params
+
+
+def restricted(view):
+ return wraps(view)(cache_control(no_cache=True, must_revalidate=True, no_store=True)(login_required(view)))
projects / qcg-portal.git / blobdiff