+# coding=utf-8
+
+from functools import wraps
+
import os
import string
import random
+from django.contrib.auth.decorators import login_required
+from django.core.cache import caches
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
+
+resources_cache = caches['resources']
+
+
def get_attributes(obj, attrs):
return {name: getattr(obj, name) for name in attrs if getattr(obj, name) is not None}
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))
+ desc = JobDescription()
direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs',
'wall_time', 'memory', 'memory_per_slot', 'modules', 'input', 'stage_in', 'native', 'notify',
desc.set_reservation(params['reservation'])
if params['watch_output']:
desc.set_watch_output(params['watch_output'], params['watch_output_pattern'])
- # TODO monitoring
+ # TODO monitoring
+
return desc
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')
+ 'wall_time', 'modules', 'input', 'stage_in', 'native', 'persistent')
params = {}
for name in direct_map:
else:
params['postprocess_type'] = JobDescriptionForm.Process.CMD
params['postprocess_cmd'] = desc.postprocess
+ if desc.memory:
+ params['memory'] = int(desc.memory)
+ if desc.memory_per_slot:
+ params['memory_per_slot'] = int(desc.memory_per_slot)
return params
+
+
+def restricted(view):
+ return wraps(view)(cache_control(no_cache=True, must_revalidate=True, no_store=True)(login_required(view)))
+
+
+def cached_resources(proxy):
+ hosts = resources_cache.get('hosts')
+ if hosts is None:
+ # prevent circular import errors
+ from qcg.service import fetch_resources
+
+ hosts, _, applications, modules = map(make_choices, fetch_resources(proxy))
+ resources_cache.set('hosts', hosts)
+ resources_cache.set('applications', applications)
+ resources_cache.set('modules', modules)
+ else:
+ applications = resources_cache.get('applications')
+ modules = resources_cache.get('modules')
+
+ return hosts, applications, modules
+
+
+def make_choices(iterable):
+ return ((None, ''),) + tuple((item, item) for item in sorted(iterable))