X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=qcg%2Futils.py;h=57cf23aa683cc60f73f4b4c0d1508b6462e1b334;hb=586209a600ac5767a48c57cae1f566c0d6aaf48a;hp=5555e16b2972a9afaf10a9a536e523b1e9a26a06;hpb=dd8e6b0785c78c42c3866f161dd853a54e47275a;p=qcg-portal.git

diff --git a/qcg/utils.py b/qcg/utils.py
index 5555e16..57cf23a 100644
--- a/qcg/utils.py
+++ b/qcg/utils.py
@@ -1,18 +1,29 @@
+# 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}
 
@@ -54,10 +65,49 @@ def random_id(size=8, chars=string.ascii_uppercase + string.digits):
 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',
@@ -90,8 +140,9 @@ def to_job_desc(params, proxy):
         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
 
 
@@ -104,7 +155,7 @@ def to_form_data(xml):
     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:
@@ -142,5 +193,34 @@ def to_form_data(xml):
         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))