3 from functools import wraps
9 from django.contrib.auth.decorators import login_required
10 from django.core.cache import caches
11 from django.core.paginator import Paginator
12 from django.utils.formats import date_format
13 from django.utils.timezone import localtime
14 from django.views.decorators.cache import cache_control
16 from pyqcg.description import JobDescription
18 from filex.ftp import FTPOperation
19 from qcg import constants
22 from django.utils import encoding
25 resources_cache = caches['resources']
28 def get_attributes(obj, attrs):
29 return {name: getattr(obj, name) for name in attrs if getattr(obj, name) is not None}
32 def username_from_dn(dn):
33 _, username = dn.rsplit('=', 1)
38 def try_parse_int(s, default=None, base=10):
41 except (TypeError, ValueError):
45 def paginator_context(request, objects, per_page=constants.PER_PAGE):
46 paginator = Paginator(objects, per_page)
48 page_num = try_parse_int(request.GET.get('page'), 1)
49 if not (1 <= page_num <= paginator.num_pages):
52 pages_range = range(max(2, min(page_num - 2, paginator.num_pages - 4)),
53 min(max(page_num + 2, 5), paginator.num_pages) + 1)
55 return {'page': paginator.page(page_num), 'num_pages': paginator.num_pages, 'pages_range': pages_range}
58 def localtime_str(datetime):
59 return date_format(localtime(datetime), 'DATETIME_FORMAT')
62 def random_id(size=8, chars=string.ascii_uppercase + string.digits):
63 return ''.join(random.choice(chars) for _ in range(size))
66 def chunks(seq, size):
67 return (seq[pos:pos + size] for pos in xrange(0, len(seq), size))
69 def generate_md_inputfile(params):
71 # Opis pliku wyjsciowego
72 opis=params['note'][:80]
73 md_input.append(encoding.smart_str(opis, encoding='ascii', errors='ignore'))
74 # Dane kontrolne obliczen
75 md_input.append('SEED=-3059743 PDBREF ONE_LETTER MD EXTCONF RESCALE_MODE=2')
76 ctl_data='nstep='+str(params['nstep'])+' ntwe='+str(params['ntwe'])
77 ctl_data+=' ntwx='+str(params['ntwx'])+' dt='+str(params['dt'])+' damax='+str(params['damax'])+'lang=1 scal_fric=0.01'
78 md_input.append('{:<79}&'.format(ctl_data))
79 md_input.append('tau_bath=1.0 t_bath=300 reset_vel=0 respa ntime_split=1 maxtime_split=512 mdpdb')
80 # Paramatry pól siłowych
81 if params['force_field'] == 'GAB':
83 md_input.append('WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &')
84 md_input.append('WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &')
85 md_input.append('WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &')
86 md_input.append('WVDWPP=0.11371 WHPB=1.00000 &')
87 md_input.append('CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0')
90 md_input.append('WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &')
91 md_input.append('WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &')
92 md_input.append('WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &')
93 md_input.append('WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &')
94 md_input.append('CUTOFF=7.00000 WCORR4=0.00000')
96 md_input.append(params['pdb_file'].split('/')[-1])
97 # Sekwencja aminokwasów
98 md_input.append(len(params['sequence']))
99 seq_str=params['sequence']
101 md_input.append(seq_str[:80])
103 md_input.append(' 0')
104 md_input.append(' 0')
109 def to_job_desc(params, proxy):
111 desc = JobDescription()
114 direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs',
115 'wall_time', 'memory', 'memory_per_slot', 'modules', 'input', 'stage_in', 'native', 'notify',
116 'preprocess', 'postprocess', 'persistent')
118 for name in direct_map:
120 setattr(desc, name, params[name])
123 if params['application']:
124 desc.set_application(*params['application'])
125 desc.stage_in += [params['master_file']]
126 desc.arguments.insert(0, os.path.basename(params['master_file']))
128 ftp = FTPOperation(proxy)
130 ftp.mkdir(constants.QCG_DATA_URL, parents=True)
131 url = os.path.join(constants.QCG_DATA_URL, 'script.{}.sh'.format(random_id()))
134 for chunk in chunks(params['script'], 4096):
135 ftp.stream.put(chunk)
139 desc.executable = url
141 desc.set_nodes(*params['nodes'])
142 if params['reservation']:
143 desc.set_reservation(params['reservation'])
144 if params['watch_output']:
145 desc.set_watch_output(params['watch_output'], params['watch_output_pattern'])
147 #print "testowanie ",
148 przemytnik = params['env_variables']
149 kontrabanda =( (u'UNRESPORTAL_FORCEFIELD', 'force_field'), (u'UNRESPORTAL_SEQUENCE', 'sequence'),
150 (u'UNRESPORTAL_PDBFILE','pdb_file'), (u'UNRESPORTAL_NSTEP','nstep'),
151 (u'UNRESPORTAL_NTWE', 'ntwe'), (u'UNRESPORTAL_NTWX','ntwx'),
152 (u'UNRESPORTAL_DT', 'dt'), (u'UNRESPORTAL_DAMAX', 'damax'))
154 print "> Przed: ",przemytnik
157 for k in kontrabanda:
163 print "> Po: ",przemytnik
167 for k in kontrabanda:
169 przemytnik.append( [ k[0], params[k[1]] ] )
175 setattr(przemytnik, k[0], params[k[1]] )
177 except AttributeError:
178 przemytnik.append( [ k[0], params[k[1]] ] )
182 if params['sequence']:
183 przemytnik.append([u'UNRESPORTAL_SEQUENCE',params['sequence']])
184 if params['pdb_file']:
185 przemytnik.append([u'UNRESPORTAL_PDBFILE',params['pdb_file']])
187 przemytnik.append([u'UNRESPORTAL_NSTEP',params['nstep']])
189 przemytnik.append([u'UNRESPORTAL_NTWE',params['ntwe']])
191 przemytnik.append([u'UNRESPORTAL_NTWX',params['ntwx']])
193 przemytnik.append([u'UNRESPORTAL_DT',params['dt']])
195 przemytnik.append([u'UNRESPORTAL_DAMAX',params['damax']])
197 setattr(desc, 'env_variables', przemytnik)
204 def to_form_data(xml):
205 # prevent circular import errors
206 from forms import JobDescriptionForm
209 desc = JobDescription()
210 desc.xml_description = xml
212 direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs',
213 'wall_time', 'modules', 'input', 'stage_in', 'native', 'persistent')
216 for name in direct_map:
217 attr = getattr(desc, name)
218 if isinstance(attr, bool) or attr:
221 if desc.application is not None:
222 app_name, app_ver = desc.application
223 params['application'] = app_name if app_ver is None else app_name + '/' + app_name
224 stage_in = params['stage_in']
225 params['stage_in'], params['master_file'] = stage_in[:-1], stage_in[-1]
226 params['arguments'] = params['arguments'][1:]
227 if desc.nodes is not None:
228 params['nodes'] = ':'.join(map(str, desc.nodes))
229 if desc.reservation is not None:
230 res_id, res_type = desc.reservation
231 params['reservation'] = res_id
232 if desc.notify is not None:
233 params['notify_type'], params['notify_address'] = desc.notify.split(':')
234 if desc.watch_output is not None:
235 watch_output, params['watch_output_pattern'] = desc.watch_output
236 params['watch_output_type'], params['watch_output_address'] = watch_output.split(':')
237 if desc.preprocess is not None:
238 if desc.preprocess.startswith('gsiftp://'):
239 params['preprocess_type'] = JobDescriptionForm.Process.SCRIPT
240 params['preprocess_script'] = desc.preprocess
242 params['preprocess_type'] = JobDescriptionForm.Process.CMD
243 params['preprocess_cmd'] = desc.preprocess
244 if desc.postprocess is not None:
245 if desc.postprocess.startswith('gsiftp://'):
246 params['postprocess_type'] = JobDescriptionForm.Process.SCRIPT
247 params['postprocess_script'] = desc.postprocess
249 params['postprocess_type'] = JobDescriptionForm.Process.CMD
250 params['postprocess_cmd'] = desc.postprocess
252 params['memory'] = int(desc.memory)
253 if desc.memory_per_slot:
254 params['memory_per_slot'] = int(desc.memory_per_slot)
256 for item in desc.env_variables:
257 if item[0] == u'UNRESPORTAL_FORCEFIELD':
258 params['force_field'] = item[1]
259 if item[0] == u'UNRESPORTAL_SEQUENCE':
260 params['sequence'] = item[1]
261 if item[0] == u'UNRESPORTAL_PDBFILE':
262 params['pdb_file'] = item[1]
263 if item[0] == u'UNRESPORTAL_NSTEP':
264 params['nstep'] = item[1]
265 if item[0] == u'UNRESPORTAL_NTWE':
266 params['ntwe'] = item[1]
267 if item[0] == u'UNRESPORTAL_NTWX':
268 params['ntwx'] = item[1]
269 if item[0] == u'UNRESPORTAL_DT':
270 params['dt'] = item[1]
271 if item[0] == u'UNRESPORTAL_DAMAX':
272 params['damax'] = item[1]
276 def restricted(view):
277 return wraps(view)(cache_control(no_cache=True, must_revalidate=True, no_store=True)(login_required(view)))
280 def cached_resources(proxy):
281 hosts = resources_cache.get('hosts')
283 # prevent circular import errors
284 from qcg.service import fetch_resources
286 hosts, _, applications, modules = map(make_choices, fetch_resources(proxy))
287 resources_cache.set('hosts', hosts)
288 resources_cache.set('applications', applications)
289 resources_cache.set('modules', modules)
291 applications = resources_cache.get('applications')
292 modules = resources_cache.get('modules')
294 return hosts, applications, modules
297 def make_choices(iterable):
298 return ((None, ''),) + tuple((item, item) for item in sorted(iterable))