3 from functools import wraps
9 from django.contrib.auth.decorators import login_required
10 from django.core.paginator import Paginator
11 from django.utils.formats import date_format
12 from django.utils.timezone import localtime
13 from django.views.decorators.cache import cache_control
15 from pyqcg.description import JobDescription
17 from filex.ftp import FTPOperation
18 from qcg import constants
20 from django.utils import encoding
22 def get_attributes(obj, attrs):
23 return {name: getattr(obj, name) for name in attrs if getattr(obj, name) is not None}
26 def username_from_dn(dn):
27 _, username = dn.rsplit('=', 1)
32 def try_parse_int(s, default=None, base=10):
35 except (TypeError, ValueError):
39 def paginator_context(request, objects, per_page=constants.PER_PAGE):
40 paginator = Paginator(objects, per_page)
42 page_num = try_parse_int(request.GET.get('page'), 1)
43 if not (1 <= page_num <= paginator.num_pages):
46 pages_range = range(max(2, min(page_num - 2, paginator.num_pages - 4)),
47 min(max(page_num + 2, 5), paginator.num_pages) + 1)
49 return {'page': paginator.page(page_num), 'num_pages': paginator.num_pages, 'pages_range': pages_range}
52 def localtime_str(datetime):
53 return date_format(localtime(datetime), 'DATETIME_FORMAT')
56 def random_id(size=8, chars=string.ascii_uppercase + string.digits):
57 return ''.join(random.choice(chars) for _ in range(size))
60 def chunks(seq, size):
61 return (seq[pos:pos + size] for pos in xrange(0, len(seq), size))
63 def generate_md_inputfile(params):
65 # Opis pliku wyjsciowego
66 opis=params['note'][:80]
67 md_input.append(encoding.smart_str(opis, encoding='ascii', errors='ignore'))
68 # Dane kontrolne obliczen
69 md_input.append('SEED=-3059743 PDBREF ONE_LETTER MD EXTCONF RESCALE_MODE=2')
70 ctl_data='nstep='+str(params['nstep'])+' ntwe='+str(params['ntwe'])
71 ctl_data+=' ntwx='+str(params['ntwx'])+' dt='+str(params['dt'])+' damax='+str(params['damax'])+'lang=0 tbf'
72 md_input.append('{:<79}&'.format(ctl_data))
73 md_input.append('tau_bath=1.0 t_bath=300 reset_vel=10000 respa ntime_split=1 maxtime_split=512')
74 # Paramatry pól siłowych
75 if params['force_field'] == 'GAB':
77 md_input.append('WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &')
78 md_input.append('WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &')
79 md_input.append('WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &')
80 md_input.append('WVDWPP=0.11371 WHPB=1.00000 &')
81 md_input.append('CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0')
84 md_input.append('WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &')
85 md_input.append('WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &')
86 md_input.append('WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &')
87 md_input.append('WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &')
88 md_input.append('CUTOFF=7.00000 WCORR4=0.00000')
90 md_input.append(params['pdb_file'].split('/')[-1])
91 # Sekwencja aminokwasów
92 md_input.append(len(params['sequence']))
93 seq_str=params['sequence']
95 md_input.append(seq_str[:80])
103 def to_job_desc(params, proxy):
105 desc = JobDescription()
107 direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs',
108 'wall_time', 'memory', 'memory_per_slot', 'modules', 'input', 'stage_in', 'native', 'notify',
109 'preprocess', 'postprocess', 'persistent')
111 for name in direct_map:
113 setattr(desc, name, params[name])
115 if params['application']:
116 desc.set_application(*params['application'])
117 desc.stage_in += [params['master_file']]
118 desc.arguments.insert(0, os.path.basename(params['master_file']))
120 ftp = FTPOperation(proxy)
122 ftp.mkdir(constants.QCG_DATA_URL, parents=True)
123 url = os.path.join(constants.QCG_DATA_URL, 'script.{}.sh'.format(random_id()))
126 for chunk in chunks(params['script'], 4096):
127 ftp.stream.put(chunk)
131 desc.executable = url
133 desc.set_nodes(*params['nodes'])
134 if params['reservation']:
135 desc.set_reservation(params['reservation'])
136 if params['watch_output']:
137 desc.set_watch_output(params['watch_output'], params['watch_output_pattern'])
144 def to_form_data(xml):
145 # prevent circular import errors
146 from forms import JobDescriptionForm
149 desc = JobDescription()
150 desc.xml_description = xml
152 direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs',
153 'wall_time', 'memory', 'memory_per_slot', 'modules', 'input', 'stage_in', 'native', 'persistent')
156 for name in direct_map:
157 attr = getattr(desc, name)
158 if isinstance(attr, bool) or attr:
161 if desc.application is not None:
162 app_name, app_ver = desc.application
163 params['application'] = app_name if app_ver is None else app_name + '/' + app_name
164 stage_in = params['stage_in']
165 params['stage_in'], params['master_file'] = stage_in[:-1], stage_in[-1]
166 params['arguments'] = params['arguments'][1:]
167 if desc.nodes is not None:
168 params['nodes'] = ':'.join(map(str, desc.nodes))
169 if desc.reservation is not None:
170 res_id, res_type = desc.reservation
171 params['reservation'] = res_id
172 if desc.notify is not None:
173 params['notify_type'], params['notify_address'] = desc.notify.split(':')
174 if desc.watch_output is not None:
175 watch_output, params['watch_output_pattern'] = desc.watch_output
176 params['watch_output_type'], params['watch_output_address'] = watch_output.split(':')
177 if desc.preprocess is not None:
178 if desc.preprocess.startswith('gsiftp://'):
179 params['preprocess_type'] = JobDescriptionForm.Process.SCRIPT
180 params['preprocess_script'] = desc.preprocess
182 params['preprocess_type'] = JobDescriptionForm.Process.CMD
183 params['preprocess_cmd'] = desc.preprocess
184 if desc.postprocess is not None:
185 if desc.postprocess.startswith('gsiftp://'):
186 params['postprocess_type'] = JobDescriptionForm.Process.SCRIPT
187 params['postprocess_script'] = desc.postprocess
189 params['postprocess_type'] = JobDescriptionForm.Process.CMD
190 params['postprocess_cmd'] = desc.postprocess
195 def restricted(view):
196 return wraps(view)(cache_control(no_cache=True, must_revalidate=True, no_store=True)(login_required(view)))