from filex.views import make_url
from qcg.forms import FiltersForm, ColumnsForm, JobDescriptionForm, EnvFormSet, JobTemplateForm
from qcg.models import JobTemplate
-from qcg.utils import paginator_context, to_job_desc, to_form_data
+<<<<<<< HEAD
+from qcg.utils import paginator_context, to_job_desc, to_form_data, generate_md_inputfile
+=======
+from qcg.utils import paginator_context, to_job_desc, to_form_data, restricted
+>>>>>>> 4a588e0... set Cache-Control header for restricted views
from qcg.service import update_user_data, update_job, cancel, clean
import string
import random
import os
+from qcg import constants
+from qcg.utils import chunks
# for Debugging
from pprint import pprint
return datetime.strptime(string.strip(), "%d.%m.%Y").replace(tzinfo=UTC())
-@login_required
+@restricted
def jobs_list(request):
update_user_data(request.user, request.session['proxy'])
return render(request, 'qcg/jobs.html', context)
-@login_required
+@restricted
def job_details(request, job_id):
- job = get_object_or_404(request.user.jobs.prefetch_related('tasks'), job_id=job_id)
+ job = get_object_or_404(request.user.jobs.select_related('owner').prefetch_related('tasks'), job_id=job_id)
return render(request, 'qcg/job.html', process_details(request, job))
-@login_required
+@restricted
def task_details(request, job_id, task_id):
- task = get_object_or_404(request.user.tasks.select_related('job').prefetch_related('allocations'),
+ task = get_object_or_404(request.user.tasks.select_related('job__owner').prefetch_related('allocations'),
job__job_id=job_id, task_id=task_id)
return render(request, 'qcg/task.html', process_details(request, task.job, task))
return {'job': job, 'task': task, 'form': form, 'env_formset': env_formset, 'template_form': template_form}
-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 obliczeń
- md_input.append('SEED=-3059743 PDBREF 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 id_generator(size=6, chars=string.ascii_uppercase + string.digits):
return ''.join(random.choice(chars) for _ in range(size))
-@login_required
+@restricted
def job_submit(request, template_id=None):
save_template = 'save-template' in request.POST
template = get_object_or_404(request.user.templates, id=template_id) if template_id is not None else None
for env in env_formset.cleaned_data if env and not env['DELETE']]
# Generowanie pliku inputowego
- #md_input=list()
md_input=generate_md_inputfile(params)
- filename='input.'+id_generator(6)+'.tmp'
- f = open(filename, 'w')
- # for Debugging
- for idx in md_input:
- print idx
- f.write("%s\n" % idx)
- f.close()
- os.remove(filename)
-
+ url=os.path.splitext(params['pdb_file'])[0]+'_MD_genarated.inp'
+ params['master_file']=url
+ params['stage_in'].append(params['pdb_file'])
# Upload
-
+ ftp = FTPOperation(request.session['proxy'])
+ ftp.put(url)
+ for chunk in chunks('\n'.join([str(i) for i in md_input] ), 4096):
+ ftp.stream.put(chunk)
+ ftp.stream.put(None)
+ ftp.wait()
+
params['persistent'] = True
- # Debugging parametrów
- pprint(params)
job_desc = to_job_desc(params, request.session['proxy'])
+
if save_template:
template = template_form.save(commit=False)
return redirect(template)
- # wyłączenie wysyłania zadania
- '''
+ # wyłączenie wysyłania zadania - zakomentować poniżej
+
job = job_desc.submit()
messages.success(request,
format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> '
u'Zlecono zadanie <em>{}</em>.', job.job_id))
- '''
+
return redirect('jobs')
else:
form = JobDescriptionForm(initial=form_data)
return redirect(obj)
-@login_required
+@restricted
def gridftp(request):
return render(request, 'qcg/gridftp.html',
{'new_dir_form': HostPathNameForm(), 'rename_form': RenameForm(), 'archive_form': ArchiveForm()})
-@login_required
+@restricted
def gridftp_upload(request):
form = HostPathForm(request.GET)
'sep': '/' if form.cleaned_data['path'].startswith('~') else ''})
-@login_required
+@restricted
def job_templates(request):
return render(request, 'qcg/job_templates.html', {'templates': request.user.templates.all()})
projects / qcg-portal.git / blobdiff