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
-from qcg.service import update_user_data, update_job, cancel, clean
+from qcg.utils import paginator_context, to_job_desc, to_form_data, restricted, cached_resources
+from qcg import service
from django.utils import encoding
import random
import os
from qcg import constants
-from qcg.utils import chunks
+from qcg.utils import chunks, generate_md_inputfile
# 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'])
+ service.update_user_data(request.user, request.session['proxy'])
tasks = request.user.tasks.order_by('-job__submission_time', '-submission_time') \
.select_related('job').prefetch_related('allocations__nodes')
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))
def process_details(request, job, task=None):
if not job.terminated or not job.purged:
- update_job(job, request.session['proxy'])
+ service.update_job(job, request.session['proxy'])
form_data = to_form_data(job.qcg_description)
env_formset_data = [{'name': name, 'value': value} for name, value in form_data.pop('env_variables', ())]
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
env_formset_data = [{'name': name, 'value': value} for name, value in form_data.pop('env_variables', ())]
else:
form_data, env_formset_data = None, None
+ hosts, applications, modules = cached_resources(request.session['proxy'])
if request.method == 'POST':
- form = JobDescriptionForm(request.POST, initial=form_data)
+ form = JobDescriptionForm(request.POST, form_data, hosts, applications, modules)
env_formset = EnvFormSet(request.POST, initial=env_formset_data)
template_form = JobTemplateForm(request.POST, prefix='template', instance=template)
md_input=generate_md_inputfile(params)
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)
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 - zakomentować poniżej
- job = job_desc.submit()
+ job = service.submit(job_desc, request.session['proxy'])
+
messages.success(request,
- format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> '
+ format_html(u'<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)
+ form = JobDescriptionForm(initial=form_data, hosts=hosts, applications=applications, modules=modules)
env_formset = EnvFormSet(initial=env_formset_data)
template_form = JobTemplateForm(prefix='template', instance=template)
@require_POST
@login_required
def job_cancel(request, job_id):
- return obj_cancel(request, get_object_or_404(request.user.jobs, job_id=job_id))
+ job = get_object_or_404(request.user.jobs, job_id=job_id)
+ return obj_run(request, job, service.cancel, u'Zadanie anulowano.')
@require_POST
@login_required
def task_cancel(request, job_id, task_id):
- return obj_cancel(request, get_object_or_404(request.user.tasks, job__job_id=job_id, task_id=task_id))
-
-
-def obj_cancel(request, obj):
- try:
- cancel(obj, request.session['proxy'])
- except PyqcgException as e:
- messages.error(request, format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> {}',
- e.message))
- else:
- messages.success(request, format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> '
- 'Zadanie anulowano.'))
-
- return redirect(obj)
+ task = get_object_or_404(request.user.tasks, job__job_id=job_id, task_id=task_id)
+ return obj_run(request, task, service.cancel, u'Zadanie anulowano.')
@require_POST
@login_required
def job_clean(request, job_id):
- return obj_clean(request, get_object_or_404(request.user.jobs, job_id=job_id))
+ job = get_object_or_404(request.user.jobs, job_id=job_id)
+ return obj_run(request, job, service.clean, u'Usunięto katalog roboczy.')
@require_POST
@login_required
def task_clean(request, job_id, task_id):
- return obj_clean(request, get_object_or_404(request.user.tasks, job__job_id=job_id, task_id=task_id))
+ task = get_object_or_404(request.user.tasks, job__job_id=job_id, task_id=task_id)
+ return obj_run(request, task, service.clean, u'Usunięto katalog roboczy.')
-def obj_clean(request, obj):
+def obj_run(request, obj, func, msg):
try:
- clean(obj, request.session['proxy'])
+ func(obj, request.session['proxy'])
except PyqcgException as e:
messages.error(request, format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> {}',
e.message))
else:
- messages.success(request, format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> '
- 'Usunięto katalog roboczy.'))
+ messages.success(request,
+ format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> {}', msg))
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()})
template = get_object_or_404(request.user.templates, id=template_id)
template.delete()
- messages.success(request, format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> '
+ messages.success(request, format_html(u'<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> '
u'Usunięto szablon <em>{}</em>.', template.name))
return redirect('job_templates')
return redirect(template)
- messages.error(request, format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> {}'
- 'Nie udało się zapisać szablonu!', template_form.errors))
+ messages.error(request, format_html(u'<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> {}'
+ u'Nie udało się zapisać szablonu!', template_form.errors))
return redirect(job)
projects / qcg-portal.git / blobdiff