def _run_job(ssh, sftp, gjfstring, jobstring=None, **kwargs):
try:
error = _make_folders(ssh)
if error:
return None, "folder - " + error
name = kwargs.get("name", "chemtoolsjob")
gjfname = "chemtools/%s.gjf" % name
jobname = "chemtools/%s.job" % name
f = sftp.open(gjfname, 'w')
f.write(gjfstring)
f.close()
if jobstring is None:
jobstring = JobTemplate.render(internal=True, **kwargs)
f2 = sftp.open(jobname, 'w')
f2.write(jobstring)
f2.close()
# TODO: Make this safer, this should fail before
# TODO: Make test for failing before
s = "cd chemtools; qsub %s.job" % name
_, stdout, stderr = ssh.exec_command(s)
stderr = stderr.readlines()
if stderr:
return None, "qsub - " + stderr[0]
jobid = stdout.readlines()[0].split(".")[0]
except Exception as e:
logger.warn("Could not run the job: %s" % e)
return None, str(e)
return jobid, None
def get_results(self, request, string, mol_form):
job_settings = dict(self.cleaned_data)
mol_settings = dict(mol_form.cleaned_data)
if request.method == "GET":
if request.REQUEST.get('molname'):
job_settings['name'] = request.REQUEST.get('molname')
job_string = JobTemplate.render(**job_settings)
response = HttpResponse(job_string, content_type="text/plain")
filename = '%s.job' % job_settings['name']
add = "" if request.REQUEST.get("view") else "attachment; "
response['Content-Disposition'] = add + 'filename=' + filename
return response
elif request.method == "POST":
cred = job_settings.pop("credential")
do_html = request.REQUEST.get("html", False)
results = run_standard_jobs(
cred, string, mol_settings, job_settings)
if results["failed"]:
failed_names = zip(*results['failed'])[0]
results["failed_mols"] = ','.join(failed_names)
if do_html:
html = render_to_string("chem/multi_submit.html", results)
temp = {"success": True, "html": html}
return HttpResponse(json.dumps(temp),
content_type="application/json")
else:
return HttpResponse(json.dumps(results),
content_type="application/json")
def get_results(self, request, string, mol_form):
job_settings = dict(self.cleaned_data)
mol_settings = dict(mol_form.cleaned_data)
if request.method == "GET":
if request.REQUEST.get('molname'):
job_settings['name'] = request.REQUEST.get('molname')
job_string = JobTemplate.render(**job_settings)
response = HttpResponse(job_string, content_type="text/plain")
filename = '%s.job' % job_settings['name']
add = "" if request.REQUEST.get("view") else "attachment; "
response['Content-Disposition'] = add + 'filename=' + filename
return response
elif request.method == "POST":
cred = job_settings.pop("credential")
do_html = request.REQUEST.get("html", False)
results = run_standard_jobs(cred, string, mol_settings,
job_settings)
if results["failed"]:
failed_names = zip(*results['failed'])[0]
results["failed_mols"] = ','.join(failed_names)
if do_html:
html = render_to_string("chem/multi_submit.html", results)
temp = {"success": True, "html": html}
return HttpResponse(json.dumps(temp),
content_type="application/json")
else:
return HttpResponse(json.dumps(results),
content_type="application/json")
def get_multi_job(string, form):
buff = StringIO()
zfile = zipfile.ZipFile(buff, 'w', zipfile.ZIP_DEFLATED)
for name in mol_name.name_expansion(string):
if not name:
continue
name, _ = os.path.splitext(name)
dnew = form.get_single_data(name)
zfile.writestr("%s.job" % dnew["name"], JobTemplate.render(**dnew))
zfile.close()
buff.flush()
ret_zip = buff.getvalue()
buff.close()
return ret_zip
def template_settings(request, username):
state = "Change Settings"
if request.method == "POST":
if "delete" in request.POST:
i = 0
for i, template in enumerate(get_templates_from_request(request)):
template.delete()
logger.info("%s deleted %d template(s)" % (username, i + 1))
state = "Settings Successfully Saved"
form = JobTemplateForm(request.user)
elif "save" in request.POST:
form = JobTemplateForm(request.user, request.POST)
if form.is_valid():
try:
name = form.cleaned_data.get("name")
obj = JobTemplate.objects.get(creator=request.user,
name=name)
obj.template.delete(False)
obj.template = form.cleaned_data.get("template")
obj.save()
except JobTemplate.DoesNotExist:
obj = form.save(commit=False)
obj.creator = request.user
obj.save()
state = "Settings Successfully Saved"
form = JobTemplateForm(request.user)
else:
form = JobTemplateForm(request.user)
else:
form = JobTemplateForm(request.user)
c = {
"pages": PAGES,
"page": "templates",
"state": state,
"form": form,
"templates": JobTemplate.get_templates(request.user),
}
return render(request, "data/template_settings.html", c)
def get_multi_molecule(molecules, options, mol_form, job_form):
buff = StringIO()
zfile = zipfile.ZipFile(buff, "w", zipfile.ZIP_DEFLATED)
mol_settings = dict(mol_form.cleaned_data)
generrors = []
for name in molecules:
try:
dnew = job_form.get_single_data(name)
mol_name = dnew['name']
except AttributeError:
mol_name = name
try:
out = gjfwriter.NamedMolecule(name, **mol_settings)
others = False
if "image" in options:
zfile.writestr(mol_name + ".png", out.get_png(10))
others = True
if "mol2" in options:
zfile.writestr(mol_name + ".mol2", out.get_mol2())
others = True
if "job" in options:
zfile.writestr(mol_name + ".job", JobTemplate.render(**dnew))
others = True
if "gjf" in options or not others:
zfile.writestr(mol_name + ".gjf", out.get_gjf())
except Exception as e:
logger.warn("Multigen error: %s - %s" % (name, e))
generrors.append("%s - %s" % (name, e))
if generrors:
zfile.writestr("errors.txt", '\n'.join(generrors))
zfile.close()
buff.flush()
ret_zip = buff.getvalue()
buff.close()
return ret_zip
def template_settings(request, username):
state = "Change Settings"
if request.method == "POST":
if "delete" in request.POST:
i = 0
for i, template in enumerate(get_templates_from_request(request)):
template.delete()
logger.info("%s deleted %d template(s)" % (username, i+1))
state = "Settings Successfully Saved"
form = JobTemplateForm(request.user)
elif "save" in request.POST:
form = JobTemplateForm(request.user, request.POST)
if form.is_valid():
try:
name = form.cleaned_data.get("name")
obj = JobTemplate.objects.get(creator=request.user, name=name)
obj.template.delete(False)
obj.template = form.cleaned_data.get("template")
obj.save()
except JobTemplate.DoesNotExist:
obj = form.save(commit=False)
obj.creator = request.user
obj.save()
state = "Settings Successfully Saved"
form = JobTemplateForm(request.user)
else:
form = JobTemplateForm(request.user)
else:
form = JobTemplateForm(request.user)
c = {
"pages": PAGES,
"page": "templates",
"state": state,
"form": form,
"templates": JobTemplate.get_templates(request.user),
}
return render(request, "data/template_settings.html", c)