def multi_molecule(request, string):
if request.REQUEST.get("random"):
amount = int(request.REQUEST.get("random"))
string = ','.join(name_expansion(string, rand=amount))
job_form = JobForm.get_form(request, "{{ name }}")
mol_form = MoleculeForm(request.REQUEST)
job_is_valid = job_form.is_valid(request.method)
mol_is_valid = mol_form.is_valid()
if job_is_valid and mol_is_valid:
return job_form.get_results(request, string, mol_form)
elif request.is_ajax():
job_form_html = render_crispy_form(
job_form, context=RequestContext(request))
mol_form_html = render_crispy_form(
mol_form, context=RequestContext(request))
a = {
"success": False,
"job_form_html": job_form_html,
"mol_form_html": mol_form_html,
}
return HttpResponse(json.dumps(a), content_type="application/json")
c = {
"pagename": string,
"job_form": job_form,
"mol_form": MoleculeForm(),
"gjf": "checked",
"autoflip": request.REQUEST.get("autoflip"),
}
return render(request, "chem/multi_molecule.html", c)
def multi_molecule(request, string):
if request.REQUEST.get("random"):
amount = int(request.REQUEST.get("random"))
string = ','.join(name_expansion(string, rand=amount))
job_form = JobForm.get_form(request, "{{ name }}")
mol_form = MoleculeForm(request.REQUEST)
job_is_valid = job_form.is_valid(request.method)
mol_is_valid = mol_form.is_valid()
if job_is_valid and mol_is_valid:
return job_form.get_results(request, string, mol_form)
elif request.is_ajax():
job_form_html = render_crispy_form(job_form,
context=RequestContext(request))
mol_form_html = render_crispy_form(mol_form,
context=RequestContext(request))
a = {
"success": False,
"job_form_html": job_form_html,
"mol_form_html": mol_form_html,
}
return HttpResponse(json.dumps(a), content_type="application/json")
c = {
"pagename": string,
"job_form": job_form,
"mol_form": MoleculeForm(),
"gjf": "checked",
"autoflip": request.REQUEST.get("autoflip"),
}
return render(request, "chem/multi_molecule.html", c)
def get_multi_molecule_status(string, autoflip=False):
unique_molecules = collections.OrderedDict()
start = time.time()
for name in name_expansion(string):
if time.time() - start > 1:
logger.warn("%s -- The operation timed out" % (string))
raise ValueError("The operation has timed out.")
mol, name_error, error_report, new = get_molecule_status(name, autoflip=autoflip)
exact_spacer = mol.get_exact_name(spacers=True)
if not exact_spacer:
exact_spacer = name
if exact_spacer not in unique_molecules:
unique_molecules[exact_spacer] = [mol.name, error_report,
name_error, new]
return zip(*unique_molecules.values())
def get_multi_molecule_status(string, autoflip=False):
unique_molecules = collections.OrderedDict()
start = time.time()
for name in name_expansion(string):
if time.time() - start > 1:
logger.warn("%s -- The operation timed out" % (string))
raise ValueError("The operation has timed out.")
mol, name_error, error_report, new = get_molecule_status(
name, autoflip=autoflip)
exact_spacer = mol.get_exact_name(spacers=True)
if not exact_spacer:
exact_spacer = name
if exact_spacer not in unique_molecules:
unique_molecules[exact_spacer] = [
mol.name, error_report, name_error, new
]
return zip(*unique_molecules.values())
def run_standard_jobs(credential, string, mol_settings, job_settings):
results = {
"worked": [],
"failed": [],
"error": None,
}
# This is to catch invalid users early on
try:
results["cluster"] = credential.cluster.name
if not credential.user.is_staff:
results["error"] = "You must be a staff user to submit a job."
return results
except Exception as e:
results["error"] = "Invalid credential"
results["cluster"] = None
return results
names = []
gjfs = []
for mol in name_expansion(string):
try:
out = gjfwriter.NamedMolecule(mol, **mol_settings)
# This instantiation needs to be done here because of the errors
# in a structure are calculated lazily.
gjf = out.get_gjf()
names.append(mol)
gjfs.append(gjf)
except Exception as e:
logger.warn("Failed gjf write -- %s -- %s" % (mol, e))
results["failed"].append((mol, str(e)))
continue
if names:
settings = {
k: v
for k, v in job_settings.items() + mol_settings.items()
}
temp = run_jobs(credential, names, gjfs, **settings)
results["worked"] = temp["worked"]
results["failed"].extend(temp["failed"])
results["error"] = temp["error"]
return results
def run_standard_jobs(credential, string, mol_settings, job_settings):
results = {
"worked": [],
"failed": [],
"error": None,
}
# This is to catch invalid users early on
try:
results["cluster"] = credential.cluster.name
if not credential.user.is_staff:
results["error"] = "You must be a staff user to submit a job."
return results
except Exception as e:
results["error"] = "Invalid credential"
results["cluster"] = None
return results
names = []
gjfs = []
for mol in name_expansion(string):
try:
out = gjfwriter.NamedMolecule(mol, **mol_settings)
# This instantiation needs to be done here because of the errors
# in a structure are calculated lazily.
gjf = out.get_gjf()
names.append(mol)
gjfs.append(gjf)
except Exception as e:
logger.warn("Failed gjf write -- %s -- %s" % (mol, e))
results["failed"].append((mol, str(e)))
continue
if names:
settings = {
k: v for k, v in job_settings.items() + mol_settings.items()}
temp = run_jobs(credential, names, gjfs, **settings)
results["worked"] = temp["worked"]
results["failed"].extend(temp["failed"])
results["error"] = temp["error"]
return results