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 molecule_detail(request, molecule):
job_form = JobForm.get_form(request, molecule)
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, molecule, 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")
a = get_molecule_info_status(molecule)
a["job_form"] = job_form
a["mol_form"] = MoleculeForm()
return render(request, "chem/molecule_detail.html", a)
def molecule_detail(request, molecule):
job_form = JobForm.get_form(request, molecule)
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, molecule, 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")
a = get_molecule_info_status(molecule)
a["job_form"] = job_form
a["mol_form"] = MoleculeForm()
return render(request, "chem/molecule_detail.html", a)
def upload_data(request):
switch = {
"logparse": parse_log,
"longchain": long_chain_limit,
"gjfreset": reset_gjf,
"structureview": view_structure,
}
if request.method == "POST":
upload_form = UploadForm(request.POST or None, files=request.FILES)
if upload_form.is_valid():
return switch[request.POST["options"]](request, upload_form)
else:
upload_form = UploadForm()
c = {
"upload_form": upload_form,
"job_form": JobForm.get_form(request, "{{ name }}", initial=True),
}
return render(request, "chem/upload_log.html", c)
def upload_data(request):
switch = {
"logparse": parse_log,
"longchain": long_chain_limit,
"gjfreset": reset_gjf,
"structureview": view_structure,
"percent": get_percent,
}
if request.method == "POST":
upload_form = UploadForm(request.POST or None, files=request.FILES)
if upload_form.is_valid():
return switch[request.POST["options"]](request, upload_form)
else:
upload_form = UploadForm()
c = {
"upload_form": upload_form,
"job_form": JobForm.get_form(request, "{{ name }}", initial=True),
}
return render(request, "chem/upload_log.html", c)
def multi_job(request):
form = JobForm.get_form(request, "{{ name }}")
c = {
"form": form,
}
if not form.is_valid(request.method):
if request.is_ajax():
job_form_html = render_crispy_form(
form, context=RequestContext(request))
a = {
"success": False,
"job_form_html": job_form_html,
"mol_form_html": '',
}
return HttpResponse(json.dumps(a),
content_type="application/json")
return render(request, "chem/multi_job.html", c)
d = dict(form.cleaned_data)
if request.method == "POST":
cred = d.pop("credential")
files = request.FILES.getlist("files")
strings = [''.join(f.readlines()) for f in files]
names = [os.path.splitext(f.name)[0] for f in files]
a = cluster.interface.run_jobs(cred, names, strings, **d)
do_html = request.REQUEST.get("html", False)
if do_html:
html = render_to_string("chem/multi_submit.html", a)
temp = {"success": True, "html": html}
return HttpResponse(json.dumps(temp),
content_type="application/json")
else:
return HttpResponse(json.dumps(a),
content_type="application/json")
string = request.REQUEST.get('filenames', '').replace('\r\n', ',').replace('\n', ',')
ret_zip = get_multi_job(string, form)
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=output.zip"
return response
def multi_molecule_zip(request, string):
try:
autoflip = request.REQUEST.get("autoflip")
molecules, warnings, errors, news = get_multi_molecule_status(
string, autoflip=autoflip)
except ValueError as e:
logger.warn(str(e))
c = {
"error": str(e)
}
return render(request, "chem/multi_molecule.html", c)
mol_form = MoleculeForm(request.REQUEST)
mol_form.is_valid()
if request.REQUEST.get("job"):
job_form = JobForm.get_form(request, "{{ name }}")
if not job_form.is_valid():
f = lambda x: 'checked' if request.REQUEST.get(x) else ''
c = {
"pagename": string,
"job_form": job_form,
"mol_form": mol_form,
"gjf": f("gjf"),
"mol2": f("mol2"),
"image": f("image"),
"job": f("job"),
}
return render(request, "chem/multi_molecule.html", c)
else:
job_form = None
selection = ("image", "mol2", "job", "gjf")
options = [x for x in selection if request.REQUEST.get(x)]
if request.REQUEST.get("new", ''):
molecules = [x for i, x in enumerate(molecules) if news[i]]
ret_zip = get_multi_molecule(molecules, options, mol_form, job_form)
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=molecules.zip"
return response
def multi_job(request):
form = JobForm.get_form(request, "{{ name }}")
c = {
"form": form,
}
if not form.is_valid(request.method):
if request.is_ajax():
job_form_html = render_crispy_form(form,
context=RequestContext(request))
a = {
"success": False,
"job_form_html": job_form_html,
"mol_form_html": '',
}
return HttpResponse(json.dumps(a), content_type="application/json")
return render(request, "chem/multi_job.html", c)
d = dict(form.cleaned_data)
if request.method == "POST":
cred = d.pop("credential")
files = request.FILES.getlist("files")
strings = [''.join(f.readlines()) for f in files]
names = [os.path.splitext(f.name)[0] for f in files]
a = cluster.interface.run_jobs(cred, names, strings, **d)
do_html = request.REQUEST.get("html", False)
if do_html:
html = render_to_string("chem/multi_submit.html", a)
temp = {"success": True, "html": html}
return HttpResponse(json.dumps(temp),
content_type="application/json")
else:
return HttpResponse(json.dumps(a), content_type="application/json")
string = request.REQUEST.get('filenames',
'').replace('\r\n', ',').replace('\n', ',')
ret_zip = get_multi_job(string, form)
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=output.zip"
return response
def multi_molecule_zip(request, string):
try:
autoflip = request.REQUEST.get("autoflip")
molecules, warnings, errors, news = get_multi_molecule_status(
string, autoflip=autoflip)
except ValueError as e:
logger.warn(str(e))
c = {"error": str(e)}
return render(request, "chem/multi_molecule.html", c)
mol_form = MoleculeForm(request.REQUEST)
mol_form.is_valid()
if request.REQUEST.get("job"):
job_form = JobForm.get_form(request, "{{ name }}")
if not job_form.is_valid():
f = lambda x: 'checked' if request.REQUEST.get(x) else ''
c = {
"pagename": string,
"job_form": job_form,
"mol_form": mol_form,
"gjf": f("gjf"),
"mol2": f("mol2"),
"image": f("image"),
"job": f("job"),
}
return render(request, "chem/multi_molecule.html", c)
else:
job_form = None
selection = ("image", "mol2", "job", "gjf")
options = [x for x in selection if request.REQUEST.get(x)]
if request.REQUEST.get("new", ''):
molecules = [x for i, x in enumerate(molecules) if news[i]]
ret_zip = get_multi_molecule(molecules, options, mol_form, job_form)
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=molecules.zip"
return response
def reset_gjf(request, upload_form):
job_form = JobForm.get_form(request, "{{ name }}")
errors = []
strings = []
names = []
for f in upload_form.cleaned_data["files"]:
try:
parser = fileparser.Log(f)
name, _ = os.path.splitext(f.name)
td = False
if request.REQUEST.get("td_reset"):
name += '_TD'
td = True
strings.append(parser.format_gjf(td=td))
names.append(name)
except Exception as e:
logger.warn("There was an error when trying to reset a gjf: '%s'" % str(e))
errors.append((f.name, e))
if request.REQUEST.get("gjf_submit"):
if not job_form.is_valid(request.method):
if request.is_ajax():
upload_form_html = render_crispy_form(upload_form,
context=RequestContext(request))
job_form_html = render_crispy_form(job_form,
context=RequestContext(request))
a = {
"success": False,
"job_form_html": job_form_html,
"upload_form_html": upload_form_html,
}
return HttpResponse(json.dumps(a),
content_type="application/json")
c = {
"job_form": job_form,
"upload_form": upload_form,
}
return render(request, "chem/upload_log.html", c)
d = dict(job_form.cleaned_data)
cred = d.pop("credential")
a = cluster.interface.run_jobs(cred, names, strings, **d)
a["failed"].extend(errors)
do_html = request.REQUEST.get("html", False)
if do_html:
html = render_to_string("chem/multi_submit.html", a)
temp = {"success": True, "html": html}
return HttpResponse(json.dumps(temp),
content_type="application/json")
else:
return HttpResponse(json.dumps(a),
content_type="application/json")
buff = StringIO()
zfile = zipfile.ZipFile(buff, 'w', zipfile.ZIP_DEFLATED)
for name, string in zip(names, strings):
zfile.writestr("%s.gjf" % name, string)
if errors:
temp = ['%s - %s' % (name, error) for (name, error) in errors]
zfile.writestr("errors.txt", '\n'.join(temp))
zfile.close()
buff.flush()
ret_zip = buff.getvalue()
buff.close()
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=output.zip"
return response
def reset_gjf(request, upload_form):
job_form = JobForm.get_form(request, "{{ name }}")
errors = []
strings = []
names = []
for f in upload_form.cleaned_data["files"]:
try:
parser = fileparser.Log(f)
name, _ = os.path.splitext(f.name)
td = False
if request.REQUEST.get("td_reset"):
name += '_TD'
td = True
strings.append(parser.format_gjf(td=td))
names.append(name)
except Exception as e:
logger.warn("There was an error when trying to reset a gjf: '%s'" %
str(e))
errors.append((f.name, e))
if request.REQUEST.get("gjf_submit"):
if not job_form.is_valid(request.method):
if request.is_ajax():
upload_form_html = render_crispy_form(
upload_form, context=RequestContext(request))
job_form_html = render_crispy_form(
job_form, context=RequestContext(request))
a = {
"success": False,
"job_form_html": job_form_html,
"upload_form_html": upload_form_html,
}
return HttpResponse(json.dumps(a),
content_type="application/json")
c = {
"job_form": job_form,
"upload_form": upload_form,
}
return render(request, "chem/upload_log.html", c)
d = dict(job_form.cleaned_data)
cred = d.pop("credential")
a = cluster.interface.run_jobs(cred, names, strings, **d)
a["failed"].extend(errors)
do_html = request.REQUEST.get("html", False)
if do_html:
html = render_to_string("chem/multi_submit.html", a)
temp = {"success": True, "html": html}
return HttpResponse(json.dumps(temp),
content_type="application/json")
else:
return HttpResponse(json.dumps(a), content_type="application/json")
buff = StringIO()
zfile = zipfile.ZipFile(buff, 'w', zipfile.ZIP_DEFLATED)
for name, string in zip(names, strings):
zfile.writestr("%s.gjf" % name, string)
if errors:
temp = ['%s - %s' % (name, error) for (name, error) in errors]
zfile.writestr("errors.txt", '\n'.join(temp))
zfile.close()
buff.flush()
ret_zip = buff.getvalue()
buff.close()
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=output.zip"
return response