def dispatch(self, request, **args):
current_uri = args["uri"]
graph = graphstore.graph()
try:
iconv = grrm2.Interconversion.get(graph, current_uri)
except:
return None
ctx = {}
ctx["steps"] = []
ctx["start"] = ResultInfo()
ctx["end"] = ResultInfo()
start = grrm2.interconversionStart(iconv).get()[0]
ctx["start"].uri = start.uri()
ctx["start"].link = "/resources/%7B" + utils.uriToUuid(
start.uri()) + "%7D"
iconstorage = filestorage.ResourceIcon(
start, settings=settings.filestorage_settings)
ctx["start"].icon = iconstorage.url(filestorage.ResourceIcon.STATIC)
ctx["start"].energy = grrm2.energy(start).get()
ctx["start"].label = _getLabel(start)
end = grrm2.interconversionEnd(iconv).get()[0]
ctx["end"].uri = end.uri()
ctx["end"].link = "/resources/%7B" + utils.uriToUuid(end.uri()) + "%7D"
iconstorage = filestorage.ResourceIcon(
end, settings=settings.filestorage_settings)
ctx["end"].icon = iconstorage.url(filestorage.ResourceIcon.STATIC)
ctx["end"].energy = grrm2.energy(end).get()
ctx["end"].label = _getLabel(end)
for s in grrm2.interconversionStep(iconv).getAll():
step = s[0]
iconstorage = filestorage.ResourceIcon(
step, settings=settings.filestorage_settings)
info = StepInfo()
info.link = "/resources/%7B" + utils.uriToUuid(step.uri()) + "%7D"
info.icon = iconstorage.url(filestorage.ResourceIcon.STATIC)
info.uri = step.uri()
info.energy = grrm2.energy(step).get()
info.number = grrm2.stepNumber(step).get()
ctx["steps"].append(info)
def cmpFunc(x, y):
return cmp(x.number, y.number)
ctx["steps"] = sorted(ctx["steps"], cmp=cmpFunc)
return ctx
def dispatch(self, request, **args):
current_uri = args["uri"]
graph = graphstore.graph()
try:
route = grrm2.Interconversion.get(graph, current_uri)
except:
return None
start = grrm2.interconversionStart(route).get()[0]
end = grrm2.interconversionEnd(route).get()[0]
iconstorage_start = filestorage.ResourceIcon(start, settings=settings.filestorage_settings)
iconstorage_end = filestorage.ResourceIcon(end, settings=settings.filestorage_settings)
iconstorage_route = filestorage.ResourceIcon(route, settings=settings.filestorage_settings)
ctx = {}
ctx["startUrl"] = "/resources/%7B"+utils.uriToUuid(start.uri())+"%7D"
ctx["endUrl"] = "/resources/%7B"+utils.uriToUuid(end.uri())+"%7D"
ctx["startIcon"] = iconstorage_start.url(filestorage.ResourceIcon.STATIC)
ctx["endIcon"] = iconstorage_end.url(filestorage.ResourceIcon.STATIC)
ctx["connectionRouteIcon"] = iconstorage_route.url(filestorage.ResourceIcon.ANIMATED)
ctx["startStructureLabel"] = _getLabel(start)
ctx["endStructureLabel"] = _getLabel(end)
energies = {}
for step in grrm2.interconversionStep(route).getAll():
step = step[0]
energies[grrm2.stepNumber(step).get()] = grrm2.energy(step).get()
energies[0] = grrm2.energy(start).get()
energies[max(energies.keys())+1] = grrm2.energy(end).get()
chart_query = http.QueryDict("").copy()
chart_query.update( {
"cht": "lxy",
"chs": "400x400",
"chd": "t:"+",".join([ str(x) for x in energies.keys()])+"|"+",".join( [str(x) for x in energies.values()]),
"chds": str(min(energies.keys()))+","+str(max(energies.keys()))+","+str(min(energies.values()))+","+str(max(energies.values())),
"chco": "3072F3,ff0000,00aaaa",
"chls": "2,4,1",
"chf": "bg,s,F0F0FF",
"chm": "s,FF0000,0,-1,5|s,0000ff,1,-1,5|s,00aa00,2,-1,5",
"chxt": "x,y",
"chxr": "0,"+str(min(energies.keys()))+","+str(max(energies.keys()))+"|1,"+str(min(energies.values()))+","+str(max(energies.values())),
} )
ctx["chartUrl"] = "http://chart.apis.google.com/chart?"+chart_query.urlencode()
return ctx
def _getMoleculeInfo(self, molecule):
info = MoleculeInfo()
info.icon = filestorage.ResourceIcon(
molecule, settings=settings.filestorage_settings).url(
filestorage.ResourceIcon.STATIC)
info.link = "/resources/%7B" + utils.uriToUuid(molecule.uri()) + "%7D"
info.structureLabel = "Unknown"
info.isInterconversionStep = False
interconversion_step = grrm2.InterconversionStep.tryCast(molecule)
icresult = grrm2.InterconversionResult.tryCast(molecule)
if interconversion_step:
info.isInterconversionStep = True
info.structureLabel = "IC - step " + str(
grrm2.stepNumber(interconversion_step).get())
elif icresult:
struct_number = grrm2.structureNumber(icresult).get()
if grrm2.EquilibriumStructure.tryCast(icresult):
struct_type = "EQ"
elif grrm2.TransitionState.tryCast(icresult):
struct_type = "TS"
elif grrm2.BarrierlessDissociated.tryCast(icresult):
struct_type = "DDC"
elif grrm2.BarrierDissociated.tryCast(icresult):
struct_type = "UDC"
info.structureLabel = struct_type + str(struct_number)
return info
def dispatch(self, request, **args):
graph = graphstore.graph()
try:
run = grrm2.Run.get(graph, args["uri"])
except:
return None
return { "resource_uuid" : utils.uriToUuid(run.uri())}
def _getFromRoutesContext(self, molecule):
icres = grrm2.InterconversionResult.tryCast(molecule)
context = []
iconvs = grrm2.interconversionEndOf(icres).getAll()
if iconvs is None:
return context
for iconv in iconvs:
iconv = iconv[0]
start = grrm2.interconversionStart(iconv).get()[0]
route_info = RouteInfo()
route_info.link = "/resources/%7B" + utils.uriToUuid(
iconv.uri()) + "%7D"
route_info.targetLink = "/resources/%7B" + utils.uriToUuid(
start.uri()) + "%7D"
route_info.targetIcon = filestorage.ResourceIcon(
start, settings=settings.filestorage_settings).url(
filestorage.ResourceIcon.STATIC)
struct_number = grrm2.structureNumber(start).get()
if grrm2.EquilibriumStructure.tryCast(start):
struct_type = "EQ"
elif grrm2.TransitionState.tryCast(start):
struct_type = "TS"
elif grrm2.BarrierlessDissociated.tryCast(start):
struct_type = "DDC"
elif grrm2.BarrierDissociated.tryCast(start):
struct_type = "UDC"
route_info.targetStructureLabel = struct_type + str(struct_number)
route_info.targetEnergy = grrm2.energy(start).get()
route_info.energyDifference = grrm2.energy(
start).get() - grrm2.energy(molecule).get()
route_info.icon = filestorage.ResourceIcon(
iconv, settings=settings.filestorage_settings).url(
filestorage.ResourceIcon.ANIMATED)
context.append(route_info)
return context
def foo():
end = grrm2.interconversionEnd(route).get()[0]
iconstorage_start = filestorage.ResourceIcon(
start, settings=settings.filestorage_settings)
iconstorage_end = filestorage.ResourceIcon(
end, settings=settings.filestorage_settings)
iconstorage_route = filestorage.ResourceIcon(
route, settings=settings.filestorage_settings)
ctx = {}
ctx["startUrl"] = "/resources/%7B" + utils.uriToUuid(start.uri()) + "%7D"
ctx["endUrl"] = "/resources/%7B" + utils.uriToUuid(end.uri()) + "%7D"
ctx["startIcon"] = iconstorage_start.url(filestorage.ResourceIcon.STATIC)
ctx["endIcon"] = iconstorage_end.url(filestorage.ResourceIcon.STATIC)
ctx["connectionRouteIcon"] = iconstorage_route.url(
filestorage.ResourceIcon.ANIMATED)
ctx["startStructureLabel"] = _getLabel(start)
ctx["endStructureLabel"] = _getLabel(end)
def dispatch(self, request, **args):
graph = graphstore.graph()
try:
run = grrm2.Run.get(graph, args["uri"])
except:
return None
storage = filestorage.ResourceStorage(
run, web_accessible=True, settings=settings.filestorage_settings)
return {
"connectivityUrl":
settings.HOST_BASE + storage.url("connectivity", "csv"),
"resource_uuid":
utils.uriToUuid(run.uri())
}
def dispatch(self, request, **args):
graph = graphstore.graph()
try:
run = grrm2.Run.get(graph, args["uri"])
except:
return None
return_dict = { "input" : [],
"output": [],
}
for input_tuple in grrm2.runInput(run).getAll():
resource = input_tuple[0]
input = {}
return_dict["input"].append(input)
input["uuid"] = utils.uriToUuid(resource.uri())
input["data"] = {}
run_data = grrm2.RunData.tryCast(resource)
if run_data:
input["data"]["Type"] = "RunData"
input["data"]["Basis set"] = grrm2.basisSet(run_data).get()
input["data"]["Method"] = grrm2.method(run_data).get()
input["data"]["Job"] = grrm2.job(run_data).get()
continue
molecule= grrm2.Molecule.tryCast(resource)
if molecule:
input["url"] = "/resources/%7B"+input["uuid"]+"%7D"
input["data"]["Type"] = "Molecule"
input["data"]["Hill Formula"] = grrm2.hillFormula(molecule).get()
input["data"]["Mass"] = grrm2.mass(molecule).get()
input["data"]["SMILES"] = grrm2.smiles(molecule).get()
input["data"]["InChi"] = grrm2.inchi(molecule).get()
input["data"]["Spin Multiplicity"] = grrm2.spinMultiplicity(molecule).get()
continue
input["data"]["Type"] = "Unknown"
return return_dict
def dispatch(self, request, uri):
context = {}
graph = graphstore.graph()
try:
molecule = grrm2.Molecule.get(graph, uri)
except:
return None
context["moleculeInfo"] = []
context["moleculeInfo"].append(
("Formula", grrm2.hillFormula(molecule).get(), None))
context["moleculeInfo"].append(
("Molecular Mass", grrm2.mass(molecule).get(), None))
context["moleculeInfo"].append(
("InChi", grrm2.inchi(molecule).get(), None))
context["moleculeInfo"].append(
("SMILES", grrm2.smiles(molecule).get(), None))
context["moleculeInfo"].append(
("Energy", grrm2.energy(molecule).get(), None))
context["moleculeInfo"].append(
("Charge", grrm2.charge(molecule).get(), None))
context["moleculeInfo"].append(
("Spin", grrm2.spin(molecule).get(), None))
context["moleculeInfo"].append(
("Structure Type", _getStructureType(molecule), None))
result = grrm2.InterconversionResult.tryCast(molecule)
if result:
context["moleculeInfo"].append(
("Structure Number", grrm2.structureNumber(result).get(),
None))
context["moleculeInfo"].append(
("Zero Point Vibrational Energy",
grrm2.zeroPointVibrationalEnergy(result).get(), None))
step = grrm2.InterconversionStep.tryCast(molecule)
if step:
context["moleculeInfo"].append(
("Interconversion Step", grrm2.stepNumber(step).get(), None))
context["moleculeInfo"].append(
("Belongs to interconversion",
grrm2.interconversionStepOf(step).get()[0].uri(),
"/resources/%7B" + utils.uriToUuid(
grrm2.interconversionStepOf(step).get()[0].uri()) +
"%7D"))
context["moleculeInfo"].append(
("CANOST canonical planar",
grrm2.canostSerialCanonical(molecule).get(), None))
context["moleculeInfo"].append(
("CANOST canonical serial",
grrm2.canostPlanarCanonical(molecule).get(), None))
context["moleculeInfo"].append(
("CANOST planar codes", grrm2.canostPlanar(molecule).get(), None))
context["moleculeInfo"].append(
("CANOST serial codes", grrm2.canostSerial(molecule).get(), None))
fragment_strings = []
if grrm2.fragments(molecule).get() is not None:
geometry = grrm2.geometry(molecule).get()
for fragment in grrm2.fragments(molecule).get():
symbols = [geometry["symbols"][i - 1] for i in fragment]
fragment_strings.append(chemistry.hillFormula(symbols))
context["moleculeInfo"].append(
("Fragments", "/".join(fragment_strings), None))
try:
run = grrm2.runOutputOf(molecule).get()[0]
context["moleculeInfo"].append(
("Run", run.uri(),
"/resources/%7B" + utils.uriToUuid(run.uri()) + "%7D"))
except Exception, e:
pass
def uriToUrl(value):
return "/resources/%7B" + utils.uriToUuid(value) + "%7D"
def dispatch(self, request, **args):
current_uri = args["uri"]
graph = graphstore.graph()
try:
transition_state = grrm2.TransitionState.get(graph, current_uri)
except:
return None
ctx = {}
iconv_start_tuple_list = grrm2.interconversionStartOf(
transition_state).getAll() or []
iconv_end_tuple_list = grrm2.interconversionEndOf(
transition_state).getAll() or []
if len(iconv_start_tuple_list) + len(iconv_end_tuple_list) != 2:
return None # we have a problem... a transition state must have two links
if len(iconv_start_tuple_list) == 2:
iconv_left = iconv_start_tuple_list[0][0]
iconv_right = iconv_start_tuple_list[1][0]
energies_left = _getEnergies(iconv_left)
energies_right = _getEnergies(iconv_right)
energies = {}
energies[0] = grrm2.energy(transition_state).get()
for k, v in sorted(map(lambda x:
(-x[0], x[1]), energies_left.items()) +
energies_right.items(),
key=lambda x: x[0]):
print k
energies[k] = v
end_left = grrm2.interconversionEnd(iconv_left).get()[0]
end_right = grrm2.interconversionEnd(iconv_right).get()[0]
energies[min(energies.keys()) - 1] = grrm2.energy(end_left).get()
energies[max(energies.keys()) + 1] = grrm2.energy(end_right).get()
else:
return None
chart_query = http.QueryDict("").copy()
chart_query.update({
"cht":
"lxy",
"chs":
"400x400",
"chd":
"t:" + ",".join([
str(x[0]) for x in sorted(energies.items(), key=lambda x: x[0])
]) + "|" + ",".join([
str(x[1]) for x in sorted(energies.items(), key=lambda x: x[0])
]),
"chds":
str(min(energies.keys())) + "," + str(max(energies.keys())) + "," +
str(min(energies.values())) + "," + str(max(energies.values())),
"chco":
"3072F3,ff0000,00aaaa",
"chls":
"2,4,1",
"chf":
"bg,s,F0F0FF",
"chm":
"s,FF0000,0,-1,5|s,0000ff,1,-1,5|s,00aa00,2,-1,5",
"chxt":
"x,y",
"chxr":
"0," + str(min(energies.keys())) + "," +
str(max(energies.keys())) + "|1," + str(min(energies.values())) +
"," + str(max(energies.values())),
})
ctx["chartUrl"] = "http://chart.apis.google.com/chart?" + chart_query.urlencode(
)
iconstorage = filestorage.ResourceIcon(
transition_state, settings=settings.filestorage_settings)
if iconstorage.readable(filestorage.ResourceIcon.STATIC):
icon_url = iconstorage.url(filestorage.ResourceIcon.STATIC)
elif iconstorage.readable(filestorage.ResourceIcon.ANIMATED):
icon_url = iconstorage.url(filestorage.ResourceIcon.ANIMATED)
else:
icon_url = None
ctx["transitionStateIcon"] = icon_url
iconstorage = filestorage.ResourceIcon(
end_left, settings=settings.filestorage_settings)
if iconstorage.readable(filestorage.ResourceIcon.STATIC):
icon_url = iconstorage.url(filestorage.ResourceIcon.STATIC)
elif iconstorage.readable(filestorage.ResourceIcon.ANIMATED):
icon_url = iconstorage.url(filestorage.ResourceIcon.ANIMATED)
else:
icon_url = None
ctx["leftEndIcon"] = icon_url
iconstorage = filestorage.ResourceIcon(
end_right, settings=settings.filestorage_settings)
if iconstorage.readable(filestorage.ResourceIcon.STATIC):
icon_url = iconstorage.url(filestorage.ResourceIcon.STATIC)
elif iconstorage.readable(filestorage.ResourceIcon.ANIMATED):
icon_url = iconstorage.url(filestorage.ResourceIcon.ANIMATED)
else:
icon_url = None
ctx["rightEndIcon"] = icon_url
ctx["leftEndUrl"] = "/resources/%7B" + utils.uriToUuid(
end_left.uri()) + "%7D"
ctx["rightEndUrl"] = "/resources/%7B" + utils.uriToUuid(
end_right.uri()) + "%7D"
return ctx
return struct_type+str(struct_number)
options=Options(sys.argv)
graph = Graph(graphstore.store(), identifier=rdflib.URIRef("urn:uuid:"+str(options.submission_uuid)))
runs = list(grrm2.Run.all(graph))
if len(runs) != 1:
raise Exception("Run length != 1")
storage = filestorage.ResourceStorage(runs[0], web_accessible=True, settings=settings.filestorage_settings)
print "writing file : "+storage.path("connectivity","csv")
f=file(storage.path("connectivity","csv"),"w")
for icresult in grrm2.InterconversionResult.all(graph):
label=_getLabel(icresult)
f.write("v,"+label+","+utils.uriToUuid(icresult.uri())+"\n")
for iconv in grrm2.Interconversion.all(graph):
start = grrm2.interconversionStart(iconv).get()[0]
if grrm2.interconversionStart(iconv).get() is not None:
start = grrm2.interconversionStart(iconv).get()[0]
else:
continue
if grrm2.interconversionEnd(iconv).get() is not None:
end = grrm2.interconversionEnd(iconv).get()[0]
else:
continue
start_energy = grrm2.energy(start).get()
"type"] == "ajax" and request.GET.get("receiver_plugin"):
for p in registry.allPlugins():
if p.ajaxHandlerGet() is not None and p.name() == request.GET.get(
"receiver_plugin"):
response = p.ajaxHandlerGet().dispatch(request,
uri=resource_uri)
if response is not None:
return response
else:
raise http.Http404
raise http.Http404
ctx = {}
ctx["base"] = basecontext.context()
ctx["resource"] = {}
ctx["resource"]["uuid"] = utils.uriToUuid(resource_uri)
ctx["resource"]["uri"] = resource_uri
ctx["plugins"] = []
ctx["pluginContext"] = {}
for p in registry.allPlugins():
try:
plugin_ctx = p.requestHandler().dispatch(request, uri=resource_uri)
except Exception, e:
log.warning(
str(__file__) + " : Plugin " + p.name() +
" raised exception : " + e.message + " : " +
str(traceback.print_tb(sys.exc_traceback)))
plugin_ctx = None
if plugin_ctx is not None:
ctx["plugins"].append(p)
else:
icon_url = None
resource_type = None
if grrm2.Run.tryCast(thing):
resource_type = "Run"
elif grrm2.TransitionState.tryCast(thing):
resource_type = "TransitionState"
elif grrm2.EquilibriumStructure.tryCast(thing):
resource_type = "EquilibriumStructure"
elif grrm2.BarrierDissociated.tryCast(thing):
resource_type = "BarrierDissociated"
elif grrm2.BarrierlessDissociated.tryCast(thing):
resource_type = "BarrierlessDissociated"
elif grrm2.InterconversionStep.tryCast(thing):
resource_type = "InterconversionStep"
elif grrm2.Interconversion.tryCast(thing):
resource_type = "Interconversion"
elif grrm2.RunInput.tryCast(thing):
resource_type = "RunInput"
else:
resource_type = "Thing"
return render_to_response(
'application/searchsnippets.html', {
"base": basecontext.context(),
"resource_uuid": utils.uriToUuid(resource_uri),
"resource_type": resource_type,
"icon_url": icon_url
})
