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 _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 _getTableData(self,request,uri):
try:
uris = request.GET.getlist("uris")
# page = int(request.POST['page'])
# rows_per_page = int(request.POST['rp'])
# sortname = request.POST['sortname']
# sortorder = request.POST['sortorder']
except:
return http.HttpResponseBadRequest()
json_response = {}
json_response["rows"] = []
for uri in uris:
resclass = ordfm.classByUri(graphstore.graph(),uri)
resource = resclass.get(graphstore.graph(),uri)
storage = filestorage.ResourceStorage(resource, web_accessible=True, settings=settings.filestorage_settings)
iconstorage = filestorage.ResourceIcon(resource, settings=settings.filestorage_settings)
row = {}
row["icon"] = iconstorage.url(filestorage.ResourceIcon.STATIC)
row["animatedicon"] = iconstorage.url(filestorage.ResourceIcon.ANIMATED)
row["uri"] = uri
row["url"] = utils.resourceUrl(resource)
row["type"] = resclass.visibleName()
json_response["rows"].append(row)
# if page < 0:
# return http.HttpResponseBadRequest("Invalid page number")
#
# graph = graphstore.graph()
# c = ordfm.Collection.get(graph, uri)
#
# json_response = { "page": page,
# "total": len(c.contents()),
# "rows" : []
# }
#
# for m_uri in c.contents().values()[(page-1)*rows_per_page:(page-1)*rows_per_page+rows_per_page]:
# m = ordfm.Molecule.get(graph, m_uri)
# json_response["rows"].append( { "cell" : [ "<span style=\"font-family: Courier\"><a href=\"/molecules/{"+utils.uriToUuid(m_uri)+"}\">"+utils.uriToUuid(m_uri)+"</a></span>", "", m.formula(), str(m.structureType()), str(m.energy()) ] } )
return http.HttpResponse(simplejson.dumps(json_response), mimetype='application/javascript')
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
print str(__file__) + " : Unable to convert to uri " + str(
resource_uuid) + " " + e.message
raise http.Http404()
graph = graphstore.graph()
try:
thing = grrm2.Thing.get(graph, resource_uri)
except:
log.info(str(__file__) + " : not found " + str(resource_uri))
raise http.Http404
if not thing:
log.info(str(__file__) + " : not found " + str(resource_uri))
raise http.Http404
iconstorage = filestorage.ResourceIcon(
thing, 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
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):