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 })