How to use _set_path method in autotest

Best Python code snippet using autotest_python

system_classes.py

Source:system_classes.py

1# -*- coding: utf-8 -*-2"""3Created on Fri Feb 12 18:56:07 20214@author: ilros5"""6import json7import copy8class GET_manager(object):9    def __init__(self, path):10        self.path=path11        12    def run(self):13        if self.path[0]=='sensors':14            _set_path="settings.json"15            with open(_set_path) as json_file:16                data=json.load(json_file)17            18            if self.path[1]=='house':19                #we need to send the basic setup for the sensors of the house20                resp = {21                    "broker" : data["broker"],22                    "port" : data["port"],23                    "temperature" : data["meanAndVarSensorsHouse"]["temperature"],24                    "humidity" : data["meanAndVarSensorsHouse"]["humidity"],25                    "lumen" : data["meanAndVarSensorsHouse"]["lumen"]26                    }27                28                return json.dumps(resp)29                30                31            elif self.path[1]=='house_list':32                resp = []33                34                if data["patientsList"]!=[]:35                    for patient in data["patientsList"]:36                        resp.append(patient["houseDevices"])37                    38                    return json.dumps(resp)39                #we need to get all the sensors from all the houses, publish on house-based topics40                41            elif self.path[1]=='bodydevices_list':42                resp = []43                44                if data["patientsList"]!=[]:45                    for patient in data["patientsList"]:46                        resp.append(patient["bodyDevices"])47                    48                    return json.dumps(resp)49                #we need to get all the sensors from all the houses, publish on house-based topics50                51            elif self.path[1]=='sim_values':52                53                resp = {}54                uniqueID = self.path[2]55                56                if data["patientsList"] != []:57                    for patient in data["patientsList"]:58                        if patient["uniqueID"] == uniqueID:59                            resp = patient["bodySensorsSimulation"]60                61                return json.dumps(resp)62            63            64            elif self.path[1]=='patient':65                66                resp = {67                    "broker" : data["broker"],68                    "port" : data["port"],69                    }70                71                return json.dumps(resp)72            73        elif self.path[0]=='thingspeak':74            _set_path="settings.json"75            with open(_set_path) as json_file:76                data=json.load(json_file)77            if self.path[1]=='settings':78                resp = {79                    "broker" : data["broker"],80                    "port" : data["port"],81                    "url" : data["thinkspeakSettings"]["tsURL"],82                    "key" : data["thinkspeakSettings"]["tsKEY"],83                    "clearURL" : data["thinkspeakSettings"]["tsCLEARURL"],84                    "field" : data["thinkspeakSettings"]["tsFields"]85                }86                return json.dumps(resp)87            if self.path[1]=='highlightedPatient':88                _set_path="settings.json"89                with open(_set_path) as json_file:90                    data=json.load(json_file)91            92                resp = data["highlightedPatient"]93                94                return json.dumps(resp)95            elif self.path[1]=="highlighted":96                resp = ""97                uniqueID = self.path[2]98                99                if data["patientsList"] != []:100                    for patient in data["patientsList"]:101                        if patient["uniqueID"] == uniqueID:102                            resp = patient["bodyDevices"][0]["topic"]103                104                return json.dumps(resp)105        elif self.path[0] == 'telegram':106            _set_path="settings.json"107            with open(_set_path) as json_file:108                data=json.load(json_file)109                110                111                112            if self.path[1]=='settings':113                resp={114                    "TG_Token": data['TG_Token'],115                    "broker" : data['broker'],116                    "port" : data['port'],117                    "topic_commands" : data['telegramTopics']['t_bot_topic'],118                    "topic_alarms" : data['telegramTopics']['sim_bot_topic']119                }120                121                return json.dumps(resp)122            123            124            elif self.path[1] == 'get_pins':125                126                resp = {127                    "Patient": [],128                    "Doctor": [],129                    "Caretaker": []130                    }131                132                for patient in data["patientsList"]:133                    resp["Patient"].append({"uniqueID":patient["uniqueID"], "pin":patient["pin"]})134                    135                for doctor in data["doctorsList"]:136                    resp["Doctor"].append({"uniqueID":doctor["uniqueID"], "pin":doctor["pin"]})137                138                for caretaker in data["caretakersList"]:139                    resp["Caretaker"].append({"uniqueID":caretaker["uniqueID"], "pin":caretaker["pin"]})140                    141                return json.dumps(resp)142            143            144            elif self.path[1]=="supported":145                resp = {146                    "actuators" : {},147                    "sensors" : {}148                    }149                150                resp["actuators"] = data["supportedActuators"]151                resp["sensors"] = data["supportedSensors"]152                153                return json.dumps(resp)154            elif self.path[1]=="alarm_status":155                resp = []156                157                if data["patientsList"] != []:158                    resp = data["patientsList"]159                    160                    return json.dumps(resp)161                162            elif self.path[1]=='getVals':163                164                uniqueID = self.path[2]165                166                resp = {167                    "measUnit" : {},168                    "sensValues": {}169                    }170                171                resp["measUnit"] = data["correspondentUnits"]172                173                174                if data["patientsList"]!=[]:175                    for patient in data["patientsList"]:176                        if patient["uniqueID"] == uniqueID:177                            if patient["bodyDevices"] != []:178                                for sensor in patient["bodyDevices"]:179                                    resp["sensValues"].update({sensor["e"][0]["n"] : sensor["e"][0]["n"]})180                                    181                            if patient["houseDevices"] != []:182                                for sensor in patient["houseDevices"]:183                                    resp["sensValues"].update({sensor["e"][0]["n"] : sensor["e"][0]["n"]})184                                    185                            if patient["actuatorsList"] != []:186                                for actuator in patient["actuatorsList"]:187                                    resp["sensValues"].update({actuator["name"] : actuator["state"]})188                                    189                    return json.dumps(resp)190        elif self.path[0] == 'controls':191            _set_path="settings.json"192            with open(_set_path) as json_file:193                data=json.load(json_file)194                195            if self.path[1] == 'settings':196                197                resp = {198                    "broker" : data["broker"],199                    "port" : data["port"]200                    }201                202                return json.dumps(resp)203            204            elif self.path[1] == 'house_list':205                206                resp={207                    "houses" : []208                    }209                210                if data["patientsList"]!=[]:211                    for patient in data["patientsList"]:212                        resp["houses"].append({"houseDevices" : patient["houseDevices"], "actList" : patient["actuatorsList"]})213                        214                    215                return json.dumps(resp)216            217        else:218            return "Error 400 : The request cannot be fullfilled since the URL is wrong or it refers to something which does not exist"219    220class POST_manager():221    def __init__(self, path):222        self.path=path223        224    def run(self, data):225        if self.path[0]=='trained_modelsupdate':226            _set_path='data_comparison/trained_models.json'227            json.dump(data, open(_set_path,'w'), indent = 4)228                229        elif self.path[0] == 'regression_resultupdate':230            _set_path="settings.json"231            232            with open(_set_path) as json_in:233                sens_data=json.load(json_in)234            235            smt=dict(sens_data)236            smt["Regr_Values"]["Temp"] = data["Temp"]237            smt["Regr_Values"]["Weight"] = data["Weight"]238            smt["Regr_Values"]["HeartR"] = data["HeartR"]239            240            241            f = open(_set_path, 'w')242            json.dump(smt, f, indent = 4)243            f.close()244            245            246            247        elif self.path[0] == 'updateSens':248            _set_path="settings.json"   249            with open(_set_path) as json_in:250                all_data=json.load(json_in)251                252            if self.path[1] == 'body':253                254                uniqueID = self.path[2] 255                256                dev = data257                258                if all_data["patientsList"] != []:259                    for patient in all_data["patientsList"]:260                        if patient["uniqueID"] == uniqueID:261                            if patient["bodyDevices"] != []:262                                for sensor in patient["bodyDevices"]:263                                    if sensor["e"][0]["n"] == data["e"][0]["n"]:264                                        sensor["e"][0]["v"]=data["e"][0]["v"]265                                        266                    f = open(_set_path, 'w')267                    json.dump(all_data, f, indent = 4)268                    f.close()269            270                    271            elif self.path[1] == 'house':272                273                uniqueID = self.path[2] 274                275                dev = data276                277                if all_data["patientsList"] != []:278                    for patient in all_data["patientsList"]:279                        if patient["uniqueID"] == uniqueID:280                            if patient["houseDevices"] != []:281                                for sensor in patient["houseDevices"]:282                                    if sensor["e"][0]["n"] == data["e"][0]["n"]:283                                        sensor["e"][0]["v"]=data["e"][0]["v"]284                                        285                    f = open(_set_path, 'w')286                    json.dump(all_data, f, indent = 4)287                    f.close()288                289            elif self.path[1] == 'actuator':290                291                uniqueID = self.path[2] 292                293                dev = data294                295                if all_data["patientsList"] != []:296                    for patient in all_data["patientsList"]:297                        if patient["uniqueID"] == uniqueID:298                            if patient["actuatorsList"] != []:299                                for actuator in patient["actuatorsList"]:300                                    if actuator["name"] == data["name"]:301                                        actuator["state"] = data["state"]302                                        303                    f = open(_set_path, 'w')304                    json.dump(all_data, f, indent = 4)305                    f.close()306        307            308        elif self.path[0]=="telegram":309            _set_path="settings.json"   310            with open(_set_path) as json_in:311                all_data=json.load(json_in)312            if self.path[1]=="addPatient":313                found = False314                if all_data["patientsList"] != []:315                    for patient in all_data["patientsList"]:316                        if data["uniqueID"] == patient["uniqueID"]:317                            found = True318                    319                if not found:320                    newPatient = copy.deepcopy(all_data["basePatient"])321                    322                    newPatient["name"] = data["name"]323                    newPatient["age"] = data["age"]324                    newPatient["weight"] = data["weight"]325                    newPatient["uniqueID"] = data["uniqueID"]326                    newPatient["disease"] = data["disease"]327                    newPatient["bodySensorsSimulation"] = all_data["defaultSimValues"]328                    if all_data["highlightedPatient"] == "":329                        all_data["highlightedPatient"] = newPatient["uniqueID"]330                    331                    for sens in data["bodySensors"]:332                        sens = sens.lower()333                        newSensor = copy.deepcopy(all_data["baseSensor"])334                        tresh = {335                            sens+"Low" : data["thresholds"][sens+"Low"],336                            sens+"High" : data["thresholds"][sens+"High"]337                        }338                        newSensor["simThresholds"] = tresh339                        alarm = {340                            sens+"Low" : data["alarms"][sens+"Low"],341                            sens+"High" : data["alarms"][sens+"High"]342                        }343                        newSensor["alarmThresholds"] = alarm344                        newSensor["topic"] = all_data["baseTopic"] + "/" + newPatient["uniqueID"] + "/body"345                        newSensor["patientID"] = newPatient["uniqueID"]346                        newSensor["bn"] = newPatient["uniqueID"] + "/body/" + sens347                        newSensor["e"][0]["n"] = sens      348                        newSensor["e"][0]["u"] = all_data["supportedSensors"][sens]349                    350                        newPatient["bodyDevices"].append(newSensor)351                        newSensor = None352                        353                        354                    for sens in data["houseSensors"]:355                        sens = sens.lower()356                        newSensor = copy.deepcopy(all_data["baseSensor"])357                        358                        newSensor["topic"] = all_data["baseTopic"] + "/" + newPatient["uniqueID"] + "/house"359                        newSensor["patientID"] = newPatient["uniqueID"]360                        newSensor["bn"] = newPatient["uniqueID"] + "/house/" + sens361                        newSensor["e"][0]["n"] = sens      362                        newSensor["e"][0]["u"] = all_data["supportedSensors"][sens]363                        364                        newPatient["houseDevices"].append(newSensor)365                        newSensor = None366                        367                    for actuator in data["controlledActuators"]:368                        actuator = actuator.lower()369                        newActuator = copy.deepcopy(all_data["baseActuator"])370                        371                        newActuator["topic"] = all_data["baseTopic"] + "/" + newPatient["uniqueID"] + "/actuator"372                        newActuator["patientID"] = newPatient["uniqueID"]373                        newActuator["unit"] = all_data["supportedActuators"][actuator]374                        newActuator["name"] = actuator375                        newActuator["tresholds"].append(all_data["defaultActuatorValues"][actuator+"Low"]) 376                        newActuator["tresholds"].append(all_data["defaultActuatorValues"][actuator+"High"])377                        378                        newPatient["actuatorsList"].append(newActuator)379                        newActuator = None380                        381                    all_data["patientsList"].append(newPatient)382                    383                f = open(_set_path, 'w')384                json.dump(all_data, f, indent = 4)385                f.close()386                387            elif self.path[1]=="addDoctor":388                389                newDoctor = all_data["baseDoctor"].copy()390                found = False391                392                if all_data["doctorsList"] != []:393                    for doctor in all_data["doctorsList"]:394                        if doctor["uniqueID"] == data["uniqueID"]:395                            found = True396                397                if not found:398                    newDoctor["age"] = data["age"]399                    newDoctor["name"] = data["name"]400                    newDoctor["patientsAssigned"] = data["patientsAssigned"]401                    newDoctor["uniqueID"] = data["uniqueID"]402                    403                    all_data["doctorsList"].append(newDoctor)404                f = open(_set_path, 'w')405                json.dump(all_data, f, indent = 4)406                f.close()407                408            elif self.path[1]=="addCaretaker":409                410                newCaretaker = all_data["baseCaretaker"].copy()411                found = False412                413                if all_data["caretakersList"] != []:414                    for caretaker in all_data["caretakersList"]:415                        if caretaker["uniqueID"] == data["uniqueID"]:416                            found = True417                418                if not found:419                420                    newCaretaker["age"] = data["age"]421                    newCaretaker["name"] = data["name"]422                    newCaretaker["patientAssigned"] = data["patientAssigned"]423                    newCaretaker["uniqueID"] = data["uniqueID"]424                    425                    all_data["caretakersList"].append(newCaretaker)426                    427                f = open(_set_path, 'w')428                json.dump(all_data, f, indent = 4)429                f.close()430                431                432                    433                434class PUT_manager():435    def __init__(self, path):436        self.path=path437        438    def run(self, data):439        _set_path = "settings.json"440        with open(_set_path) as json_in:441            all_data=json.load(json_in)442            443        if self.path[0] == "telegram":444            if self.path[1] == "updateAddress":445                if all_data["patientsList"] != []:446                    for patient in all_data["patientsList"]:447                        if patient["uniqueID"] == data["uniqueID"]:448                            patient["address"] = data["address"]449                            450                    f = open(_set_path, 'w')451                    json.dump(all_data, f, indent = 4)452                    f.close()453                454            elif self.path[1] == "updateActuator":455                if all_data["patientsList"] != []:456                    for patient in all_data["patientsList"]:457                        if patient["uniqueID"] == data["uniqueID"]:458                            actList = patient["actuatorsList"]459                            for actuator in actList:460                                if actuator["name"] == data["actName"]:461                                    actuator["tresholds"][0]=data["actLow"]462                                    actuator["tresholds"][1]=data["actHigh"]463                                    464                    f = open(_set_path, 'w')465                    json.dump(all_data, f, indent = 4)466                    f.close()467            elif self.path[1] == "updateAlarms":468                if all_data["patientsList"] != []:469                    for patient in all_data["patientsList"]:470                        if patient["uniqueID"] == data["uniqueID"]:471                            sensorList = patient["bodyDevices"]472                            for alarm in sensorList:473                                if alarm["e"][0]["n"] == data["sensorName"]:474                                    alarm["alarmThresholds"][alarm["e"][0]["n"]+"Low"]=data["alarmLow"]475                                    alarm["alarmThresholds"][alarm["e"][0]["n"]+"High"]=data["alarmHigh"]476                                    477                    f = open(_set_path, 'w')478                    json.dump(all_data, f, indent = 4)479                    f.close()480            elif self.path[1] == "updateSimulation":481                if all_data["patientsList"] != []:482                    for patient in all_data["patientsList"]:483                        if patient["uniqueID"] == data["uniqueID"]:484                            simsList = patient["bodySensorsSimulation"]485                            for simulation in simsList:486                                if simulation["sensorName"] == data["sensorName"]:487                                    simulation["typeSim"] = data["typeSim"]488                                    simulation["statusSim"] = data["statusSim"]489                                    490                    f = open(_set_path, 'w')491                    json.dump(all_data, f, indent = 4)492                    f.close()     493            elif self.path[1] == "registerPatient":494                if all_data["patientsList"] != []:495                    for patient in all_data["patientsList"]:496                        if patient["uniqueID"] == data["userName"]:497                            patient["pin"] = data["pin"]498                            499                            500                    f = open(_set_path, 'w')501                    json.dump(all_data, f, indent = 4)502                    f.close()503                    504            elif self.path[1] == "registerDoctor":505                if all_data["doctorsList"] != []:506                    for doctor in all_data["doctorsList"]:507                        if doctor["uniqueID"] == data["userName"]:508                            doctor["pin"] = data["pin"]509                            510                    f = open(_set_path, 'w')511                    json.dump(all_data, f, indent = 4)512                    f.close()513                    514            elif self.path[1] == "registerCaretaker":515                if all_data["caretakersList"] != []:516                    for caretaker in all_data["caretakersList"]:517                        if caretaker["uniqueID"] == data["userName"]:518                            caretaker["pin"] = data["pin"]519                            520                    f = open(_set_path, 'w')521                    json.dump(all_data, f, indent = 4)522                    f.close()523                    524                    525            elif self.path[1] == "addSensor":526                uniqueID = data["uniqueID"]527                zone = data["zone"]528                sens_name = data["sensName"]529                530                531                sens = sens_name.lower()532                newSensor = copy.deepcopy(all_data["baseSensor"])533                534                newSensor["topic"] = all_data["baseTopic"] + "/" + uniqueID + "/house/"535                newSensor["patientID"] = uniqueID536                newSensor["bn"] = uniqueID + "/house/" + sens537                newSensor["e"][0]["n"] = sens      538                newSensor["e"][0]["u"] = all_data["supportedSensors"][sens]539                540                if all_data["patientsList"] != []:541                    for patient in all_data["patientsList"]:542                        if patient["uniqueID"] == uniqueID:543                            patient[zone+"Devices"].append(newSensor)544                            545                            546                    f = open(_set_path, 'w')547                    json.dump(all_data, f, indent = 4)548                    f.close()549                    550            elif self.path[1] == "assignPatient":551                docID = data["docID"]552                patID = data["patID"]553                554                if all_data["doctorsList"]!=[]:555                    for doctor in all_data["doctorsList"]:556                        if doctor["uniqueID"] == docID:557                            doctor["patientsAssigned"].append(patID)558                            559                            560                    f = open(_set_path, 'w')561                    json.dump(all_data, f, indent = 4)562                    f.close()563                    564            elif self.path[1] == "assignPatientCaretaker":565                careID = data["careID"]566                patID = data["patID"]567                568                if all_data["caretakersList"]!=[]:569                    for caretaker in all_data["caretakersList"]:570                        if caretaker["uniqueID"] == careID:571                            caretaker["patientAssigned"] = patID572                            573                            574                    f = open(_set_path, 'w')575                    json.dump(all_data, f, indent = 4)576                    f.close()577            578            elif self.path[1] == "updateHighlighted":579                upID = data["uniqueID"]580                581                all_data["highlightedPatient"] = upID582                583                f = open(_set_path, 'w')584                json.dump(all_data, f, indent = 4)585                f.close()586            587        elif self.path[0] == "sensors":588            if self.path[1] == "updateTimeVisited":589                590                uniqueID = self.path[2]591                sens_name = self.path[3]592                593                if all_data["patientsList"] != []:594                    for patient in all_data["patientsList"]:595                        if patient["bodyDevices"] != []:596                            for device in patient["bodyDevices"]:597                                if uniqueID == device["patientID"]:598                                    if device["e"][0]["n"] == sens_name:599                                        device["timesVisited"] = data["timesVisited"]600                                    601                    f = open(_set_path, 'w')602                    json.dump(all_data, f, indent = 4)603                    f.close()604                    605            elif self.path[1] == "alarm_patient":606                607                uniqueID = self.path[2]608                sens_name = self.path[3]609                610                if all_data["patientsList"] != []:611                    for patient in all_data["patientsList"]:612                        if patient["uniqueID"] == uniqueID:613                            for key in data:614                                if data[key]!="":615                                    patient["alarms_patient"] = key616                                    617                    f = open(_set_path, 'w')618                    json.dump(all_data, f, indent = 4)619                    f.close()620            621                622class DELETE_manager():623    def __init__(self, path):624        self.path=path625        626    def run(self):627        _set_path = 'settings.json'628        with open(_set_path) as json_in:629            all_data=json.load(json_in)630        631        if self.path[0]=="telegram":632            if self.path[1]=="deletePatient":633                uniqueID = self.path[2]634                if all_data["patientsList"] != []:635                    i = 0636                    for patient in all_data["patientsList"]:637                        if patient["uniqueID"] == uniqueID:638                            all_data["patientsList"].pop(i)639                            if patient["uniqueID"] == all_data["highlightedPatient"]:640                                all_data["highlightedPatient"] = ""641                            642                        i+=1643                        644                if all_data["doctorsList"] != []:645                    i = 0646                    for doctor in all_data["doctorsList"]:647                        for patient_assigned in doctor["patientsAssigned"]:648                            if patient_assigned["uniqueID"] == uniqueID:649                                all_data["doctorsList"]["patientsAssigned"].pop(i)650                                651                            i+=1652                            653                            654                if all_data["caretakersList"] != []:655                    i = 0656                    for caretaker in all_data["caretakersList"]:657                        if caretaker["patientAssigned"] == uniqueID:658                            all_data["caretakersList"]["patientAssigned"] = ""659                            660                        i+=1661                        662                f = open(_set_path, 'w')663                json.dump(all_data, f, indent = 4)664                f.close()665                666            667            elif self.path[1]=="deleteDoctor":668                uniqueID = self.path[2]669                if all_data["doctorsList"] != []:670                    i = 0671                    for doctor in all_data["doctorsList"]:672                        if doctor["uniqueID"] == uniqueID:673                            all_data["doctorsList"].pop(i)674                            675                        i+=1676                        677                    f = open(_set_path, 'w')678                    json.dump(all_data, f, indent = 4)679                    f.close()680                    681            elif self.path[1]=="deleteCaretaker":682                uniqueID = self.path[2]683                if all_data["caretakersList"] != []:684                    i = 0685                    for caretaker in all_data["caretakersList"]:686                        if caretaker["uniqueID"] == uniqueID:687                            all_data["caretakersList"].pop(i)688                            689                        i+=1690                        691                    f = open(_set_path, 'w')692                    json.dump(all_data, f, indent = 4)693                    f.close()694        695            elif self.path[1] == "deleteSensor":696                uniqueID=self.path[2]697                zone = self.path[3]698                sens_name = self.path[4]699                700                if all_data["patientsList"] != []:701                    for patient in all_data["patientsList"]:702                        if patient["uniqueID"] == uniqueID:703                            if patient[zone+"Devices"] != []:704                                for sensor in patient[zone+"Devices"]:705                                    if sensor["e"][0]["n"]==sens_name:706                                        patient[zone+"Devices"].pop(patient[zone+"Devices"].index(sensor))707                                        708                    f = open(_set_path, 'w')709                    json.dump(all_data, f, indent = 4)...

namespace_model.py

Source:namespace_model.py

...53        self.config_file = open(config_path)54        self.config = load(self.config_file, Loader=FullLoader)55        os.environ['CUDA_VISIBLE_DEVICES'] = str(self.config[_experiment].get(_gpu,-1))56    @staticmethod57    def _set_path(config_path, local_path):58        if os.path.isabs(local_path):59            return local_path60        else:61            if local_path.startswith(("./", "../")) or regexp.search(local_path):62                return f"{config_path}/{local_path}"63            else:64                return local_path65    def fill_base(self):66        # for path in self.config[_experiment][_data_paths].keys():67        #     self.config[_experiment][_data_paths][path] = \68        #         self.config[_experiment][_data_paths][path].format(self.config[_experiment][_dataset])69        self.config[_experiment][_recs] = self.config[_experiment]\70            .get(_recs, self._set_path(self._base_folder_path_config, "../results/{0}/recs/"))\71            .format(self.config[_experiment][_dataset])72        self.config[_experiment][_weights] = self.config[_experiment]\73            .get(_weights, self._set_path(self._base_folder_path_config, "../results/{0}/weights/")) \74            .format(self.config[_experiment][_dataset])75        self.config[_experiment][_performance] = self.config[_experiment]\76            .get(_performance, self._set_path(self._base_folder_path_config, "../results/{0}/performance/")) \77            .format(self.config[_experiment][_dataset])78        self.config[_experiment][_dataloader] = self.config[_experiment].get(_dataloader, "DataSetLoader")79        manage_directories(self.config[_experiment][_recs], self.config[_experiment][_weights],80                           self.config[_experiment][_performance])81        for p in [_data_config, _weights, _recs, _dataset, _top_k, _performance, _logger_config,82                  _log_folder, _dataloader, _splitting, _prefiltering, _evaluation, _external_models_path,83                  _print_triplets, _config_test]:84            if p == _data_config:85                side_information = self.config[_experiment][p].get("side_information", {})86                side_information.update({k: self._set_path(self._base_folder_path_config,87                                                           v.format(self.config[_experiment][_dataset]))88                                         for k, v in side_information.items() if isinstance(v, str)})89                side_information = SimpleNamespace(**side_information)90                self.config[_experiment][p].update({k: self._set_path(self._base_folder_path_config,91                                                                      v.format(self.config[_experiment][_dataset]))92                                                    for k, v in self.config[_experiment][p].items() if93                                                    isinstance(v, str)})94                self.config[_experiment][p]["side_information"] = side_information95                self.config[_experiment][p][_dataloader] = self.config[_experiment][p].get(_dataloader, "DataSetLoader")96                setattr(self.base_namespace, p, SimpleNamespace(**self.config[_experiment][p]))97            elif p == _splitting and self.config[_experiment].get(p, {}):98                self.config[_experiment][p].update({k: self._set_path(self._base_folder_path_config,99                                                                      v.format(self.config[_experiment][_dataset]))100                                                    for k, v in self.config[_experiment][p].items() if101                                                    isinstance(v, str)})102                test_splitting = self.config[_experiment][p].get("test_splitting", {})103                validation_splitting = self.config[_experiment][p].get("validation_splitting", {})104                if test_splitting:105                    test_splitting = SimpleNamespace(**test_splitting)106                    self.config[_experiment][p]["test_splitting"] = test_splitting107                if validation_splitting:108                    validation_splitting = SimpleNamespace(**validation_splitting)109                    self.config[_experiment][p]["validation_splitting"] = validation_splitting110                setattr(self.base_namespace, p, SimpleNamespace(**self.config[_experiment][p]))111            elif p == _prefiltering and self.config[_experiment].get(p, {}):112                preprocessing_strategy = SimpleNamespace(**self.config[_experiment][p])113                self.config[_experiment][p] = preprocessing_strategy114                setattr(self.base_namespace, p, self.config[_experiment][p])115            elif p == _evaluation and self.config[_experiment].get(p, {}):116                complex_metrics = self.config[_experiment][p].get("complex_metrics", {})117                paired_ttest = self.config[_experiment][p].get("paired_ttest", {})118                wilcoxon_test = self.config[_experiment][p].get("wilcoxon_test", {})119                for complex_metric in complex_metrics:120                    complex_metric.update({k: self._set_path(self._base_folder_path_config,121                                                      v.format(self.config[_experiment][_dataset]))122                                    for k, v in complex_metric.items() if isinstance(v, str)})123                self.config[_experiment][p]["complex_metrics"] = complex_metrics124                self.config[_experiment][p]["paired_ttest"] = paired_ttest125                self.config[_experiment][p]["wilcoxon_test"] = wilcoxon_test126                setattr(self.base_namespace, p, SimpleNamespace(**self.config[_experiment][p]))127            elif p == _logger_config and not self.config[_experiment].get(p, False):128                setattr(self.base_namespace, p, f"{self._base_folder_path_elliot}/config/logger_config.yml")129            elif p == _log_folder and not self.config[_experiment].get(p, False):130                setattr(self.base_namespace, p, f"{self._base_folder_path_elliot}/../log/")131            elif p == _external_models_path and self.config[_experiment].get(p, False):132                self.config[_experiment][p] = self._set_path(self._base_folder_path_config, self.config[_experiment][p])133                setattr(self.base_namespace, p, self.config[_experiment][p])134            elif p == _config_test:135                setattr(self.base_namespace, p, self.config[_experiment].get(p, False))136            else:137                if self.config[_experiment].get(p):138                    setattr(self.base_namespace, p, self.config[_experiment][p])139    def fill_model(self):140        for key in self.config[_experiment][_models]:141            meta_model = self.config[_experiment][_models][key][_meta]142            model_name_space = SimpleNamespace(**self.config[_experiment][_models][key])143            setattr(model_name_space, _meta, SimpleNamespace(**meta_model))144            if any(isinstance(value, list) for value in self.config[_experiment][_models][key].values()):145                space_list = []146                for k, value in self.config[_experiment][_models][key].items():...

configuration.py

Source:configuration.py

2class Conf(object):3    def __init__(self, args):4        self.args = args5        self.dataset = args.dataset6    def _set_path(self, dataset_type):7        if self.dataset == 'TIHM':8            return './{}/tihm15'.format(dataset_type)9        elif self.dataset == 'DRI':10            return './{}/tihmdri'.format(dataset_type)11    @property12    def raw_data(self):13        return self._set_path('raw_data')14    @property15    def csv_data(self):16        return self._set_path('csv_data')17    @property18    def npy_data(self):19        return self._set_path('npy_data')20    @property21    def data_path(self):22        data_path = {23            'env': self._set_path('csv_data') + '/env/data/',24            'flag': self._set_path('csv_data') + '/env/flag/',25            'clinical': self._set_path('csv_data') + '/clinical/data/',26        }27        return data_path28    def reading_settings(self, validation):29        validation = parser_bool(validation)30        return {31            'label': True if validation else False,32            'extend_label_range': 1 if validation else 1,33            'valid': True if validation else False,34            'uti_pre_post_range': 3 if validation else 3,  # 10 days: 15,35            'extra_uti_range': 1 if validation else 1,  # 10 days: 5,36        }37# Validated UTI, may not in the flags files38def validated_date():39    patient_data = {...

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