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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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