updating the files

Author: argahsuknesib

.gitignore

@@ -1,2 +1,2 @@
 /data
-/venv
+/venv

mapper/mapper-evaluation-single-pod.py

@@ -0,0 +1,352 @@
+import logging
+import sys
+from datetime import datetime
+import pandas as pandas
+import pytz
+
+# configure logging
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+handler = logging.StreamHandler(sys.stdout)
+handler.setLevel(logging.DEBUG)
+formatter = logging.Formatter(
+    '%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+handler.setFormatter(formatter)
+logger.addHandler(handler)
+
+# template definitions
+TEMPLATE_TIME_MS = '<TIME_MS>'
+TEMPLATE_TIME_STR = '<TIME_STR>'
+
+
+# MAIN MAPPER FUNCTION
+
+def annotate_event(event, template_timestamps=False):
+    try:
+        # check if event is valid
+        valid = 'sourceId' in event and \
+                'metricId' in event and \
+                'value' in event and \
+                ('timestamp' in event or template_timestamps)
+
+        # if the event is not valid, return None
+        if not valid:
+            return None
+
+        # otherwise, return mapped event
+        rdf_event = map_observation_to_rdf(
+            event, template_timestamps=template_timestamps)
+        return remove_whitespace(rdf_event) if rdf_event is not None else rdf_event
+
+    except Exception as e:
+        print(e)
+        return None
+
+
+def map_observation_to_rdf(event, template_timestamps=False):
+    result = map_observation(source_id=event['sourceId'],
+                             metric_id=event['metricId'],
+                             value=event['value'],
+                             timestamp=event['timestamp'] if not template_timestamps else None)
+    return result
+
+
+# MAPPING FUNCTIONS OF HEADACHE PARTS
+
+def map_observation(metric_id,
+                    source_id,
+                    value,
+                    timestamp):
+    # extract patient ID from source ID
+    split = source_id.split(".", 1)
+    patient_id = split[0]
+    source_id = split[1]
+
+    # replace spaces by underscores in metricId
+    metric_id = metric_id.replace(' ', '_')
+
+    # add suffix to sensor (sourceId) based on metricId
+    source_id = update_source_id(source_id, metric_id)
+
+    # generate timestamp
+    uuid = generate_uuid(metric_id, patient_id)
+    if timestamp:
+        timestamp_utc = timestamp
+        time_str =timestamp
+    else:
+        timestamp_utc = TEMPLATE_TIME_MS
+        time_str = TEMPLATE_TIME_STR
+
+    # map value
+    value_str, metric_group = map_value(value, metric_id)
+
+    # create RDF data
+    if metric_group == "CONTEXT":
+        return OBSERVATION_TEMPLATE_CONTEXT_DAHCC % (uuid,
+                                                     uuid, source_id,
+                                                     uuid, uuid, metric_id,
+                                                     uuid, str(timestamp_utc),
+                                                     uuid, value
+                                                     )
+        # return OBSERVATION_TEMPLATE_CONTEXT % (source_id,
+        #                                        patient_id, metric_id, uuid,
+        #                                        patient_id, metric_id, uuid,
+        #                                        metric_id, time_str, str(timestamp_utc), value_str)
+    elif metric_group == "WEARABLE":
+            return OBSERVATION_TEMPLATE_CONTEXT_DAHCC % (uuid,
+                                                     uuid, source_id,
+                                                     uuid, uuid, metric_id,
+                                                     uuid, str(timestamp_utc),
+                                                     uuid, value
+                                                     )
+
+
+        # return OBSERVATION_TEMPLATE_WEARABLE % (source_id,
+        #                                         patient_id, metric_id, uuid,
+        #                                         patient_id, metric_id, uuid,
+        #                                         metric_id, time_str, str(timestamp_utc), value_str)
+
+
+def map_value(value, metric_id):
+    value_type, metric_group = float, None
+    if metric_id in METRIC_TYPES_CONTEXT:
+        value_type, metric_group = METRIC_TYPES_CONTEXT[metric_id], "CONTEXT"
+    elif metric_id in METRIC_TYPES_WEARABLE:
+        value_type, metric_group = METRIC_TYPES_WEARABLE[metric_id], "WEARABLE"
+
+    if value_type == bool:
+        processed_value = int(1) if value == 1 or value == '1' else int(0)
+    else:
+        processed_value = value
+
+    return VALUE_TEMPLATE % (processed_value, TYPE_MAP[value_type]), metric_group
+
+
+def update_source_id(source_id, metric_id):
+    if metric_id in SENSOR_SUFFIX_MAP:
+        return '%s.%s' % (source_id, SENSOR_SUFFIX_MAP[metric_id])
+    else:
+        return source_id
+
+
+# MAPPING TEMPLATES
+
+EXAMPLE_OBSERVATION = """
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs0> <http://rdfs.org/ns/void#inDataset> <https://dahcc.idlab.ugent.be/Protego/_participant1> .
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs0> <https://saref.etsi.org/core/measurementMadeBy> <https://dahcc.idlab.ugent.be/Homelab/SensorsAndActuators/70:ee:50:67:30:b2> .
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs0> <https://saref.etsi.org/core/relatesToProperty> <https://dahcc.idlab.ugent.be/Homelab/SensorsAndActuators/org.dyamand.types.common.AtmosphericPressure> .
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs0> <https://saref.etsi.org/core/hasTimestamp> "2022-01-03T09:04:55.000000"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs0> <https://saref.etsi.org/core/hasValue> "1013.1"^^<http://www.w3.org/2001/XMLSchema#float> 
+
+"""
+
+OBSERVATION_TEMPLATE_CONTEXT_DAHCC = """
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs%s> <http://rdfs.org/ns/void#inDataset> <https://dahcc.idlab.ugent.be/Protego/_participant1> .
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs%s> <https://saref.etsi.org/core/measurementMadeBy> <https://dahcc.idlab.ugent.be/Homelab/SensorsAndActuators/%s> .
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs%s> <http://purl.org/dc/terms/isVersionOf> <https://saref.etsi.org/core/Measurement> .
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs%s> <https://saref.etsi.org/core/relatesToProperty> <https://dahcc.idlab.ugent.be/Homelab/SensorsAndActuators/%s> .
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs%s> <https://saref.etsi.org/core/hasTimestamp> "%s"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
+<https://dahcc.idlab.ugent.be/Protego/_participant1/obs%s> <https://saref.etsi.org/core/hasValue> "%s"^^<http://www.w3.org/2001/XMLSchema#float> .
+
+"""
+
+OBSERVATION_TEMPLATE_CONTEXT = """
+<https://dahcc.idlab.ugent.be/Homelab/SensorsAndActuators/%s>
+    <https://saref.etsi.org/core/makesMeasurement> <http://protego.idlab.ugent.be/%s/%s/obs%s> .
+<http://protego.idlab.ugent.be/%s/%s/obs%s>
+    <https://saref.etsi.org/core/relatesToProperty> <https://dahcc.idlab.ugent.be/Homelab/SensorsAndActuators/%s> ;
+    <https://saref.etsi.org/core/hasTimestamp> "%s"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+    <https://dahcc.idlab.ugent.be/Ontology/Sensors/hasTimestampUTC> "%s"^^<http://www.w3.org/2001/XMLSchema#integer> ;
+    <https://saref.etsi.org/core/hasValue> %s .
+"""
+
+OBSERVATION_TEMPLATE_WEARABLE = """
+<https://dahcc.idlab.ugent.be/Homelab/SensorsAndWearables/%s>
+    <https://saref.etsi.org/core/makesMeasurement> <http://protego.idlab.ugent.be/%s/%s/obs%s> .
+<http://protego.idlab.ugent.be/%s/%s/obs%s>
+    <https://saref.etsi.org/core/relatesToProperty> <https://dahcc.idlab.ugent.be/Homelab/SensorsAndWearables/%s> ;
+    <https://saref.etsi.org/core/hasTimestamp> "%s"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+    <https://dahcc.idlab.ugent.be/Ontology/Sensors/hasTimestampUTC> "%s"^^<http://www.w3.org/2001/XMLSchema#integer> ;
+    <https://saref.etsi.org/core/hasValue> %s .
+"""
+
+VALUE_TEMPLATE = "\"%s\"^^%s"
+
+# CONVERTERS OF JSON VALUES TO ONTOLOGY CONCEPTS
+
+METRIC_TYPES_CONTEXT = {
+    "airquality.co2": float,
+    "airquality.voc_total": bool,
+    "energy.consumption": float,
+    "energy.power": float,
+    "environment.blind": float,
+    "environment.button": bool,
+    "environment.dimmer": float,
+    "environment.light": float,
+    "environment.lightswitch": bool,
+    "environment.motion": bool,
+    "environment.open": bool,
+    "environment.relativehumidity": float,
+    "environment.relay": bool,
+    "environment.temperature": float,
+    "environment.voltage": float,
+    "environment.waterRunning::bool": bool,
+    "mqtt.lastMessage": str,
+    "org.dyamand.aqura.AquraLocationState_Protego User": str,
+    "org.dyamand.aqura.AquraLocationState_Protego_User": str,
+    "org.dyamand.types.airquality.CO2": float,
+    "org.dyamand.types.common.AtmosphericPressure": float,
+    "org.dyamand.types.common.Loudness": float,
+    "org.dyamand.types.common.RelativeHumidity": float,
+    "org.dyamand.types.common.Temperature": float,
+    "people.presence.detected": bool,
+    "people.presence.numberDetected": float,
+    "weather.pressure": float,
+    "weather.rainrate": float,
+    "weather.windspeed": float
+}
+
+METRIC_TYPES_WEARABLE = {
+    "org.dyamand.types.health.BodyTemperature": float,
+    "org.dyamand.types.common.Load": float,
+    "org.dyamand.types.health.DiastolicBloodPressure": float,
+    "org.dyamand.types.health.HeartRate": float,
+    "org.dyamand.types.health.SystolicBloodPressure": float,
+    "org.dyamand.types.health.GlucoseLevel": float,
+    "smartphone.acceleration.x": float,
+    "smartphone.acceleration.y": float,
+    "smartphone.acceleration.z": float,
+    "smartphone.ambient_light": float,
+    "smartphone.ambient_noise.amplitude": float,
+    "smartphone.ambient_noise.frequency": float,
+    "smartphone.application": str,
+    "smartphone.gravity.x": float,
+    "smartphone.gravity.y": float,
+    "smartphone.gravity.z": float,
+    "smartphone.gyroscope.x": float,
+    "smartphone.gyroscope.y": float,
+    "smartphone.gyroscope.z": float,
+    "smartphone.keyboard": str,
+    "smartphone.linear_acceleration.x": float,
+    "smartphone.linear_acceleration.y": float,
+    "smartphone.linear_acceleration.z": float,
+    "smartphone.location.accuracy": float,
+    "smartphone.location.altitude": float,
+    "smartphone.location.bearing": float,
+    "smartphone.location.latitude": float,
+    "smartphone.location.longitude": float,
+    "smartphone.magnetometer.x": float,
+    "smartphone.magnetometer.y": float,
+    "smartphone.magnetometer.z": float,
+    "smartphone.proximity": float,
+    "smartphone.rotation.x": float,
+    "smartphone.rotation.y": float,
+    "smartphone.rotation.z": float,
+    "smartphone.screen": str,
+    "smartphone.sleepAPI.API_confidence": float,
+    "smartphone.sleepAPI.model_type": str,
+    "smartphone.sleepAPI.t_start": float,
+    "smartphone.sleepAPI.t_stop": float,
+    "smartphone.step": float,
+    "wearable.acceleration.x": float,
+    "wearable.acceleration.y": float,
+    "wearable.acceleration.z": float,
+    "wearable.battery_level": float,
+    "wearable.bvp": float,
+    "wearable.gsr": float,
+    "wearable.ibi": float,
+    "wearable.on_wrist": bool,
+    "wearable.skt": float
+}
+
+SENSOR_SUFFIX_MAP = {
+    "org.dyamand.aqura.AquraLocationState_Protego_User": "Tag",
+    "wearable.acceleration.x": 'Accelerometer',
+    "wearable.acceleration.y": 'Accelerometer',
+    "wearable.acceleration.z": 'Accelerometer',
+    "wearable.battery_level": 'BatteryLevelMeter',
+    "wearable.bvp": 'PPGSensor',
+    "wearable.gsr": 'GSRSensor',
+    "wearable.ibi": 'PPGSensor',
+    "wearable.on_wrist": 'OnWristDetector',
+    "wearable.skt": 'Thermopile'
+}
+
+TYPE_MAP = {
+    float: "<http://www.w3.org/2001/XMLSchema#float>",
+    int: "<http://www.w3.org/2001/XMLSchema#integer>",
+    bool: "<http://www.w3.org/2001/XMLSchema#integer>",
+    str: "<http://www.w3.org/2001/XMLSchema#string>"
+}
+
+
+# HELPER FUNCTIONS
+
+def convert_timestamp_to_string(timestamp):
+    return datetime.fromtimestamp(float(timestamp) / 1000.0,
+                                  pytz.timezone('Europe/Brussels')). \
+        strftime('%Y-%m-%dT%H:%M:%S')
+
+
+uuid_map = {}
+
+
+def generate_uuid(metric_id, patient_id):
+    key = '%s' % (patient_id)
+    if key not in uuid_map:
+        uuid_map[key] = 0
+    result = uuid_map[key]
+    uuid_map[key] += 1
+    return result
+
+
+def remove_whitespace(given_str):
+    return ' '.join(given_str.split())
+
+
+def map_feather(file, sensors_to_map):
+    file = pandas.read_feather(file)
+    for sensor in sensors_to_map:
+        df = file[file['Metric'] == sensor]
+        for index in df.index:
+            source = (df['Sensor'][index])
+            metric = (df['Metric'][index])
+            value = (df['Value'][index])
+            timestamp = (df['Timestamp'][index])
+            timestamp_str = str(timestamp)
+            hour = timestamp_str[0:2]
+            minute = timestamp_str[3:5]
+            second = timestamp_str[6:8]
+            millisecond = '000Z'
+            if (timestamp_str[9:12] == ''):
+                continue
+            else:
+                millisecond = timestamp_str[9:13] + 'Z'
+
+
+            current_time = datetime.now()
+            year = current_time.strftime("%Y")
+            month = current_time.strftime("%m")
+            day = current_time.strftime("%d")
+
+            try: 
+                time_value = str(year) + '-' + str(month) + '-' + str(day) + 'T' + str(hour) + ':' + str(minute) + ':' + str(second) + '.' + str(millisecond)
+            except Exception as e:
+                print('Exception is' + e)
+            
+            event = {
+                'sourceId': source,
+                'metricId': metric,
+                'value': value,
+                'timestamp': time_value
+            }
+            result = annotate_event(event)          
+
+            with open('/home/kush/Code/feather-RDF-mapper/data/rdfData/participant6.nt', 'a') as file:
+                pass
+                file.write('\n')
+                file.write(result)
+if __name__ == '__main__':
+    file = 'data/dataset_participant6.feather'  
+    sensors = ['wearable.bvp']
+    map_feather(file= file, sensors_to_map= sensors)