rapids/rules/features.smk

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rule join_features_from_providers:
input:
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sensor_features = find_features_files
wildcard_constraints:
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sensor_key = '(phone|fitbit|empatica).*'
output:
"data/processed/features/{pid}/{sensor_key}.csv"
script:
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"../src/features/utils/join_features_from_providers.R"
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rule phone_data_yield_python_features:
input:
sensor_data = "data/interim/{pid}/phone_yielded_timestamps_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
provider = lambda wildcards: config["PHONE_DATA_YIELD"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_data_yield"
output:
"data/interim/{pid}/phone_data_yield_features/phone_data_yield_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule phone_data_yield_r_features:
input:
sensor_data = "data/interim/{pid}/phone_yielded_timestamps_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
provider = lambda wildcards: config["PHONE_DATA_YIELD"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_data_yield"
output:
"data/interim/{pid}/phone_data_yield_features/phone_data_yield_r_{provider_key}.csv"
script:
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
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"../src/features/entry.R"
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rule phone_accelerometer_python_features:
input:
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sensor_data = "data/raw/{pid}/phone_accelerometer_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
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provider = lambda wildcards: config["PHONE_ACCELEROMETER"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_accelerometer"
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output:
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"data/interim/{pid}/phone_accelerometer_features/phone_accelerometer_python_{provider_key}.csv"
script:
"../src/features/entry.py"
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rule phone_accelerometer_r_features:
input:
sensor_data = "data/raw/{pid}/phone_accelerometer_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_ACCELEROMETER"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_accelerometer"
output:
"data/interim/{pid}/phone_accelerometer_features/phone_accelerometer_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule activity_recognition_episodes:
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input:
sensor_data = "data/raw/{pid}/phone_activity_recognition_with_datetime.csv"
params:
episode_threshold_between_rows = config["PHONE_ACTIVITY_RECOGNITION"]["EPISODE_THRESHOLD_BETWEEN_ROWS"]
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output:
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"data/interim/{pid}/phone_activity_recognition_episodes.csv"
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script:
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"../src/features/phone_activity_recognition/episodes/activity_recognition_episodes.R"
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rule phone_activity_recognition_python_features:
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input:
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sensor_episodes = "data/interim/{pid}/phone_activity_recognition_episodes_resampled_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
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provider = lambda wildcards: config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_activity_recognition"
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output:
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"data/interim/{pid}/phone_activity_recognition_features/phone_activity_recognition_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule phone_activity_recognition_r_features:
input:
sensor_episodes = "data/interim/{pid}/phone_activity_recognition_episodes_resampled_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_activity_recognition"
output:
"data/interim/{pid}/phone_activity_recognition_features/phone_activity_recognition_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule phone_applications_crashes_python_features:
input:
sensor_data = "data/raw/{pid}/phone_applications_crashes_with_datetime_with_categories.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_applications_crashes"
output:
"data/interim/{pid}/phone_applications_crashes_features/phone_applications_crashes_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule phone_applications_crashes_r_features:
input:
sensor_data = "data/raw/{pid}/phone_applications_crashes_with_datetime_with_categories.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_applications_crashes"
output:
"data/interim/{pid}/phone_applications_crashes_features/phone_applications_crashes_r_{provider_key}.csv"
script:
"../src/features/entry.R"
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rule phone_applications_foreground_python_features:
input:
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sensor_data = "data/raw/{pid}/phone_applications_foreground_with_datetime_with_categories.csv",
episode_data = "data/interim/{pid}/phone_app_episodes_resampled_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
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provider = lambda wildcards: config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_applications_foreground"
output:
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"data/interim/{pid}/phone_applications_foreground_features/phone_applications_foreground_python_{provider_key}.csv"
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script:
"../src/features/entry.py"
rule phone_applications_foreground_r_features:
input:
sensor_data = "data/raw/{pid}/phone_applications_foreground_with_datetime_with_categories.csv",
episode_data = "data/interim/{pid}/phone_app_episodes_resampled_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_applications_foreground"
output:
"data/interim/{pid}/phone_applications_foreground_features/phone_applications_foreground_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule phone_applications_notifications_python_features:
input:
sensor_data = "data/raw/{pid}/phone_applications_notifications_with_datetime_with_categories.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_applications_notifications"
output:
"data/interim/{pid}/phone_applications_notifications_features/phone_applications_notifications_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule phone_applications_notifications_r_features:
input:
sensor_data = "data/raw/{pid}/phone_applications_notifications_with_datetime_with_categories.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_APPLICATIONS_NOTIFICATIONS"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_applications_notifications"
output:
"data/interim/{pid}/phone_applications_notifications_features/phone_applications_notifications_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule phone_log_python_features:
input:
sensor_data = "data/raw/{pid}/phone_log_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_LOG"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_log"
output:
"data/interim/{pid}/phone_log_features/phone_log_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule phone_log_r_features:
input:
sensor_data = "data/raw/{pid}/phone_log_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_LOG"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_log"
output:
"data/interim/{pid}/phone_log_features/phone_log_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule battery_episodes:
input:
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"data/raw/{pid}/phone_battery_raw.csv"
params:
episode_threshold_between_rows = config["PHONE_BATTERY"]["EPISODE_THRESHOLD_BETWEEN_ROWS"]
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output:
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"data/interim/{pid}/phone_battery_episodes.csv"
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script:
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"../src/features/phone_battery/episodes/battery_episodes.R"
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rule phone_battery_python_features:
input:
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sensor_episodes = "data/interim/{pid}/phone_battery_episodes_resampled_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
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provider = lambda wildcards: config["PHONE_BATTERY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_battery"
output:
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"data/interim/{pid}/phone_battery_features/phone_battery_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule phone_battery_r_features:
input:
sensor_episodes = "data/interim/{pid}/phone_battery_episodes_resampled_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_BATTERY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_battery"
output:
"data/interim/{pid}/phone_battery_features/phone_battery_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule phone_bluetooth_python_features:
input:
sensor_data = "data/raw/{pid}/phone_bluetooth_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_BLUETOOTH"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_bluetooth"
output:
"data/interim/{pid}/phone_bluetooth_features/phone_bluetooth_python_{provider_key}.csv"
script:
"../src/features/entry.py"
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rule phone_bluetooth_r_features:
input:
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sensor_data = "data/raw/{pid}/phone_bluetooth_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
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provider = lambda wildcards: config["PHONE_BLUETOOTH"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_bluetooth"
output:
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"data/interim/{pid}/phone_bluetooth_features/phone_bluetooth_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule calls_episodes:
input:
calls = "data/raw/{pid}/phone_calls_raw.csv"
output:
"data/interim/{pid}/phone_calls_episodes.csv"
script:
"../src/features/phone_calls/episodes/calls_episodes.py"
rule phone_calls_python_features:
input:
sensor_data = get_calls_input,
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_CALLS"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_calls"
output:
"data/interim/{pid}/phone_calls_features/phone_calls_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule phone_calls_r_features:
input:
sensor_data = get_calls_input,
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
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provider = lambda wildcards: config["PHONE_CALLS"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_calls"
output:
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"data/interim/{pid}/phone_calls_features/phone_calls_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule conversation_python_features:
input:
sensor_data = "data/raw/{pid}/phone_conversation_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
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provider = lambda wildcards: config["PHONE_CONVERSATION"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_conversation"
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output:
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"data/interim/{pid}/phone_conversation_features/phone_conversation_python_{provider_key}.csv"
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script:
"../src/features/entry.py"
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rule conversation_r_features:
input:
sensor_data = "data/raw/{pid}/phone_conversation_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_CONVERSATION"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_conversation"
output:
"data/interim/{pid}/phone_conversation_features/phone_conversation_r_{provider_key}.csv"
script:
"../src/features/entry.R"
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rule preprocess_esm:
input: "data/raw/{pid}/phone_esm_with_datetime.csv"
params:
scales=lambda wildcards: config["PHONE_ESM"]["PROVIDERS"]["STRAW"]["SCALES"]
output: "data/interim/{pid}/phone_esm_clean.csv"
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script:
"../src/features/phone_esm/straw/preprocess.py"
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rule esm_features:
input:
sensor_data = "data/interim/{pid}/phone_esm_clean.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_ESM"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_esm",
scales=lambda wildcards: config["PHONE_ESM"]["PROVIDERS"][wildcards.provider_key.upper()]["SCALES"]
output: "data/interim/{pid}/phone_esm_features/phone_esm_python_{provider_key}.csv"
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script:
"../src/features/entry.py"
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rule phone_keyboard_python_features:
input:
sensor_data = "data/raw/{pid}/phone_keyboard_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_KEYBOARD"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_keyboard"
output:
"data/interim/{pid}/phone_keyboard_features/phone_keyboard_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule phone_keyboard_r_features:
input:
sensor_data = "data/raw/{pid}/phone_keyboard_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_KEYBOARD"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_keyboard"
output:
"data/interim/{pid}/phone_keyboard_features/phone_keyboard_r_{provider_key}.csv"
script:
"../src/features/entry.R"
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rule phone_light_python_features:
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input:
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sensor_data = "data/raw/{pid}/phone_light_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
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provider = lambda wildcards: config["PHONE_LIGHT"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_light"
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output:
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"data/interim/{pid}/phone_light_features/phone_light_python_{provider_key}.csv"
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script:
"../src/features/entry.py"
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rule phone_light_r_features:
input:
sensor_data = "data/raw/{pid}/phone_light_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_LIGHT"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_light"
output:
"data/interim/{pid}/phone_light_features/phone_light_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule phone_locations_add_doryab_extra_columns:
input:
sensor_input = "data/interim/{pid}/phone_locations_processed_with_datetime.csv",
params:
provider = config["PHONE_LOCATIONS"]["PROVIDERS"]["DORYAB"]
output:
"data/interim/{pid}/phone_locations_processed_with_datetime_with_doryab_columns_episodes.csv"
script:
"../src/features/phone_locations/doryab/add_doryab_extra_columns.py"
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rule phone_locations_python_features:
input:
sensor_data = get_locations_python_input,
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
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provider = lambda wildcards: config["PHONE_LOCATIONS"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_locations"
output:
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"data/interim/{pid}/phone_locations_features/phone_locations_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule phone_locations_barnett_daily_features:
input:
sensor_data = "data/interim/{pid}/phone_locations_processed_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv",
params:
provider = lambda wildcards: config["PHONE_LOCATIONS"]["PROVIDERS"]["BARNETT"],
output:
"data/interim/{pid}/phone_locations_barnett_daily.csv"
script:
"../src/features/phone_locations/barnett/daily_features.R"
rule phone_locations_r_features:
input:
sensor_data = "data/interim/{pid}/phone_locations_processed_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv",
barnett_daily = get_barnett_daily
params:
provider = lambda wildcards: config["PHONE_LOCATIONS"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_locations"
output:
"data/interim/{pid}/phone_locations_features/phone_locations_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule phone_messages_python_features:
input:
sensor_data = "data/raw/{pid}/phone_messages_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_MESSAGES"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_messages"
output:
"data/interim/{pid}/phone_messages_features/phone_messages_python_{provider_key}.csv"
script:
"../src/features/entry.py"
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rule phone_messages_r_features:
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input:
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sensor_data = "data/raw/{pid}/phone_messages_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
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provider = lambda wildcards: config["PHONE_MESSAGES"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_messages"
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output:
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"data/interim/{pid}/phone_messages_features/phone_messages_r_{provider_key}.csv"
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script:
"../src/features/entry.R"
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rule screen_episodes:
input:
screen = "data/raw/{pid}/phone_screen_with_datetime.csv"
output:
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"data/interim/{pid}/phone_screen_episodes.csv"
script:
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"../src/features/phone_screen/episodes/screen_episodes.R"
rule app_episodes:
input:
screen = "data/interim/{pid}/phone_screen_episodes.csv",
app = "data/raw/{pid}/phone_applications_foreground_with_datetime_with_categories.csv"
output:
"data/interim/{pid}/phone_app_episodes.csv"
script:
"../src/features/phone_applications_foreground/episodes/app_episodes.R"
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rule phone_screen_python_features:
input:
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sensor_episodes = "data/interim/{pid}/phone_screen_episodes_resampled_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
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provider = lambda wildcards: config["PHONE_SCREEN"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_screen"
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output:
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"data/interim/{pid}/phone_screen_features/phone_screen_python_{provider_key}.csv"
script:
"../src/features/entry.py"
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rule phone_screen_r_features:
input:
sensor_episodes = "data/interim/{pid}/phone_screen_episodes_resampled_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_SCREEN"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_screen"
output:
"data/interim/{pid}/phone_screen_features/phone_screen_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule phone_wifi_connected_python_features:
input:
sensor_data = "data/raw/{pid}/phone_wifi_connected_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_wifi_connected"
output:
"data/interim/{pid}/phone_wifi_connected_features/phone_wifi_connected_python_{provider_key}.csv"
script:
"../src/features/entry.py"
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rule phone_wifi_connected_r_features:
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input:
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sensor_data = "data/raw/{pid}/phone_wifi_connected_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
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provider = lambda wildcards: config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_wifi_connected"
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output:
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"data/interim/{pid}/phone_wifi_connected_features/phone_wifi_connected_r_{provider_key}.csv"
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script:
"../src/features/entry.R"
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rule phone_wifi_visible_python_features:
input:
sensor_data = "data/raw/{pid}/phone_wifi_visible_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "phone_wifi_visible"
output:
"data/interim/{pid}/phone_wifi_visible_features/phone_wifi_visible_python_{provider_key}.csv"
script:
"../src/features/entry.py"
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rule phone_wifi_visible_r_features:
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input:
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sensor_data = "data/raw/{pid}/phone_wifi_visible_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
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provider = lambda wildcards: config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
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sensor_key = "phone_wifi_visible"
output:
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"data/interim/{pid}/phone_wifi_visible_features/phone_wifi_visible_r_{provider_key}.csv"
script:
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"../src/features/entry.R"
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rule fitbit_calories_intraday_python_features:
input:
sensor_data = "data/raw/{pid}/fitbit_calories_intraday_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_calories_intraday"
output:
"data/interim/{pid}/fitbit_calories_intraday_features/fitbit_calories_intraday_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule fitbit_calories_intraday_r_features:
input:
sensor_data = "data/raw/{pid}/fitbit_calories_intraday_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_calories_intraday"
output:
"data/interim/{pid}/fitbit_calories_intraday_features/fitbit_calories_intraday_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule fitbit_data_yield_python_features:
input:
sensor_data = "data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_DATA_YIELD"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_data_yield"
output:
"data/interim/{pid}/fitbit_data_yield_features/fitbit_data_yield_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule fitbit_data_yield_r_features:
input:
sensor_data = "data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_DATA_YIELD"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_data_yield"
output:
"data/interim/{pid}/fitbit_data_yield_features/fitbit_data_yield_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule fitbit_heartrate_summary_python_features:
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input:
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sensor_data = "data/raw/{pid}/fitbit_heartrate_summary_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
provider = lambda wildcards: config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"][wildcards.provider_key.upper()],
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provider_key = "{provider_key}",
sensor_key = "fitbit_heartrate_summary"
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output:
"data/interim/{pid}/fitbit_heartrate_summary_features/fitbit_heartrate_summary_python_{provider_key}.csv"
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script:
"../src/features/entry.py"
rule fitbit_heartrate_summary_r_features:
input:
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sensor_data = "data/raw/{pid}/fitbit_heartrate_summary_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_heartrate_summary"
output:
"data/interim/{pid}/fitbit_heartrate_summary_features/fitbit_heartrate_summary_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule fitbit_heartrate_intraday_python_features:
input:
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sensor_data = "data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_heartrate_intraday"
output:
"data/interim/{pid}/fitbit_heartrate_intraday_features/fitbit_heartrate_intraday_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule fitbit_heartrate_intraday_r_features:
input:
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sensor_data = "data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_heartrate_intraday"
output:
"data/interim/{pid}/fitbit_heartrate_intraday_features/fitbit_heartrate_intraday_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule fitbit_steps_summary_python_features:
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input:
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sensor_data = "data/raw/{pid}/fitbit_steps_summary_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
provider = lambda wildcards: config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][wildcards.provider_key.upper()],
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provider_key = "{provider_key}",
sensor_key = "fitbit_steps_summary"
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output:
"data/interim/{pid}/fitbit_steps_summary_features/fitbit_steps_summary_python_{provider_key}.csv"
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script:
"../src/features/entry.py"
rule fitbit_steps_summary_r_features:
input:
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sensor_data = "data/raw/{pid}/fitbit_steps_summary_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_steps_summary"
output:
"data/interim/{pid}/fitbit_steps_summary_features/fitbit_steps_summary_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule fitbit_steps_intraday_python_features:
input:
sensor_data = optional_steps_intraday_input,
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_steps_intraday"
output:
"data/interim/{pid}/fitbit_steps_intraday_features/fitbit_steps_intraday_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule fitbit_steps_intraday_r_features:
input:
sensor_data = optional_steps_intraday_input,
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_steps_intraday"
output:
"data/interim/{pid}/fitbit_steps_intraday_features/fitbit_steps_intraday_r_{provider_key}.csv"
script:
"../src/features/entry.R"
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rule fitbit_sleep_summary_python_features:
input:
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sensor_data = "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_sleep_summary"
output:
"data/interim/{pid}/fitbit_sleep_summary_features/fitbit_sleep_summary_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule fitbit_sleep_summary_r_features:
input:
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sensor_data = "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_sleep_summary"
output:
"data/interim/{pid}/fitbit_sleep_summary_features/fitbit_sleep_summary_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule sleep_intraday_episodes:
input:
sleep_intraday = "data/raw/{pid}/fitbit_sleep_intraday_with_datetime.csv"
output:
"data/interim/{pid}/fitbit_sleep_intraday_episodes.csv"
script:
"../src/features/fitbit_sleep_intraday/episodes/sleep_intraday_episodes.py"
rule fitbit_sleep_intraday_python_features:
input:
sensor_data = "data/interim/{pid}/fitbit_sleep_intraday_episodes_resampled_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_sleep_intraday"
output:
"data/interim/{pid}/fitbit_sleep_intraday_features/fitbit_sleep_intraday_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule fitbit_sleep_intraday_r_features:
input:
sensor_data = "data/interim/{pid}/fitbit_sleep_intraday_episodes_resampled_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "fitbit_sleep_intraday"
output:
"data/interim/{pid}/fitbit_sleep_intraday_features/fitbit_sleep_intraday_r_{provider_key}.csv"
script:
"../src/features/entry.R"
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rule empatica_accelerometer_python_features:
input:
sensor_data = "data/raw/{pid}/empatica_accelerometer_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_ACCELEROMETER"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_accelerometer"
output:
"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}.csv",
"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}_windows.csv"
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script:
"../src/features/entry.py"
rule empatica_accelerometer_python_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_accelerometer",
provider_main = config["EMPATICA_ACCELEROMETER"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_accelerometer_features/z_empatica_accelerometer_python_{provider_key}.csv",
"data/interim/{pid}/empatica_accelerometer_features/z_empatica_accelerometer_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
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rule empatica_accelerometer_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_accelerometer_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_ACCELEROMETER"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_accelerometer"
output:
"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule empatica_heartrate_python_features:
input:
sensor_data = "data/raw/{pid}/empatica_heartrate_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_HEARTRATE"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_heartrate"
output:
"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}.csv",
"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}_windows.csv"
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script:
"../src/features/entry.py"
rule empatica_heartrate_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_heartrate_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_HEARTRATE"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_heartrate"
output:
"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule empatica_temperature_python_features:
input:
sensor_data = "data/raw/{pid}/empatica_temperature_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_TEMPERATURE"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_temperature"
output:
"data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}.csv",
"data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}_windows.csv"
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script:
"../src/features/entry.py"
rule empatica_temperature_python_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_temperature",
provider_main = config["EMPATICA_TEMPERATURE"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_temperature_features/z_empatica_temperature_python_{provider_key}.csv",
"data/interim/{pid}/empatica_temperature_features/z_empatica_temperature_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
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rule empatica_temperature_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_temperature_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_TEMPERATURE"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_temperature"
output:
"data/interim/{pid}/empatica_temperature_features/empatica_temperature_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule empatica_electrodermal_activity_python_features:
input:
sensor_data = "data/raw/{pid}/empatica_electrodermal_activity_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_electrodermal_activity"
output:
"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}.csv",
"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}_windows.csv"
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script:
"../src/features/entry.py"
rule empatica_electrodermal_activity_python_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_electrodermal_activity",
provider_main = config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_electrodermal_activity_features/z_empatica_electrodermal_activity_python_{provider_key}.csv",
"data/interim/{pid}/empatica_electrodermal_activity_features/z_empatica_electrodermal_activity_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
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rule empatica_electrodermal_activity_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_electrodermal_activity_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_electrodermal_activity"
output:
"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule empatica_blood_volume_pulse_python_features:
input:
sensor_data = "data/raw/{pid}/empatica_blood_volume_pulse_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_blood_volume_pulse"
output:
"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}.csv",
"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}_windows.csv"
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script:
"../src/features/entry.py"
rule empatica_blood_volume_pulse_python_cr_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_blood_volume_pulse",
provider_main = config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_blood_volume_pulse_features/z_empatica_blood_volume_pulse_python_{provider_key}.csv",
"data/interim/{pid}/empatica_blood_volume_pulse_features/z_empatica_blood_volume_pulse_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
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rule empatica_blood_volume_pulse_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_blood_volume_pulse_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_blood_volume_pulse"
output:
"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule empatica_inter_beat_interval_python_features:
input:
sensor_data = "data/raw/{pid}/empatica_inter_beat_interval_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_inter_beat_interval"
output:
"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}.csv",
"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}_windows.csv"
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script:
"../src/features/entry.py"
rule empatica_inter_beat_interval_python_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_inter_beat_interval",
provider_main = config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_inter_beat_interval_features/z_empatica_inter_beat_interval_python_{provider_key}.csv",
"data/interim/{pid}/empatica_inter_beat_interval_features/z_empatica_inter_beat_interval_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
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rule empatica_inter_beat_interval_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_inter_beat_interval_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_inter_beat_interval"
output:
"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule empatica_tags_python_features:
input:
sensor_data = "data/raw/{pid}/empatica_tags_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_TAGS"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_tags"
output:
"data/interim/{pid}/empatica_tags_features/empatica_tags_python_{provider_key}.csv"
script:
"../src/features/entry.py"
rule empatica_tags_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_tags_with_datetime.csv",
time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
params:
provider = lambda wildcards: config["EMPATICA_TAGS"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
sensor_key = "empatica_tags"
output:
"data/interim/{pid}/empatica_tags_features/empatica_tags_r_{provider_key}.csv"
script:
"../src/features/entry.R"
rule merge_sensor_features_for_individual_participants:
input:
feature_files = input_merge_sensor_features_for_individual_participants
output:
"data/processed/features/{pid}/all_sensor_features.csv"
script:
"../src/features/utils/merge_sensor_features_for_individual_participants.R"
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
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rule join_standardized_features_from_empatica:
input:
sensor_features = find_empaticas_standardized_features_files
wildcard_constraints:
sensor_key = '(empatica).*'
output:
"data/processed/features/{pid}/z_{sensor_key}.csv"
script:
"../src/features/utils/join_features_from_providers.R"
rule standardize_features_from_providers_no_empatica:
input:
sensor_features = find_joint_non_empatica_sensor_files
wildcard_constraints:
sensor_key = '(phone|fitbit).*'
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["OTHER"],
provider_key = "OTHER",
sensor_key = "{sensor_key}"
output:
"data/processed/features/{pid}/z_{sensor_key}.csv"
script:
"../src/features/standardization/main.py"
rule merge_standardized_sensor_features_for_individual_participants:
input:
feature_files = input_merge_standardized_sensor_features_for_individual_participants
output:
"data/processed/features/{pid}/z_all_sensor_features.csv"
script:
"../src/features/utils/merge_sensor_features_for_individual_participants.R"
rule merge_sensor_features_for_all_participants:
input:
feature_files = expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"])
output:
"data/processed/features/all_participants/all_sensor_features.csv"
script:
"../src/features/utils/merge_sensor_features_for_all_participants.R"
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
2022-07-20 15:51:22 +02:00
rule merge_standardized_sensor_features_for_all_participants:
input:
feature_files = expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"])
output:
"data/processed/features/all_participants/z_all_sensor_features.csv"
script:
"../src/features/utils/merge_standardized_sensor_features_for_all_participants.R"
rule clean_sensor_features_for_individual_participants:
input:
sensor_data = rules.merge_sensor_features_for_individual_participants.output
wildcard_constraints:
pid = "("+"|".join(config["PIDS"])+")"
params:
provider = lambda wildcards: config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
2022-07-20 15:51:22 +02:00
script_extension = "{script_extension}",
sensor_key = "all_cleaning_individual"
output:
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
2022-07-20 15:51:22 +02:00
"data/processed/features/{pid}/all_sensor_features_cleaned_{provider_key}_{script_extension}.csv" # bo predstavljalo probleme za naprej (kako iskati datoteke + standardizacija itd.)
script:
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
2022-07-20 15:51:22 +02:00
"../src/features/entry.{params.script_extension}"
rule clean_sensor_features_for_all_participants:
input:
sensor_data = rules.merge_sensor_features_for_all_participants.output
params:
provider = lambda wildcards: config["ALL_CLEANING_OVERALL"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
2022-07-20 15:51:22 +02:00
script_extension = "{script_extension}",
sensor_key = "all_cleaning_overall"
output:
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
2022-07-20 15:51:22 +02:00
"data/processed/features/all_participants/all_sensor_features_cleaned_{provider_key}_{script_extension}.csv"
script:
Squashed commit of the following: commit 31a47a5ee4569264e39d7c445525a6e64bb7700a Author: Primoz <sisko.primoz@gmail.com> Date: Wed Jul 20 13:49:22 2022 +0000 Environment version change. commit 5b274ed8993f58e783bda6d82fce936764209c28 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 16:10:07 2022 +0000 Enabled cleaning for all participants + standardization files. commit 203fdb31e0f3c647ef8c8a60cb9531831b7ab924 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 14:14:51 2022 +0000 Features cleaning fixes after testing. Visualization script for phone features values. commit 176178d73b154c30b9eb9eb4a67514f00d6a924e Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 19 09:05:14 2022 +0000 Revert "Necessary config changes." This reverts commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0. commit 26ea6512c9d512f95837e7b047fe510c1d196403 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 13:19:47 2022 +0000 Adding cleaning function condition and cleaning functionality. commit 575c29eef9c21e6f2d7832871e73bc0941643734 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:51:56 2022 +0000 Translation of the cleaning individual RAPIDS function from R to py. commit 6ec1ef50430d2e1f5ce4670d505d5e84ac47f0a0 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 18 12:02:18 2022 +0000 Necessary config changes. commit b5669f51612fbd8378848615d639677851ab032f Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 15:26:00 2022 +0000 Modified snakemake rule to dynamically choose script extention. commit 66636be1e8ae4828228b37c59b9df1faf3fc3d3d Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 14:43:08 2022 +0000 Trying to modify the snakefile rule to execute scripts in two languages depended on the provider. commit 574778b00f3cbb368ef4bc74de15cf5070c65ea9 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 09:49:41 2022 +0000 gitignore: adding required files so that RAPIDS can be run successfully. commit 71018ab178256970535e78961602ab8c7f0ebb14 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 15 08:34:19 2022 +0000 Standardization bug fixes commit 6253c470a624e6bfbb02e0c453b652452eb2dbbc Author: Primoz <sisko.primoz@gmail.com> Date: Thu Jul 14 15:28:02 2022 +0000 Seperate rules for empatica vs. nonempatica standardization. Parameter in config that controls the creation of standardized merged files for individual and all participants.. commit 90f902778565e0896d3bae22ae8551be8b487e67 Author: Primoz <sisko.primoz@gmail.com> Date: Tue Jul 12 14:23:03 2022 +0000 Preparing for final csvs' standardization. commit d25dde3998786a9a582f5cda544ee104386778f9 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:47 2022 +0000 Revert "Changes in config to be reverted." This reverts commit bea7608e7095021fb7c53a9afa07074448fe4313. commit 6b23e70857e63deda98eb98d190af9090626c84b Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 12:08:26 2022 +0000 Enabled standardization for rest (previously active) phone features. Testing still needed. commit 8ec58a6f34ba3d42e5cc71d26e6d91837472ca5f Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 09:07:55 2022 +0000 Enabled standardization for phone calls. All steps completed and tested. commit bea7608e7095021fb7c53a9afa07074448fe4313 Author: Primoz <sisko.primoz@gmail.com> Date: Mon Jul 11 07:47:51 2022 +0000 Changes in config to be reverted. commit 4e84ca0e51bf709bff56fd09437b95310ec6bedd Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:24 2022 +0000 Standardization for the rest of the features. commit cc581aa788e3d5c17131af8f3d5dd6b0c3b5aff7 Author: Primoz <sisko.primoz@gmail.com> Date: Fri Jul 8 14:11:08 2022 +0000 README update again
2022-07-20 15:51:22 +02:00
"../src/features/entry.{params.script_extension}"
rule clean_standardized_sensor_features_for_individual_participants:
input:
sensor_data = rules.merge_standardized_sensor_features_for_individual_participants.output
wildcard_constraints:
pid = "("+"|".join(config["PIDS"])+")"
params:
provider = lambda wildcards: config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
script_extension = "{script_extension}",
sensor_key = "all_cleaning_individual"
output:
"data/processed/features/{pid}/z_all_sensor_features_cleaned_{provider_key}_{script_extension}.csv" # bo predstavljalo probleme za naprej (kako iskati datoteke + standardizacija itd.)
script:
"../src/features/entry.{params.script_extension}"
rule clean_standardized_sensor_features_for_all_participants:
input:
sensor_data = rules.merge_standardized_sensor_features_for_all_participants.output
params:
provider = lambda wildcards: config["ALL_CLEANING_OVERALL"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
script_extension = "{script_extension}",
sensor_key = "all_cleaning_overall"
output:
"data/processed/features/all_participants/z_all_sensor_features_cleaned_{provider_key}_{script_extension}.csv"
script:
"../src/features/entry.{params.script_extension}"