Refactor snakefiles to smk files and create common.smk
JulioV
parent
1dec6764f8
commit
b83f8ead44
11
Snakefile
11
Snakefile
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@ -1,9 +1,10 @@
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configfile: "config.yaml"
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include: "rules/renv.snakefile"
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include: "rules/preprocessing.snakefile"
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include: "rules/features.snakefile"
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include: "rules/models.snakefile"
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include: "rules/reports.snakefile"
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include: "rules/common.smk"
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include: "rules/renv.smk"
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include: "rules/preprocessing.smk"
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include: "rules/features.smk"
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include: "rules/models.smk"
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include: "rules/reports.smk"
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import itertools
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@ -0,0 +1,113 @@
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# Common.smk ##########################################################################################################
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def infer_participant_platform(participant_file):
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with open(participant_file, encoding="ISO-8859-1") as external_file:
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external_file_content = external_file.readlines()
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platforms = external_file_content[1].strip().split(",")
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if platforms[0] == "multiple" or (len(platforms) > 1 and "android" in platforms and "ios" in platforms):
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platform = "android"
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else:
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platform = platforms[0]
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if platform not in ["android", "ios"]:
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raise ValueError("Platform (line 2) in a participant file should be 'android', 'ios', or 'multiple'. You typed '" + platforms + "'")
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return platform
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# Preprocessing.smk ####################################################################################################
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def optional_phone_sensed_bins_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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tables_platform = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]]] # for android, discard any ios tables that may exist
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elif platform == "ios":
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tables_platform = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"]]] # for ios, discard any android tables that may exist
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return expand("data/raw/{{pid}}/{table}_with_datetime.csv", table = tables_platform)
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# Features.smk #########################################################################################################
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def optional_ar_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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return ["data/raw/{pid}/" + config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"] + "_with_datetime_unified.csv",
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"data/processed/{pid}/" + config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"] + "_deltas.csv"]
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elif platform == "ios":
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return ["data/raw/{pid}/"+config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]+"_with_datetime_unified.csv",
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"data/processed/{pid}/"+config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]+"_deltas.csv"]
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def optional_conversation_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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return ["data/raw/{pid}/" + config["CONVERSATION"]["DB_TABLE"]["ANDROID"] + "_with_datetime_unified.csv"]
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elif platform == "ios":
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return ["data/raw/{pid}/" + config["CONVERSATION"]["DB_TABLE"]["IOS"] + "_with_datetime_unified.csv"]
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def optional_location_barnett_input(wildcards):
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if config["BARNETT_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
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return expand("data/raw/{{pid}}/{sensor}_resampled.csv", sensor=config["BARNETT_LOCATION"]["DB_TABLE"])
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else:
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return expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["BARNETT_LOCATION"]["DB_TABLE"])
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def optional_location_doryab_input(wildcards):
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if config["DORYAB_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
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return expand("data/raw/{{pid}}/{sensor}_resampled.csv", sensor=config["DORYAB_LOCATION"]["DB_TABLE"])
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else:
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return expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["DORYAB_LOCATION"]["DB_TABLE"])
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def optional_steps_sleep_input(wildcards):
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if config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"] == True and config["STEP"]["EXCLUDE_SLEEP"]["TYPE"] == "FITBIT_BASED":
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return "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv"
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else:
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return []
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def optional_wifi_input(wildcards):
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if len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0 and len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) == 0:
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return {"visible_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"])}
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elif len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) == 0 and len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
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return {"connected_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"])}
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elif len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0 and len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
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return {"visible_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]), "connected_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"])}
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else:
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raise ValueError("If you are computing WIFI features you need to provide either VISIBLE_ACCESS_POINTS, CONNECTED_ACCESS_POINTS or both")
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# Models.smk ###########################################################################################################
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def input_merge_features_of_single_participant(wildcards):
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if wildcards.source == "phone_fitbit_features":
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return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"]["PHONE_FEATURES"] + config["PARAMS_FOR_ANALYSIS"]["FITBIT_FEATURES"], day_segment=wildcards.day_segment)
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else:
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return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"][wildcards.source.upper()], day_segment=wildcards.day_segment)
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def optional_input_days_to_include(wildcards):
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if config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["ENABLED"]:
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# This input automatically trigers the rule days_to_analyse in mystudy.snakefile
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return ["data/interim/{pid}/days_to_analyse" + \
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"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_BEFORE_SURGERY"]) + \
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"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_IN_HOSPITAL"]) + \
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"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_AFTER_DISCHARGE"]) + ".csv"]
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else:
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return []
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def optional_input_valid_sensed_days(wildcards):
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if config["PARAMS_FOR_ANALYSIS"]["DROP_VALID_SENSED_DAYS"]["ENABLED"]:
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# This input automatically trigers the rule phone_valid_sensed_days in preprocessing.snakefile
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return ["data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv"]
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else:
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return []
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# Reports.smk ###########################################################################################################
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def optional_heatmap_days_by_sensors_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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tables_platform = [table for table in config["HEATMAP_DAYS_BY_SENSORS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]]] # for android, discard any ios tables that may exist
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elif platform == "ios":
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tables_platform = [table for table in config["HEATMAP_DAYS_BY_SENSORS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"]]] # for ios, discard any android tables that may exist
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return expand("data/raw/{{pid}}/{table}_with_datetime.csv", table = tables_platform)
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@ -1,63 +1,3 @@
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def infer_participant_platform(participant_file):
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with open(participant_file, encoding="ISO-8859-1") as external_file:
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external_file_content = external_file.readlines()
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platforms = external_file_content[1].strip().split(",")
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if platforms[0] == "multiple" or (len(platforms) > 1 and "android" in platforms and "ios" in platforms):
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platform = "android"
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else:
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platform = platforms[0]
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return platform
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def optional_ar_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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return ["data/raw/{pid}/" + config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"] + "_with_datetime_unified.csv",
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"data/processed/{pid}/" + config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"] + "_deltas.csv"]
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elif platform == "ios":
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return ["data/raw/{pid}/"+config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]+"_with_datetime_unified.csv",
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"data/processed/{pid}/"+config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]+"_deltas.csv"]
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else:
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raise ValueError("Platform (line 2) in a participant file should be 'android', 'ios', or 'multiple'. You typed '" + platforms + "'")
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def optional_conversation_input(wildcards):
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platform = infer_participant_platform("data/external/"+wildcards.pid)
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if platform == "android":
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return ["data/raw/{pid}/" + config["CONVERSATION"]["DB_TABLE"]["ANDROID"] + "_with_datetime_unified.csv"]
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elif platform == "ios":
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return ["data/raw/{pid}/" + config["CONVERSATION"]["DB_TABLE"]["IOS"] + "_with_datetime_unified.csv"]
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else:
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raise ValueError("Platform (line 2) in a participant file should be 'android' or 'ios', or 'multiple'. You typed '" + platforms + "'")
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def optional_location_input(wildcards):
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if config["BARNETT_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
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return expand("data/raw/{{pid}}/{sensor}_resampled.csv", sensor=config["BARNETT_LOCATION"]["DB_TABLE"])
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else:
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return expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["BARNETT_LOCATION"]["DB_TABLE"])
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def optional_location_doryab_input(wildcards):
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if config["DORYAB_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
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return expand("data/raw/{{pid}}/{sensor}_resampled.csv", sensor=config["DORYAB_LOCATION"]["DB_TABLE"])
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else:
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return expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["DORYAB_LOCATION"]["DB_TABLE"])
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def optional_steps_sleep_input(wildcards):
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if config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"] == True and config["STEP"]["EXCLUDE_SLEEP"]["TYPE"] == "FITBIT_BASED":
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return "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv"
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else:
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return []
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def optional_wifi_input(wildcards):
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if len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0 and len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) == 0:
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return {"visible_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"])}
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elif len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) == 0 and len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
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return {"connected_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"])}
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elif len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0 and len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
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return {"visible_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]), "connected_access_points": expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"])}
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else:
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raise ValueError("If you are computing WIFI features you need to provide either VISIBLE_ACCESS_POINTS, CONNECTED_ACCESS_POINTS or both")
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rule messages_features:
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input:
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expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["MESSAGES"]["DB_TABLE"])
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@ -116,7 +56,7 @@ rule ios_activity_recognition_deltas:
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rule location_barnett_features:
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input:
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locations = optional_location_input
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locations = optional_location_barnett_input
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params:
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features = config["BARNETT_LOCATION"]["FEATURES"],
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locations_to_use = config["BARNETT_LOCATION"]["LOCATIONS_TO_USE"],
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@ -36,29 +36,6 @@ rule demographic_features:
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script:
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"../src/features/demographic_features.py"
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def input_merge_features_of_single_participant(wildcards):
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if wildcards.source == "phone_fitbit_features":
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return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"]["PHONE_FEATURES"] + config["PARAMS_FOR_ANALYSIS"]["FITBIT_FEATURES"], day_segment=wildcards.day_segment)
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else:
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return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"][wildcards.source.upper()], day_segment=wildcards.day_segment)
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def optional_input_days_to_include(wildcards):
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if config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["ENABLED"]:
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# This input automatically trigers the rule days_to_analyse in mystudy.snakefile
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return ["data/interim/{pid}/days_to_analyse" + \
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"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_BEFORE_SURGERY"]) + \
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"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_IN_HOSPITAL"]) + \
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"_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_AFTER_DISCHARGE"]) + ".csv"]
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else:
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return []
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def optional_input_valid_sensed_days(wildcards):
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if config["PARAMS_FOR_ANALYSIS"]["DROP_VALID_SENSED_DAYS"]["ENABLED"]:
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# This input automatically trigers the rule phone_valid_sensed_days in preprocessing.snakefile
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return ["data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv"]
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else:
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return []
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rule merge_features_for_individual_model:
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input:
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feature_files = input_merge_features_of_single_participant,
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@ -1,22 +0,0 @@
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# --- Packrat Rules --- #
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## Taken from https://github.com/lachlandeer/snakemake-econ-r
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## packrat_install: installs packrat onto machine
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rule packrat_install:
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shell:
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"R -e 'install.packages(\"packrat\", repos=\"http://cran.us.r-project.org\")'"
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## packrat_install: initialize a packrat environment for this project
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rule packrat_init:
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shell:
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"R -e 'packrat::init()'"
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## packrat_snap : Look for new R packages in files & archives them
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rule packrat_snap:
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shell:
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"R -e 'packrat::snapshot()'"
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## packrat_restore: Installs archived packages onto a new machine
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rule packrat_restore:
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shell:
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"R -e 'packrat::restore()'"
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@ -1,22 +1,3 @@
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def optional_phone_sensed_bins_input(wildcards):
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with open("data/external/"+wildcards.pid, encoding="ISO-8859-1") as external_file:
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external_file_content = external_file.readlines()
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platforms = external_file_content[1].strip().split(",")
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if platforms[0] == "multiple" or (len(platforms) > 1 and "android" in platforms and "ios" in platforms):
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platform = "android"
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else:
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platform = platforms[0]
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if platform not in ["android", "ios"]:
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raise ValueError("Platform (line 2) in a participant file should be 'android', 'ios', or 'multiple'. You typed '" + platforms + "'")
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if platform == "android":
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tables_platform = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["IOS"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"]]] # for android, discard any ios tables that may exist
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elif platform == "ios":
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tables_platform = [table for table in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"] if table not in [config["CONVERSATION"]["DB_TABLE"]["ANDROID"], config["ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"]]] # for ios, discard any android tables that may exist
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return expand("data/raw/{{pid}}/{table}_with_datetime.csv", table = tables_platform)
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rule restore_sql_file:
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input:
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sql_file = "data/external/rapids_example.sql",
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@ -1,27 +1,3 @@
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def optional_heatmap_days_by_sensors_input(wildcards):
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with open("data/external/"+wildcards.pid, encoding="ISO-8859-1") as external_file:
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external_file_content = external_file.readlines()
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platforms = external_file_content[1].strip().split(",")
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if platforms[0] == "multiple" or (len(platforms) > 1 and "android" in platforms and "ios" in platforms):
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platform = "android"
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else:
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platform = platforms[0]
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if platform not in ["android", "ios"]:
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raise ValueError("Platform (line 2) in a participant file should be 'android', 'ios', or 'multiple'. You typed '" + platforms + "'")
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input_for_heatmap_days_by_sensors, tables = [], config["HEATMAP_DAYS_BY_SENSORS"]["DB_TABLES"]
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for sensor in ["ACTIVITY_RECOGNITION", "CONVERSATION"]:
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table = config[sensor]["DB_TABLE"][platform.upper()]
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if table in tables:
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input_for_heatmap_days_by_sensors.append("data/raw/{pid}/" + table + "_with_datetime.csv")
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tables = [x for x in tables if x not in config[sensor]["DB_TABLE"].values()]
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for table in tables:
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input_for_heatmap_days_by_sensors.append("data/raw/{pid}/" + table + "_with_datetime.csv")
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return input_for_heatmap_days_by_sensors
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rule heatmap_features_correlations:
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input:
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features = expand("data/processed/{pid}/{sensor}_{day_segment}.csv", pid=config["PIDS"], sensor=config["HEATMAP_FEATURES_CORRELATIONS"]["PHONE_FEATURES"]+config["HEATMAP_FEATURES_CORRELATIONS"]["FITBIT_FEATURES"], day_segment=config["DAY_SEGMENTS"]),
|
||||
|
|
@ -98,36 +74,3 @@ rule overall_compliance_heatmap:
|
|||
"reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/overall_compliance_heatmap.html"
|
||||
script:
|
||||
"../src/visualization/overall_compliance_heatmap.py"
|
||||
|
||||
# rule heatmap_rows:
|
||||
# input:
|
||||
# sensor = "data/raw/{pid}/{sensor}_with_datetime.csv",
|
||||
# pid_file = "data/external/{pid}"
|
||||
# params:
|
||||
# table = "{sensor}",
|
||||
# pid = "{pid}",
|
||||
# bin_size = config["PHONE_VALID_SENSED_BINS"]["BIN_SIZE"]
|
||||
# output:
|
||||
# "reports/figures/{pid}/{sensor}_heatmap_rows.html"
|
||||
# script:
|
||||
# "../src/visualization/heatmap_rows.py"
|
||||
|
||||
# rule battery_consumption_rates_barchart:
|
||||
# input:
|
||||
# sensor = "data/processed/{pid}/battery_daily.csv",
|
||||
# pid_file = "data/external/{pid}"
|
||||
# params:
|
||||
# pid = "{pid}"
|
||||
# output:
|
||||
# "reports/figures/{pid}/battery_consumption_rates_barchart.html"
|
||||
# script:
|
||||
# "../src/visualization/battery_consumption_rates_barchart.py"
|
||||
|
||||
# rule compliance_report:
|
||||
# input:
|
||||
# sensor_heatmaps = expand("reports/figures/{{pid}}/{sensor}_heatmap_rows.html", sensor=PHONE_SENSORS),
|
||||
# compliance_heatmap = rules.compliance_heatmap.output
|
||||
# output:
|
||||
# "reports/compliance/{pid}/compliance_report.html",
|
||||
# script:
|
||||
# "../src/visualization/compliance_report.Rmd"
|
||||
|
|
@ -19,7 +19,7 @@ cp tests/data/external/* data/external
|
|||
# cp rules/preprocessing.snakefile bak
|
||||
|
||||
echo Disabling downloading of dataset...
|
||||
sed -e '46,58 s/^/#/' -e 's/rules.download_dataset.output/"data\/raw\/\{pid\}\/\{sensor\}_raw\.csv"/' rules/preprocessing.snakefile > tmp
|
||||
sed -e '27,39 s/^/#/' -e 's/rules.download_dataset.output/"data\/raw\/\{pid\}\/\{sensor\}_raw\.csv"/' rules/preprocessing.snakefile > tmp
|
||||
cp tmp rules/preprocessing.snakefile
|
||||
|
||||
echo Running RAPIDS Pipeline on testdata...
|
||||
|
|
|
|||
Loading…
Reference in New Issue