Add check for non-overlapping event day segments

data/external/daysegments_event.csv

@@ -1,9 +1,9 @@
-label,event_timestamp,length,shift,shift_direction,pid
+label,event_timestamp,length,shift,shift_direction,device_id
-stress,1587661220000,1hours,0minutes,1,test01
+stress,1587661220000,1hours,0minutes,1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
-stress,1587747620000,4hours,4hours,-1,test01
+stress,1587747620000,4hours,4hours,-1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
-stress,1587906020000,3hours,0minutes,1,test01
+stress,1587906020000,3hours,0minutes,1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
-stress,1588003220000,7hours,4hours,-1,test01
+stress,1588003220000,7hours,4hours,-1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
-stress,1588172420000,9hours,0,-1,test01
+stress,1588172420000,9hours,0,-1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
-mood,1587661220000,7days,0,0,p02
+mood,1587661220000,1hour,0,0,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
-mood,1587747620000,7days,0,0,p02
+mood,1587747620000,1days,0,0,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
-mood,1587906020000,7days,0,0,p02
+mood,1587906020000,7days,0,0,a748ee1a-1d0b-4ae9-9074-279a2b6ba524

rules/preprocessing.smk

@@ -53,7 +53,8 @@ rule download_fitbit_data:
 
 rule compute_day_segments:
     input: 
-        config["DAY_SEGMENTS"]["FILE"]
+        config["DAY_SEGMENTS"]["FILE"],
+        "data/external/participant_files/{pid}.yaml"
     params:
         day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
         pid = "{pid}"

src/data/assign_to_day_segment.R

@@ -138,22 +138,33 @@ assign_to_day_segment <- function(sensor_data, day_segments, day_segments_type,
     sensor_data <- sensor_data %>% 
       group_by(local_timezone) %>% 
       nest() %>% 
-      mutate(inferred_day_segments = map(local_timezone, ~ day_segments %>% 
+      mutate(inferred_day_segments = map(local_timezone, function(tz){ 
+                                         inferred <- day_segments %>% 
                                            mutate(shift = ifelse(shift == "0", "0seconds", shift),
                                                   segment_start_ts = event_timestamp + (as.integer(seconds(lubridate::duration(shift))) * ifelse(shift_direction >= 0, 1, -1) * 1000),
                                                   segment_end_ts = segment_start_ts + (as.integer(seconds(lubridate::duration(length))) * 1000),
                                                   # these start and end datetime objects are for labeling only
-                                                  segment_id_start = lubridate::as_datetime(segment_start_ts/1000, tz = .x), 
+                                                  segment_id_start = lubridate::as_datetime(segment_start_ts/1000, tz = tz), 
-                                                  segment_id_end = lubridate::as_datetime(segment_end_ts/1000, tz = .x),
+                                                  segment_id_end = lubridate::as_datetime(segment_end_ts/1000, tz = tz),
                                                   segment_end_ts = segment_end_ts + 999,
                                                   segment_id = paste0("[",
                                                                       paste0(label,"#",
                                                                              paste0(lubridate::date(segment_id_start), " ",
-                                                                             paste(str_pad(hour(segment_id_start),2, pad="0"), str_pad(minute(segment_id_start),2, pad="0"), str_pad(second(segment_id_start),2, pad="0"),sep =":"), ",",
+                                                                                    paste(str_pad(hour(segment_id_start),2, pad="0"), str_pad(minute(segment_id_start),2, pad="0"), str_pad(second(segment_id_start),2, pad="0"),sep =":"), ",",
-                                                                             lubridate::date(segment_id_end), " ",
+                                                                                    lubridate::date(segment_id_end), " ",
-                                                                             paste(str_pad(hour(segment_id_end),2, pad="0"), str_pad(minute(segment_id_end),2, pad="0"), str_pad(second(segment_id_end),2, pad="0"),sep =":")),";",
+                                                                                    paste(str_pad(hour(segment_id_end),2, pad="0"), str_pad(minute(segment_id_end),2, pad="0"), str_pad(second(segment_id_end),2, pad="0"),sep =":")),";",
                                                                              paste0(segment_start_ts, ",", segment_end_ts)),
-                                                                     "]"))),
+                                                                      "]"))
+                                         # Check that for overlapping segments (not allowed because our resampling episode algorithm would have to have a second instead of minute granularity that increases storage and computation time)
+                                         overlapping <-  inferred  %>% group_by(label) %>% arrange(segment_start_ts) %>% 
+                                           mutate(overlaps = if_else(segment_start_ts <= lag(segment_end_ts), TRUE, FALSE),
+                                                  overlapping_segments = paste(paste(lag(label), lag(event_timestamp), lag(length), lag(shift), lag(shift_direction), lag(device_id), sep = ","),"and",
+                                                                                paste(label, event_timestamp, length, shift, shift_direction, device_id, sep = ",")))
+                                         if(any(overlapping$overlaps, na.rm = TRUE)){
+                                           stop(paste0("\n\nOne or more event day segments overlap for ",overlapping$device_id[[1]],", modify their lengths so they don't:\n", paste0(overlapping %>% filter(overlaps == TRUE) %>% pull(overlapping_segments), collapse = "\n"), "\n\n"))
+                                         } else{
+                                           return(inferred)
+                                         }}),
              data = map2(data, inferred_day_segments, assign_rows_to_segments)) %>% 
       select(-inferred_day_segments) %>% 
       unnest(data) %>% 

src/data/compute_day_segments.py

@@ -1,5 +1,6 @@
 import pandas as pd
 import warnings
+import yaml
 
 def is_valid_frequency_segments(day_segments, day_segments_file):
     """
@@ -107,9 +108,9 @@ def is_valid_periodic_segments(day_segments, day_segments_file):
 def is_valid_event_segments(day_segments, day_segments_file):
     day_segments = day_segments.copy(deep=True)
 
-    valid_columns = ["label", "event_timestamp", "length", "shift", "shift_direction", "pid"]
+    valid_columns = ["label", "event_timestamp", "length", "shift", "shift_direction", "device_id"]
     if len(list(set(day_segments.columns) - set(valid_columns))) > 0:
-        error_message = 'The EVENT day segments file in [DAY_SEGMENTS][FILE] must have six columns: label, event_timestamp, length, shift, shift_direction and pid ' \
+        error_message = 'The EVENT day segments file in [DAY_SEGMENTS][FILE] must have six columns: label, event_timestamp, length, shift, shift_direction and device_id ' \
                   'but instead we found {}. Modify {}'.format(list(day_segments.columns), day_segments_file)
         raise ValueError(error_message)
 
@@ -167,10 +168,10 @@ def parse_periodic_segments(day_segments):
     day_segments.loc[day_segments["repeats_on"] == "every_day", "repeats_value"] = 0
     return day_segments
 
-def parse_event_segments(day_segments, pid):
+def parse_event_segments(day_segments, device_id):
-    return day_segments.query("pid == @pid")
+    return day_segments.query("device_id == @device_id")
 
-def parse_day_segments(day_segments_file, segments_type, pid):
+def parse_day_segments(day_segments_file, segments_type, device_id):
     # Add code to validate and parse frequencies, intervals, and events
     # Expected formats:
     # Frequency: label, length columns (e.g. my_prefix, 5) length has to be in minutes (int)
@@ -195,12 +196,15 @@ def parse_day_segments(day_segments_file, segments_type, pid):
     elif(segments_type == "PERIODIC" and is_valid_periodic_segments(day_segments, day_segments_file)):
         day_segments = parse_periodic_segments(day_segments)
     elif(segments_type == "EVENT" and is_valid_event_segments(day_segments, day_segments_file)):
-        day_segments = parse_event_segments(day_segments, pid)
+        day_segments = parse_event_segments(day_segments, device_id)
     else:
         raise ValueError("{} does not have a format compatible with frequency, periodic or event day segments. Please refer to [LINK]".format(day_segments_file))
     return day_segments
 
-final_day_segments = parse_day_segments(snakemake.input[0], snakemake.params["day_segments_type"], snakemake.params["pid"])
+participant_file = yaml.load(open(snakemake.input[1], 'r'), Loader=yaml.FullLoader)
+device_id = participant_file["PHONE"]["DEVICE_IDS"]
+device_id = device_id[len(device_id) -1 ]
+final_day_segments = parse_day_segments(snakemake.input[0], snakemake.params["day_segments_type"], device_id)
 
 if snakemake.params["day_segments_type"] == "EVENT" and final_day_segments.shape[0] == 0:
     warnings.warn("There are no event day segments for {}. Check your day segment file {}".format(snakemake.params["pid"], snakemake.input[0]))