Update create participant files section

config.yaml

@@ -10,15 +10,12 @@ CREATE_PARTICIPANT_FILES:
   CSV_FILE_PATH: "data/external/example_participants.csv" # see docs for required format
   PHONE_SECTION:
     ADD: True
-    DEVICE_ID_COLUMN: device_id # column name
     IGNORED_DEVICE_IDS: []
   FITBIT_SECTION:
     ADD: True
-    DEVICE_ID_COLUMN: fitbit_id # column name
     IGNORED_DEVICE_IDS: []
   EMPATICA_SECTION:
     ADD: True
-    DEVICE_ID_COLUMN: empatica_id # column name
     IGNORED_DEVICE_IDS: []
 
 # See https://www.rapids.science/latest/setup/configuration/#time-segments

docs/setup/configuration.md

@@ -134,14 +134,14 @@ Your CSV file (`[CSV_FILE_PATH]`) should have the following columns (headers) bu
 
 | Column           | Description                                                                                               |
 |------------------|-----------------------------------------------------------------------------------------------------------|
-| phone device id  | The name of this column has to match `[PHONE_SECTION][DEVICE_ID_COLUMN]`. Separate multiple ids with `;`  |
+| device_id        | Phone device id. Separate multiple ids with `;`   |
-| fitbit device id | The name of this column has to match `[FITBIT_SECTION][DEVICE_ID_COLUMN]`. Separate multiple ids with `;`  |
+| fitbit_id        | Fitbit device id. Separate multiple ids with `;`  |
-| empatica device id | The name of this column has to match `[EMPATICA_SECTION][DEVICE_ID_COLUMN]`. Since the most common use case involves having multiple zip files from a single device for each person, set this device id to an arbitrary string (we usually use their `pid`)  |
+| empatica_id      | Empatica device id. Since the most common use case involves having multiple zip files from a single device for each person, set this device id to an arbitrary string (we usually use their `pid`)  |
 | pid              | Unique identifiers with the format pXXX (your participant files will be named with this string)            |
 | platform         | Use `android`, `ios` or `infer` as explained above, separate values with `;`            |
 | label            | A human readable string that is used in reports and visualizations.                                       |
-| start_date       | A string with format `YYY-MM-DD`. |
+| start_date       | A string with format `YYY-MM-DD` or `YYYY-MM-DD HH:MM:SS`. By default, `YYYY-MM-DD` is interpreted as `YYYY-MM-DD 00:00:00`. |
-| end_date         | A string with format `YYY-MM-DD`. |
+| end_date         | A string with format `YYY-MM-DD` or `YYYY-MM-DD HH:MM:SS`. By default, `YYYY-MM-DD` is interpreted as `YYYY-MM-DD 00:00:00`. |
 
 !!! example
     We added white spaces to this example to make it easy to read but you don't have to.

example_profile/example_config.yaml

@@ -5,22 +5,6 @@
 # See https://www.rapids.science/latest/setup/configuration/#participant-files
 PIDS: [example01, example02]
 
-# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
-CREATE_PARTICIPANT_FILES:
-  CSV_FILE_PATH: "data/external/example_participants.csv" # see docs for required format
-  PHONE_SECTION:
-    ADD: True
-    DEVICE_ID_COLUMN: device_id # column name
-    IGNORED_DEVICE_IDS: []
-  FITBIT_SECTION:
-    ADD: True
-    DEVICE_ID_COLUMN: fitbit_id # column name
-    IGNORED_DEVICE_IDS: []
-  EMPATICA_SECTION:
-    ADD: False
-    DEVICE_ID_COLUMN: empatica_id # column name
-    IGNORED_DEVICE_IDS: []
-
 # See https://www.rapids.science/latest/setup/configuration/#time-segments
 TIME_SEGMENTS: &time_segments
   TYPE: PERIODIC # FREQUENCY, PERIODIC, EVENT

src/data/create_participants_files.R

@@ -9,9 +9,9 @@ library("dplyr", warn.conflicts = F)
 config <- snakemake@params[["config"]]
 group <- config$SOURCE$DATABASE_GROUP
 timezone <- config$SOURCE$TIMEZONE
-phone_device_id_column = config$PHONE_SECTION$DEVICE_ID_COLUMN
+phone_device_id_column = "device_id"
-fitbit_device_id_column = config$FITBIT_SECTION$DEVICE_ID_COLUMN
+fitbit_device_id_column = "fitbit_id"
-empatica_device_id_column = config$EMPATICA_SECTION$DEVICE_ID_COLUMN
+empatica_device_id_column = "empatica_id"
 add_phone_section = config$PHONE_SECTION$ADD
 add_fitbit_section = config$FITBIT_SECTION$ADD
 add_empatica_section = config$EMPATICA_SECTION$ADD
@@ -22,7 +22,7 @@ empatica_ignored = config$EMPATICA_SECTION$IGNORED_DEVICE_IDS
 rmysql.settingsfile <- "./.env"
 
 participants <- read_csv(config$CSV_FILE_PATH, col_types=cols_only(device_id="c",pid="c",label="c",platform="c",
-                          start_date=col_date(format = "%Y-%m-%d"),end_date=col_date(format = "%Y-%m-%d"),fitbit_id="c",empatica_id="c")) %>% 
+                          start_date=col_datetime(),end_date=col_datetime(),fitbit_id="c",empatica_id="c")) %>% 
                           mutate(start_date = as.character(start_date), end_date = as.character(end_date)) # we read as date to validate format
 participants <- participants %>% 
 mutate(!!phone_device_id_column := str_replace(!!rlang::sym(phone_device_id_column), ";",","),