Set the timezone.csv path in config.

Take into account that TZCODES_FILE can be created with a rule.

config.yaml

@@ -31,6 +31,7 @@ TIMEZONE:
     SINGLE:
       TZCODE: Europe/Ljubljana
     MULTIPLE:
+      TZ_FILE: data/external/timezone.csv
       TZCODES_FILE: data/external/multiple_timezones.csv
       IF_MISSING_TZCODE: USE_DEFAULT
       DEFAULT_TZCODE: Europe/Ljubljana
@@ -110,6 +111,7 @@ PHONE_APPLICATIONS_FOREGROUND:
   APPLICATION_CATEGORIES:
     CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
     CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
+    PACKAGE_NAMES_HASHED: True
     UPDATE_CATALOGUE_FILE: False # if CATALOGUE_SOURCE is equal to FILE, whether or not to update CATALOGUE_FILE, if CATALOGUE_SOURCE is equal to GOOGLE all scraped genres will be saved to CATALOGUE_FILE
     SCRAPE_MISSING_CATEGORIES: False # whether or not to scrape missing genres, only effective if CATALOGUE_SOURCE is equal to FILE. If CATALOGUE_SOURCE is equal to GOOGLE, all genres are scraped anyway
   PROVIDERS:

problems/app_categories.txt

@@ -0,0 +1,33 @@
+Warning: 1241 parsing failures.
+row           col   expected actual                                                                            file
+  1 is_system_app an integer  TRUE  'data/raw/p011/phone_applications_foreground_with_datetime_with_categories.csv'
+  2 is_system_app an integer  FALSE 'data/raw/p011/phone_applications_foreground_with_datetime_with_categories.csv'
+  3 is_system_app an integer  TRUE  'data/raw/p011/phone_applications_foreground_with_datetime_with_categories.csv'
+  4 is_system_app an integer  TRUE  'data/raw/p011/phone_applications_foreground_with_datetime_with_categories.csv'
+  5 is_system_app an integer  TRUE  'data/raw/p011/phone_applications_foreground_with_datetime_with_categories.csv'
+... ............. .......... ...... ...............................................................................
+See problems(...) for more details.
+
+Warning message:
+The following named parsers don't match the column names: application_name
+Error: Problem with `filter()` input `..1`.
+✖ object 'application_name' not found
+ℹ Input `..1` is `!is.na(application_name)`.
+Backtrace:
+     █
+  1. ├─`%>%`(...)
+  2. ├─dplyr::mutate(...)
+  3. ├─utils::head(., -1)
+  4. ├─dplyr::select(., -c("timestamp"))
+  5. ├─dplyr::filter(., !is.na(application_name))
+  6. ├─dplyr:::filter.data.frame(., !is.na(application_name))
+  7. │ └─dplyr:::filter_rows(.data, ...)
+  8. │   ├─base::withCallingHandlers(...)
+  9. │   └─mask$eval_all_filter(dots, env_filter)
+ 10. └─base::.handleSimpleError(...)
+ 11.   └─dplyr:::h(simpleError(msg, call))
+Execution halted
+[Mon Dec 13 17:19:06 2021]
+Error in rule app_episodes:
+    jobid: 54
+    output: data/interim/p011/phone_app_episodes.csv

problems/locations_barnett.txt

@@ -0,0 +1,5 @@
+Warning message:
+In barnett_daily_features(snakemake) :
+  Barnett's location features cannot be computed for data or time segments that do not span one or more entire days (00:00:00 to 23:59:59). Values below point to the problem:
+Location data rows within a daily time segment: 0
+Location data time span in days: 398.6

rules/common.smk

@@ -114,7 +114,16 @@ def input_tzcodes_file(wilcards):
         if not config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"].lower().endswith(".csv"):
             raise ValueError("[TIMEZONE][MULTIPLE][TZCODES_FILE] should point to a CSV file, instead you typed: " + config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"])
         if not Path(config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"]).exists():
-            raise ValueError("[TIMEZONE][MULTIPLE][TZCODES_FILE] should point to a CSV file, the file in the path you typed does not exist: " + config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"])
+            try:
+                config["TIMEZONE"]["MULTIPLE"]["TZ_FILE"]
+            except KeyError:
+                raise ValueError("To create TZCODES_FILE, a list of timezones should be created " +
+                                 "with the rule preprocessing.smk/prepare_tzcodes_file " +
+                                 "which will create a file specified as config['TIMEZONE']['MULTIPLE']['TZ_FILE']." +
+                                 "\n An alternative is to provide the file manually:" +
+                                 "[TIMEZONE][MULTIPLE][TZCODES_FILE] should point to a CSV file," +
+                                 "but the file in the path you typed does not exist: " +
+                                 config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"])
         return [config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"]]
     return []
 

rules/preprocessing.smk

@@ -9,13 +9,13 @@ rule query_usernames_device_empatica_ids:
         baseline_folder = "/mnt/e/STRAWbaseline/"
     output:
         usernames_file = config["CREATE_PARTICIPANT_FILES"]["USERNAMES_CSV"],
-        timezone_file = "data/external/timezone.csv"
+        timezone_file = config["TIMEZONE"]["MULTIPLE"]["TZ_FILE"]
     script:
         "../../participants/prepare_usernames_file.py"
 
 rule prepare_tzcodes_file:
     input:
-        timezone_file = "data/external/timezone.csv"
+        timezone_file = config["TIMEZONE"]["MULTIPLE"]["TZ_FILE"]
     output:
         tzcodes_file = config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"]
     script:

src/data/application_categories.R

@@ -29,6 +29,7 @@ get_genre <- function(apps){
 apps <- read.csv(snakemake@input[[1]], stringsAsFactors = F)
 genre_catalogue <- data.frame()
 catalogue_source <- snakemake@params[["catalogue_source"]]
+package_names_hashed <- snakemake@params[["package_names_hashed"]]
 update_catalogue_file <- snakemake@params[["update_catalogue_file"]]
 scrape_missing_genres <- snakemake@params[["scrape_missing_genres"]]
 apps_with_genre <- data.frame(matrix(ncol=length(colnames(apps)) + 1,nrow=0, dimnames=list(NULL, c(colnames(apps), "genre"))))
@@ -38,8 +39,12 @@ if(nrow(apps) > 0){
     apps_with_genre <- apps %>% mutate(genre = NA_character_)
   } else if(catalogue_source == "FILE"){
     genre_catalogue <- read.csv(snakemake@params[["catalogue_file"]], colClasses = c("character", "character"))
+    if (package_names_hashed) {
+      apps_with_genre <- left_join(apps, genre_catalogue, by = "package_hash")
+    } else {
       apps_with_genre <- left_join(apps, genre_catalogue, by = "package_name")
     }
+  }
 
   if(catalogue_source == "GOOGLE" || (catalogue_source == "FILE" && scrape_missing_genres)){
     apps_without_genre <- (apps_with_genre %>% filter(is.na(genre)) %>% distinct(package_name))$package_name

src/data/streams/aware_postgresql/format.yaml

@@ -67,10 +67,12 @@ PHONE_APPLICATIONS_FOREGROUND:
       TIMESTAMP: timestamp
       DEVICE_ID: device_id
       PACKAGE_NAME: package_hash
+      APPLICATION_NAME: FLAG_TO_MUTATE
       IS_SYSTEM_APP: is_system_app
     MUTATION:
       COLUMN_MAPPINGS:
-      SCRIPTS: # List any python or r scripts that mutate your raw data
+      SCRIPTS:
+        - src/data/streams/mutations/phone/straw/app_add_name.py
 
 PHONE_APPLICATIONS_NOTIFICATIONS:
   ANDROID:
@@ -78,11 +80,13 @@ PHONE_APPLICATIONS_NOTIFICATIONS:
       TIMESTAMP: timestamp
       DEVICE_ID: device_id
       PACKAGE_NAME: package_hash
+      APPLICATION_NAME: FLAG_TO_MUTATE
       SOUND: sound
       VIBRATE: vibrate
     MUTATION:
       COLUMN_MAPPINGS:
-      SCRIPTS: # List any python or r scripts that mutate your raw data
+      SCRIPTS:
+        - src/data/streams/mutations/phone/straw/app_add_name.py
 
 PHONE_BATTERY:
   ANDROID:

src/data/streams/mutations/phone/straw/app_add_name.py

@@ -0,0 +1,5 @@
+import pandas as pd
+
+def main(data, stream_parameters):
+    data["application_name"] = "hashed"
+    return(data)

src/data/streams/rapids_columns.yaml

@@ -27,12 +27,14 @@ PHONE_APPLICATIONS_FOREGROUND:
   - TIMESTAMP
   - DEVICE_ID
   - PACKAGE_NAME
+  - APPLICATION_NAME
   - IS_SYSTEM_APP
 
 PHONE_APPLICATIONS_NOTIFICATIONS:
   - TIMESTAMP
   - DEVICE_ID
   - PACKAGE_NAME
+  - APPLICATION_NAME
   - SOUND
   - VIBRATE
 

src/visualization/heatmap_sensors_per_minute_per_time_segment.py

@@ -38,6 +38,7 @@ def getDataForPlot(phone_data_yield_per_segment):
     for columns in columns_for_full_index:
         full_index = full_index + columns
     full_index = pd.MultiIndex.from_tuples(full_index, names=("local_segment_start_datetimes", "minutes_after_segment_start"))
+    phone_data_yield_per_segment = phone_data_yield_per_segment.drop_duplicates(subset=["local_segment_start_datetimes", "minutes_after_segment_start"], keep="first")
     phone_data_yield_per_segment = phone_data_yield_per_segment.set_index(["local_segment_start_datetimes", "minutes_after_segment_start"]).reindex(full_index).reset_index().fillna(0)
     
     # transpose the dataframe per local start datetime of the segment and discard the useless index layer

src/visualization/merge_heatmap_sensors_per_minute_per_time_segment.Rmd

@@ -22,7 +22,7 @@ output:
 </style>
 
 ```{r include=FALSE}
-source("renv/activate.R")
+source("/mnt/c/Users/junos/Documents/FWO-ARRS/Analysis/straw2analysis/rapids/renv/activate.R")
 ```