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Migrate messages to new file structure

pull/103/head
JulioV 2020-08-31 13:34:15 -04:00
parent e269062439
commit 132311da77
6 changed files with 98 additions and 39 deletions
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10
Snakefile
View File

@ -32,10 +32,12 @@ if config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]:
min_valid_hours_per_day=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS_PER_DAY"],
min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))
if config["MESSAGES"]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["MESSAGES"]["DB_TABLE"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["MESSAGES"]["DB_TABLE"]))
files_to_compute.extend(expand("data/processed/{pid}/messages_{messages_type}.csv", pid=config["PIDS"], messages_type = config["MESSAGES"]["TYPES"]))
for provider in config["MESSAGES"]["PROVIDERS"].keys():
if config["MESSAGES"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["MESSAGES"]["DB_TABLE"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["MESSAGES"]["DB_TABLE"]))
files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["MESSAGES"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="MESSAGES".lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="MESSAGES".lower()))
for provider in config["CALLS"]["PROVIDERS"].keys():
if config["CALLS"]["PROVIDERS"][provider]["COMPUTE"]:

24
config.yaml
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@ -42,28 +42,30 @@ PHONE_VALID_SENSED_DAYS:
# Communication SMS features config, TYPES and FEATURES keys need to match
MESSAGES:
COMPUTE: False
DB_TABLE: messages
TYPES : [received, sent]
FEATURES:
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
DAY_SEGMENTS: *day_segments
PROVIDERS:
RAPIDS:
COMPUTE: False
MESSAGES_TYPES : [received, sent]
FEATURES:
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/messages
# Communication call features config, TYPES and FEATURES keys need to match
CALLS:
DB_TABLE: calls
PROVIDERS:
RAPIDS:
COMPUTE: True
COMPUTE: False
CALL_TYPES: [missed, incoming, outgoing]
FEATURES:
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
incoming: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
outgoing: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
DAY_SEGMENTS: *day_segments
SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids"
SRC_FOLDER: "rapids" # inside src/features/calls
APPLICATION_GENRES:
CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
@ -87,7 +89,7 @@ LOCATIONS:
MAXIMUM_GAP_ALLOWED: 300
MINUTES_DATA_USED: False
SAMPLING_FREQUENCY: 0
SRC_FOLDER: "doryab"
SRC_FOLDER: "doryab" # inside src/features/locations
SRC_LANGUAGE: "python"
BARNETT:
@ -96,7 +98,7 @@ LOCATIONS:
ACCURACY_LIMIT: 51 # meters, drops location coordinates with an accuracy higher than this. This number means there's a 68% probability the true location is within this radius
TIMEZONE: *timezone
MINUTES_DATA_USED: False # Use this for quality control purposes, how many minutes of data (location coordinates gruped by minute) were used to compute features
SRC_FOLDER: "barnett"
SRC_FOLDER: "barnett" # inside src/features/locations
SRC_LANGUAGE: "r"
BLUETOOTH:

26
rules/features.smk
View File

@ -6,17 +6,29 @@ rule join_features_from_providers:
script:
"../src/features/join_features_from_providers.R"
rule messages_features:
rule messages_r_features:
input:
expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["MESSAGES"]["DB_TABLE"]),
day_segments_labels = expand("data/interim/{sensor}_day_segments_labels.csv", sensor=config["MESSAGES"]["DB_TABLE"])
sensor_data = expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["MESSAGES"]["DB_TABLE"]),
day_segments_labels = "data/interim/day_segments_labels.csv"
params:
messages_type = "{messages_type}",
features = lambda wildcards: config["MESSAGES"]["FEATURES"][wildcards.messages_type]
provider = lambda wildcards: config["MESSAGES"]["PROVIDERS"][wildcards.provider_key],
provider_key = "{provider_key}"
output:
"data/processed/{pid}/messages_{messages_type}.csv"
"data/interim/{pid}/messages_features/messages_r_{provider_key}.csv"
script:
"../src/features/messages_features.R"
"../src/features/messages/messages_entry.R"
rule messages_python_features:
input:
sensor_data = expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["MESSAGES"]["DB_TABLE"]),
day_segments_labels = "data/interim/day_segments_labels.csv"
params:
provider = lambda wildcards: config["MESSAGES"]["PROVIDERS"][wildcards.provider_key],
provider_key = "{provider_key}"
output:
"data/interim/{pid}/messages_features/messages_python_{provider_key}.csv"
script:
"../src/features/messages/messages_entry.py"
rule calls_python_features:
input:

13
src/features/messages/messages_entry.R 100644
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@ -0,0 +1,13 @@
source("renv/activate.R")
source("src/features/utils/utils.R")
library("dplyr")
library("tidyr")
sensor_data_file <- snakemake@input[["sensor_data"]]
day_segments_file <- snakemake@input[["day_segments_labels"]]
provider <- snakemake@params["provider"][["provider"]]
provider_key <- snakemake@params["provider_key"]
sensor_features <- fetch_provider_features(provider, provider_key, "messages", sensor_data_file, day_segments_file)
write.csv(sensor_features, snakemake@output[[1]], row.names = FALSE)

18
src/features/messages/messages_entry.py 100644
View File

@ -0,0 +1,18 @@
import pandas as pd
from importlib import import_module, util
from pathlib import Path
# import fetch_provider_features from src/features/utils/utils.py
spec = util.spec_from_file_location("util", str(Path(snakemake.scriptdir).parent / "utils" / "utils.py"))
mod = util.module_from_spec(spec)
spec.loader.exec_module(mod)
fetch_provider_features = getattr(mod, "fetch_provider_features")
sensor_data_file = snakemake.input["sensor_data"][0]
day_segments_file = snakemake.input["day_segments_labels"]
provider = snakemake.params["provider"]
provider_key = snakemake.params["provider_key"]
sensor_features = fetch_provider_features(provider, provider_key, "messages", sensor_data_file, day_segments_file)
sensor_features.to_csv(snakemake.output[0], index=False)

44
src/features/messages/messages_base.R → src/features/messages/rapids/main.R
View File

@ -1,7 +1,7 @@
library('tidyr')
library('stringr')
base_messages_features <- function(messages, messages_type, day_segment, requested_features){
message_features_of_type <- function(messages, messages_type, day_segment, requested_features){
# Output dataframe
features = data.frame(local_segment = character(), stringsAsFactors = FALSE)
@ -11,20 +11,11 @@ base_messages_features <- function(messages, messages_type, day_segment, request
# The subset of requested features this function can compute
features_to_compute <- intersect(base_features_names, requested_features)
# Filter the rows that belong to day_segment, and put the segment full name in a new column for grouping
date_regex = "[0-9]{4}[\\-|\\/][0-9]{2}[\\-|\\/][0-9]{2}"
hour_regex = "[0-9]{2}:[0-9]{2}:[0-9]{2}"
messages <- messages %>%
filter(message_type == ifelse(messages_type == "received", "1", ifelse(messages_type == "sent", 2, NA))) %>%
filter(grepl(paste0("\\[", day_segment, "#"),assigned_segments)) %>%
mutate(local_segment = str_extract(assigned_segments, paste0("\\[", day_segment, "#", date_regex, "#", hour_regex, "#", date_regex, "#", hour_regex, "\\]")),
local_segment = str_sub(local_segment, 2, -2)) # get rid of first and last character([])
# If there are not features or data to work with, return an empty df with appropiate columns names
if(length(features_to_compute) == 0)
return(features)
if(nrow(messages) < 1)
return(cbind(features, read.csv(text = paste(paste("messages", messages_type, features_to_compute, sep = "_"), collapse = ","), stringsAsFactors = FALSE)))
return(cbind(features, read.csv(text = paste(paste("messages_rapids", messages_type, features_to_compute, sep = "_"), collapse = ","), stringsAsFactors = FALSE)))
for(feature_name in features_to_compute){
if(feature_name == "countmostfrequentcontact"){
@ -39,7 +30,7 @@ base_messages_features <- function(messages, messages_type, day_segment, request
feature <- messages %>%
filter(trace == mostfrequentcontact) %>%
group_by(local_segment) %>%
summarise(!!paste("messages", messages_type, feature_name, sep = "_") := n()) %>%
summarise(!!paste("messages_rapids", messages_type, feature_name, sep = "_") := n()) %>%
replace(is.na(.), 0)
features <- merge(features, feature, by="local_segment", all = TRUE)
} else {
@ -47,10 +38,10 @@ base_messages_features <- function(messages, messages_type, day_segment, request
group_by(local_segment)
feature <- switch(feature_name,
"count" = feature %>% summarise(!!paste("messages", messages_type, feature_name, sep = "_") := n()),
"distinctcontacts" = feature %>% summarise(!!paste("messages", messages_type, feature_name, sep = "_") := n_distinct(trace)),
"timefirstmessage" = feature %>% summarise(!!paste("messages", messages_type, feature_name, sep = "_") := first(local_hour) * 60 + first(local_minute)),
"timelastmessage" = feature %>% summarise(!!paste("messages", messages_type, feature_name, sep = "_") := last(local_hour) * 60 + last(local_minute)))
"count" = feature %>% summarise(!!paste("messages_rapids", messages_type, feature_name, sep = "_") := n()),
"distinctcontacts" = feature %>% summarise(!!paste("messages_rapids", messages_type, feature_name, sep = "_") := n_distinct(trace)),
"timefirstmessage" = feature %>% summarise(!!paste("messages_rapids", messages_type, feature_name, sep = "_") := first(local_hour) * 60 + first(local_minute)),
"timelastmessage" = feature %>% summarise(!!paste("messages_rapids", messages_type, feature_name, sep = "_") := last(local_hour) * 60 + last(local_minute)))
features <- merge(features, feature, by="local_segment", all = TRUE)
}
@ -58,3 +49,24 @@ base_messages_features <- function(messages, messages_type, day_segment, request
features <- features %>% mutate_at(vars(contains("countmostfrequentcontact")), list( ~ replace_na(., 0)))
return(features)
}
rapids_features <- function(messages, day_segment, provider){
messages <- messages %>% filter_data_by_segment(day_segment)
messages_types = provider[["MESSAGES_TYPES"]]
messages_features <- setNames(data.frame(matrix(ncol=1, nrow=0)), c("local_segment"))
for(message_type in messages_types){
# Filter rows that belong to the message type and day segment of interest
message_type_label = ifelse(message_type == "received", "1", ifelse(message_type == "sent", "2", NA))
if(is.na(message_type_label))
stop(paste("Message type can online be received or sent but instead you typed: ", message_type, " in config[MESSAGES][MESSAGES_TYPES]"))
requested_features <- provider[["FEATURES"]][[message_type]]
messages_of_type <- messages %>% filter(message_type == message_type_label)
features <- message_features_of_type(messages_of_type, message_type, day_segment, requested_features)
messages_features <- merge(messages_features, features, all=TRUE)
}
return(messages_features)
}