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Add date filter for download_dataset

pull/95/head
Meng Li 2020-02-20 15:51:22 -05:00
parent 3369a97d0e
commit 579df6325f
2 changed files with 13 additions and 2 deletions
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3
rules/preprocessing.snakefile
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@ -11,7 +11,8 @@ rule download_dataset:
"data/external/{pid}"
params:
group = config["DOWNLOAD_DATASET"]["GROUP"],
table = "{sensor}"
table = "{sensor}",
timezone = config["TIMEZONE"]
output:
"data/raw/{pid}/{sensor}_raw.csv"
script:

12
src/data/download_dataset.R
View File

@ -7,14 +7,24 @@ library(dplyr)
participant <- snakemake@input[[1]]
group <- snakemake@params[["group"]]
table <- snakemake@params[["table"]]
timezone <- snakemake@params[["timezone"]]
sensor_file <- snakemake@output[[1]]
device_ids <- readLines(participant, n=1)
unified_device_id <- tail(strsplit(device_ids, ",")[[1]], 1)
start_date <- strsplit(readLines(participant, n=4)[4], ",")[[1]][1]
end_date <- strsplit(readLines(participant, n=4)[4], ",")[[1]][2]
start_datetime_utc = format(as.POSIXct(paste0(start_date, " 00:00:00"),format="%Y/%m/%d %H:%M:%S",origin="1970-01-01",tz=timezone), tz="UTC")
end_datetime_utc = format(as.POSIXct(paste0(end_date, " 23:59:59"),format="%Y/%m/%d %H:%M:%S",origin="1970-01-01",tz=timezone), tz="UTC")
rmysql.settingsfile <- "./.env"
stopDB <- dbConnect(MySQL(), default.file = rmysql.settingsfile, group = group)
query <- paste0("SELECT * FROM ", table, " WHERE device_id IN ('", gsub(",", "','", device_ids), "')")
if(!(is.na(start_datetime_utc)) && !(is.na(end_datetime_utc)) && start_datetime_utc < end_datetime_utc){
query <- paste0(query, "AND timestamp BETWEEN 1000*UNIX_TIMESTAMP('", start_datetime_utc, "') AND 1000*UNIX_TIMESTAMP('", end_datetime_utc, "')")
}
sensor_data <- dbGetQuery(stopDB, query)
sensor_data <- sensor_data %>%
arrange(timestamp) %>%
@ -23,4 +33,4 @@ sensor_data <- sensor_data %>%
# Droping duplicates on all columns except for _id
sensor_data <- sensor_data %>% distinct(!!!syms(setdiff(names(sensor_data), "_id")))
write.csv(sensor_data, sensor_file, row.names = FALSE)
dbDisconnect(stopDB)
dbDisconnect(stopDB)