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Update 'np_glass.R'

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Steven Uggowitzer 4 years ago
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1 changed files with 172 additions and 172 deletions
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      np_glass.R

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np_glass.R
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library(RPostgreSQL) library(RPostgreSQL)
library(rlang) library(rlang)
library(plyr) library(plyr)
library(dplyr) library(dplyr)
library(DBI) library(DBI)
library(RCurl) library(RCurl)
con <- dbConnect(PostgreSQL(), dbname = 'np_glass', host = 'xxxxxxxx', port = 5432, user = 'xxxxxx', password = 'xxxxxxx') con <- dbConnect(PostgreSQL(), dbname = 'xxDBxx', host = 'xxHOSTxx', port = 5432, user = 'xxUSERxx', password = 'xxPASSxx')
glass <- getURL(paste0("https://ohp.staging.np.amr.health/api/29/analytics/events/aggregate/wsHfxYEgte5.csv?dimension=ou:isF1Ffne2Ik&dimension=pe:THIS_YEAR;LAST_5_YEARS&dimension=opkhFoeEz9m:IN:eco;sal&dimension=DYsNDR4nCWB&dimension=TRm4iaYikdK-oPyVHCMErH0&dimension=NoTuZ3jydbw:IN:ur;bl&dimension=JkrGmcLg6Zm.gaCDwmKm768&dimension=JkrGmcLg6Zm.C25kY3E21zv&stage=JkrGmcLg6Zm&displayProperty=NAME&outputType=EVENT&outputIdScheme=CODE"), userpwd="api:Pa55word!", httpauth = 1L) glass <- getURL(paste0("https://ohp.staging.np.amr.health/api/29/analytics/events/aggregate/wsHfxYEgte5.csv?dimension=ou:isF1Ffne2Ik&dimension=pe:THIS_YEAR;LAST_5_YEARS&dimension=opkhFoeEz9m:IN:eco;sal&dimension=DYsNDR4nCWB&dimension=TRm4iaYikdK-oPyVHCMErH0&dimension=NoTuZ3jydbw:IN:ur;bl&dimension=JkrGmcLg6Zm.gaCDwmKm768&dimension=JkrGmcLg6Zm.C25kY3E21zv&stage=JkrGmcLg6Zm&displayProperty=NAME&outputType=EVENT&outputIdScheme=CODE"), userpwd="api:Pa55word!", httpauth = 1L)
glass <- read.table(text = glass, sep =",", header = TRUE, stringsAsFactors = FALSE) glass <- read.table(text = glass, sep =",", header = TRUE, stringsAsFactors = FALSE)
glass glass
# Renaming the header # Renaming the header
names(glass)[1] <- "pathogen" names(glass)[1] <- "pathogen"
names(glass)[2] <- "sex" names(glass)[2] <- "sex"
names(glass)[3] <- "age" names(glass)[3] <- "age"
names(glass)[4] <- "specimen" names(glass)[4] <- "specimen"
names(glass)[5] <- "antibiotic" names(glass)[5] <- "antibiotic"
names(glass)[6] <- "status" names(glass)[6] <- "status"
names(glass)[7] <- "country" names(glass)[7] <- "country"
names(glass)[8] <- "year" names(glass)[8] <- "year"
names(glass)[9] <- "value" names(glass)[9] <- "value"
# Replace NA with blank # Replace NA with blank
glass <- glass %>% replace(., is.na(.), "") glass <- glass %>% replace(., is.na(.), "")
# Replacing null status by replacing with X # Replacing null status by replacing with X
glass <- glass %>% mutate(status = ifelse(status == '', 'X', status)) glass <- glass %>% mutate(status = ifelse(status == '', 'X', status))
# Replacing null age with UNK # Replacing null age with UNK
glass <- glass %>% mutate(age = ifelse(age == '', 'UNK', age)) glass <- glass %>% mutate(age = ifelse(age == '', 'UNK', age))
# Changing gender with capital latter # Changing gender with capital latter
glass <- glass %>% mutate(sex = ifelse(sex == 'f', 'F', sex)) glass <- glass %>% mutate(sex = ifelse(sex == 'f', 'F', sex))
glass <- glass %>% mutate(sex = ifelse(sex == 'm', 'M', sex)) glass <- glass %>% mutate(sex = ifelse(sex == 'm', 'M', sex))
glass <- glass %>% mutate(sex = ifelse(sex == '', 'UNK', sex)) glass <- glass %>% mutate(sex = ifelse(sex == '', 'UNK', sex))
# glass # glass
# Renaming age from uid to code # Renaming age from uid to code
glass <- glass %>% mutate(age = ifelse(age == 'y6vwuHXxddO', '<1', age)) glass <- glass %>% mutate(age = ifelse(age == 'y6vwuHXxddO', '<1', age))
glass <- glass %>% mutate(age = ifelse(age == 'jf5Zr4sleyX', '01<04', age)) glass <- glass %>% mutate(age = ifelse(age == 'jf5Zr4sleyX', '01<04', age))
glass <- glass %>% mutate(age = ifelse(age == 'VUF8eXjrbjC', '05<14', age)) glass <- glass %>% mutate(age = ifelse(age == 'VUF8eXjrbjC', '05<14', age))
glass <- glass %>% mutate(age = ifelse(age == 'LF7HNYtqIr5', '15<24', age)) glass <- glass %>% mutate(age = ifelse(age == 'LF7HNYtqIr5', '15<24', age))
glass <- glass %>% mutate(age = ifelse(age == 'T51pNS4GE9a', '25<34', age)) glass <- glass %>% mutate(age = ifelse(age == 'T51pNS4GE9a', '25<34', age))
glass <- glass %>% mutate(age = ifelse(age == 'eQslOKgf0Wp', '35<44', age)) glass <- glass %>% mutate(age = ifelse(age == 'eQslOKgf0Wp', '35<44', age))
glass <- glass %>% mutate(age = ifelse(age == 'G2ur1JRd6uL', '45<54', age)) glass <- glass %>% mutate(age = ifelse(age == 'G2ur1JRd6uL', '45<54', age))
glass <- glass %>% mutate(age = ifelse(age == 'Dh89WgJK9vt', '55<64', age)) glass <- glass %>% mutate(age = ifelse(age == 'Dh89WgJK9vt', '55<64', age))
glass <- glass %>% mutate(age = ifelse(age == 'dGbMkILwzzN', '65<74', age)) glass <- glass %>% mutate(age = ifelse(age == 'dGbMkILwzzN', '65<74', age))
glass <- glass %>% mutate(age = ifelse(age == 'Z6eawM1m33G', '75<84', age)) glass <- glass %>% mutate(age = ifelse(age == 'Z6eawM1m33G', '75<84', age))
glass <- glass %>% mutate(age = ifelse(age == 'VKJhxU3XeVU', '85<', age)) glass <- glass %>% mutate(age = ifelse(age == 'VKJhxU3XeVU', '85<', age))
glass <- glass %>% mutate(age = ifelse(age == '', 'UNK', age)) glass <- glass %>% mutate(age = ifelse(age == '', 'UNK', age))
glass glass
# # Renaming specimen # # Renaming specimen
glass <- glass %>% mutate(specimen = ifelse(specimen == 'bl', 'BLOOD', specimen)) glass <- glass %>% mutate(specimen = ifelse(specimen == 'bl', 'BLOOD', specimen))
glass <- glass %>% mutate(specimen = ifelse(specimen == 'ur', 'URINE', specimen)) glass <- glass %>% mutate(specimen = ifelse(specimen == 'ur', 'URINE', specimen))
# glass <- glass %>% mutate(specimen = ifelse(specimen == 'st', 'STOOL', specimen)) # glass <- glass %>% mutate(specimen = ifelse(specimen == 'st', 'STOOL', specimen))
# glass <- glass %>% mutate(specimen = ifelse(specimen == 'gn', 'GENITAL', specimen)) # glass <- glass %>% mutate(specimen = ifelse(specimen == 'gn', 'GENITAL', specimen))
glass$code = paste(glass$pathogen, glass$specimen, glass$sex, glass$age, glass$antibiotic, glass$year, sep="=") glass$code = paste(glass$pathogen, glass$specimen, glass$sex, glass$age, glass$antibiotic, glass$year, sep="=")
glass glass
# year <- tail(glass$year, 1) # year <- tail(glass$year, 1)
glass_unique <- paste0(unlist(unique(glass$year)), collapse = ',') glass_unique <- paste0(unlist(unique(glass$year)), collapse = ',')
# glass_unique <- unique(glass_unique) # glass_unique <- unique(glass_unique)
# glass_unique <- paste0(unlist(glass_unique), collapse = ',') # glass_unique <- paste0(unlist(glass_unique), collapse = ',')
glass_unique glass_unique
# //////////////---------------- Sample file starting -------------///////////////////// # //////////////---------------- Sample file starting -------------/////////////////////
Sample_file <- getURL(paste0("https://ohp.staging.np.amr.health/api/29/analytics/events/aggregate/wsHfxYEgte5.csv?dimension=ou:isF1Ffne2Ik&dimension=pe:THIS_YEAR;LAST_5_YEARS&dimension=JkrGmcLg6Zm.DYsNDR4nCWB&dimension=JkrGmcLg6Zm.TRm4iaYikdK-oPyVHCMErH0&dimension=JkrGmcLg6Zm.NoTuZ3jydbw:IN:ur;bl&stage=JkrGmcLg6Zm&displayProperty=NAME&outputType=EVENT&outputIdScheme=CODE"), userpwd="api:Pa55word!", httpauth = 1L) Sample_file <- getURL(paste0("https://ohp.staging.np.amr.health/api/29/analytics/events/aggregate/wsHfxYEgte5.csv?dimension=ou:isF1Ffne2Ik&dimension=pe:THIS_YEAR;LAST_5_YEARS&dimension=JkrGmcLg6Zm.DYsNDR4nCWB&dimension=JkrGmcLg6Zm.TRm4iaYikdK-oPyVHCMErH0&dimension=JkrGmcLg6Zm.NoTuZ3jydbw:IN:ur;bl&stage=JkrGmcLg6Zm&displayProperty=NAME&outputType=EVENT&outputIdScheme=CODE"), userpwd="api:Pa55word!", httpauth = 1L)
Sample_file <- read.table(text = Sample_file, sep =",", header = TRUE, stringsAsFactors = FALSE) Sample_file <- read.table(text = Sample_file, sep =",", header = TRUE, stringsAsFactors = FALSE)
Sample_file Sample_file
# Renaming the header # Renaming the header
names(Sample_file)[1] <- "sex" names(Sample_file)[1] <- "sex"
names(Sample_file)[2] <- "age" names(Sample_file)[2] <- "age"
names(Sample_file)[3] <- "specimen" names(Sample_file)[3] <- "specimen"
names(Sample_file)[4] <- "country" names(Sample_file)[4] <- "country"
names(Sample_file)[5] <- "year" names(Sample_file)[5] <- "year"
names(Sample_file)[6] <- "value" names(Sample_file)[6] <- "value"
# Replacing null age with UNK # Replacing null age with UNK
Sample_file <- Sample_file %>% mutate(age = ifelse(age == '', 'UNK', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == '', 'UNK', age))
# Changing gender with capital latter # Changing gender with capital latter
Sample_file <- Sample_file %>% mutate(sex = ifelse(sex == 'f', 'F', sex)) Sample_file <- Sample_file %>% mutate(sex = ifelse(sex == 'f', 'F', sex))
Sample_file <- Sample_file %>% mutate(sex = ifelse(sex == 'm', 'M', sex)) Sample_file <- Sample_file %>% mutate(sex = ifelse(sex == 'm', 'M', sex))
Sample_file <- Sample_file %>% mutate(sex = ifelse(sex == '', 'UNK', sex)) Sample_file <- Sample_file %>% mutate(sex = ifelse(sex == '', 'UNK', sex))
# Renaming age from uid to code # Renaming age from uid to code
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'y6vwuHXxddO', '<1', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'y6vwuHXxddO', '<1', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'jf5Zr4sleyX', '01<04', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'jf5Zr4sleyX', '01<04', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'VUF8eXjrbjC', '05<14', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'VUF8eXjrbjC', '05<14', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'LF7HNYtqIr5', '15<24', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'LF7HNYtqIr5', '15<24', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'T51pNS4GE9a', '25<34', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'T51pNS4GE9a', '25<34', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'eQslOKgf0Wp', '35<44', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'eQslOKgf0Wp', '35<44', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'G2ur1JRd6uL', '45<54', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'G2ur1JRd6uL', '45<54', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'Dh89WgJK9vt', '55<64', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'Dh89WgJK9vt', '55<64', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'dGbMkILwzzN', '65<74', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'dGbMkILwzzN', '65<74', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'Z6eawM1m33G', '75<84', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'Z6eawM1m33G', '75<84', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'VKJhxU3XeVU', '85<', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == 'VKJhxU3XeVU', '85<', age))
Sample_file <- Sample_file %>% mutate(age = ifelse(age == '', 'UNK', age)) Sample_file <- Sample_file %>% mutate(age = ifelse(age == '', 'UNK', age))
# # Renaming specimen # # Renaming specimen
Sample_file <- Sample_file %>% mutate(specimen = ifelse(specimen == 'bl', 'BLOOD', specimen)) Sample_file <- Sample_file %>% mutate(specimen = ifelse(specimen == 'bl', 'BLOOD', specimen))
Sample_file <- Sample_file %>% mutate(specimen = ifelse(specimen == 'ur', 'URINE', specimen)) Sample_file <- Sample_file %>% mutate(specimen = ifelse(specimen == 'ur', 'URINE', specimen))
Sample_file <- Sample_file %>% mutate(specimen = ifelse(specimen == 'st', 'STOOL', specimen)) Sample_file <- Sample_file %>% mutate(specimen = ifelse(specimen == 'st', 'STOOL', specimen))
Sample_file <- Sample_file %>% mutate(specimen = ifelse(specimen == 'gn', 'GENITAL', specimen)) Sample_file <- Sample_file %>% mutate(specimen = ifelse(specimen == 'gn', 'GENITAL', specimen))
Sample_file$code = paste(Sample_file$specimen, Sample_file$sex, Sample_file$age, Sample_file$year, sep="=") Sample_file$code = paste(Sample_file$specimen, Sample_file$sex, Sample_file$age, Sample_file$year, sep="=")
Sample_file Sample_file
# ========================PROCCESSING==================== # ========================PROCCESSING====================
# RIS starting execution ---------------------------------- # RIS starting execution ----------------------------------
delete_RIS_data <- function(glass_unique){ delete_RIS_data <- function(glass_unique){
query <- paste("delete from ris where year in ", paste("(", glass_unique, ")")) query <- paste("delete from ris where year in ", paste("(", glass_unique, ")"))
# query <- paste("delete from irsxes where year in 2015, 2016") # query <- paste("delete from irsxes where year in 2015, 2016")
dbSendQuery(con, query) dbSendQuery(con, query)
print('========= RIS REPORT =========') print('========= RIS REPORT =========')
msg <- paste("Successfully deleted RIS data for: ", glass_unique) msg <- paste("Successfully deleted RIS data for: ", glass_unique)
print(msg) print(msg)
} }
# Save to database # Save to database
insert_RIS_data <- function(){ insert_RIS_data <- function(){
dbWriteTable(con, name = 'ris', value = as.data.frame(glass), row.names = FALSE, append = TRUE) dbWriteTable(con, name = 'ris', value = as.data.frame(glass), row.names = FALSE, append = TRUE)
msg <- paste("Successfully uploaded RIS data for: ", glass_unique) msg <- paste("Successfully uploaded RIS data for: ", glass_unique)
print(msg) print(msg)
} }
delete_RIS_data(glass_unique) delete_RIS_data(glass_unique)
insert_RIS_data() insert_RIS_data()
# ========================== END for RIS ================================ # ========================== END for RIS ================================
# Sample file starting execution ---------------------------------- # Sample file starting execution ----------------------------------
delete_SF_data <- function(glass_unique){ delete_SF_data <- function(glass_unique){
query <- paste("delete from sample_files where year in ", paste("(", glass_unique, ")")) query <- paste("delete from sample_files where year in ", paste("(", glass_unique, ")"))
dbSendQuery(con, query) dbSendQuery(con, query)
print('========= SAMPLE FILE REPORT =========') print('========= SAMPLE FILE REPORT =========')
msg <- paste("Successfully deleted Sample File data for: ", glass_unique) msg <- paste("Successfully deleted Sample File data for: ", glass_unique)
print(msg) print(msg)
} }
# Save to database # Save to database
insert_SF_data <- function(){ insert_SF_data <- function(){
myquery <- dbWriteTable(con, name = 'sample_files', value = as.data.frame(Sample_file), row.names = FALSE, append = TRUE) myquery <- dbWriteTable(con, name = 'sample_files', value = as.data.frame(Sample_file), row.names = FALSE, append = TRUE)
msg <- paste("Successfully uploaded Sample File data for: ", glass_unique) msg <- paste("Successfully uploaded Sample File data for: ", glass_unique)
print(msg) print(msg)
} }
delete_SF_data(glass_unique) delete_SF_data(glass_unique)
insert_SF_data() insert_SF_data()
# ========================== END for Sample file ================================ # ========================== END for Sample file ================================
dbDisconnect(con) dbDisconnect(con)

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