From 62a38741be72f4a5a4a86c1cd36b6301c6cc6e36 Mon Sep 17 00:00:00 2001 From: Steven Uggowitzer Date: Sun, 9 Jan 2022 19:47:34 +0000 Subject: [PATCH] Update 'np_glass.R' --- np_glass.R | 344 ++++++++++++++++++++++++++++++------------------------------- 1 file changed, 172 insertions(+), 172 deletions(-) diff --git a/np_glass.R b/np_glass.R index 9a499101..5bbcf06e 100644 --- a/np_glass.R +++ b/np_glass.R @@ -1,172 +1,172 @@ -library(RPostgreSQL) -library(rlang) -library(plyr) -library(dplyr) -library(DBI) -library(RCurl) - -con <- dbConnect(PostgreSQL(), dbname = 'np_glass', host = 'xxxxxxxx', port = 5432, user = 'xxxxxx', password = 'xxxxxxx') - -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 - -# Renaming the header -names(glass)[1] <- "pathogen" -names(glass)[2] <- "sex" -names(glass)[3] <- "age" -names(glass)[4] <- "specimen" -names(glass)[5] <- "antibiotic" -names(glass)[6] <- "status" -names(glass)[7] <- "country" -names(glass)[8] <- "year" -names(glass)[9] <- "value" - -# Replace NA with blank -glass <- glass %>% replace(., is.na(.), "") - -# Replacing null status by replacing with X -glass <- glass %>% mutate(status = ifelse(status == '', 'X', status)) - -# Replacing null age with UNK -glass <- glass %>% mutate(age = ifelse(age == '', 'UNK', age)) - -# Changing gender with capital latter -glass <- glass %>% mutate(sex = ifelse(sex == 'f', 'F', sex)) -glass <- glass %>% mutate(sex = ifelse(sex == 'm', 'M', sex)) -glass <- glass %>% mutate(sex = ifelse(sex == '', 'UNK', sex)) - -# glass - -# Renaming age from uid to code -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 == 'VUF8eXjrbjC', '05<14', 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 == 'eQslOKgf0Wp', '35<44', 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 == 'dGbMkILwzzN', '65<74', 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 == '', 'UNK', age)) - -glass - -# # Renaming 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 == 'st', 'STOOL', specimen)) -# glass <- glass %>% mutate(specimen = ifelse(specimen == 'gn', 'GENITAL', specimen)) - -glass$code = paste(glass$pathogen, glass$specimen, glass$sex, glass$age, glass$antibiotic, glass$year, sep="=") - -glass - -# year <- tail(glass$year, 1) -glass_unique <- paste0(unlist(unique(glass$year)), collapse = ',') -# glass_unique <- unique(glass_unique) -# glass_unique <- paste0(unlist(glass_unique), collapse = ',') - -glass_unique - -# //////////////---------------- 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 <- read.table(text = Sample_file, sep =",", header = TRUE, stringsAsFactors = FALSE) - -Sample_file - - -# Renaming the header -names(Sample_file)[1] <- "sex" -names(Sample_file)[2] <- "age" -names(Sample_file)[3] <- "specimen" -names(Sample_file)[4] <- "country" -names(Sample_file)[5] <- "year" -names(Sample_file)[6] <- "value" - -# Replacing null age with UNK -Sample_file <- Sample_file %>% mutate(age = ifelse(age == '', 'UNK', age)) - -# Changing gender with capital latter -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 == '', 'UNK', sex)) - -# 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 == 'jf5Zr4sleyX', '01<04', 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 == 'T51pNS4GE9a', '25<34', 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 == 'Dh89WgJK9vt', '55<64', 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 == 'VKJhxU3XeVU', '85<', age)) -Sample_file <- Sample_file %>% mutate(age = ifelse(age == '', 'UNK', age)) - -# # Renaming 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 == 'st', 'STOOL', 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 - -# ========================PROCCESSING==================== - -# RIS starting execution ---------------------------------- -delete_RIS_data <- function(glass_unique){ - - query <- paste("delete from ris where year in ", paste("(", glass_unique, ")")) - # query <- paste("delete from irsxes where year in 2015, 2016") - dbSendQuery(con, query) - - print('========= RIS REPORT =========') - msg <- paste("Successfully deleted RIS data for: ", glass_unique) - print(msg) -} - -# Save to database -insert_RIS_data <- function(){ - dbWriteTable(con, name = 'ris', value = as.data.frame(glass), row.names = FALSE, append = TRUE) - msg <- paste("Successfully uploaded RIS data for: ", glass_unique) - print(msg) -} - -delete_RIS_data(glass_unique) -insert_RIS_data() -# ========================== END for RIS ================================ - -# Sample file starting execution ---------------------------------- -delete_SF_data <- function(glass_unique){ - query <- paste("delete from sample_files where year in ", paste("(", glass_unique, ")")) - dbSendQuery(con, query) - - print('========= SAMPLE FILE REPORT =========') - msg <- paste("Successfully deleted Sample File data for: ", glass_unique) - print(msg) -} - - -# Save to database -insert_SF_data <- function(){ - 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) - print(msg) -} - -delete_SF_data(glass_unique) -insert_SF_data() -# ========================== END for Sample file ================================ - - -dbDisconnect(con) - +library(RPostgreSQL) +library(rlang) +library(plyr) +library(dplyr) +library(DBI) +library(RCurl) + +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 <- read.table(text = glass, sep =",", header = TRUE, stringsAsFactors = FALSE) + +glass + +# Renaming the header +names(glass)[1] <- "pathogen" +names(glass)[2] <- "sex" +names(glass)[3] <- "age" +names(glass)[4] <- "specimen" +names(glass)[5] <- "antibiotic" +names(glass)[6] <- "status" +names(glass)[7] <- "country" +names(glass)[8] <- "year" +names(glass)[9] <- "value" + +# Replace NA with blank +glass <- glass %>% replace(., is.na(.), "") + +# Replacing null status by replacing with X +glass <- glass %>% mutate(status = ifelse(status == '', 'X', status)) + +# Replacing null age with UNK +glass <- glass %>% mutate(age = ifelse(age == '', 'UNK', age)) + +# Changing gender with capital latter +glass <- glass %>% mutate(sex = ifelse(sex == 'f', 'F', sex)) +glass <- glass %>% mutate(sex = ifelse(sex == 'm', 'M', sex)) +glass <- glass %>% mutate(sex = ifelse(sex == '', 'UNK', sex)) + +# glass + +# Renaming age from uid to code +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 == 'VUF8eXjrbjC', '05<14', 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 == 'eQslOKgf0Wp', '35<44', 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 == 'dGbMkILwzzN', '65<74', 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 == '', 'UNK', age)) + +glass + +# # Renaming 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 == 'st', 'STOOL', specimen)) +# glass <- glass %>% mutate(specimen = ifelse(specimen == 'gn', 'GENITAL', specimen)) + +glass$code = paste(glass$pathogen, glass$specimen, glass$sex, glass$age, glass$antibiotic, glass$year, sep="=") + +glass + +# year <- tail(glass$year, 1) +glass_unique <- paste0(unlist(unique(glass$year)), collapse = ',') +# glass_unique <- unique(glass_unique) +# glass_unique <- paste0(unlist(glass_unique), collapse = ',') + +glass_unique + +# //////////////---------------- 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 <- read.table(text = Sample_file, sep =",", header = TRUE, stringsAsFactors = FALSE) + +Sample_file + + +# Renaming the header +names(Sample_file)[1] <- "sex" +names(Sample_file)[2] <- "age" +names(Sample_file)[3] <- "specimen" +names(Sample_file)[4] <- "country" +names(Sample_file)[5] <- "year" +names(Sample_file)[6] <- "value" + +# Replacing null age with UNK +Sample_file <- Sample_file %>% mutate(age = ifelse(age == '', 'UNK', age)) + +# Changing gender with capital latter +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 == '', 'UNK', sex)) + +# 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 == 'jf5Zr4sleyX', '01<04', 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 == 'T51pNS4GE9a', '25<34', 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 == 'Dh89WgJK9vt', '55<64', 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 == 'VKJhxU3XeVU', '85<', age)) +Sample_file <- Sample_file %>% mutate(age = ifelse(age == '', 'UNK', age)) + +# # Renaming 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 == 'st', 'STOOL', 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 + +# ========================PROCCESSING==================== + +# RIS starting execution ---------------------------------- +delete_RIS_data <- function(glass_unique){ + + query <- paste("delete from ris where year in ", paste("(", glass_unique, ")")) + # query <- paste("delete from irsxes where year in 2015, 2016") + dbSendQuery(con, query) + + print('========= RIS REPORT =========') + msg <- paste("Successfully deleted RIS data for: ", glass_unique) + print(msg) +} + +# Save to database +insert_RIS_data <- function(){ + dbWriteTable(con, name = 'ris', value = as.data.frame(glass), row.names = FALSE, append = TRUE) + msg <- paste("Successfully uploaded RIS data for: ", glass_unique) + print(msg) +} + +delete_RIS_data(glass_unique) +insert_RIS_data() +# ========================== END for RIS ================================ + +# Sample file starting execution ---------------------------------- +delete_SF_data <- function(glass_unique){ + query <- paste("delete from sample_files where year in ", paste("(", glass_unique, ")")) + dbSendQuery(con, query) + + print('========= SAMPLE FILE REPORT =========') + msg <- paste("Successfully deleted Sample File data for: ", glass_unique) + print(msg) +} + + +# Save to database +insert_SF_data <- function(){ + 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) + print(msg) +} + +delete_SF_data(glass_unique) +insert_SF_data() +# ========================== END for Sample file ================================ + + +dbDisconnect(con) +