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update query choices
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the dropdown query options should be updated frequently

the siteid list could not be updated. this is a WQP issue. for now, I removed the siteid option here.
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@cristinamullin
cristinamullin committed Sep 16, 2024
1 parent 467d41b commit 0cf1ce8
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Showing 2 changed files with 43 additions and 39 deletions.
82 changes: 43 additions & 39 deletions R/mod_query_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,25 +16,27 @@ load("inst/extdata/query_choices.Rdata")
# new (2024-05-23) list for new Country/Ocean(s) Query the Water Quality Portal option. Not included in saved query_choices file
library(jsonlite)
library(dplyr)
url <- 'https://www.waterqualitydata.us/Codes/countrycode?mimeType=json'
countryocean_source <- fromJSON(txt=url)
countrycode_url <- 'https://www.waterqualitydata.us/Codes/countrycode?mimeType=json'
countryocean_source <- fromJSON(txt=countrycode_url)
countryocean_source <- countryocean_source$codes %>% select(-one_of('providers'))
countryocean_source <- countryocean_source[order(countryocean_source$desc),]
countryocean_choices <- countryocean_source$value
names(countryocean_choices) <- countryocean_source$desc

# Last run by EDH on 08/25/23
# Last run by CAM on 09/16/24
# county = readr::read_tsv(url("https://www2.census.gov/geo/docs/reference/codes/files/national_county.txt"), col_names = FALSE)
# county = county%>%tidyr::separate(X1,into = c("STUSAB","STATE","COUNTY","COUNTY_NAME","COUNTY_ID"), sep=",")
# orgs = unique(utils::read.csv(url("https://cdx.epa.gov/wqx/download/DomainValues/Organization.CSV"))$ID)
# chars = unique(utils::read.csv(url("https://cdx.epa.gov/wqx/download/DomainValues/Characteristic.CSV"))$Name)
# chargroup = unique(utils::read.csv(url("https://cdx.epa.gov/wqx/download/DomainValues/CharacteristicGroup.CSV"))$Name)
# media = c(unique(utils::read.csv(url("https://cdx.epa.gov/wqx/download/DomainValues/ActivityMedia.CSV"))$Name),"water","Biological Tissue","No media")
# # sitetype = unique(utils::read.csv(url("https://cdx.epa.gov/wqx/download/DomainValues/MonitoringLocationType.CSV"))$Name)
# sitetype = unique(utils::read.csv(url("https://cdx.epa.gov/wqx/download/DomainValues/MonitoringLocationType.CSV"))$Name)
# sitetype = c("Aggregate groundwater use","Aggregate surface-water-use","Aggregate water-use establishment","Atmosphere","Estuary","Facility","Glacier","Lake, Reservoir, Impoundment","Land","Not Assigned","Ocean","Spring","Stream","Subsurface","Well","Wetland")
# projects = unique(data.table::fread("https://www.waterqualitydata.us/data/Project/search?mimeType=csv&zip=no&providers=NWIS&providers=STEWARDS&providers=STORET")$ProjectIdentifier)
# mlids = unique(data.table::fread("https://www.waterqualitydata.us/data/Station/search?mimeType=csv&zip=no&providers=NWIS&providers=STEWARDS&providers=STORET")$MonitoringLocationIdentifier)
# save(orgs, chars, chargroup, media, county, sitetype, projects, mlids, file = "inst/extdata/query_choices.Rdata")
# # not working
# # mlids = unique(data.table::fread("https://www.waterqualitydata.us/data/Station/search?mimeType=csv&zip=no&providers=NWIS&providers=STEWARDS&providers=STORET")$MonitoringLocationIdentifier)
# # removing mlids for now
# save(orgs, chars, chargroup, media, county, sitetype, projects, file = "inst/extdata/query_choices.Rdata")

mod_query_data_ui <- function(id) {
ns <- NS(id)
Expand Down Expand Up @@ -102,11 +104,11 @@ mod_query_data_ui <- function(id) {
)
),
shiny::fluidRow(
column(4,
shiny::selectizeInput(ns("siteid"),
"Monitoring Location ID(s)",
choices = NULL,
multiple = TRUE)),
# column(4,
# shiny::selectizeInput(ns("siteid"),
# "Monitoring Location ID(s)",
# choices = NULL,
# multiple = TRUE)),
column(4,
shiny::selectizeInput(ns("countryocean"),
"Country/Ocean(s)",
Expand All @@ -121,6 +123,7 @@ mod_query_data_ui <- function(id) {
ns("org"),
"Organization(s)",
choices = NULL,
options = list(placeholder = "Start typing or use drop down menu"),
multiple = TRUE
)
),
Expand All @@ -130,6 +133,7 @@ mod_query_data_ui <- function(id) {
ns("project"),
"Project(s)",
choices = NULL,
options = list(placeholder = "Start typing or use drop down menu"),
multiple = TRUE
)
),
Expand All @@ -139,6 +143,7 @@ mod_query_data_ui <- function(id) {
ns("type"),
"Site Type(s)",
choices = c(sitetype),
options = list(placeholder = "Start typing or use drop down menu"),
multiple = TRUE
)
)
Expand All @@ -164,20 +169,22 @@ mod_query_data_ui <- function(id) {
column(
4,
shiny::selectizeInput(
ns("chargroup"),
"Characteristic Group",
ns("characteristic"),
"Characteristic(s)",
choices = NULL,
options = list(placeholder = "Start typing or use drop down menu"),
multiple = TRUE
)
)
),
column(
4,
shiny::selectizeInput(
ns("characteristic"),
"Characteristic(s)",
ns("chargroup"),
"Characteristic Group",
choices = NULL,
options = list(placeholder = "Start typing or use drop down menu"),
multiple = TRUE
)
)
)
),
shiny::fluidRow(
Expand Down Expand Up @@ -323,8 +330,9 @@ mod_query_data_server <- function(id, tadat) {
session,
"chargroup",
choices = c(chargroup),
selected = character(0),
options = list(placeholder = ""),
# selected = character(0),
# options = list(placeholder = ""),
options = list(placeholder = "Start typing or use drop down menu"),
server = TRUE
)
shiny::updateSelectizeInput(session,
Expand All @@ -335,17 +343,16 @@ mod_query_data_server <- function(id, tadat) {
shiny::updateSelectizeInput(session,
"project",
choices = c(projects),
server = TRUE
)
shiny::updateSelectizeInput(
session,
"siteid",
choices = c(mlids),
options = list(placeholder = "Start typing or use drop down menu"),
server = TRUE
)


# shiny::updateSelectizeInput(
# session,
# "siteid",
# choices = c(mlids),
# options = list(placeholder = "Start typing or use drop down menu"),
# server = TRUE
# )
shiny::updateSelectizeInput(
session,
"countryocean",
Expand Down Expand Up @@ -407,6 +414,11 @@ mod_query_data_server <- function(id, tadat) {
} else {
tadat$huc <- input$huc
}
# if (is.null(input$siteid)) {
# tadat$siteid <- "null"
# } else {
# tadat$siteid <- input$siteid
# }
if (is.null(input$type)) {
tadat$siteType <- "null"
} else {
Expand Down Expand Up @@ -437,12 +449,7 @@ mod_query_data_server <- function(id, tadat) {
} else {
tadat$organization <- input$org
}
if (is.null(input$siteid)) {
tadat$siteid <- "null"
} else {
tadat$siteid <- input$siteid
# siteid = stringr::str_trim(unlist(strsplit(input$siteids,",")))
}

if (length(input$endDate) == 0) {
# ensure if date is empty, the query receives a proper input ("null")
tadat$endDate <- "null"
Expand All @@ -469,7 +476,7 @@ mod_query_data_server <- function(id, tadat) {
countycode = tadat$countycode,
countrycode = tadat$countrycode,
huc = tadat$huc,
siteid = tadat$siteid,
# siteid = tadat$siteid,
siteType = tadat$siteType,
characteristicName = tadat$characteristicName,
characteristicType = tadat$characteristicType,
Expand Down Expand Up @@ -513,12 +520,9 @@ mod_query_data_server <- function(id, tadat) {
shiny::updateSelectizeInput(session, "state", selected = tadat$statecode)
shiny::updateSelectizeInput(session, "county", selected = tadat$countycode)
shiny::updateTextInput(session, "huc")
shiny::updateSelectizeInput(session, "siteid", selected = tadat$siteid)
# shiny::updateSelectizeInput(session, "siteid", selected = tadat$siteid)
shiny::updateSelectizeInput(session, "type", selected = tadat$siteType)
shiny::updateSelectizeInput(session,
"characteristic",
selected = tadat$characteristicName
)
shiny::updateSelectizeInput(session, "characteristic", selected = tadat$characteristicName)
shiny::updateSelectizeInput(session, "chargroup", selected = tadat$characteristicType)
shiny::updateSelectizeInput(session, "media", selected = tadat$sampleMedia)
shiny::updateSelectizeInput(session, "project", selected = tadat$project)
Expand Down
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