R/check.R

In poissonconsulting/nrp: Kootenay Lake Nutrient Restoration Program Data Loading

check_chr_date <- function(x) {
 x_name <- chk::deparse_backtick_chk((substitute(x)))
 chk::chk_character(x, x_name = x_name)
 chk::chk_scalar(x, x_name = x_name)

 date <- tryCatch(dttr2::dtt_date(x), error = function(e) e, warning = function(w) w)

 if(inherits(date, "error") | inherits(date, "warning")) {
   err("Invalid date for ", x_name, ". Please use format: yyyy-mm-dd.")
 } else if(date > Sys.Date()) {
   err(x_name, " is beyond current date.")
 }
 invisible(x)
}

check_chr_datetime <- function(x) {
  x_name <- chk::deparse_backtick_chk((substitute(x)))
  chk::chk_character(x, x_name = x_name)
  chk::chk_scalar(x, x_name = x_name)

  datetime <- tryCatch(dttr2::dtt_date_time(x), error = function(e) e, warning = function(w) w)

  if(inherits(datetime, "error") | inherits(datetime, "warning")) {
    err("Invalid date-time for ", x_name, ". Please use format: yyyy-mm-dd hh:mm:ss with 24 hour time.")
  } else if(datetime > dttr2::dtt_date_time(Sys.Date())) {
    err(x_name, " is beyond current date.")
  }
  invisible(x)
}

check_path <- function(path) {
  chk_string(path)
  path
}

check_ext <- function(path, ext = "sqlite") {
  check_path(path)
  if(!identical(path_ext(path), ext))
    err("path '", path, "' extension must be '", ext, "',")
  path
}

check_file_exists <- function(path) {
  check_path(path)
  if(!file_exists(path)) err("path '", path, "' must exist")
  if(!is_file(path)) err("path '", path, "' must be a file")
  path
}

check_dir_exists <- function(path) {
  check_path(path)
  if(!file_exists(path)) err("path '", path, "' must exist")
  if(!is_dir(path)) err("path '", path, "' must be a directory")
  path
}

check_ctd_data <- function(data, exclusive = FALSE, order = FALSE) {
  check_data(
    data,
    values = list(
      FileID = as.integer(),
      SiteID = "character",
      Date = as.Date("2018-01-01"),
      Time = dttr2::dtt_time(c(NA_real_, "00:00:00")),
      Depth = units::as_units(c(NA, 1), "m"),
      Temperature = units::as_units(c(NA, 1), "degC"),
      Oxygen = units::as_units(c(NA, 1), "mg/l"),
      Oxygen2 = units::as_units(c(NA, 1), "percent"),
      Conductivity = units::as_units(c(NA, 1), "uS/cm"),
      Conductivity2 = units::as_units(c(NA, 1), "mu * S/cm"),
      Salinity = units::as_units(c(NA, 1), "PSU"),
      Backscatter = units::as_units(c(NA, 1), "NTU"),
      Fluorescence = units::as_units(c(NA, 1), "ug/L"),
      Frequency = units::as_units(c(NA, 1), "Hz"),
      Flag = 1,
      Pressure = units::as_units(c(NA, 1), "dbar"),
      Retain = TRUE,
      File = as.character()),
    exclusive = exclusive, order = order
  )
}

check_ems_metals_data <- function(data, exclusive = FALSE, order = FALSE){
  check_data(
    data,
    values = list(
      SiteID = "character" ,
      COLLECTION_START = Sys.time(),
      COLLECTION_END = Sys.time(),
      REQUISITION_ID = 1,
      ANALYZING_AGENCY = "character",
      UPPER_DEPTH = units::as_units("m"),
      LOWER_DEPTH = units::as_units("m"),
      ReplicateID = as.integer(1),
      `Alkalinity Phen. 8.3` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Alkalinity Phen. 8.3` = units::as_units(c(NA, 1), "mg/l"),
      `Aluminum Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Aluminum Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Aluminum Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Aluminum Total` = units::as_units(c(NA, 1), "mg/l"),
      `Antimony Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Antimony Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Antimony Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Antimony Total` = units::as_units(c(NA, 1), "mg/l"),
      `Arsenic Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Arsenic Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Arsenic Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Arsenic Total` = units::as_units(c(NA, 1), "mg/l"),
      `Barium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Barium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Barium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Barium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Beryllium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Beryllium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Beryllium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Beryllium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Bicarbonate Alkalinity` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Bicarbonate Alkalinity` = units::as_units(c(NA, 1), "mg/l"),
      `Bismuth Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Bismuth Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Bismuth Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Bismuth Total` = units::as_units(c(NA, 1), "mg/l"),
      `Boron Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Boron Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Boron Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Boron Total` = units::as_units(c(NA, 1), "mg/l"),
      `Cadmium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Cadmium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Cadmium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Cadmium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Calcium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Calcium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Calcium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Calcium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Carbonate Alkalinity` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Carbonate Alkalinity` = units::as_units(c(NA, 1), "mg/l"),
      `Chromium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Chromium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Chromium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Chromium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Cobalt Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Cobalt Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Cobalt Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Cobalt Total` = units::as_units(c(NA, 1), "mg/l"),
      `Copper Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Copper Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Copper Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Copper Total` = units::as_units(c(NA, 1), "mg/l"),
      `Hardness (Dissolved)` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Hardness (Dissolved)` = units::as_units(c(NA, 1), "mg/l"),
      `Hardness Total (Total)` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Hardness Total (Total)` = units::as_units(c(NA, 1), "mg/l"),
      `Hydroxide Alkalinity` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Hydroxide Alkalinity` = units::as_units(c(NA, 1), "mg/l"),
      `Iron Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Iron Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Iron Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Iron Total` = units::as_units(c(NA, 1), "mg/l"),
      `Lead Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Lead Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Lead Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Lead Total` = units::as_units(c(NA, 1), "mg/l"),
      `Magnesium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Magnesium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Magnesium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Magnesium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Manganese Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Manganese Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Manganese Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Manganese Total` = units::as_units(c(NA, 1), "mg/l"),
      `Molybdenum Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Molybdenum Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Molybdenum Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Molybdenum Total` = units::as_units(c(NA, 1), "mg/l"),
      `Nickel Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Nickel Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Nickel Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Nickel Total` = units::as_units(c(NA, 1), "mg/l"),
      `Phosphorus Total Dissolved metals` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Phosphorus Total Dissolved metals` = units::as_units(c(NA, 1), "mg/l"),
      `Phosphorus Total metals` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Phosphorus Total metals` = units::as_units(c(NA, 1), "mg/l"),
      `Potassium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Potassium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Potassium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Potassium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Selenium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Selenium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Selenium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Selenium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Silicon Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Silicon Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Silicon Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Silicon Total` = units::as_units(c(NA, 1), "mg/l"),
      `Silver Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Silver Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Silver Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Silver Total` = units::as_units(c(NA, 1), "mg/l"),
      `Sodium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Sodium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Sodium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Sodium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Strontium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Strontium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Strontium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Strontium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Sulfur Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Sulfur Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Sulfur Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Sulfur Total` = units::as_units(c(NA, 1), "mg/l"),
      `Thallium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Thallium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Thallium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Thallium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Tin Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Tin Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Tin Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Tin Total` = units::as_units(c(NA, 1), "mg/l"),
      `Titanium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Titanium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Titanium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Titanium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Uranium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Uranium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Uranium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Uranium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Vanadium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Vanadium Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Vanadium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Vanadium Total` = units::as_units(c(NA, 1), "mg/l"),
      `Zinc Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Zinc Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Zinc Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Zinc Total` = units::as_units(c(NA, 1), "mg/l")),
      key = c("SiteID", "COLLECTION_START", "COLLECTION_END", "REQUISITION_ID",
                       "ANALYZING_AGENCY", "UPPER_DEPTH", "LOWER_DEPTH", "ReplicateID"),
    exclusive = exclusive, order = order
  )
}


check_ems_standard_data <- function(data, exclusive = FALSE, order = FALSE){
  check_data(
    data,
    values = list(
      SiteID = "character" ,
      COLLECTION_START = Sys.time(),
      COLLECTION_END = Sys.time(),
      REQUISITION_ID = 1,
      ANALYZING_AGENCY = "character",
      UPPER_DEPTH = units::as_units("m"),
      LOWER_DEPTH = units::as_units("m"),
      ReplicateID = as.integer(1),
      `Alkalinity Total 4.5` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Alkalinity Total 4.5` = units::as_units(c(NA, 1), "mg/l"),
      `Carbon Total Inorganic` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Carbon Total Inorganic` = units::as_units(c(NA, 1), "mg/l"),
      `Carbon Total Organic` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Carbon Total Organic` = units::as_units(c(NA, 1), "mg/l"),
      `Carbon Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Carbon Total` = units::as_units(c(NA, 1), "mg/l"),
      `Chlorophyll A` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Chlorophyll A` = units::as_units(c(NA, 1), "mg/l"),
      `Nitrate (NO3) Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Nitrate (NO3) Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Nitrate(NO3) + Nitrite(NO2) Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Nitrate(NO3) + Nitrite(NO2) Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Nitrogen - Nitrite Dissolved (NO2)` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Nitrogen - Nitrite Dissolved (NO2)` = units::as_units(c(NA, 1), "mg/l"),
      `Nitrogen Ammonia Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Nitrogen Ammonia Total` = units::as_units(c(NA, 1), "mg/l"),
      `Nitrogen Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Nitrogen Total` = units::as_units(c(NA, 1), "mg/l"),
      `Phosphorus Ort.Dis-P` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Phosphorus Ort.Dis-P` = units::as_units(c(NA, 1), "mg/l"),
      `Phosphorus Total Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Phosphorus Total Dissolved` = units::as_units(c(NA, 1), "mg/l"),
      `Phosphorus Total` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Phosphorus Total` = units::as_units(c(NA, 1), "mg/l"),
      `pH` = units::as_units(c(NA, 1), "pH"),
      `Limit pH` = units::as_units(c(NA, 1), "pH"),
      `Silica Reactive Diss` = units::as_units(c(NA, 1), "mg/l"),
      `Limit Silica Reactive Diss` = units::as_units(c(NA, 1), "mg/l"),
      `Turbidity` = units::as_units(c(NA, 1), "NTU"),
      `Limit Turbidity` = units::as_units(c(NA, 1), "NTU")),
      key = c("SiteID", "COLLECTION_START", "COLLECTION_END", "REQUISITION_ID",
          "ANALYZING_AGENCY", "UPPER_DEPTH", "LOWER_DEPTH", "ReplicateID"),
    exclusive = exclusive, order = order
  )
}

check_ems_raw_data <- function(data, exclusive = FALSE, order = FALSE){
  chk_data(data)
  check_names(
    data,
    names = c(
      "EMS_ID",
      "REQUISITION_ID",
      "MONITORING_LOCATION",
      "LATITUDE",
      "LONGITUDE",
      "LOCATION_TYPE",
      "COLLECTION_START",
      "LOCATION_PURPOSE",
      "PERMIT",
      "SAMPLE_CLASS",
      "SAMPLE_STATE",
      "SAMPLE_DESCRIPTOR",
      "PARAMETER_CODE",
      "PARAMETER",
      "ANALYTICAL_METHOD_CODE",
      "ANALYTICAL_METHOD",
      "RESULT_LETTER",
      "RESULT",
      "UNIT",
      "METHOD_DETECTION_LIMIT",
      "MDL_UNIT",
      "QA_INDEX_CODE",
      "UPPER_DEPTH",
      "LOWER_DEPTH"),
    exclusive = exclusive, order = order
  )
  data
}

check_site_date_lookup <- function(data, exclusive = FALSE, order = FALSE) {
  check_data(
    data,
    values = list(
      File = "character",
      Date = "character",
      SiteID = "character"),
    key = c("File"),
    exclusive = exclusive, order = order
  )
}

check_mysid_raw_data <- function(data, exclusive = TRUE, order = TRUE){
  chk_data(data)
  data <- try(check_names(
    data,
    names = names(nrp::mysid_input_cols),
    exclusive = exclusive, order = order),
    silent = TRUE)

  if(inherits(data, "try-error")){
    err("Columns in data do not match template for mysid raw data. see `nrp::mysid_input_cols` for correct column names and order.")
  }
  invisible(data)
}

check_zoo_raw_data <- function(data, exclusive = TRUE, order = TRUE){
  chk_data(data)
  data <- try(check_names(
    data,
    names = names(nrp::zoo_input_cols),
    exclusive = exclusive, order = order),
    silent = TRUE)

  if(inherits(data, "try-error")){
    err("Columns in data do not match template for zooplankton raw data. see `nrp::zoo_input_cols` for correct column names and order.")
  }
  invisible(data)
}

check_phyto_raw_data <- function(data, exclusive = TRUE, order = TRUE){
  chk_data(data)
  data <- try(check_names(
    data,
    names = names(nrp::phyto_input_cols),
    exclusive = exclusive, order = order),
    silent = TRUE)

  if(inherits(data, "try-error")){
    err("Columns in data do not match template for phytoplankton raw data. see `nrp::phyto_input_cols` for correct column names and order.")
  }
  invisible(data)
}

check_new_phyto_species <- function(data) {
  check_data(
    data,
    values = list(
      Taxa = "character",
      Genus = c("character", NA),
      ClassName = "character",
      ClassAlias = c("character", NA)
    ),
    key = c("Taxa"),
    exclusive = TRUE,
    order = TRUE
  )
}

check_new_site <- function(data) {
  check_data(
    data,
    values = list(
      SiteID = "character",
      EmsSiteNumber = c("character", NA),
      SiteName = "character",
      EmsSiteName = c("character", NA),
      BasinArm = "character",
      MaxDepth = 1.1,
      Easting = 1.1,
      Northing = 1.1
    ),
    key = c("SiteID"),
    exclusive = TRUE,
    order = TRUE
  )
}