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fetchNASISWebReport.R
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fetchNASISWebReport.R
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#' Get component tables from NASIS Web Reports
#'
#' @aliases fetchNASISWebReport get_project_from_NASISWebReport
#' get_progress_from_NASISWebReport get_project_correlation_from_NASISWebReport
#' get_legend_from_NASISWebReport get_mapunit_from_NASISWebReport
#' get_projectmapunit_from_NASISWebReport
#' get_projectmapunit2_from_NASISWebReport get_component_from_NASISWebReport
#' get_chorizon_from_NASISWebReport get_cosoilmoist_from_NASISWebReport
#' get_sitesoilmoist_from_NASISWebReport get_lmuaoverlap_from_NASISWebReport
#'
#' @param projectname text string vector of project names to be inserted into a
#' SQL WHERE clause (default: `NA`)
#' @param mlraoffice text string value identifying the MLRA Regional Soil
#' Survey Office group name inserted into a SQL WHERE clause (default: `NA`)
#' @param mlrassoarea text string value identifying the MLRA Soil Survey Office
#' areasymbol symbol inserted into a SQL WHERE clause (default: `NA`)
#' @param fiscalyear text string value identifying the fiscal year inserted
#' into a SQL WHERE clause (default: `NA`)
#' @param projecttypename text string value identifying the project type name
#' inserted into a SQL WHERE clause (default: `NA`)
#' @param areasymbol text string value identifying the area symbol (e.g.
#' `IN001` or `IN%`) inserted into a SQL WHERE clause (default: `NA`)
#' `NULL` (default: `TRUE`)
#' @param fill should rows with missing component ids be removed (default: `FALSE`)
#' @param rmHzErrors should pedons with horizonation errors be removed from the
#' results? (default: `FALSE`)
#' @param stringsAsFactors deprecated
#' @param droplevels logical: indicating whether to drop unused levels in
#' classifying factors. This is useful when a class has large number of unused
#' classes, which can waste space in tables and figures.
#' @param impute replace missing (i.e. `NULL`) values with `"Not_Populated"` for
#' categorical data, or the "RV" for numeric data or `201` cm if the "RV" is also
#' `NULL` (default: `TRUE`)
#' @param usiteid character: User Site IDs
#' @return A data.frame or list with the results.
#' @author Stephen Roecker
#' @keywords manip
#'
#' @export fetchNASISWebReport
fetchNASISWebReport <- function(projectname, rmHzErrors = FALSE, fill = FALSE,
stringsAsFactors = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}
# load data in pieces
f.mapunit <- get_projectmapunit_from_NASISWebReport(projectname)
f.component <- get_component_from_NASISWebReport(projectname)
f.chorizon <- get_chorizon_from_NASISWebReport(projectname, fill)
# return NULL if one of the required pieces is missing
if(is.null(f.mapunit) | is.null(f.component) | is.null(f.chorizon)) {
message("One or more inputs for fetchNASISWebReport (mapunit, component, or horizon) is NULL, returning NULL.")
return(NULL)
}
# optionally test for bad horizonation... flag, and remove
if (rmHzErrors) {
f.chorizon.test <- aqp::checkHzDepthLogic(f.chorizon,
hzdepths = c('hzdept_r', 'hzdepb_r'),
idname = 'coiid', fast = TRUE)
# which are the good (valid) ones?
good.ids <- as.character(f.chorizon.test$coiid[which(f.chorizon.test$valid)])
bad.ids <- as.character(f.chorizon.test$coiid[which(! f.chorizon.test$valid)])
# keep the good ones
f.chorizon <- f.chorizon[which(f.chorizon$coiid %in% good.ids), ]
# keep track of those components with horizonation errors
if(length(bad.ids) > 0)
assign('component.hz.problems', value=bad.ids, envir=get_soilDB_env())
}
# upgrade to SoilProfilecollection
depths(f.chorizon) <- coiid ~ hzdept_r + hzdepb_r
## TODO: this will fail in the presence of duplicates
## TODO: make this error more informative
# add site data to object
site(f.chorizon) <- f.component # left-join via coiid
# set NASIS-specific horizon identifier
hzidname(f.chorizon) <- 'chiid'
# print any messages on possible data quality problems:
if (exists('component.hz.problems', envir=get_soilDB_env()))
message("-> QC: horizon errors detected:\n\tUse `get('component.hz.problems', envir=get_soilDB_env())` for component keys (cokey)")
# done, return SPC
return(list(spc = f.chorizon, mapunit = f.mapunit))
}
#' @rdname fetchNASISWebReport
#' @export
get_component_from_NASISWebReport <- function(projectname, stringsAsFactors = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}
url <- "https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_component_from_NASISWebReport"
d.component <- lapply(projectname, function(x) {
message("getting project '", x, "' from NasisReportsWebSite \n", sep = "")
args = list(p_projectname = x)
d = tryCatch(parseWebReport(url, args),
error = function(e) {
message(e)
return(NULL)
})
})
d.component <- do.call("rbind", d.component)
if (is.null(d.component))
return(NULL)
# set factor levels according to metadata domains
d.component <- uncode(d.component)
# prep
d.component <- .cogmd_prep(d.component, db = "LIMS")
# return data.frame
return(d.component)
}
#' @rdname fetchNASISWebReport
#' @export
get_chorizon_from_NASISWebReport <- function(projectname, fill = FALSE, stringsAsFactors = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}
url <- "https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_chorizon_from_NASISWebReport"
d.chorizon <- lapply(projectname, function(x) {
args = list(p_projectname = x)
d = parseWebReport(url, args)
})
d.chorizon <- do.call("rbind", d.chorizon)
## TODO: might be nice to abstract this into a new function
# hacks to make R CMD check --as-cran happy:
metadata <- NULL
# load local copy of metadata
load(system.file("data/metadata.rda", package="soilDB")[1])
# transform variables and metadata
if (!all(is.na(d.chorizon$chiid))) {
d.chorizon <- within(d.chorizon, {
texture = tolower(texture)
if (getOption("stringsAsFactors", default = FALSE)) {
texcl = factor(texcl,
levels = metadata[metadata$ColumnPhysicalName == "texcl", "ChoiceValue"],
labels = metadata[metadata$ColumnPhysicalName == "texcl", "ChoiceName"]
)
}
})
}
# fill
if (fill == FALSE) {
d.chorizon <- d.chorizon[!is.na(d.chorizon$chiid), ]
}
# return data.frame
return(d.chorizon)
}
#' @rdname fetchNASISWebReport
#' @export
get_legend_from_NASISWebReport <- function(mlraoffice, areasymbol, droplevels = TRUE, stringsAsFactors = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}
url <- "https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_legend_from_NASISWebReport"
args <- list(p_mlraoffice = mlraoffice, p_areasymbol = areasymbol)
d.legend <- parseWebReport(url, args)
# set factor levels according to metadata domains
d.legend <- uncode(d.legend, droplevels = droplevels)
# date
d.legend$cordate <- as.Date(d.legend$cordate)
# return data.frame
return(d.legend)
}
#' @rdname fetchNASISWebReport
#' @export
get_lmuaoverlap_from_NASISWebReport <- function(areasymbol, droplevels = TRUE, stringsAsFactors = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}
url <- "https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_lmuaoverlap_from_NASISWebReport"
d <- lapply(areasymbol, function(x) {
message("getting legend for '", x, "' from NasisReportsWebSite \n", sep = "")
args = list(p_areasymbol = x)
d = parseWebReport(url, args)
})
d <- do.call("rbind", d)
# set factor levels according to metadata domains
d <- uncode(d, droplevels = droplevels)
# return data.frame
return(d)
}
#' @rdname fetchNASISWebReport
#' @export
get_mapunit_from_NASISWebReport <- function(areasymbol, droplevels = TRUE, stringsAsFactors = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}
url <- "https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_mapunit_from_NASISWebReport"
d.mapunit <- lapply(areasymbol, function(x) {
message("getting map units for '", x, "' from NasisReportsWebSite \n", sep = "")
args = list(p_areasymbol = x)
d = parseWebReport(url, args)
})
d.mapunit <- do.call("rbind", d.mapunit)
d.mapunit$musym = as.character(d.mapunit$musym)
# set factor levels according to metadata domains
d.mapunit <- uncode(d.mapunit, droplevels = droplevels
)
# return data.frame
return(d.mapunit)
}
#' @rdname fetchNASISWebReport
#' @export
get_projectmapunit_from_NASISWebReport <- function(projectname, stringsAsFactors = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}
url <-"https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_projectmapunit_from_NASISWebReport"
d.mapunit <- lapply(projectname, function(x) {
args = list(p_projectname = x)
d = parseWebReport(url, args)
})
d.mapunit <- do.call("rbind", d.mapunit)
d.mapunit$musym = as.character(d.mapunit$musym)
# set factor levels according to metadata domains
d.mapunit <- uncode(d.mapunit)
# return data.frame
return(d.mapunit)
}
#' @rdname fetchNASISWebReport
#' @export
get_projectmapunit2_from_NASISWebReport <- function(mlrassoarea, fiscalyear, projectname, stringsAsFactors = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}
url <-"https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_projectmapunit2_from_NASISWebReport"
args = list(p_mlrassoarea = mlrassoarea, p_fy = fiscalyear, p_projectname = projectname)
d.mapunit = parseWebReport(url, args)
d.mapunit$musym = as.character(d.mapunit$musym)
# set factor levels according to metadata domains
# data is coming back uncoded from LIMS so db is set to "SDA"
d.mapunit <- uncode(d.mapunit)
# return data.frame
return(d.mapunit)
}
#' @rdname fetchNASISWebReport
#' @export
get_project_from_NASISWebReport <- function(mlrassoarea, fiscalyear) {
url <-"https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_project_from_NASISWebReport"
args <- list(p_mlrassoarea = mlrassoarea, p_fy = fiscalyear)
d.project <- parseWebReport(url, args)
# prep
idx <- unlist(lapply(names(d.project), function(x) grepl("date_", x)))
if (any(idx)) {
d.project[idx] <- lapply(d.project[idx], function(x) as.Date(x, format = "%Y/%m/%d"))
}
# return data.frame
return(d.project)
}
#' @rdname fetchNASISWebReport
#' @export
get_progress_from_NASISWebReport <- function(mlrassoarea, fiscalyear, projecttypename) {
url <-"https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_progress_from_NASISWebReport"
args <- list(p_mlrassoarea = mlrassoarea, p_fy = fiscalyear, p_projecttypename = projecttypename)
d.progress <- parseWebReport(url, args)
# return data.frame
return(d.progress)
}
#' @rdname fetchNASISWebReport
#' @export
get_project_correlation_from_NASISWebReport <- function(mlrassoarea, fiscalyear, projectname) {
# nasty hack to trick R CMD check
musym <- NULL
new_musym <- NULL
url <-"https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_project_correlation_from_NASISWebReport"
args <- list(p_mlrassoarea = mlrassoarea, p_fy = fiscalyear, p_projectname = projectname)
d.rcor <- parseWebReport(url, args)
# compute musym_orig for additional lmapunits, necessary to catch changes to the original musym, due to a constraint on the lmapunit table that prevents duplicate musym for additional mapunits
if (! is.null(d.rcor)) {
d.rcor <- within(d.rcor, {
n = nchar(musym)
begin_1 = substr(musym, 2, n)
end_1 = substr(musym, 1, n - 1)
end_4 = substr(musym, 1, n - 4)
idx = musym != new_musym & !is.na(new_musym)
orig_musym = ifelse(idx & musym != begin_1 & (new_musym == begin_1 | substr(musym, 1, 1) %in% c("x", "z")), begin_1, musym)
# Joe recommended using |\\+${1}, but appears to be legit in some cases
orig_musym = ifelse(idx & musym != end_1 & new_musym == end_1 , end_1 , orig_musym)
orig_musym = ifelse(idx & musym != end_4 & new_musym == end_4 , end_4 , orig_musym)
})
}
d.rcor[c("n", "begin_1", "end_1", "end_4", "idx")] <- NULL
# return data.frame
return(d.rcor)
}