Merge pull request #298 from ncss-tech/sdaquery-errors1

Fix some SDA-related errors and formatting in WCS vignette

R/SDA_query.R

@@ -140,18 +140,27 @@ SDA_query <- function(q) {
 
   # error message is encapsulated in XML, use xml2 library functions to extract
   if (inherits(request.status, 'try-error')) {
-
+    
     # get the request response, this will contain an error message
-    r.content <- httr::content(r, as = 'parsed', encoding = 'UTF-8')
-
-    # parse the XML to get the error message
-    error.msg <- xml2::xml_text(r.content)
-
-    ## message about bad result (previously error/warning)
-    message(error.msg)
-
+    r.content <- try(httr::content(r, as = 'parsed', encoding = 'UTF-8'), silent = TRUE)
+
+    if (!inherits(r.content, 'try-error')) {
+
+      # parse the XML to get the error message
+      error.msg <- try(xml2::xml_text(r.content), silent = TRUE)
+
+      if (inherits(error.msg, 'try-error')) {
+        error.msg <- "Unable to parse error message from XML response"
+      }
+
+      ## message about bad result (previously error/warning)
+      message(error.msg)
+
+    }
+
     # return the error object so calling function/user can handle it
     return(invisible(request.status))
+
   }
 
   # the result is JSON:

R/get_SDA_muaggatt.R

@@ -25,7 +25,7 @@ get_SDA_muaggatt <- function(areasymbols = NULL, mukeys = NULL, WHERE = NULL, qu
     WHERE <- paste("legend.areasymbol IN", format_SQL_in_statement(areasymbols))
   } 
 
-  q <- sprintf("SELECT mapunit.mukey, muaggatt.*
+  q <- sprintf("SELECT muaggatt.mukey, muaggatt.*
                 FROM legend 
                 INNER JOIN mapunit ON mapunit.lkey = legend.lkey
                 INNER JOIN muaggatt ON mapunit.mukey = muaggatt.mukey
@@ -51,6 +51,9 @@ get_SDA_muaggatt <- function(areasymbols = NULL, mukeys = NULL, WHERE = NULL, qu
     warnings()
     stop(attr(res, 'condition'))
   }
+
+  # remove duplicated mukey column
+  res[[ncol(res)]] <- NULL
 
   return(res)
 }

vignettes/wcs-ssurgo.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Map Unit Key Grids and Thematic Maps of SSURGO Data"
+title: "Map Unit Key Grids and Thematic Maps of Soil Survey Geographic (SSURGO) Data"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Map Unit Key Grids and Thematic Maps of SSURGO Data}
@@ -26,7 +26,7 @@ options(width = 100, stringsAsFactors = FALSE)
 ```
 
 
-This vignette will explore how to use the soilDB package to create thematic maps of SSURGO data via Soil Data Access and SoilWeb coverage services.
+This vignette will explore how to use the soilDB package to create thematic maps of the Soil Survey Geographic Database (SSURGO) via Soil Data Access (SDA) and SoilWeb coverage services.
 
 # Introduction
 
@@ -527,6 +527,7 @@ aws <- catalyze(mu2)
 plot(
   aws,
   axes = FALSE,
+  cex.main = 0.7,
   main = c(
     'Plant Available Water Storage (cm)\nWeighted Mean over Components, 0-50cm',
     'Plant Available Water Storage (cm)\nWeighted Mean over Components, 0-100cm'
@@ -576,6 +577,7 @@ tab$class_ENGConstructionMaterialsRoadfill <- factor(
 par(mar = c(4, 12, 3, 3))
 boxplot(
   rating_ENGConstructionMaterialsRoadfill ~ class_ENGConstructionMaterialsRoadfill,
+  cex.main = 0.7,
   main = 'ENG - Construction Materials; Roadfill',
   ylab = "",
   data = tab,
@@ -603,6 +605,7 @@ rating <- catalyze(mu2)
 plot(
   rating,
   axes = FALSE,
+  cex.main = 0.7,
   main = c(
     'Construction Materials; Roadfill\nWeighted Mean over Components',
     'Irrigation Disposal of Wastewater\nWeighted Mean over Components'
@@ -665,6 +668,7 @@ plot(
   mu, 
   legend = FALSE, 
   axes = FALSE, 
+  cex.main = 0.7,
   main = 'gSSURGO Map Unit Key Grid'
 )
 ```
@@ -759,13 +763,13 @@ box()
 Plot aggregate soil properties.
 
 ```{r}
-plot(mu2[['dbthirdbar_r']],
+plot(mu2[['dbthirdbar_r']], cex.main = 0.7,
      main = '1/3 Bar Bulk Density (g/cm^3)\nDominant Component\n0-25cm')
 
-plot(mu2[['awc_r']],
+plot(mu2[['awc_r']], cex.main = 0.7,
      main = 'AWC (cm/cm)\nDominant Component\n0-25cm')
 
-plot(mu2[['ph1to1h2o_r']],
+plot(mu2[['ph1to1h2o_r']], cex.main = 0.7,
      main = 'pH 1:1 H2O\nDominant Component\n0-25cm')
 ```
 
@@ -836,6 +840,7 @@ r <- c(ssc, texture.class)
 # graphical check
 plot(
   r,
+  cex.main = 0.7,
   main = paste0(names(r), " - 25-50cm\nDominant Component")
 )
 ```