createSSURGO() updates

[brownag]

• Cleanup overwrite logic to close createSSURGO() does not append records when overwrite = FALSE #400; now throws an error when filename exists and overwrite=FALSE
• Adds append argument for unambiguous option to append rows to existing layers in a database

Also, corrects some other situations:

• Using filename and conn with SQLite driver with .sqlite rather than .gpkg output
• Better handling of missing export files, with better messages when quiet=FALSE
• Skip executing commands that rely on a table being present (empty SSURGO export files currently can leaves gaps in the database)

library(soilDB)
library(RSQLite)

base_dir <- "D:/workspace/scratch"
.exdir1 <- file.path(base_dir, "ssurgo", "ssurgo1")
.exdir2 <- file.path(base_dir, "ssurgo", "ssurgo2")

# # download a single SSA
# downloadSSURGO(areasymbols = "ca113", destdir = .exdir1, include_template = FALSE, extract = TRUE, remove_zip = TRUE, db = "SSURGO")
# 
# # download another SSA in a different directory
# downloadSSURGO(areasymbols = "ca654", destdir = .exdir2, include_template = FALSE, extract = TRUE, remove_zip = TRUE, db = "SSURGO")

# init DB file, delete if already existing
.dbfile1 <- file.path(base_dir, "ssurgo1.sqlite")
unlink(.dbfile1)

# init SQLite DB with CA113
createSSURGO(filename = .dbfile1, exdir = .exdir1, include_spatial = FALSE, overwrite = TRUE, quiet = FALSE)
#> Loading required namespace: sf

# append existing SQLite DB with CA654
createSSURGO(filename = .dbfile1, exdir = .exdir2, include_spatial = FALSE, overwrite = FALSE, quiet = TRUE)
#> Error: File 'D:/workspace/scratch/ssurgo1.sqlite' exists and overwrite = FALSE

soilDB::SDA_query("SELECT DISTINCT areasymbol FROM legend ;", .dbfile1)
#>   areasymbol
#> 1      CA113

# init DB file, delete if already existing
.dbfile2 <- file.path(base_dir, "ssurgo2.sqlite")
unlink(.dbfile2)

# init SQLite DB with CA113 and CA654
createSSURGO(filename = .dbfile2, exdir = dirname(.exdir1), include_spatial = FALSE, overwrite = TRUE, quiet = TRUE)

soilDB::SDA_query("SELECT DISTINCT areasymbol FROM legend ;", .dbfile2)
#>   areasymbol
#> 1      CA113
#> 2      CA654

[brownag]

Added append argument and added a bit more to the special cases of the sdv* and mds* tables which you only need one instance of.

library(soilDB)
library(RSQLite)

base_dir <- "D:/workspace/scratch"
.exdir1 <- file.path(base_dir, "ssurgo", "ssurgo1")
.exdir2 <- file.path(base_dir, "ssurgo", "ssurgo2")

# # download a single SSA
# downloadSSURGO(areasymbols = "ca113", destdir = .exdir1, include_template = FALSE, extract = TRUE, remove_zip = TRUE, db = "SSURGO")
# 
# # download another SSA in a different directory
# downloadSSURGO(areasymbols = "ca654", destdir = .exdir2, include_template = FALSE, extract = TRUE, remove_zip = TRUE, db = "SSURGO")

# init DB file, delete if already existing
.dbfile1 <- file.path(base_dir, "ssurgo1.sqlite")
unlink(.dbfile1)

# init SQLite DB with CA113
createSSURGO(filename = .dbfile1, exdir = .exdir1, include_spatial = FALSE, overwrite = TRUE, quiet = FALSE)
#> Loading required namespace: sf
#> File D:/workspace/scratch/ssurgo/ssurgo1/CA113/tabular/cfprodo.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo1/CA113/tabular/chtext.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo1/CA113/tabular/cpwndbrk.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo1/CA113/tabular/csmormr.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo1/CA113/tabular/cstemp.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo1/CA113/tabular/ltext.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo1/CA113/tabular/mutext.txt contains no data

# this "works" (appending three tables we just inserted) but fails uniqueness constraints so nothing happens
createSSURGO(filename = .dbfile1, exdir = .exdir1,
             include_tabular = c("legend", "mapunit", "component"),
             include_spatial = FALSE, append = TRUE, quiet = FALSE)
#> Error : UNIQUE constraint failed: component.cokey
#> Error : UNIQUE constraint failed: legend.lkey
#> Error : UNIQUE constraint failed: mapunit.mukey

# try to write to existing SQLite DB with CA654 [error because file exists]
createSSURGO(filename = .dbfile1, exdir = .exdir2, include_spatial = FALSE, overwrite = FALSE, quiet = FALSE)
#> Error: File 'D:/workspace/scratch/ssurgo1.duckdb' exists and overwrite=FALSE; use append=TRUE to append to an existing file

# append existing SQLite DB with CA654 [no uniqueness issues with metadata tables]
createSSURGO(filename = .dbfile1, exdir = .exdir2, include_spatial = FALSE, append = TRUE, quiet = FALSE)
#> File D:/workspace/scratch/ssurgo/ssurgo2/CA654/tabular/ccancov.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo2/CA654/tabular/cfprodo.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo2/CA654/tabular/chtext.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo2/CA654/tabular/cstemp.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo2/CA654/tabular/ltext.txt contains no data
#> File D:/workspace/scratch/ssurgo/ssurgo2/CA654/tabular/mutext.txt contains no data

soilDB::SDA_query("SELECT DISTINCT areasymbol FROM legend ;", .dbfile1)
#>   areasymbol
#> 1      CA113
#> 2      CA654