Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

get_chorizon_from_SDA: concatenate many:1 texcl, lieutex within RV chtexturegrp #353

Merged
merged 3 commits into from
Jun 10, 2024
Merged

get_chorizon_from_SDA: concatenate many:1 texcl, lieutex within RV chtexturegrp #353

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
60037f8
get_chorizon_from_SDA: concatenate many:1 texcl, lieutex within RV ch…
brownag May 16, 2024
bc0cba6
left join for horizonless components
brownag May 17, 2024
0bf6dbc
Merge branch 'master' into sda-chorizon1
brownag Jun 10, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
88 changes: 47 additions & 41 deletions R/get_component_from_SDA.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -655,46 +655,55 @@ get_chorizon_from_SDA <- function(WHERE = NULL, duplicates = FALSE,
childs = TRUE,
nullFragsAreZero = TRUE,
droplevels = TRUE,
stringsAsFactors = NULL
) {
stringsAsFactors = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}

q.chorizon <- paste("
SELECT", if (duplicates == FALSE) {"DISTINCT"}
, "hzname, hzdept_r, hzdepb_r, texture, texcl, lieutex,
fragvol_l, fragvol_r, fragvol_h,
sandtotal_l, sandtotal_r, sandtotal_h,
silttotal_l, silttotal_r, silttotal_h,
claytotal_l, claytotal_r, claytotal_h,
om_l, om_r, om_h,
dbthirdbar_l, dbthirdbar_r, dbthirdbar_h,
ksat_l, ksat_r, ksat_h,
awc_l, awc_r, awc_h,
lep_r, sar_r, ec_r, cec7_r, sumbases_r,
ph1to1h2o_l, ph1to1h2o_r, ph1to1h2o_h,
caco3_l, caco3_r, caco3_h,
kwfact, kffact, c.cokey, ch.chkey
FROM legend l INNER JOIN
mapunit mu ON mu.lkey = l.lkey",
if (duplicates == FALSE) { paste(" INNER JOIN
(SELECT MIN(nationalmusym) nationalmusym2, MIN(mukey) AS mukey2
FROM mapunit
GROUP BY nationalmusym) AS mu2 ON mu2.mukey2 = mu.mukey
")
} else { paste(" INNER JOIN
(SELECT nationalmusym, mukey
FROM mapunit) AS mu2 ON mu2.mukey = mu.mukey
")
SELECT ", ifelse(!duplicates, "DISTINCT", ""),
" hzname, hzdept_r, hzdepb_r, texture, texcl, lieutex,
fragvol_l, fragvol_r, fragvol_h,
sandtotal_l, sandtotal_r, sandtotal_h,
silttotal_l, silttotal_r, silttotal_h,
claytotal_l, claytotal_r, claytotal_h,
om_l, om_r, om_h,
dbthirdbar_l, dbthirdbar_r, dbthirdbar_h,
ksat_l, ksat_r, ksat_h,
awc_l, awc_r, awc_h,
lep_r, sar_r, ec_r, cec7_r, sumbases_r,
ph1to1h2o_l, ph1to1h2o_r, ph1to1h2o_h,
caco3_l, caco3_r, caco3_h,
kwfact, kffact, c.cokey, ch.chkey
FROM legend l INNER JOIN
mapunit mu ON mu.lkey = l.lkey",

if (duplicates == FALSE) {
paste(
"INNER JOIN
(SELECT MIN(nationalmusym) nationalmusym2, MIN(mukey) AS mukey2
FROM mapunit
GROUP BY nationalmusym) AS mu2 ON mu2.mukey2 = mu.mukey
"
)
} else {
paste(
"INNER JOIN
(SELECT nationalmusym, mukey
FROM mapunit) AS mu2 ON mu2.mukey = mu.mukey
"
)
},
"INNER JOIN
component c ON c.mukey = mu.mukey LEFT JOIN
chorizon ch ON ch.cokey = c.cokey LEFT OUTER JOIN
chtexturegrp chtg ON chtg.chkey = ch.chkey AND rvindicator = 'Yes' RIGHT JOIN
chtexture cht ON cht.chtgkey = chtg.chtgkey

"INNER JOIN component c ON c.mukey = mu.mukey
LEFT JOIN chorizon ch ON ch.cokey = c.cokey
LEFT JOIN (SELECT ch2.chkey, texture,
STRING_AGG(texcl, ',') texcl,
STRING_AGG(lieutex, ',') lieutex
FROM chorizon ch2
LEFT JOIN chtexturegrp chtg ON chtg.chkey = ch2.chkey AND rvindicator = 'Yes'
LEFT JOIN chtexture cht ON cht.chtgkey = chtg.chtgkey
GROUP BY ch2.chkey, chtg.texture) texagg ON texagg.chkey = ch.chkey
LEFT OUTER JOIN
(SELECT SUM(fragvol_l) fragvol_l, SUM(fragvol_r) fragvol_r, SUM(fragvol_h) fragvol_h, ch2.chkey
FROM chorizon ch2
Expand All @@ -705,19 +714,16 @@ get_chorizon_from_SDA <- function(WHERE = NULL, duplicates = FALSE,
WHERE", WHERE,

"ORDER BY c.cokey, hzdept_r ASC;")

# exec query
d.chorizon <- SDA_query(q.chorizon)

# get metadata
metadata <- get_NASIS_metadata()

if (inherits(d.chorizon, 'try-error')) {
return(invisible(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 (!is.null(d.chorizon) && nrow(d.chorizon) > 0){
Expand Down Expand Up @@ -854,7 +860,7 @@ get_chorizon_from_SDA <- function(WHERE = NULL, duplicates = FALSE,
d.chfrags[idx] <- lapply(d.chfrags[idx], function(x) ifelse(is.na(x), 0, x))
}

d.chorizon <- merge(d.chorizon, d.chfrags, all.x = TRUE, by = "chkey")
d.chorizon <- merge(d.chorizon, d.chfrags, all.x = TRUE, by = "chkey", sort = FALSE)

}
# } else {
Expand Down
Loading