fix(OSD): validate OSD called on completely empty OSD .txt file

.github/workflows/R-CMD-check.yml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-latest, r: 'release'}
+          - { os: ubuntu-latest, r: "release" }
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -32,22 +32,21 @@ jobs:
           r-version: ${{ matrix.config.r }}
 
       - uses: r-lib/actions/setup-pandoc@v2
-    
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, any::aqp
           needs: check
-          
+
       - name: Install SoilKnowledgeBase
         run: |
           sudo apt install poppler-utils
-        
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          
+
       - name: Post-processing
         run: |
           Rscript misc/OSD-error-reporting/typical-pedon.R
           Rscript misc/OSD-error-reporting/osd-sections.R
-

R/create_OSD.R

@@ -97,6 +97,11 @@ validateOSD <- function(logfile, filepath) {
 
   raw <- trimws(raw[trimws(raw) != ""])
 
+  if (length(raw) == 0) {
+    logmsg(logfile, "EMPTY OSD FILE: %s", filepath)
+    return(FALSE)
+  }
+
   ser.raw.idx <- grep("SERIES$", raw)[1]
   tax.raw.idx <- grep("TAXONOMIC CLASS[:]", raw)[1]
   brief.desc.idx <- which(1:length(raw) > ser.raw.idx &
@@ -390,15 +395,16 @@ osd_to_json <- function(logfile = file.path(output_dir, "OSD.log"),
 
     x <- validateOSD(logfile, filepath)
 
+    if (is.logical(x)) {
+      if (!x) return(FALSE)
+    }
+
     parsed.OSD <- .doParseOSD(x, logfile, filepath)
 
     # SPC-style components from parseOSD returned as nested data.frames in JSON
     x$SITE <- I(list(parsed.OSD$`site-data`))
     x$HORIZONS <- I(list(parsed.OSD$`hz-data`))
 
-    if (is.logical(x))
-      if (!x) return(FALSE)
-
     fld <- file.path(output_dir, substr(x$SERIES, 1, 1))
 
     if (!dir.exists(fld))

inst/extdata/OSD-error-reporting/log.txt

@@ -1,6 +1,6 @@
 ### Problems by RO  ###
     auburn, al    bozeman, mt      davis, ca morgantown, wv     salina, ks 
-            81            840            833            107             94 
+            81            840            830            107             94 
     temple, tx    wasilla, AK 
             55            281 
 --------------------------------------------------------
@@ -9,7 +9,7 @@
                  FALSE TRUE
   auburn, al        67   14
   bozeman, mt      501  339
-  davis, ca        460  373
+  davis, ca        457  373
   morgantown, wv    93   14
   salina, ks        49   45
   temple, tx        34   21
@@ -20,7 +20,7 @@
                  FALSE TRUE
   auburn, al        74    7
   bozeman, mt      508  332
-  davis, ca        472  361
+  davis, ca        469  361
   morgantown, wv    94   13
   salina, ks        52   42
   temple, tx        47    8
@@ -33,7 +33,7 @@
   AL     2    0
   AR     6    5
   AZ     8    4
-  CA   230  229
+  CA   224  229
   CO    67   30
   CT     4    0
   DE     2    0
@@ -81,7 +81,7 @@
   VA    22    6
   VT     7    1
   WA   104  184
-  WI     8    3
+  WI     5    3
   WV     4    0
   WY   208    5
 --------------------------------------------------------
@@ -92,7 +92,7 @@
   AL     2    0
   AR     8    3
   AZ     9    3
-  CA   225  234
+  CA   219  234
   CO    73   24
   CT     4    0
   DE     2    0
@@ -140,7 +140,7 @@
   VA    24    4
   VT     7    1
   WA   101  187
-  WI     9    2
+  WI     6    2
   WV     4    0
   WY   208    5
 --------------------------------------------------------
@@ -151,7 +151,7 @@
   AL     1    1
   AR     8    3
   AZ     5    7
-  CA   444   15
+  CA   438   15
   CO    80   17
   CT     4    0
   DE     2    0
@@ -199,7 +199,7 @@
   VA    18   10
   VT     5    3
   WA   233   55
-  WI     7    4
+  WI     4    4
   WV     1    3
   WY   202   11
 --------------------------------------------------------
@@ -210,7 +210,7 @@
   AL     2    0
   AR    11    0
   AZ    12    0
-  CA   459    0
+  CA   453    0
   CO    92    5
   CT     4    0
   DE     2    0
@@ -258,7 +258,7 @@
   VA    28    0
   VT     8    0
   WA   248   40
-  WI    11    0
+  WI     8    0
   WV     4    0
   WY   212    1
 --------------------------------------------------------
@@ -269,7 +269,7 @@
   AL     2    0
   AR    11    0
   AZ    12    0
-  CA   459    0
+  CA   453    0
   CO    90    7
   CT     4    0
   DE     2    0
@@ -317,7 +317,7 @@
   VA    19    9
   VT     8    0
   WA   251   37
-  WI    11    0
+  WI     8    0
   WV     4    0
   WY   212    1
 --------------------------------------------------------

inst/extdata/OSD-error-reporting/misc-errors.txt

@@ -8,7 +8,6 @@ GUALALA
 HATU
 KANA`A
 LONOKE
-MECCA
 NEOLA
 NUTALL
 ODESANGEL

inst/extdata/OSD/A/ALBEPEAKE.json

@@ -2,7 +2,7 @@
   "SERIES": "ALBEPEAKE",
   "STATUS": "Tentative Series",
   "BYREV": "JDK-RBT",
-  "REVDATE": "06/2026",
+  "REVDATE": "09/2026",
   "STATES": "NC,VA",
   "OVERVIEW": "MLRA(s)--153B\nDepth class--Very deep\nDrainage class--Subaqueous\nWater depth range--0 to 2 meters (0 to 7 feet)\nParent material--Human-transported materials over loamy estuarine deposits\nGeomorphic location--Dredge-deposit shoals\nSlope range--0 to 1 percent\nMean annual air temperature--17 degrees C (63 degrees F)\nMean annual water temperature--15 degrees C (59 degrees F)",
   "TAXONOMIC CLASS": {
@@ -11,7 +11,7 @@
   },
   "TYPICAL PEDON": {
     "section": "TYPICAL PEDON",
-    "content": "TYPICAL PEDON: Albepeake loamy sand in a dredge-deposit shoal under 1.2 meters of brackish water (colors are for moist soil unless otherwise stated; electrical conductivity is 1:5 by volume solution mixture unless otherwise stated).\n^Aseg--0 to 12 centimeters; 60 percent black (N 2.5/) and 40 percent greenish gray (10Y 5/1) loamy sand; structureless, single grain; nonsticky, nonplastic; slightly fluid; common medium and common fine roots throughout; no sulfurous odor; color change with 3 percent hydrogen peroxide; slight effervescence with 30 percent hydrogen peroxide; nonsaline (0.6 dS/m); neutral (pH 7.0); clear boundary.\n^Cseg1--12 to 34 centimeters; dark greenish gray (10Y 4/1) loamy sand; structureless, single grain; nonsticky, nonplastic; nonfluid; few fine roots throughout; slight sulfurous odor; color change with 3 percent hydrogen peroxide; no effervescence with 30 percent hydrogen peroxide; nonsaline (0.7 dS/m); neutral (pH 6.8); abrupt boundary.\n^Cseg2--34 to 73 centimeters; very dark gray (N 3/) silt loam; structureless, massive; slightly sticky, slightly plastic; very fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; slight effervescence with 30 percent hydrogen peroxide; nonsaline (0.7 dS/m); neutral (pH 7.0); clear boundary.\n^Cseg3--73 to 97 centimeters; dark gray (N 4/) silt loam; structureless, massive; slightly sticky, slightly plastic; very fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; moderate effervescence with 30 percent hydrogen peroxide; nonsaline (0.8 dS/m); neutral (pH 7.2); abrupt boundary.\n^Cseg4--97 to 122 centimeters; dark greenish gray (10Y 4/1) fine sandy loam; structureless, massive; slightly sticky, slightly plastic; slightly fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; moderate effervescence with 30 percent hydrogen peroxide; nonsaline (1.0 dS/m); neutral (pH 7.2); clear boundary.\nCseg5--122 to 205 centimeters; dark gray (N 4/) silty clay loam; structureless, massive; moderately sticky, moderately plastic; very fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; slight effervescence with 30 percent hydrogen peroxide; nonsaline (1.3 dS/m); slightly alkaline (pH 7.8)."
+    "content": "TYPICAL PEDON: Albepeake loamy sand in a dredge-deposit shoal under 1.2 meters of brackish water (colors are for moist soil unless otherwise stated; electrical conductivity is 1:5 by volume solution mixture unless otherwise stated).\n^Aseg--0 to 12 centimeters; 60 percent black (N 2.5/) and 40 percent greenish gray (10Y 5/1) loamy sand; structureless, single grain; nonsticky, nonplastic; slightly fluid; common medium and common fine roots throughout; no sulfurous odor; color change with 3 percent hydrogen peroxide; slight effervescence with 30 percent hydrogen peroxide; nonsaline (0.6 dS/m); neutral (pH 7.0); clear boundary.\n^Cseg1--12 to 34 centimeters; dark greenish gray (10Y 4/1) loamy sand; structureless, single grain; nonsticky, nonplastic; nonfluid; few fine roots throughout; slight sulfurous odor; color change with 3 percent hydrogen peroxide; no effervescence with 30 percent hydrogen peroxide; nonsaline (0.7 dS/m); neutral (pH 6.8); abrupt boundary.\n^Cseg2--34 to 73 centimeters; very dark gray (N 3/) silt loam; structureless, massive; slightly sticky, slightly plastic; very fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; slight effervescence with 30 percent hydrogen peroxide; nonsaline (0.7 dS/m); neutral (pH 7.0); clear boundary.\n^Cseg3--73 to 97 centimeters; dark gray (N 4/) silt loam; structureless, massive; slightly sticky, slightly plastic; very fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; moderate effervescence with 30 percent hydrogen peroxide; nonsaline (0.8 dS/m); neutral (pH 7.2); abrupt boundary.\n^Cseg4--97 to 122 centimeters; dark greenish gray (10Y 4/1) fine sandy loam; structureless, massive; slightly sticky, slightly plastic; slightly fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; moderate effervescence with 30 percent hydrogen peroxide; nonsaline (1.0 dS/m); neutral (pH 7.2); clear boundary.\n2Cseg5--122 to 205 centimeters; dark gray (N 4/) silty clay loam; structureless, massive; moderately sticky, moderately plastic; very fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; slight effervescence with 30 percent hydrogen peroxide; nonsaline (1.3 dS/m); slightly alkaline (pH 7.8)."
   },
   "TYPE LOCATION": {
     "section": "TYPE LOCATION",
@@ -187,7 +187,7 @@
         "narrative": "^Cseg4--97 to 122 centimeters; dark greenish gray (10Y 4/1) fine sandy loam; structureless, massive; slightly sticky, slightly plastic; slightly fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; moderate effervescence with 30 percent hydrogen peroxide; nonsaline (1.0 dS/m); neutral (pH 7.2); clear boundary."
       },
       {
-        "name": "Cseg5",
+        "name": "2Cseg5",
         "top": 122,
         "bottom": 205,
         "dry_hue": "NA",
@@ -207,7 +207,7 @@
         "eff_class": "slight effervescence",
         "distinctness": "NA",
         "topography": "NA",
-        "narrative": "Cseg5--122 to 205 centimeters; dark gray (N 4/) silty clay loam; structureless, massive; moderately sticky, moderately plastic; very fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; slight effervescence with 30 percent hydrogen peroxide; nonsaline (1.3 dS/m); slightly alkaline (pH 7.8)."
+        "narrative": "2Cseg5--122 to 205 centimeters; dark gray (N 4/) silty clay loam; structureless, massive; moderately sticky, moderately plastic; very fluid; no sulfurous odor; no color change with 3 percent hydrogen peroxide; slight effervescence with 30 percent hydrogen peroxide; nonsaline (1.3 dS/m); slightly alkaline (pH 7.8)."
       }
     ]
   ]