Mercurial > repos > siwaa > redelac_stics_t

changeset 22:15317ef4816b draft default tip

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 3867fb88de7181d8703dec0b69d1f03a9a36b34b"
author siwaa
date Tue, 21 Jul 2026 14:23:47 +0000
parents 5dcba002e019
children
files redelacSticsTool.R redelacSticsTool.xml
diffstat 2 files changed, 48 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/redelacSticsTool.R	Fri Jul 10 15:02:33 2026 +0000
+++ b/redelacSticsTool.R	Tue Jul 21 14:23:47 2026 +0000
@@ -66,6 +66,53 @@
 # Tec files loading and generating xml
 
 tec_param <- read_params_table(file.path(workspace, TecFile))
+
+# sanitizing (trying to)
+
+paramDesc = SticsRFiles:::get_param_desc()
+
+paramTecDesc <- paramDesc[paramDesc$kind=="PARTEC",]
+
+expectedTypes <- setNames(as.list(paramTecDesc$type), paramTecDesc$name)
+
+expectedTypes <- lapply(expectedTypes, function(x) {
+  if (identical(x, "real")) "numeric" else x
+})
+
+check <- sapply(names(tec_param), function(col) {
+colref <- col                     
+col <- sub("_[0-9]+$", "", col)
+if (!col %in% names(expectedTypes)) { 
+    NA
+  } else {
+class(tec_param[[colref]])[1] == expectedTypes[[col]]
+  }
+})
+
+finalCheck <- check[!is.na(check)]
+                                  
+toFix <- finalCheck[sapply(finalCheck, function(x) x == FALSE)]                                      
+
+converters <- list(
+  integer   = as.integer,
+  numeric   = as.numeric,
+  character = as.character,
+  logical   = as.logical,
+  factor    = as.factor,
+  Date      = as.Date
+)
+
+for (col in names(toFix)) {
+  if (col %in% names(tec_param)) {
+    type <- expectedTypes[[sub("_[0-9]+$", "", col)]]
+    if (type %in% names(converters)) {
+      tec_param[[col]] <- converters[[type]](tec_param[[col]])
+    } else {
+      warning(sprintf("Unknown type '%s' for column '%s'", type, col))
+    }
+  }
+ }
+
 columnToRemove <-
   names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
 columnToKeep <-
--- a/redelacSticsTool.xml	Fri Jul 10 15:02:33 2026 +0000
+++ b/redelacSticsTool.xml	Tue Jul 21 14:23:47 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.23">
+<tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.24">
   <description>to run Stics for REDELAC</description>
   <requirements>
     <container type="singularity">docker://registry.forge.inrae.fr/redelac/redelac-toolbox/sticsrpacks:5337507635242b3ad0f3559a1a6b666512ecf002