Mercurial > repos > siwaa > redelac_stics_t

comparison redelacSticsTool.R @ 22:15317ef4816b draft

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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 3b44cb0a1e76
comparison
equal deleted inserted replaced
21:5dcba002e019 22:15317ef4816b
64 ) 64 )
65 65
66 # Tec files loading and generating xml 66 # Tec files loading and generating xml
67 67
68 tec_param <- read_params_table(file.path(workspace, TecFile)) 68 tec_param <- read_params_table(file.path(workspace, TecFile))
69
70 # sanitizing (trying to)
71
72 paramDesc = SticsRFiles:::get_param_desc()
73
74 paramTecDesc <- paramDesc[paramDesc$kind=="PARTEC",]
75
76 expectedTypes <- setNames(as.list(paramTecDesc$type), paramTecDesc$name)
77
78 expectedTypes <- lapply(expectedTypes, function(x) {
79 if (identical(x, "real")) "numeric" else x
80 })
81
82 check <- sapply(names(tec_param), function(col) {
83 colref <- col
84 col <- sub("_[0-9]+$", "", col)
85 if (!col %in% names(expectedTypes)) {
86 NA
87 } else {
88 class(tec_param[[colref]])[1] == expectedTypes[[col]]
89 }
90 })
91
92 finalCheck <- check[!is.na(check)]
93
94 toFix <- finalCheck[sapply(finalCheck, function(x) x == FALSE)]
95
96 converters <- list(
97 integer = as.integer,
98 numeric = as.numeric,
99 character = as.character,
100 logical = as.logical,
101 factor = as.factor,
102 Date = as.Date
103 )
104
105 for (col in names(toFix)) {
106 if (col %in% names(tec_param)) {
107 type <- expectedTypes[[sub("_[0-9]+$", "", col)]]
108 if (type %in% names(converters)) {
109 tec_param[[col]] <- converters[[type]](tec_param[[col]])
110 } else {
111 warning(sprintf("Unknown type '%s' for column '%s'", type, col))
112 }
113 }
114 }
115
69 columnToRemove <- 116 columnToRemove <-
70 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))]) 117 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
71 columnToKeep <- 118 columnToKeep <-
72 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE] 119 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
73 120