Mercurial > repos > siwaa > redelac_stics_g

changeset 5:4f8d87b9c246 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
author siwaa
date Tue, 04 Jul 2023 16:37:44 +0000
parents af7d9ca55205
children bb1ac57f8545
files redelacSticsInputGenerator.R redelacSticsInputGenerator.bash redelacSticsInputGenerator.xml
diffstat 3 files changed, 33 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/redelacSticsInputGenerator.R	Thu Jun 29 11:03:20 2023 +0000
+++ b/redelacSticsInputGenerator.R	Tue Jul 04 16:37:44 2023 +0000
@@ -17,13 +17,11 @@
 # USMs file
 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
   select(usm_name,datedebut,datefin,finit,nomsol,fstation,fclim1,fclim2,culturean,nbplantes,codesimul,fplt_1,ftec_1,flai_1,fplt_2,ftec_2,flai_2)
-gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = usms_param)
 
 # Tec files
 tec_param <- read_params_table(file.path(workspace, TecFile)) %>%
    select(!c(annee, date_min, date_max, Date_res_1, Date_res_2, Type_res_1, Type_res_2, Date_trav_1, Date_trav_2, Date_trav_3, Type_trav_1, Type_trav_2 ,Type_trav_3, plante_sem, date_sem, starts_with("nom_vari"), date_ferti_1, date_ferti_2, date_ferti_3, type_eng_1, type_eng_2, type_eng_3, date_rec, date_des, juleclair, nbinfloecl))
 gen_tec_xml(param_df = tec_param, out_dir = workspace)
-#   select(!c(annee, date_min, date_max, Date_res_1, Date_res_2, Type_res_1, Type_res_2, Date_trav_1, Date_trav_2, Date_trav_3, Type_trav_1, Type_trav_2 ,Type_trav_3, plante_sem, date_sem)
 
 # Ini files
 ini_param <- read_params_table(file.path(workspace, IniFile))
@@ -35,14 +33,18 @@
 
 # Generate STICS txt files------------------------------------------------------------------------------
 # List of USMs
-list_usms <- SticsRFiles::get_usms_list(file = file.path(workspace,"usms.xml"))
 
 ### Generate txt files into individual folders
 
-# generate text files
-gen_usms_xml2txt(javastics = javastics_path,
-	         workspace = workspace, 
-                 out_dir = txt_path,
-                 verbose = TRUE,
-                 usm = list_usms)
+for(i in 1:nrow(usms_param)) {
+   row <- usms_param[i,]
+   # do stuff with row
+    
+   gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = row)
+
+   gen_usms_xml2txt(javastics = javastics_path,
+	            workspace = workspace, 
+                    out_dir = txt_path,
+                    verbose = TRUE)
+}
     
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/redelacSticsInputGenerator.bash	Tue Jul 04 16:37:44 2023 +0000
@@ -0,0 +1,20 @@
+cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . &&
+rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
+cp -r $1/config JavaSTICS-1.5.1-STICS-10.0.0 &&
+unzip $2 -d TMP &&
+export WSname=$(ls TMP) &&
+mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
+cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
+cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
+unzip $3 -d TMPbis &&
+mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
+cp $4 JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
+cp $5 JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
+cp $6 JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
+cp $7 JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
+cd JavaSTICS-1.5.1-STICS-10.0.0 &&
+Rscript --verbose $1/redelacSticsInputGenerator.R &&
+rm WS/1* &&
+mv WS $WSname &&
+zip -r $WSname $WSname &&
+cp $WSname.zip $8
--- a/redelacSticsInputGenerator.xml	Thu Jun 29 11:03:20 2023 +0000
+++ b/redelacSticsInputGenerator.xml	Tue Jul 04 16:37:44 2023 +0000
@@ -4,27 +4,8 @@
     <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_test:10.0.0</container>
   </requirements>
   <command detect_errors="aggressive">
-    <![CDATA[ 
-	     cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . &&
-	     rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
-             cp -r $__tool_directory__/config JavaSTICS-1.5.1-STICS-10.0.0 &&
-	     unzip ${Workspace} -d TMP &&
-             export WSname=\$(ls TMP) &&
-	     mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
-             cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
-             cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
-	     unzip ${Climat} -d TMPbis &&
-             mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
-	     cp ${USMs} JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
-	     cp ${Tec} JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
-	     cp ${Ini} JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
-	     cp ${Station} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
-	     cd JavaSTICS-1.5.1-STICS-10.0.0 &&
-	     Rscript --verbose $__tool_directory__/redelacSticsInputGenerator.R &&
-             rm WS/1* &&
-             mv WS \$WSname &&
-	     zip -r \$WSname \$WSname &&
-	     cp \$WSname.zip ${GeneratedWorkspace}
+    <![CDATA[
+	     bash $__tool_directory__/redelacSticsInputGenerator.bash $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} ${GeneratedWorkspace}
      ]]>
   </command>
   <inputs>