# HG changeset patch
# User siwaa
# Date 1724407777 0
# Node ID d753f34309701aea3c18d3792d16f152e7f05588
# Parent  d78961e3f5ca82b51cc047b2c4c5593a805c75f1
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/cc777c42662683b47bdcdcd72d65e0087962b794/toos/CarboSeqSimulator commit cc777c42662683b47bdcdcd72d65e0087962b794-dirty"

diff -r d78961e3f5ca -r d753f3430970 carboseqSimulator.xml
--- a/carboseqSimulator.xml	Fri Aug 23 09:22:12 2024 +0000
+++ b/carboseqSimulator.xml	Fri Aug 23 10:09:37 2024 +0000
@@ -1,7 +1,7 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.9">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.10">
   <description>To run the CarboSeq simulator</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop-cec3a421</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:74-considering-java21</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
   mkdir data &&
diff -r d78961e3f5ca -r d753f3430970 config_mappers/aial.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config_mappers/aial.json	Fri Aug 23 10:09:37 2024 +0000
@@ -0,0 +1,504 @@
+[
+    {
+        "extFileName": "mat_rot_cult",
+        "appFiles": [
+            {
+                "appFileName": "matRotCults",
+                "columns": [
+                    {
+                        "extColumnName": "id_profil_csopra",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_succession",
+                        "appColumnName": "id_succession",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_culture",
+                        "appColumnName": "id_culture",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "nom_culture",
+                        "appColumnName": "nom_culture",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "type_culture",
+                        "appColumnName": "type_culture",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_fin",
+                        "appColumnName": "date_fin",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_fin_text",
+                        "appColumnName": "date_fin_text",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "type_gestion_res",
+                        "appColumnName": "type_gestion_res",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "culture_intermediaire",
+                        "appColumnName": "culture_intermediaire",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_semis",
+                        "appColumnName": "date_semis",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_semis_text",
+                        "appColumnName": "date_semis_text",
+                        "urifyHeader": true
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "extFileName": "mat_rot_fert_min",
+        "appFiles": [
+            {
+                "appFileName": "matRotFertMin",
+                "columns": [
+                    {
+                        "extColumnName": "id_profil_csopra",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_succession",
+                        "appColumnName": "id_succession",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_ferti_min",
+                        "appColumnName": "id_ferti_min",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_ferti_min",
+                        "appColumnName": "date_ferti_min",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "dose_n",
+                        "appColumnName": "dose_n",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "dose_p",
+                        "appColumnName": "dose_p",
+                        "urifyHeader": true
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "extFileName": "mat_rot_fert_org",
+        "appFiles": [
+            {
+                "appFileName": "matRotFertOrg",
+                "columns": [
+                    {
+                        "extColumnName": "id_profil_csopra",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_succession",
+                        "appColumnName": "id_succession",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_ferti_org",
+                        "appColumnName": "id_ferti_org",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "type_ferti_org",
+                        "appColumnName": "type_ferti_org",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_ferti_org",
+                        "appColumnName": "date_ferti_org",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "masse_carb",
+                        "appColumnName": "masse_carb",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "fraction_lignine",
+                        "appColumnName": "fraction_lignine",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "ratio_c_n",
+                        "appColumnName": "ratio_c_n",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "ratio_c_p",
+                        "appColumnName": "ratio_c_p",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "ratio_c_s",
+                        "appColumnName": "ratio_c_s",
+                        "urifyHeader": true
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "extFileName": "mat_rot_irrigation",
+        "appFiles": [
+            {
+                "appFileName": "matRotIrrigation",
+                "columns": [
+                    {
+                        "extColumnName": "id_profil_csopra",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_succession",
+                        "appColumnName": "id_succession",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_irrigation",
+                        "appColumnName": "id_irrigation",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_irrig",
+                        "appColumnName": "date_irrig",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "dose_irrig",
+                        "appColumnName": "dose_irrig",
+                        "urifyHeader": true
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "extFileName": "mat_rot_obs_cult",
+        "appFiles": [
+            {
+                "appFileName": "matRotObsCult",
+                "columns": [
+                    {
+                        "extColumnName": "id_profil_csopra",
+                        "appColumnName": "id_profil_csopra",
+                        "index": 0,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_succession",
+                        "appColumnName": "id_succession",
+                        "index": 1,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_culture",
+                        "appColumnName": "id_culture",
+                        "index": 2,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "nom_culture",
+                        "appColumnName": "nom_culture",
+                        "index": 3,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "type_culture",
+                        "appColumnName": "type_culture",
+                        "index": 4
+                    },
+                    {
+                        "extColumnName": "num_ordre",
+                        "appColumnName": "num_ordre",
+                        "index": 6,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_fin",
+                        "appColumnName": "date_fin",
+                        "index": 7,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_fin_text",
+                        "appColumnName": "date_fin_text",
+                        "index": 8,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "culture_intermediaire",
+                        "appColumnName": "culture_intermediaire",
+                        "index": 9,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "rendement",
+                        "appColumnName": "rendement",
+                        "index": 10,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "c_plante_aerien_c",
+                        "appColumnName": "c_plante_aerien_c",
+                        "index": 11,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "c_plante_racine_c",
+                        "appColumnName": "c_plante_racine_c",
+                        "index": 12,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "frac_of_stem_that_remains",
+                        "appColumnName": "frac_of_stem_that_remains",
+                        "index": 13,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "flag_yield_remains",
+                        "appColumnName": "flag_yield_remains",
+                        "index": 14,
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "c_woody_elements",
+                        "appColumnName": "c_woody_elements",
+                        "index": 15,
+                        "urifyHeader": true
+                    }
+                ],
+                "additionalColumns": [
+                    {
+                        "columnName": "weather_data_id",
+                        "columnValue": "",
+                        "urifyHeader": true,
+                        "index": 5
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "extFileName": "mat_rot_trav_sol",
+        "appFiles": [
+            {
+                "appFileName": "matRotTravSol",
+                "columns": [
+                    {
+                        "extColumnName": "id_profil_csopra",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_succession",
+                        "appColumnName": "id_succession",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_culture",
+                        "appColumnName": "id_culture",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "type_travsol",
+                        "appColumnName": "type_travsol",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_travsol",
+                        "appColumnName": "date_travsol",
+                        "urifyHeader": true
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "extFileName": "usm_data",
+        "appFiles": [
+            {
+                "appFileName": "usmData",
+                "columns": [
+                    {
+                        "extColumnName": "id_profil_csopra",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "no_horizon",
+                        "appColumnName": "no_horizon",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "prof_sup",
+                        "appColumnName": "prof_sup",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "prof_inf",
+                        "appColumnName": "prof_inf",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "clay",
+                        "appColumnName": "clay",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "sand",
+                        "appColumnName": "sand",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "silt",
+                        "appColumnName": "silt",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "bulkd",
+                        "appColumnName": "bulkd",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "ph",
+                        "appColumnName": "ph",
+                        "urifyHeader": true
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "extFileName": "usm_data_site_succ",
+        "appFiles": [
+            {
+                "appFileName": "usmDataSiteSucc",
+                "columns": [
+                    {
+                        "extColumnName": "id_profil_csopra",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "id_succession",
+                        "appColumnName": "id_succession",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "periode_debut",
+                        "appColumnName": "periode_debut",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "periode_fin",
+                        "appColumnName": "periode_fin",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "latitude",
+                        "appColumnName": "latitude",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "longitude",
+                        "appColumnName": "longitude",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "x_lambert2_etendu",
+                        "appColumnName": "x_lambert2_etendu",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "y_lambert2_etendu",
+                        "appColumnName": "y_lambert2_etendu",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "drain",
+                        "appColumnName": "drain",
+                        "urifyHeader": true
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "extFileName": "usm_soil_data_timed",
+        "appFiles": [
+            {
+                "appFileName": "usmSoilDataTimed",
+                "columns": [
+                    {
+                        "extColumnName": "id_profil_csopra",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "stock_soc",
+                        "appColumnName": "stock_soc",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "var_stock_soc",
+                        "appColumnName": "var_stock_soc",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "date_annee",
+                        "appColumnName": "date_annee",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "demi_ic_stock_soc",
+                        "appColumnName": "demi_ic_stock_soc",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "d13c",
+                        "appColumnName": "d13c",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "stock_n",
+                        "appColumnName": "stock_n",
+                        "urifyHeader": true
+                    },
+                    {
+                        "extColumnName": "c_n",
+                        "appColumnName": "c_n",
+                        "urifyHeader": true
+                    }
+                ]
+            }
+        ]
+    }
+]
diff -r d78961e3f5ca -r d753f3430970 config_mappers/aial/mapping.csv
--- a/config_mappers/aial/mapping.csv	Fri Aug 23 09:22:12 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-"extFileName","extColumnName","appFileName","appColumnName"
-"mat_rot_cult","id_culture","matRotCults","id_culture"
-"mat_rot_cult","id_succession","matRotCults","id_succession"
-"mat_rot_cult","id_profil_csopra","matRotCults","id_profil_csopra"
-"mat_rot_cult","nom_culture","matRotCults","nom_culture"
-"mat_rot_cult","type_culture","matRotCults","type_culture"
-"mat_rot_cult","date_semis","matRotCults","date_semis"
-"mat_rot_cult","date_fin","matRotCults","date_fin"
-"mat_rot_cult","date_semis_text","matRotCults","date_semis_text"
-"mat_rot_cult","date_fin_text","matRotCults","date_fin_text"
-"mat_rot_cult","culture_intermediaire","matRotCults","culture_intermediaire"
-"mat_rot_cult","type_gestion_res","matRotCults","type_gestion_res"
-"mat_rot_fert_min","id_profil_csopra","matRotFertMin","id_profil_csopra"
-"mat_rot_fert_min","id_ferti_min","matRotFertMin","id_ferti_min"
-"mat_rot_fert_min","id_succession","matRotFertMin","id_succession"
-"mat_rot_fert_min","date_ferti_min","matRotFertMin","date_ferti_min"
-"mat_rot_fert_min","dose_n","matRotFertMin","dose_n"
-"mat_rot_fert_min","dose_p","matRotFertMin","dose_p"
-"mat_rot_fert_org","id_profil_csopra","matRotFertOrg","id_profil_csopra"
-"mat_rot_fert_org","id_ferti_org","matRotFertOrg","id_ferti_org"
-"mat_rot_fert_org","date_ferti_org","matRotFertOrg","date_ferti_org"
-"mat_rot_fert_org","type_ferti_org","matRotFertOrg","type_ferti_org"
-"mat_rot_fert_org","masse_carb","matRotFertOrg","masse_carb"
-"mat_rot_fert_org","fraction_lignine","matRotFertOrg","fraction_lignine"
-"mat_rot_fert_org","ratio_c_n","matRotFertOrg","ratio_c_n"
-"mat_rot_fert_org","ratio_c_p","matRotFertOrg","ratio_c_p"
-"mat_rot_fert_org","ratio_c_s","matRotFertOrg","ratio_c_s"
-"mat_rot_fert_org","id_succession","matRotFertOrg","id_succession"
-"mat_rot_irrigation","id_profil_csopra","matRotIrrigation","id_profil_csopra"
-"mat_rot_irrigation","id_irrigation","matRotIrrigation","id_irrigation"
-"mat_rot_irrigation","date_irrig","matRotIrrigation","date_irrig"
-"mat_rot_irrigation","dose_irrig","matRotIrrigation","dose_irrig"
-"mat_rot_irrigation","id_succession","matRotIrrigation","id_succession"
-"mat_rot_obs_cult","id_culture","matRotObsCult","id_culture"
-"mat_rot_obs_cult","id_succession","matRotObsCult","id_succession"
-"mat_rot_obs_cult","id_profil_csopra","matRotObsCult","id_profil_csopra"
-"mat_rot_obs_cult","nom_culture","matRotObsCult","nom_culture"
-"mat_rot_obs_cult","type_culture","matRotObsCult","type_culture"
-"mat_rot_obs_cult","date_fin","matRotObsCult","date_fin"
-"mat_rot_obs_cult","num_ordre","matRotObsCult","num_ordre"
-"mat_rot_obs_cult","date_fin_text","matRotObsCult","date_fin_text"
-"mat_rot_obs_cult","culture_intermediaire","matRotObsCult","culture_intermediaire"
-"mat_rot_obs_cult","rendement","matRotObsCult","rendement"
-"mat_rot_obs_cult","c_plante_aerien_c","matRotObsCult","c_plante_aerien_c"
-"mat_rot_obs_cult","c_plante_aerien_c_ref","matRotObsCult","c_plante_aerien_c_ref"
-"mat_rot_obs_cult","c_plante_racine_c","matRotObsCult","c_plante_racine_c"
-"mat_rot_obs_cult","c_plante_racine_c_ref","matRotObsCult","c_plante_racine_c_ref"
-"mat_rot_obs_cult","frac_of_stem_that_remains","matRotObsCult","frac_of_stem_that_remains"
-"mat_rot_obs_cult","flag_yield_remains","matRotObsCult","flag_yield_remains"
-"mat_rot_trav_sol","id_profil_csopra","matRotTravSol","id_profil_csopra"
-"mat_rot_trav_sol","id_succession","matRotTravSol","id_succession"
-"mat_rot_trav_sol","id_culture","matRotTravSol","id_culture"
-"mat_rot_trav_sol","type_travsol","matRotTravSol","type_travsol"
-"mat_rot_trav_sol","date_travsol","matRotTravSol","date_travsol"
-"usm_data","id_profil_csopra","usmData","id_profil_csopra"
-"usm_data","id_profil_aial","usmData","id_profil_aial"
-"usm_data","no_horizon","usmData","no_horizon"
-"usm_data","prof_sup","usmData","prof_sup"
-"usm_data","prof_inf","usmData","prof_inf"
-"usm_data","clay","usmData","clay"
-"usm_data","silt","usmData","silt"
-"usm_data","sand","usmData","sand"
-"usm_data","bulkd","usmData","bulkd"
-"usm_data","ph","usmData","ph"
-"usm_data_site_succ","id_profil_csopra","usmDataSiteSucc","id_profil_csopra"
-"usm_data_site_succ","longitude","usmDataSiteSucc","longitude"
-"usm_data_site_succ","latitude","usmDataSiteSucc","latitude"
-"usm_data_site_succ","drain","usmDataSiteSucc","drain"
-"usm_data_site_succ","periode_debut","usmDataSiteSucc","periode_debut"
-"usm_data_site_succ","periode_fin","usmDataSiteSucc","periode_fin"
-"usm_data_site_succ","id_succession","usmDataSiteSucc","id_succession"
-"usm_data_site_succ","x_lambert2_etendu","usmDataSiteSucc","x_lambert2_etendu"
-"usm_data_site_succ","y_lambert2_etendu","usmDataSiteSucc","y_lambert2_etendu"
-"usm_soil_data_timed","id_profil_csopra","usmSoilDataTimed","id_profil_csopra"
-"usm_soil_data_timed","stock_soc","usmSoilDataTimed","stock_soc"
-"usm_soil_data_timed","var_stock_soc","usmSoilDataTimed","var_stock_soc"
-"usm_soil_data_timed","demi_ic_stock_soc","usmSoilDataTimed","demi_ic_stock_soc"
-"usm_soil_data_timed","d13c","usmSoilDataTimed","d13c"
-"usm_soil_data_timed","stock_n","usmSoilDataTimed","stock_n"
-"usm_soil_data_timed","c_n","usmSoilDataTimed","c_n"
-"usm_soil_data_timed","date_annee","usmSoilDataTimed","date_annee"
diff -r d78961e3f5ca -r d753f3430970 config_mappers/carboSeq.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config_mappers/carboSeq.json	Fri Aug 23 10:09:37 2024 +0000
@@ -0,0 +1,674 @@
+[
+    {
+        "extFileName": "soil_all",
+        "appFiles": [
+            {
+                "appFileName": "usmDataSiteSucc",
+                "columns": [
+                    {
+                        "extColumnName": "ID",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true,
+                        "index": 0
+                    },
+                    {
+                        "extColumnName": "LAT",
+                        "appColumnName": "latitude",
+                        "urifyHeader": true,
+                        "index": 4
+                    },
+                    {
+                        "extColumnName": "LON",
+                        "appColumnName": "longitude",
+                        "urifyHeader": true,
+                        "index": 5
+                    }
+                ],
+                "additionalColumns": [
+                    {
+                        "columnName": "id_succession",
+                        "urifyHeader": true,
+                        "columnValue": "1",
+                        "index": 1
+                    },
+                    {
+                        "columnName": "periode_debut",
+                        "columnValue": "2000-01-01",
+                        "index": 2
+                    },
+                    {
+                        "columnName": "periode_fin",
+                        "columnValue": "",
+                        "index": 3
+                    },
+                    {
+                        "columnName": "x_lambert2_etendu",
+                        "columnValue": ""
+                    },
+                    {
+                        "columnName": "y_lambert2_etendu",
+                        "columnValue": ""
+                    },
+                    {
+                        "columnName": "drain",
+                        "columnValue": "1"
+                    }
+                ]
+            },
+            {
+                "appFileName": "usmData",
+                "columns": [
+                    {
+                        "extColumnName": "ID",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true,
+                        "index": 0
+                    },
+                    {
+                        "extColumnName": "CLAY",
+                        "appColumnName": "clay",
+                        "urifyHeader": true,
+                        "index": 4
+                    },
+                    {
+                        "extColumnName": "SILT",
+                        "appColumnName": "silt",
+                        "urifyHeader": true,
+                        "index": 6
+                    },
+                    {
+                        "extColumnName": "pH",
+                        "appColumnName": "ph",
+                        "urifyHeader": true,
+                        "index": 8
+                    }
+                ],
+                "additionalColumns": [
+                    {
+                        "columnName": "no_horizon",
+                        "columnValue": "1",
+                        "index": 1
+                    },
+                    {
+                        "columnName": "prof_sup",
+                        "columnValue": "0",
+                        "index": 2
+                    },
+                    {
+                        "columnName": "prof_inf",
+                        "columnValue": "30",
+                        "index": 3
+                    },
+                    {
+                        "columnName": "sand",
+                        "columnValue": "",
+                        "index": 5
+                    },
+                    {
+                        "columnName": "bulkd",
+                        "columnValue": "",
+                        "index": 7
+                    }
+                ]
+            },
+            {
+                "appFileName": "usmSoilDataTimed",
+                "columns": [
+                    {
+                        "extColumnName": "ID",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true,
+                        "index": 0
+                    },
+                    {
+                        "extColumnName": "OC_THA",
+                        "appColumnName": "stock_soc",
+                        "urifyHeader": true,
+                        "index": 1
+                    }
+                ],
+                "additionalColumns": [
+                    {
+                        "columnName": "var_stock_soc",
+                        "columnValue": "",
+                        "index": 2
+                    },
+                    {
+                        "columnName": "date_annee",
+                        "columnValue": "2000-01-01",
+                        "index": 3
+                    },
+                    {
+                        "columnName": "demi_ic_stock_soc",
+                        "columnValue": "",
+                        "index": 4
+                    },
+                    {
+                        "columnName": "d13c",
+                        "columnValue": "",
+                        "index": 5
+                    },
+                    {
+                        "columnName": "stock_n",
+                        "columnValue": "",
+                        "index": 6
+                    },
+                    {
+                        "columnName": "c_n",
+                        "columnValue": "",
+                        "index": 7
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "extFileName": "crop_all",
+        "appFiles": [
+            {
+                "appFileName": "matRotCults",
+                "columns": [
+                    {
+                        "extColumnName": "ID",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true,
+                        "index": 0
+                    },
+                    {
+                        "extColumnName": "CROP",
+                        "appColumnName": "nom_culture",
+                        "urifyHeader": true,
+                        "urifyValues": true,
+                        "urifyInAdditionalRows": true,
+                        "index": 3
+                    },
+                    {
+                        "extColumnName": "HARVEST_DATE",
+                        "appColumnName": "date_fin_text",
+                        "urifyHeader": false,
+                        "index": 6
+                    },
+                    {
+                        "extColumnName": "SOWING_DATE",
+                        "appColumnName": "date_semis_text",
+                        "index": 10
+                    }
+                ],
+                "additionalColumns": [
+                    {
+                        "columnName": "id_succession",
+                        "urifyHeader": true,
+                        "columnValue": "1",
+                        "index": 1
+                    },
+                    {
+                        "columnName": "id_culture",
+                        "columnValue": "",
+                        "index": 2,
+                        "rules": [
+                            {
+                                "type": "concat",
+                                "arguments": {
+                                    "columns": "ID,id_succession,NUM",
+                                    "separator": "_",
+                                    "useCounter": false,
+                                    "constant": ""
+                                }
+                            }
+                        ]
+                    },
+                    {
+                        "columnName": "type_culture",
+                        "columnValue": "",
+                        "index": 4
+                    },
+                    {
+                        "columnName": "date_fin",
+                        "columnValue": "",
+                        "index": 5
+                    },
+                    {
+                        "columnName": "type_gestion_res",
+                        "columnValue": "Paille exportée",
+                        "urifyHeader": true,
+                        "urifyValues": true,
+                        "urifyInAdditionalRows": true,
+                        "index": 7
+                    },
+                    {
+                        "columnName": "culture_intermediaire",
+                        "columnValue": "0",
+                        "index": 8
+                    },
+                    {
+                        "columnName": "date_semis",
+                        "columnValue": "",
+                        "index": 9
+                    }
+                ],
+                "additionalRows": [
+                    {
+                        "rules": [
+                            {
+                                "type": "composite",
+                                "arguments": {
+                                    "condition": "CI_CC > 0",
+                                    "rules": [
+                                        {
+                                            "type": "setEmpty",
+                                            "arguments": {
+                                                "columns": "date_fin,SOWING_DATE,HARVEST_DATE"
+                                            }
+                                        },
+                                        {
+                                            "type": "setMultipleValues",
+                                            "arguments": {
+                                                "values": [
+                                                    {
+                                                        "columns": "CROP",
+                                                        "constant": "Cover crop"
+                                                    },
+                                                    {
+                                                        "columns": "type_gestion_res",
+                                                        "constant": "Laissé sur place"
+                                                    },
+                                                    {
+                                                        "columns": "culture_intermediaire",
+                                                        "constant": "1"
+                                                    }
+                                                ]
+                                            }
+                                        },
+                                        {
+                                            "type": "concat",
+                                            "arguments": {
+                                                "columnName": "id_culture",
+                                                "columns": "ID,id_succession,NUM",
+                                                "separator": "_",
+                                                "useCounter": false,
+                                                "constant": "CC"
+                                            }
+                                        }
+                                    ]
+                                }
+                            }
+                        ]
+                    }
+                ]
+            },
+            {
+                "appFileName": "matRotObsCult",
+                "columns": [
+                    {
+                        "extColumnName": "ID",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true,
+                        "index": 0
+                    },
+                    {
+                        "extColumnName": "CROP",
+                        "appColumnName": "nom_culture",
+                        "urifyHeader": true,
+                        "urifyValues": true,
+                        "urifyInAdditionalRows": true,
+                        "index": 3
+                    },
+                    {
+                        "extColumnName": "Yield",
+                        "appColumnName": "rendement",
+                        "urifyHeader": true,
+                        "index": 10
+                    },
+                    {
+                        "extColumnName": "prop_residue_removal",
+                        "appColumnName": "frac_of_stem_that_remains",
+                        "index": 13,
+                        "rules": [
+                            {
+                                "type": "proportion",
+                                "arguments": {
+                                    "columns": "prop_residue_removal",
+                                    "columnName": "prop_residue_removal"
+                                }
+                            }
+                        ]
+                    },
+                    {
+                        "extColumnName": "C_WOODY_ELEMENTS",
+                        "appColumnName": "c_woody_elements",
+                        "urifyHeader": true,
+                        "index": 15
+                    }
+                ],
+                "additionalColumns": [
+                    {
+                        "columnName": "id_succession",
+                        "urifyHeader": true,
+                        "columnValue": "1",
+                        "index": 1
+                    },
+                    {
+                        "columnName": "id_culture",
+                        "columnValue": "",
+                        "index": 2,
+                        "rules": [
+                            {
+                                "type": "concat",
+                                "arguments": {
+                                    "columns": "ID,id_succession,NUM",
+                                    "separator": "_",
+                                    "useCounter": false,
+                                    "constant": ""
+                                }
+                            }
+                        ]
+                    },
+                    {
+                        "columnName": "type_culture",
+                        "columnValue": "",
+                        "index": 4
+                    },
+                    {
+                        "columnName": "weather_data_id",
+                        "columnValue": "",
+                        "index": 5
+                    },
+                    {
+                        "columnName": "num_ordre",
+                        "columnValue": "",
+                        "index": 6
+                    },
+                    {
+                        "columnName": "date_fin",
+                        "columnValue": "",
+                        "index": 7
+                    },
+                    {
+                        "columnName": "date_fin_text",
+                        "columnValue": "",
+                        "index": 8
+                    },
+                    {
+                        "columnName": "culture_intermediaire",
+                        "columnValue": "0",
+                        "index": 9
+                    },
+                    {
+                        "columnName": "c_plante_aerien_c",
+                        "columnValue": "",
+                        "index": 11
+                    },
+                    {
+                        "columnName": "c_plante_racine_c",
+                        "columnValue": "",
+                        "index": 12
+                    },
+                    {
+                        "columnName": "flag_yield_remains",
+                        "columnValue": "",
+                        "index": 14
+                    }
+                ],
+                "additionalRows": [
+                    {
+                        "rules": [
+                            {
+                                "type": "composite",
+                                "arguments": {
+                                    "condition": "CI_CC > 0",
+                                    "rules": [
+                                        {
+                                            "type": "setEmpty",
+                                            "arguments": {
+                                                "columns": "date_fin,SOWING_DATE,HARVEST_DATE"
+                                            }
+                                        },
+                                        {
+                                            "type": "setMultipleValues",
+                                            "arguments": {
+                                                "values": [
+                                                    {
+                                                        "columns": "CROP",
+                                                        "constant": "Cover crop"
+                                                    },
+                                                    {
+                                                        "columns": "prop_residue_removal,culture_intermediaire",
+                                                        "constant": "1"
+                                                    },
+                                                    {
+                                                        "columns": "C_WOODY_ELEMENTS",
+                                                        "constant": "0"
+                                                    },
+                                                    {
+                                                        "columns": "Yield",
+                                                        "columnName": "CI_CC"
+                                                    }
+                                                ]
+                                            }
+                                        },
+                                        {
+                                            "type": "concat",
+                                            "arguments": {
+                                                "columnName": "id_culture",
+                                                "columns": "ID,id_succession,NUM",
+                                                "separator": "_",
+                                                "useCounter": false,
+                                                "constant": "CC"
+                                            }
+                                        }
+                                    ]
+                                }
+                            }
+                        ]
+                    }
+                ]
+            },
+            {
+                "appFileName": "matRotTravSol",
+                "columns": [
+                    {
+                        "extColumnName": "ID",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true,
+                        "index": 0
+                    }
+                ],
+                "additionalColumns": [
+                    {
+                        "columnName": "id_succession",
+                        "urifyHeader": true,
+                        "columnValue": "1",
+                        "index": 1
+                    },
+                    {
+                        "columnName": "id_culture",
+                        "index": 2,
+                        "rules": [
+                            {
+                                "type": "concat",
+                                "arguments": {
+                                    "columns": "ID,id_succession,NUM",
+                                    "separator": "_"
+                                }
+                            }
+                        ]
+                    },
+                    {
+                        "columnName": "type_travsol",
+                        "index": 3,
+                        "rules": [
+                            {
+                                "type": "conditional",
+                                "arguments": {
+                                    "condition": "Till = 0",
+                                    "value_if_true": {
+                                        "constant": "Zero tillage"
+                                    },
+                                    "value_if_false": {
+                                        "constant": "Inversion tillage"
+                                    }
+                                }
+                            }
+                        ]
+                    },
+                    {
+                        "columnName": "date_travsol",
+                        "columnValue": "",
+                        "index": 4
+                    }
+                ]
+            },
+            {
+                "appFileName": "matRotIrrigation",
+                "columns": [
+                    {
+                        "extColumnName": "ID",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true,
+                        "index": 0
+                    },
+                    {
+                        "extColumnName": "Irrig",
+                        "appColumnName": "dose_irrig",
+                        "urifyHeader": false,
+                        "index": 4
+                    }
+                ],
+                "additionalColumns": [
+                    {
+                        "columnName": "id_succession",
+                        "urifyHeader": true,
+                        "columnValue": "1",
+                        "index": 1
+                    },
+                    {
+                        "columnName": "id_irrigation",
+                        "index": 2,
+                        "rules": [
+                            {
+                                "type": "concat",
+                                "arguments": {
+                                    "columns": "ID,id_succession,NUM",
+                                    "separator": "_"
+                                }
+                            }
+                        ]
+                    },
+                    {
+                        "columnName": "date_irrig",
+                        "columnValue": "",
+                        "index": 3
+                    }
+                ]
+            },
+            {
+                "appFileName": "matRotFertOrg",
+                "columns": [
+                    {
+                        "extColumnName": "ID",
+                        "appColumnName": "id_profil_csopra",
+                        "urifyHeader": true,
+                        "index": 0
+                    },
+                    {
+                        "extColumnName": "EOM_TYPE",
+                        "appColumnName": "type_ferti_org",
+                        "urifyHeader": false,
+                        "urifyValues": true,
+                        "urifyInAdditionalRows": true,
+                        "index": 3
+                    },
+                    {
+                        "extColumnName": "EOM_C",
+                        "appColumnName": "masse_carb",
+                        "index": 5
+                    }
+                ],
+                "additionalColumns": [
+                    {
+                        "columnName": "id_succession",
+                        "urifyHeader": true,
+                        "columnValue": "1",
+                        "index": 1
+                    },
+                    {
+                        "columnName": "id_ferti_org",
+                        "index": 2,
+                        "rules": [
+                            {
+                                "type": "concat",
+                                "arguments": {
+                                    "columns": "ID,id_succession,NUM",
+                                    "separator": "_"
+                                }
+                            }
+                        ]
+                    },
+                    {
+                        "columnName": "date_ferti_org",
+                        "columnValue": "",
+                        "index": 4
+                    },
+                    {
+                        "columnName": "fraction_lignine",
+                        "columnValue": "",
+                        "index": 6
+                    },
+                    {
+                        "columnName": "ratio_c_n",
+                        "columnValue": "",
+                        "index": 7
+                    },
+                    {
+                        "columnName": "ratio_c_p",
+                        "columnValue": "",
+                        "index": 8
+                    },
+                    {
+                        "columnName": "ratio_c_s",
+                        "columnValue": "",
+                        "index": 9
+                    }
+                ],
+                "additionalRows": [
+                    {
+                        "rules": [
+                            {
+                                "type": "composite",
+                                "arguments": {
+                                    "condition": "BIOCHAR_C > 0",
+                                    "rules": [
+                                        {
+                                            "type": "setValue",
+                                            "arguments": {
+                                                "columns": "EOM_C",
+                                                "columnName": "BIOCHAR_C"
+                                            }
+                                        },
+                                        {
+                                            "type": "setValue",
+                                            "arguments": {
+                                                "columns": "EOM_TYPE",
+                                                "constant": "BioChar"
+                                            }
+                                        },
+                                        {
+                                            "type": "concat",
+                                            "arguments": {
+                                                "columnName": "id_ferti_org",
+                                                "columns": "id_ferti_org",
+                                                "separator": "_",
+                                                "useCounter": false,
+                                                "constant": "BC"
+                                            }
+                                        }
+                                    ]
+                                }
+                            }
+                        ]
+                    }
+                ]
+            }
+        ]
+    }
+]
diff -r d78961e3f5ca -r d753f3430970 config_mappers/carboseq/mapping.csv
--- a/config_mappers/carboseq/mapping.csv	Fri Aug 23 09:22:12 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-"extFileName","extColumnName","appFileName","appColumnName"
-"soil","ID","usmDataSiteSucc","id_profil_csopra"
-"soil","LAT","usmDataSiteSucc","latitude"
-"soil","LON","usmDataSiteSucc","longitude"
-"soil","ID","usmData","id_profil_csopra"
-"soil","CLAY","usmData","clay"
-"soil","pH","usmData","ph"
-"soil","SILT","usmData","silt"
-"soil","ID","usmSoilDataTimed","id_profil_csopra"
-"soil","OC_THA","usmSoilDataTimed","stock_soc"
-"crop","ID","matRotCult","id_profil_csopra"
-"crop","NUM","matRotCult","num"
-"crop","CI_CC","matRotCult","ci_cc"
-"crop","CROP","matRotCult","crop_code"
-"crop","SOWING_DATE","matRotCult","date_semis_text"
-"crop","HARVEST_DATE","matRotCult","date_fin_text"
-"crop","ID","matRotObsCult","id_profil_csopra"
-"crop","NUM","matRotObsCult","num"
-"crop","CI_CC","matRotObsCult","ci_cc"
-"crop","Yield","matRotObsCult","yield"
-"crop","prop_residue_removal","matRotObsCult","frac_of_stem_that_remains"
-"crop","C_WOODY_ELEMENTS","matRotObsCult","c_woody_elements"
-"crop","ID","matRotTravSol","id_profil_csopra"
-"crop","Till","matRotTravSol","till"
-"crop","NUM","matRotTravSol","num"
-"crop","ID","matRotIrrigation","id_profil_csopra"
-"crop","Irrig","matRotIrrigation","dose_irrig"
-"crop","NUM","matRotIrrigation","num"
-"crop","ID","matRotFertOrg","id_profil_csopra"
-"crop","NUM","matRotFertOrg","num"
-"crop","EOM_TYPE","matRotFertOrg","eom_type"
-"crop","BIOCHAR_C","matRotFertOrg","biochar_c"
diff -r d78961e3f5ca -r d753f3430970 config_mappers/mapper.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config_mappers/mapper.json	Fri Aug 23 10:09:37 2024 +0000
@@ -0,0 +1,14 @@
+{
+   "config": {
+      "parallelism": {
+          "csv": 8,
+          "zip": 12
+      },
+      "perf-mode": 1
+   },
+   
+   "mappers": {
+      "carboSeq": "carboSeq.json",
+      "aial": "aial.json"
+   }
+}
diff -r d78961e3f5ca -r d753f3430970 semantifier.jar
Binary file semantifier.jar has changed