Mercurial > repos > siwaa > carboseq_s
changeset 3:d753f3430970 draft
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/cc777c42662683b47bdcdcd72d65e0087962b794/toos/CarboSeqSimulator commit cc777c42662683b47bdcdcd72d65e0087962b794-dirty"
| author | siwaa |
|---|---|
| date | Fri, 23 Aug 2024 10:09:37 +0000 |
| parents | d78961e3f5ca |
| children | a069fc43b0b1 |
| files | carboseqSimulator.xml config_mappers/aial.json config_mappers/aial/mapping.csv config_mappers/carboSeq.json config_mappers/carboseq/mapping.csv config_mappers/mapper.json semantifier.jar |
| diffstat | 7 files changed, 1194 insertions(+), 115 deletions(-) [+] |
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--- 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 &&
--- /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 + } + ] + } + ] + } +]
--- 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"
--- /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" + } + } + ] + } + } + ] + } + ] + } + ] + } +]
--- 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"