# HG changeset patch # User siwaa # Date 1724419144 0 # Node ID a069fc43b0b16f08fe7001ccadccc8561bbd4d0e # Parent d753f34309701aea3c18d3792d16f152e7f05588 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7/toos/CarboSeqSimulator commit ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7-dirty" diff -r d753f3430970 -r a069fc43b0b1 carboseqSimulator.xml --- a/carboseqSimulator.xml Fri Aug 23 10:09:37 2024 +0000 +++ b/carboseqSimulator.xml Fri Aug 23 13:19:04 2024 +0000 @@ -1,20 +1,14 @@ - + To run the CarboSeq simulator - docker://registry.forgemia.inra.fr/csopra/csopralibs:74-considering-java21 + docker://registry.forgemia.inra.fr/csopra/csopralibs:siwa @@ -29,7 +23,7 @@ - + diff -r d753f3430970 -r a069fc43b0b1 config_mappers/aial.json --- a/config_mappers/aial.json Fri Aug 23 10:09:37 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,504 +0,0 @@ -[ - { - "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 d753f3430970 -r a069fc43b0b1 config_mappers/carboSeq.json --- a/config_mappers/carboSeq.json Fri Aug 23 10:09:37 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,674 +0,0 @@ -[ - { - "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 d753f3430970 -r a069fc43b0b1 config_mappers/mapper.json --- a/config_mappers/mapper.json Fri Aug 23 10:09:37 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -{ - "config": { - "parallelism": { - "csv": 8, - "zip": 12 - }, - "perf-mode": 1 - }, - - "mappers": { - "carboSeq": "carboSeq.json", - "aial": "aial.json" - } -} diff -r d753f3430970 -r a069fc43b0b1 ontology.owl --- a/ontology.owl Fri Aug 23 10:09:37 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2811 +0,0 @@ - - - - - - - - alliumcepa - - - - onions - Allium cepa - AlliumCepa - allium cepa - onion - Allium cepa - AlliumCepa - - - Unique identifier used for designating a simulation site, that is, a 10x10 km pixel. - - id - - - - Id - id_profil_csopra - Id - - ID - Id - - - leaf lettuce - lactuca sativa var. crispa - Lactuca sativa var. crispa - Lactuca sativa var. crispa - - - - lactucasativavar.crispa - LactucaSativaVar.Crispa - LactucaSativaVar.Crispa - - - - - - green fallow - grasslandarea - Grassland area - ray - GrasslandArea - pasture - Grassland area - extensive grassland - mowing pasture - ryegrass - GrasslandArea - grassland area - Ray - grassland annual - sedge - ryegrass annual - - - broccoli - brassica oleracea var. italica - Brassica oleracea var. italica - Brassica oleracea var. italica - - - - brassicaoleraceavar.italica - BrassicaOleraceaVar.Italica - BrassicaOleraceaVar.Italica - - - Moutarde blanche - white mustard - SinapisAlba - - - - sinapisalba - sinapis alba - Sinapis alba - moutarde blanche - Sinapis alba - SinapisAlba - - - Composted bovine solid manure - compost de fumier - compost de fumier de bovins - CompostedBovineSolidManure - compostedbovinesolidmanure - CompostedBovineSolidManure - CFB - composted bovine solid manure - cfb - Composted bovine solid manure - - - - - - triticum spelta - triticumspelta - TriticumSpelta - TriticumSpelta - dinkel wheat - Triticum spelta - spelt - - - - Triticum spelta - - - Variable - variable - Variable - Variable - - - soilorganiccarbonstock - - - oc_tha - CMassMeas - - - - CMassMeas - CMassMeas - OC_THA - - cmassmeas - stock_soc - - - Generic soil organic stock. Should have an informed soil layer attached to it. - - - SoilOrganicCarbonStock - - - - - - - - - - SOCMaxDepthMeas - - - - socmaxdepthmeas - SOCMaxDepthMeas - SOCMaxDepthMeas - - - - - - - - - MaxDepthMeas - - - - maxdepthmeas - MaxDepthMeas - MaxDepthMeas - - - - soillayerobs - - - - - - - MinDepthMeas - - - - mindepthmeas - MinDepthMeas - MinDepthMeas - - - - SoilLayerObs - SoilLayerObs - SoilLayerObs - - - - - - SOCMinDepthMeas - - - - socmindepthmeas - SOCMinDepthMeas - SOCMinDepthMeas - - - - - - SoilOrganicCarbonStock - - SoilOrganicCarbonStock - - - Max - max - Max - Max - - - white clover - trifolium repens - Trifolium repens - Trifolium repens - - - - trifoliumrepens - TrifoliumRepens - TrifoliumRepens - - - - - - Year number in the 20-year crop rotations (1-20). - - NUM - num - NUM - NUM - - - lupine - Lupinus - - - - lupinus - Lupinus - Lupinus - - - cover crop - intermediate crop - ci_cc - - - - CI_CC - CI_CC - Amount of organic matter input through intermediate crops. Unit: t/ha/yr. - - CI_CC - Cover crop - - - shrub fruit - Shrub fruit - Shrub fruit - - - - shrubfruit - ShrubFruit - ShrubFruit - - - sugar beet vinasse - Sugar beet vinasse - Sugar beet vinasse - sugarbeetvinasse - SugarBeetVinasse - SugarBeetVinasse - - - - - - Sludge - sludge - Sludge - Sludge - - - spinach - spinacia oleracea - Spinacia oleracea - Spinacia oleracea - - - - spinaciaoleracea - SpinaciaOleracea - SpinaciaOleracea - - - - - - Compost - compost - Compost - Compost - - - full tillage - Full tillage - Full tillage - - - - fulltillage - FullTillage - FullTillage - - - GreenWasteAndBiowasteCompost - green waste and biowaste compost - BIOW-Qua - GreenWasteAndBiowasteCompost - - bio - Green waste and biowaste compost - bio_feucherolles - BIO - greenwasteandbiowastecompost - biow-qua - Green waste and biowaste compost - BIO_Feucherolles - - - red clover - trifolium pratense - Trifolium pratense - Trifolium pratense - - - - trifoliumpratense - TrifoliumPratense - TrifoliumPratense - - - brassica oleracea var. botrytis - caouliflower - - - - cauliflower - BrassicaOleraceaVar.Botrytis - brassicaoleraceavar.botrytis - BrassicaOleraceaVar.Botrytis - Brassica oleracea var. botrytis - Brassica oleracea var. botrytis - - - orchard grass - dactylis glomerata - Dactylis glomerata - Dactylis glomerata - - - - dactylisglomerata - DactylisGlomerata - DactylisGlomerata - - - - - - Type of organic fertilization. See the list of Organic products in the ontology. - - EOM_TYPE - eom_type - EOM_TYPE - EOM_TYPE - - - mm - Millimeter - - - - millimeter - Millimeter - Millimeter - - - commercial organic fertilizer - Commercial organic fertilizer - Commercial organic fertilizer - - - - commercialorganicfertilizer - CommercialOrganicFertilizer - CommercialOrganicFertilizer - - - agro-industrial wastewater - Agro-industrial wastewater - Agro-industrial wastewater - - - - agro-industrialwastewater - Agro-industrialWastewater - Agro-industrialWastewater - - - file inputs - File inputs - File inputs - fileinputs - FileInputs - FileInputs - - - soil tillage - Soil tillage - Soil tillage - soiltillage - SoilTillage - SoilTillage - - - DVB_Feucherolles - bovine compost - Bovine solid manure - FB_Feucherolles - fb_feucherolles - bovinesolidmanure - fumier de bovin - BovineSolidManure - BovineSolidManure - - - - fumier de bovins (génisses) - bovine solid manure - fym-qua - FYM-Qua - fumier de bovins - dvb - DVB - Bovine solid manure - dvb_feucherolles - default_FYM - fb - FB - default_fym - - - - - - Winter barley - Winter barley - WinterBarley - Orge Hiver - WinterBarley - winter barley - winterbarley - orge hiver - - - Carbon Input From Organic fertilization - carbon input from organic fertilization - carboninputfromorganicfertilization - CarbonInputFromOrganicFertilization - - - Carbon Input From Organic fertilization - CarbonInputFromOrganicFertilization - - - eom_c - EOM_C - CFluxFromOrganicFertilization - - - - cfluxfromorganicfertilization - CFluxFromOrganicFertilization - CFluxFromOrganicFertilization - - - - - - tomato - solanum lycopersicum - Solanum lycopersicum - Solanum lycopersicum - - - - solanumlycopersicum - SolanumLycopersicum - SolanumLycopersicum - - - BioChar - Biochar - - - - biochar - Biochar - Biochar - - - - - - - rr - RR - Rainfall - - - Total rainfall in mm per month - - RainfallMeas - - - - rainfallmeas - RainfallMeas - RainfallMeas - - - - rainfall - Rainfall - Rainfall - - - Climate - climate - Climate - Climate - - - marrow-stem kale - brassica oleracea var. medullosa - Brassica oleracea var. medullosa - Brassica oleracea var. medullosa - - - - brassicaoleraceavar.medullosa - BrassicaOleraceaVar.Medullosa - BrassicaOleraceaVar.Medullosa - - - raw digestate of biowaste and other wastes - Raw digestate of biowaste and other wastes - Raw digestate of biowaste and other wastes - rawdigestateofbiowasteandotherwastes - RawDigestateOfBiowasteAndOtherWastes - RawDigestateOfBiowasteAndOtherWastes - - - other vegetal residue - Other vegetal residue - Other vegetal residue - - - - othervegetalresidue - OtherVegetalResidue - OtherVegetalResidue - - - raw digestate of livestock effluents and other wastes - Raw digestate of livestock effluents and other wastes - Raw digestate of livestock effluents and other wastes - rawdigestateoflivestockeffluentsandotherwastes - RawDigestateOfLivestockEffluentsAndOtherWastes - RawDigestateOfLivestockEffluentsAndOtherWastes - - - winter turnip - Winter turnip - Winter turnip - - - - winterturnip - WinterTurnip - WinterTurnip - - - dried chicken droppings - Dried chicken droppings - Dried chicken droppings - - - - driedchickendroppings - DriedChickenDroppings - DriedChickenDroppings - - - whole-plant silage rye - Whole-plant silage rye - Whole-plant silage rye - - - - whole-plantsilagerye - Whole-plantSilageRye - Whole-plantSilageRye - - - ramtilla - guizotia abyssinica - Guizotia abyssinica - Guizotia abyssinica - - - - guizotiaabyssinica - GuizotiaAbyssinica - GuizotiaAbyssinica - - - sheep manure - Sheep manure - Sheep manure - - - - sheepmanure - SheepManure - SheepManure - - - sol nu - Sol nu - bare fallow - Bare fallow - Bare fallow - barefallow - BareFallow - BareFallow - - - Id_succession - id_succession - Id_succession - Id_succession - - - flax - linum usitatissimum - Linum usitatissimum - Linum usitatissimum - - - - linumusitatissimum - LinumUsitatissimum - LinumUsitatissimum - - - other animal manure - Other animal manure - Other animal manure - - - - otheranimalmanure - OtherAnimalManure - OtherAnimalManure - - - - vegetal residue - Vegetal residue - Vegetal residue - vegetalresidue - VegetalResidue - VegetalResidue - - - liquid phase of digestate of biowaste and other wastes - Liquid phase of digestate of biowaste and other wastes - Liquid phase of digestate of biowaste and other wastes - liquidphaseofdigestateofbiowasteandotherwastes - LiquidPhaseOfDigestateOfBiowasteAndOtherWastes - LiquidPhaseOfDigestateOfBiowasteAndOtherWastes - - - legume mixture - Legume mixture - Legume mixture - - - - legumemixture - LegumeMixture - LegumeMixture - - - winter rye - Winter rye - Winter rye - - - - winterrye - WinterRye - WinterRye - - - Vicia lens - lentils - vicia lens - lentil - ViciaLens - - - - vicialens - ViciaLens - Vicia lens - - - Year - year - Year - Year - - - other animal residue - Other animal residue - Other animal residue - otheranimalresidue - OtherAnimalResidue - OtherAnimalResidue - - - - Amount of clay. Unit: %. - - CLAY - clay - clay - clay - - - Legume(whole) - Legume(whole) - Legume (whole) - legume hay - Legume (whole) - - - - grassland with legumes - legume(whole) - legume (whole) - - - potatoes - Solanum tuberosum - potato - SolanumTuberosum - - - - Pomme de terre Plants - Solanum tuberosum - SolanumTuberosum - solanum tuberosum - pomme de terre plants - solanumtuberosum - - - Minimum temperature - MinimumTemperature - minimum temperature - TN - tn - minimumtemperature - Minimum temperature - - - - - Temperature - - - TempMeas - - - - tempmeas - TempMeas - TempMeas - - - - temperature - Temperature - Temperature - - - - MinimumTemperature - - - brassicaoleraceavar.sabauda - Brassica oleracea var. sabauda - cabbage - Brassica oleracea var. sabauda - brassica oleracea var. sabauda - BrassicaOleraceaVar.Sabauda - BrassicaOleraceaVar.Sabauda - - - - savoy cabbage - - - reduce tillage - Reduce tillage - Reduce tillage - - reducetillage - ReduceTillage - ReduceTillage - - - Others - - - - others - Others - Others - - - Sorghum - Sorgho Grain(es) - - - - hemisorghum - sorgho grain(es) - sorgum - Sorghum - sorghum - Sorghum - - - solid phase of digestate of cover crops and other wastes - Solid phase of digestate of cover crops and other wastes - Solid phase of digestate of cover crops and other wastes - solidphaseofdigestateofcovercropsandotherwastes - SolidPhaseOfDigestateOfCoverCropsAndOtherWastes - SolidPhaseOfDigestateOfCoverCropsAndOtherWastes - - - paper mill sludge - Paper mill sludge - Paper mill sludge - - papermillsludge - PaperMillSludge - PaperMillSludge - - - swedish clover - trifolium hybridum - Trifolium hybridum - Trifolium hybridum - - - - trifoliumhybridum - TrifoliumHybridum - TrifoliumHybridum - - - meadow fescue - festuca pratensis - Festuca pratensis - Festuca pratensis - - - - festucapratensis - FestucaPratensis - FestucaPratensis - - - Raphanus sativus var. oleiformis - RaphanusSativusVar.Oleiformis - oilradish - oil radish - raphanussativusvar.oleiformis - radis fourrager / fourrage - Raphanus sativus var. oleiformis - - - - RaphanusSativusVar.Oleiformis - raphanus sativus var. oleiformis - Radis Fourrager / Fourrage - - - solid phase of pig slurry - Solid phase of pig slurry - Solid phase of pig slurry - - - - solidphaseofpigslurry - SolidPhaseOfPigSlurry - SolidPhaseOfPigSlurry - - - avena strigosa - avoine noir(e) - Avena strigosa - Avena strigosa - - - - Avoine Noir(e) - AvenaStrigosa - avenastrigosa - black oat - AvenaStrigosa - - - Simulated Site - - - id_profil_aial - id in source db - ID in source DB - ID in source DB - idinsourcedb - IDInSourceDB - IDInSourceDB - - - - - - year - YEAR - StartYear - - startyear - StartYear - StartYear - - - - SimulatedSite - simulatedsite - - - Simulated Site - SimulatedSite - - simulated site - - - - PET - Potential Evapotranspiration - - Potential Evapotranspiration - potentialevapotranspiration - PotentialEvapotranspiration - - - Potential Evapotranspiration in mm per month - - PETMeas - - - - petmeas - PETMeas - PETMeas - - - - potential evapotranspiration - pet - PotentialEvapotranspiration - - - perennial ryegrass - lolium perenne - Lolium perenne - Lolium perenne - - - - loliumperenne - LoliumPerenne - LoliumPerenne - - - - - - kilogram/m2/yr - KilogramPerSquaredMeterPerYear - - - - - - 0.001 - - - - KgPerM2PerYrToMgPerHaPerYrConversion - kgperm2peryrtomgperhaperyrconversion - KgPerM2PerYrToMgPerHaPerYrConversion - KgPerM2PerYrToMgPerHaPerYrConversion - - - - kilogrampersquaredmeterperyear - KilogramPerSquaredMeterPerYear - KilogramPerSquaredMeterPerYear - - - - greenwastecompost - omr_feucherolles - OMR_Feucherolles - GreenWasteCompost - Green waste compost - green waste compost - Green waste compost - GreenWasteCompost - - - mm/month - MillimeterPerMonth - - - - millimeterpermonth - MillimeterPerMonth - MillimeterPerMonth - - - http://ecoinformatics.org/oboe/oboe.1.0/oboe.owl#kilogramPerHectarePerYear - KilogramPerHectare - - - - kilogramperhectare - KilogramPerHectare - KilogramPerHectare - - - bovine slurry - Bovine slurry - Bovine slurry - - - - bovineslurry - BovineSlurry - BovineSlurry - - - municipal solid waste compost - Municipal solid waste compost - Municipal solid waste compost - - municipalsolidwastecompost - MunicipalSolidWasteCompost - MunicipalSolidWasteCompost - - - - Digestate - digestate - Digestate - Digestate - - - - other organic products - Other organic products - Other organic products - otherorganicproducts - OtherOrganicProducts - OtherOrganicProducts - - - winter triticale - Winter triticale - Winter triticale - - - - wintertriticale - WinterTriticale - WinterTriticale - - - Blé tendre Printemps - soft wheat - - - - WinterWheat - blé tendre printemps - winterwheat - Winter wheat - WinterWheat - winter wheat - blé tendre hiver - Winter wheat - wheat - Blé tendre Hiver - blé tendre - - - megagram/ha/yr - - - - MegagramPerHectarePerYear - megagramperhectareperyear - MegagramPerHectarePerYear - MegagramPerHectarePerYear - - - green waste and chicken droppings compost - Green waste and chicken droppings compost - Green waste and chicken droppings compost - - greenwasteandchickendroppingscompost - GreenWasteAndChickenDroppingsCompost - GreenWasteAndChickenDroppingsCompost - - - - - - Degree - degree - Degree - Degree - - - - animal manure - Animal manure - Animal manure - animalmanure - AnimalManure - AnimalManure - - - cf - gravel - Proportion of coarse fragments. Unit: %. - - - CF - coarse fraction - gravel - coarse - coarse elements - gravel - - - Pisum sativum - pea - Pois Protéagineux - pisum sativum - PisumSativum - pisum - pisumsativum - pois protéagineux - fodder pea frostresistent - PisumSativum - Pisum sativum - fodder pea - - - - - - raw digestate of municipal solid waste - Raw digestate of municipal solid waste - Raw digestate of municipal solid waste - rawdigestateofmunicipalsolidwaste - RawDigestateOfMunicipalSolidWaste - RawDigestateOfMunicipalSolidWaste - - - bean - Phaseolus vulgaris - phaseolus vulgaris - PhaseolusVulgaris - Phaseolus vulgaris - - - - common bean - phaseolusvulgaris - PhaseolusVulgaris - - - compost de fumier de volailles - composted chicken manure - Composted chicken manure - Composted chicken manure - - compostedchickenmanure - CompostedChickenManure - CompostedChickenManure - - - black mustard - brassica nigra - Brassica nigra - Brassica nigra - - - - brassicanigra - BrassicaNigra - BrassicaNigra - - - green waste and sludge compost - Green waste and sludge compost - Green waste and sludge compost - - greenwasteandsludgecompost - GreenWasteAndSludgeCompost - GreenWasteAndSludgeCompost - - - aboveground carbon input - Aboveground Carbon Input - Aboveground Carbon Input - - - - abovegroundcarboninput - AbovegroundCarbonInput - AbovegroundCarbonInput - - - irrig - volumeOfIrrigationWater - volumeOfIrrigationWater - Irrigation amount. Unit: mm/yr. - - volumeofirrigationwater - - volume of irrigation water - volume of irrigation water - Irrig - - - fumier de volailles - chicken manure - Chicken manure - Chicken manure - - chickenmanure - ChickenManure - ChickenManure - - - solid phase of digestate of biowaste and other wastes - Solid phase of digestate of biowaste and other wastes - Solid phase of digestate of biowaste and other wastes - solidphaseofdigestateofbiowasteandotherwastes - SolidPhaseOfDigestateOfBiowasteAndOtherWastes - SolidPhaseOfDigestateOfBiowasteAndOtherWastes - - - Molasse - - molasse - Molasse - Molasse - - - celery - apium graveolens - Apium graveolens - Apium graveolens - - - - apiumgraveolens - ApiumGraveolens - ApiumGraveolens - - - horse manure - Horse manure - Horse manure - - horsemanure - HorseManure - HorseManure - - - other compost - Other Compost - Other Compost - - othercompost - OtherCompost - OtherCompost - - - phacelia - phacelia tanacetifolia - Phacelia tanacetifolia - Phacelia tanacetifolia - - - - phaceliatanacetifolia - PhaceliaTanacetifolia - PhaceliaTanacetifolia - - - Pig manure - PigManure - pig manure - - pigmanure - fumier de porcs - Pig manure - PigManure - fumier de porc - - - colza h - summer oil seed rape - summer rapeseed - Colza Hiver - oilseed rape - Colza H - winter rapeseed - BrassicaNapusSubsp.Napus - Brassica napus subsp. napus - winter oil seed rape - rapeseed - brassicanapussubsp.napus - winter oilseed winter rape - - - - oil seed rape - Brassica napus subsp. napus - colza hiver - summer oilseed rape - brassica napus subsp. napus - BrassicaNapusSubsp.Napus - - - T/ha - t/ha - - - - MegagramPerHectare - megagramperhectare - MegagramPerHectare - MegagramPerHectare - - - urban sewage sludge - Urban sewage sludge - Urban sewage sludge - - urbansewagesludge - UrbanSewageSludge - UrbanSewageSludge - - - vetch-rye mixture - Vetch-rye mixture - Vetch-rye mixture - - - - vetch-ryemixture - Vetch-ryeMixture - Vetch-ryeMixture - - - plant species - nom_culture - CROP - Name of the crop cultivated on a specific simulation unit and a specific year. - - PlantSpecies - crop - PlantSpecies - - plantspecies - Plant species - plant_name - Plant species - - - Ray-grass d'Italie - italian ryegrass - - Lolium multiflorum - annual ryegrass - ray-grass d'italie - loliummultiflorum - Lolium multiflorum - LoliumMultiflorum - lolium multiflorum - LoliumMultiflorum - - - DegreeCelcius - degreecelcius - DegreeCelcius - DegreeCelcius - - - - Amount of carbon brought by organic fertilization. Unit: tC/ha/yr. - - EOM_C - eom_c - EOM_C - EOM_C - - - Vicia faba - viciafaba - - fèverole - vicia faba - faba bean - ViciaFaba - fava bean - ViciaFaba - broad bean - Fèverole - Vicia faba - - - composted pig slurry and vegetal residues - Composted pig slurry and vegetal residues - Composted pig slurry and vegetal residues - - compostedpigslurryandvegetalresidues - CompostedPigSlurryAndVegetalResidues - CompostedPigSlurryAndVegetalResidues - - - - BrassicaRapaSubsp.Rapa - Brassica rapa subsp. rapa - brassicarapasubsp.rapa - autumn turnip - rutabaga - Brassica rapa subsp. rapa - brassica rapa subsp. rapa - rutabagas - Rutabaga - BrassicaRapaSubsp.Rapa - - - green rye - Green rye - Green rye - - greenrye - GreenRye - GreenRye - - - Bark - - bark - Bark - Bark - - - Guano - guano - Guano - Guano - - - hay - - Meadow ecosystem - MeadowEcosystem - meadow ecosystem - MeadowEcosystem - non-legume hay - meadowecosystem - Meadow ecosystem - - - lisier de porc - lisier de porc (m3/ha) - pigslurry - PigSlurry - - Lisier de Porc - Pig slurry - Pig slurry - PigSlurry - Lisier de Porc (m3/ha) - pig slurry - - - liquid phase of digestate of livestock effluents and other wastes - Liquid phase of digestate of livestock effluents and other wastes - Liquid phase of digestate of livestock effluents and other wastes - liquidphaseofdigestateoflivestockeffluentsandotherwastes - LiquidPhaseOfDigestateOfLivestockEffluentsAndOtherWastes - LiquidPhaseOfDigestateOfLivestockEffluentsAndOtherWastes - - - Amount of silt. Unit: %. - - SILT - silt - silt - silt - - - chicken droppings - Chicken droppings - Chicken droppings - - chickendroppings - ChickenDroppings - ChickenDroppings - - - hemp - cannabis sativa - Cannabis sativa - Cannabis sativa - - cannabissativa - CannabisSativa - CannabisSativa - - - composted goat manure - Composted goat manure - Composted goat manure - - compostedgoatmanure - CompostedGoatManure - CompostedGoatManure - - - Units - units - Units - Units - - - Min - min - Min - Min - - - Avena sativa - summer oat - - avenasativa - oat - avena sativa - AvenaSativa - winter oat - Avena sativa - AvenaSativa - - - m - Meter - - meter - Meter - Meter - - - AsparagusOfficinalis - - AsparagusOfficinalis - garden asparagus - Asparagus officinalis - asparagusofficinalis - asparagus - asparagus officinalis - Asparagus officinalis - - - herbs - spice or flavor-producing plant - Spice or flavor-producing plant - Spice or flavor-producing plant - - spiceorflavor-producingplant - SpiceOrFlavor-producingPlant - SpiceOrFlavor-producingPlant - - - dried urban sewage sludge - Dried urban sewage sludge - Dried urban sewage sludge - - driedurbansewagesludge - DriedUrbanSewageSludge - DriedUrbanSewageSludge - - - grain maize - Grain corn - - GrainCorn - graincorn - maïs grain(es) - grain corn - Grain corn - GrainCorn - Maïs Grain(es) - - - vetch summer - vicia - vetch winter - Vicia - Vicia - - Vicia - vicia - Vicia - hairy vetch - vetch - - - DepthRelativeToSurface - depthrelativetosurface - DepthRelativeToSurface - DepthRelativeToSurface - - - composted sheep manure - Composted sheep manure - Composted sheep manure - - compostedsheepmanure - CompostedSheepManure - CompostedSheepManure - - - buckwheat - fagopyrum esculentum - Fagopyrum esculentum - Fagopyrum esculentum - - fagopyrumesculentum - FagopyrumEsculentum - FagopyrumEsculentum - - - alexandrian clover - trifolium alexandrinum - Trifolium alexandrinum - Trifolium alexandrinum - - trifoliumalexandrinum - TrifoliumAlexandrinum - TrifoliumAlexandrinum - - - tree fruit - Tree fruit - Tree fruit - - treefruit - TreeFruit - TreeFruit - - - green waste and bovine manure compost - Green waste and bovine manure compost - Green waste and bovine manure compost - - greenwasteandbovinemanurecompost - GreenWasteAndBovineManureCompost - GreenWasteAndBovineManureCompost - - - boue - Other sludge - othersludge - other sludge - OtherSludge - Other sludge - OtherSludge - BOUE - - - - luzerne - lucerne - MedicagoSativa - Luzerne - medicago sativa - alfalfa - MedicagoSativa - Medicago sativa - medicagosativa - - Medicago sativa - - - Sowing date of the crop. Format: DD-MM. - - - seedingdate - Seeding date - sowing_date - SeedingDate - seeding date - Seeding date - SOWING_DATE - SeedingDate - - - summer rye - Summer rye - Summer rye - - summerrye - SummerRye - SummerRye - - - - Yield of the crop in term of dry matter. Unit: t/ha/yr - - rendement - Yield - yield - Yield - Yield - - - solid phase of digestate of livestock effluents and other wastes - Solid phase of digestate of livestock effluents and other wastes - Solid phase of digestate of livestock effluents and other wastes - solidphaseofdigestateoflivestockeffluentsandotherwastes - SolidPhaseOfDigestateOfLivestockEffluentsAndOtherWastes - SolidPhaseOfDigestateOfLivestockEffluentsAndOtherWastes - - - compost de fumier de porcs - composted pig manure - Composted pig manure - Composted pig manure - - compostedpigmanure - CompostedPigManure - CompostedPigManure - - - - - - - 0.01 - - CentimeterToMeterConversion - centimetertometerconversion - CentimeterToMeterConversion - CentimeterToMeterConversion - - - - cm - Centimeter - - - - 10.0 - - CentimeterToMillimeterConversion - centimetertomillimeterconversion - CentimeterToMillimeterConversion - CentimeterToMillimeterConversion - - - - centimeter - Centimeter - Centimeter - - - Maximum temperature - MaximumTemperature - TX - tx - maximumtemperature - - MaximumTemperature - Maximum temperature - maximum temperature - - - - carboninputobs - CarbonInputObs - - Ceci est une note test - - - - CarbonInputObs - - - belowground carbon - aboveground carbon - CFluxMeas - - cfluxmeas - CFluxMeas - CFluxMeas - - - - CarbonInputObs - - - - Ornithopus sativus - seradella - serradella - OrnithopusSativus - ornithopussativus - OrnithopusSativus - ornithopus sativus - Ornithopus sativus - - - limed urban sewage sludge - Limed urban sewage sludge - Limed urban sewage sludge - - limedurbansewagesludge - LimedUrbanSewageSludge - LimedUrbanSewageSludge - - - glycine max - glycinemax - GlycineMax - Soybean - soja - soy - soybean - Glycine max - Glycine max - soya bean - soya - GlycineMax - soy bean - - Soja - - - composted horse manure - Composted horse manure - Composted horse manure - - compostedhorsemanure - CompostedHorseManure - CompostedHorseManure - - - spring turnip - Spring turnip - Spring turnip - - springturnip - SpringTurnip - SpringTurnip - - - KilogramPerM2ToMegagramPerHectareConversion - kilogramperm2tomegagramperhectareconversion - KilogramPerM2ToMegagramPerHectareConversion - KilogramPerM2ToMegagramPerHectareConversion - - - composted solid phase of digestate - Composted solid phase of digestate - Composted solid phase of digestate - - compostedsolidphaseofdigestate - CompostedSolidPhaseOfDigestate - CompostedSolidPhaseOfDigestate - - - liquid phase of digestate of cover crops and other wastes - Liquid phase of digestate of cover crops and other wastes - Liquid phase of digestate of cover crops and other wastes - liquidphaseofdigestateofcovercropsandotherwastes - LiquidPhaseOfDigestateOfCoverCropsAndOtherWastes - LiquidPhaseOfDigestateOfCoverCropsAndOtherWastes - - - CaCO3 - - calcium carbonate - calciumCarbonate - calciumcarbonate - calcium carbonate - calciumCarbonate - pH of the soil in water. - - caco3 - - - summer barley - Summer barley - Summer barley - - summerbarley - SummerBarley - SummerBarley - - - - animal residue - Animal residue - Animal residue - animalresidue - AnimalResidue - AnimalResidue - - - - kg/m2 - KilogramPerM2 - - kilogramperm2 - KilogramPerM2 - KilogramPerM2 - - - digestate of bovine manure (dry ad) - Digestate of bovine manure (dry AD) - Digestate of bovine manure (dry AD) - digestateofbovinemanure(dryad) - DigestateOfBovineManure(dryAD) - DigestateOfBovineManure(dryAD) - - - SummerWheat - Summer wheat - Summer wheat - summer wheat - blé dur - - SummerWheat - durum wheat - summerwheat - - - summer triticale - Summer triticale - Summer triticale - - summertriticale - SummerTriticale - SummerTriticale - - - no till - No till - No till - - notill - NoTill - NoTill - - - dwarf mallow - feed mallow - MalvaNeglecta - Malva neglecta - roundleaf mallow - cheeseplant - buttonweed - MalvaNeglecta - Malva neglecta - malva neglecta - mallow - malvaneglecta - cheeseweed - common mallow - - - - betterave sucrière - SugarBeets - - sugarbeets - sugar beets - SugarBeets - Sugar beets - Betterave Sucrière - Sugar beets - - - bare soil - Bare Soil - Bare Soil - - baresoil - BareSoil - BareSoil - - - helianthusannuus - HelianthusAnnuus - - Helianthus annuus - Helianthus annuus - tournesol - Tournesol - sunflower - HelianthusAnnuus - helianthus annuus - - - pH of the soil in water. - - pH - - ph - pH - pH - - - agro-industrial sludge - Agro-industrial sludge - Agro-industrial sludge - - agro-industrialsludge - Agro-industrialSludge - Agro-industrialSludge - - - lettuce - lactuca sativa - Lactuca sativa - Lactuca sativa - - lactucasativa - LactucaSativa - LactucaSativa - - - pea-vetch mixture - Pea-vetch mixture - Pea-vetch mixture - - pea-vetchmixture - Pea-vetchMixture - Pea-vetchMixture - - - other digestate - Other digestate - Other digestate - otherdigestate - OtherDigestate - OtherDigestate - - - clover mixture - Clover mixture - Clover mixture - - clovermixture - CloverMixture - CloverMixture - - - TrifoliumIncarnatum - Trifolium incarnatum - - trifolium incarnatum - winter incarnate clover - summer incarnate clover - TrifoliumIncarnatum - trifoliumincarnatum - Trifolium incarnatum - incarnate clover - - - raw digestate of cover crops and other wastes - Raw digestate of cover crops and other wastes - Raw digestate of cover crops and other wastes - rawdigestateofcovercropsandotherwastes - RawDigestateOfCoverCropsAndOtherWastes - RawDigestateOfCoverCropsAndOtherWastes - - - Maïs Fourrage - silagecorn - SilageCorn - SilageCorn - Silage corn - silage maize - Silage corn - maïs fourrage - - silage corn - - - Algae - - algae - Algae - Algae - - - creeping clover - trifolium subterraneum - Trifolium subterraneum - Trifolium subterraneum - - trifoliumsubterraneum - TrifoliumSubterraneum - TrifoliumSubterraneum - - - compost de fientes - composted chicken droppings - Composted chicken droppings - Composted chicken droppings - - compostedchickendroppings - CompostedChickenDroppings - CompostedChickenDroppings - - - fodder beets - Fodder beets - Fodder beets - - fodderbeets - FodderBeets - FodderBeets - - - feather meal - Feather meal - Feather meal - feathermeal - FeatherMeal - FeatherMeal - - - grapes - VitisVinifera - vitisvinifera - - grape - vitis vinifera - Vitis vinifera - Vitis vinifera - VitisVinifera - - - - Amount of biochar added to the field. Unit: t/ha/yr. - - BIOCHAR_C - biochar_c - BIOCHAR_C - BIOCHAR_C - - - fallow - fallow land - FallowLand - - black fallow - Fallow land - fallowland - FallowLand - Fallow land - - - belowground carbon input - Belowground Carbon Input - Belowground Carbon Input - - belowgroundcarboninput - BelowgroundCarbonInput - BelowgroundCarbonInput - - - - Daucus carota subsp. sativus - daucus carota subsp. sativus - carrot - daucuscarotasubsp.sativus - carrots - DaucusCarotaSubsp.Sativus - Daucus carota subsp. sativus - DaucusCarotaSubsp.Sativus - - - strawberry - fragaria ananassa - Fragaria ananassa - Fragaria ananassa - - fragariaananassa - FragariaAnanassa - FragariaAnanassa - - - HarvestingDate - harvest_date - - Harvesting date - harvestingdate - Harvesting date - HarvestingDate - harvesting date - HARVEST_DATE - Harvesting date of the crop. Format: DD-MM. - - - - persian clover - trifolium resupinatum - Trifolium resupinatum - Trifolium resupinatum - - trifoliumresupinatum - TrifoliumResupinatum - TrifoliumResupinatum - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Longitude - LON - - - lon - Longitude - Longitude - - longitude - - - GeographicCoordinates - GeographicCoordinates - geographic coordinates - - Geographic coordinates - Geographic coordinates - - - - latitude - - - Latitude - lat - Latitude - LAT - - Latitude - - - geographiccoordinates - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CFromWood - c from wood - - CFromWood - cfromwood - c_woody_elements - - - - CFromWood - C_WOODY_ELEMENTS - Amount of organic matter from hedges or agroforestry. Unit: t/ha/yr. - - C from wood - C from wood - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d753f3430970 -r a069fc43b0b1 run.r --- a/run.r Fri Aug 23 10:09:37 2024 +0000 +++ b/run.r Fri Aug 23 13:19:04 2024 +0000 @@ -7,7 +7,7 @@ # Default values for optional parameters url <- "https://coby.infosol.inrae.fr:8080/semantify/" srcDir <- NULL - part <- "modeltoolbox_sem_sep" + part <- "modeltoolbox" DS <- T NBCores <- 1 # Parse arguments @@ -35,14 +35,10 @@ if (grepl("^--srcOut=", arg)) { srcOut <- sub("^--srcOut=", "", arg) } - - if (grepl("^--semPath=", arg)) { - semPath <- sub("^--semPath=", "", arg) - } } - list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut, semPath = semPath) + list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut) } argus <- parse_args() @@ -53,7 +49,6 @@ NBCores <- argus[["NBCores"]] srcOut <- argus[["srcOut"]] -semPath <- argus[["semPath"]] if (!endsWith(srcOut, "/")) { srcOut <- paste0(srcOut, "/") @@ -66,6 +61,14 @@ # DS=TRUE # NBCores=10 +ppi <- list( + weatherRetrievalMethod = "service", + srcDir = srcDir, + doSemantify = DS, + weatherRetrievalURL = "https://147.100.203.110/climate", + semantifierServiceURL = url + ) + # MTB{{{ if (part == "modeltoolbox") { @@ -81,40 +84,19 @@ } #}}} -if (part == "modeltoolbox_sem_sep") { - DS <- F - print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions") - f0 <- function(){ - csopratools::semantify( - inputDir = srcDir, - outputDir = srcDir, - name = "carboseq", - # use = "service", - URL = url, - use = "java", - semantifierRootPath = semPath, - extFileNames = paste0(c("crop", "soil", "units"), ".csv") - ) - print("between semantify and load") - modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest", - preprocessorInputs = ppi) - print("between load an sim") - modeltoolbox::runSims(maxCores = NBCores) - res <- modeltoolbox::getYearlySOCResults() - fileName <- "resRun.RData" - filePath <- file.path(srcOut, fileName) - save(res, file = filePath) - } +# prepro{{ +if (part == "csoprapreprocessor") { +f0 <- function(){ + path <- this.path::this.dir() + print(path) + setwd(path) + setwd("../..") + source("src/csoprapreprocessor/src-utils.r") + CsopPre$Tool$sourceCodeFiles() + CsopPre$runPreprocessor(name = "carboseq", maxCores = NBCores, preprocessorInputs = ppi) } - -ppi <- list( - weatherRetrievalMethod = "service", - srcDir = srcDir, - doSemantify = DS, - weatherRetrievalURL = "https://147.100.203.110/climate", - semantifierServiceURL = url - ) - +} +#}}} print(url) print(srcDir) @@ -122,7 +104,6 @@ print(DS) print(NBCores) print(f0) - f0() diff -r d753f3430970 -r a069fc43b0b1 semantifier.jar Binary file semantifier.jar has changed diff -r d753f3430970 -r a069fc43b0b1 test-data/input/40Sites.zip Binary file test-data/input/40Sites.zip has changed diff -r d753f3430970 -r a069fc43b0b1 test-data/input/40Sites/40Sites.zip Binary file test-data/input/40Sites/40Sites.zip has changed