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J.W. Smith authored
crontab and ewsdev configs now refer to configs in project-specific resources directories.
J.W. Smith authoredcrontab and ewsdev configs now refer to configs in project-specific resources directories.
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config_EastAfrica_fc_ewsdev_MF.json 14.27 KiB
{
"RegionName" : "EastAfrica",
"SubRegionNames" : ["EastAfrica"],
"StartTime" : "?",
"StartString" : "?",
"WorkspacePathout" : "/storage/home/tm689/EWS-Coordinator-Dev/scratch_EastAfrica/",
"WorkspacePath" : "/storage/home/tm689/EWS-Coordinator-Dev/scratch_EastAfrica/",
"ServerPath" : "/storage/moved/Ethiopia/",
"ServerName" : "willow.csx.cam.ac.uk",
"ServerKey" : "/storage/app/EWS/Ethiopia/Resources/EWS-Coordinator/ssh_key_willow",
"Survey" : {
"ProcessPreJob" : "process_pre_job_survey",
"ProcessInJob" : "process_in_job_survey",
"ProcessEWSPlotting" : "process_EWS_plotting_survey",
"ServerCredentialsFile" : "/storage/app/EWS/Ethiopia/Resources/EWS-Coordinator/Cred-ODK-EIAR.json",
"ServerPathExtra" : "/storage/sftp/metofficeupload/upload/Ethiopia/toMO/",
"FormEdits" : {
"wheat_rust_survey_1_0" : {},
"akpyJHvYxkLKPkxFJnPyTW" : {
"filter": {
"surveyor_infromation-country" : "Kenya"
}
}
},
"SourcesConfigFilename" : "/storage/app/EWS/General/wheat-source-generation/data/config_EastAfrica_mapspam2017.R",
"SourcesRegionName" : "EastAfrica"
},
"Environment" : {
"ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
"InputFileTemplate" : "WR_EnvSuit_Met_Ethiopia_${StartString}_fc",
"TimeExpectedAvailable" : "0800",
"ProcessPreJob" : "process_pre_job_server_download",
"ProcessInJob" : "process_in_job_env2_0",
"ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
"BIN_PATH" : "/storage/app/EWS/General/EWS-met_extractor/",
"TEMPLATE_PATH": "/storage/app/EWS/General/EWS-met_extractor/configs/",
"WORK_PATH": "/storage/home/tm689/EWS-Coordinator-Dev/scratch_EastAfrica/",
"INPUT_PATH": "/storage/home/tm689/EWS-Coordinator-Dev/scratch_EastAfrica/",
"OUTPUT_PATH": "/storage/home/tm689/EWS-Coordinator-Dev/scratch_EastAfrica/",
"RUN_TYPE": "operational",
"EXTRACTION_DAYS": 7,
"FORECAST_DAYS": 6,
"STRAINS": ["LeafRust", "StemRust", "StripeRust", "LeafRust_MF", "StemRust_MF", "StripeRust_MF"],
"PARAMS": {
"LeafRust": {
"suitability_modules": ["semibool_dewperiod"],
"past_steps": 0,
"future_steps": 7,
"thresholds": {
"temperature": [2,15,20,30],
"precipitation": 0,
"relative_humidity": 90
}
},
"StemRust": {
"suitability_modules": ["semibool_dewperiod"],
"past_steps": 0,
"future_steps": 7,
"thresholds": {
"temperature": [2,15,24,30],
"precipitation": 0,
"relative_humidity": 90
}
},
"StripeRust": {
"suitability_modules": ["v1_dewperiod"],
"past_steps": 0,
"future_steps": 7,
"thresholds": {
"temperature": [2.37,19.8], "precipitation": 0,
"relative_humidity": 90
}
},
"LeafRust_MF": {
"suitability_modules": ["semibool_dewperiod"],
"past_steps": 0,
"future_steps": 7,
"thresholds": {
"temperature": [2,15,20,30],
"precipitation": -1,
"relative_humidity": -90
}
},
"StemRust_MF": {
"suitability_modules": ["semibool_dewperiod"],
"past_steps": 0,
"future_steps": 7,
"thresholds": {
"temperature": [2,15,24,30],
"precipitation": -1,
"relative_humidity": -90
}
},
"StripeRust_MF": {
"suitability_modules": ["v1_dewperiod"],
"past_steps": 0,
"future_steps": 7,
"thresholds": {
"temperature": [2.37,19.8],
"precipitation": -1,
"relative_humidity": -90
}
}
},
"EWS-Plotting" : {
"Path" : "/storage/app/EWS/General/EWS-Plotting-Dev/",
"SysConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/sys/SYS_CONFIG_PINE.json",
"RunConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/env_suit/RUN_CONFIG_ENV.json",
"EastAfrica" : {
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/chart/CHART_CONFIG_EAST_AFRICA_PINE.json",
"PythonScript" : "/storage/home/tm689/EWS-Coordinator-Dev/custom_plotting.py"
}
}
},
"Deposition" : {
"ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
"InputFileTemplate" : "WR_NAME_Ethiopia_${StartString}_fc",
"TimeExpectedAvailable" : "0800",
"ProcessPreJob" : "process_pre_job_server_download",
"ProcessInJob" : "process_in_job_dep",
"ProcessEWSPlotting" : "process_EWS_plotting_dep",
"EWS-Plotting" : {
"Path" : "/storage/app/EWS/General/EWS-Plotting/",
"SysConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/sys/SYS_CONFIG_PINE.json",
"NameExtractionConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/ews/name_extraction/NAME_EXTRACTION_CONFIG.json",
"RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/ews/deposition/RUN_CONFIG_DEPO.json",
"RunConfigNorm" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/ews/deposition/RUN_CONFIG_DEPO_NORMALIZED.json",
"EastAfrica" : {
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/ews/chart/CHART_CONFIG_EAST_AFRICA_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/chart_areas/east_africa/ews_plotting_depo_east_africa_main.py"
},
"Ethiopia" : {
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/ews/chart/CHART_CONFIG_ETHIOPIA_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/chart_areas/ethiopia/ews_plotting_depo_ethiopia_main.py"
},
"Kenya" : {
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/ews/chart/CHART_CONFIG_KENYA_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/chart_areas/kenya/ews_plotting_depo_kenya_main.py"
} }
},
"Epidemiology" : {
"ProcessPreJob" : "process_pre_job_epi",
"ProcessInJob" : "process_in_job_epi",
"ProcessEWSPlotting" : "process_EWS_plotting_epi",
"Host" : {
"MaxFieldsPerCell" : "1000",
"HostRaster" : "/storage/app/EWS/General/EWS-EpiModel/SAsiaInputs/HostData/WheatRaster.tif"
},
"Deposition" : {
"VariableName" : "P_RECONDITA_DEPOSITION",
"PathTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/WR_NAME_SouthAsia_${StartString}/",
"SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/DEPOSITION_SUCCESS.txt",
"FileNameTemplate" : "deposition_srcs_allregions_C1_T${tIndexPlusOneString}_${iTimeString}.txt",
"FileNamePrepared" : "?"
},
"Environment" : {
"PathTemplate" : "${WorkspacePath}ENVIRONMENT_${StartString}/WR_EnvSuit_SouthAsia_${StartString}/${DiseaseName}Rust_${RegionName}/${StartString}0000/",
"SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_${StartString}/ENVIRONMENT_SUCCESS.txt",
"FileNameTemplate" : "RIE_value.csv",
"FileNamePrepared" : "?"
},
"Epi" : [
{
"model" : "Env",
"modelArguments" : {},
"infectionRasterFileName" : "?",
"description": "env. suitability",
"analysis" : {
"vmin" : 0.0e+0,
"vmax" : 1.5e+1,
"subplot_position" : [0,0],
"cmapString" : "CMRmap_r",
"bounds" : [87.9, 92.7, 20.5, 26.7],
"UTMprojection" : 45
}
},{
"model" : "log10Dep",
"modelArguments" : {},
"infectionRasterFileName" : "?",
"description": "log(spore deposition)",
"analysis" : {
"vmin" : 0.0e+0,
"vmax" : 3.0e+2,
"subplot_position" : [0,1],
"cmapString" : "CMRmap_r",
"bounds" : [87.9, 92.7, 20.5, 26.7],
"UTMprojection" : 45
}
},{
"model" : "log10DepEnv",
"modelArguments" : {},
"infectionRasterFileName" : "?",
"description": "EPI: env.suit $\\times$ log(dep.)",
"analysis" : {
"vmin" : 0.0e+0,
"vmax" : 1.5e+1,
"subplot_position" : [0,2],
"cmapString" : "CMRmap_r",
"bounds" : [87.9, 92.7, 20.5, 26.7],
"UTMprojection" : 45
}
}
],
"EWS-Plotting" : {
"Path" : "/storage/app/EWS/General/EWS-Plotting/",
"RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_ETH_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_epi_ethiopia_main.py",
"EpiCase" : "log10DepEnv" }
},
"Advisory" :
{
"ProcessPreJob" : "query_past_successes",
"ProcessInJob" : "process_in_job_advisory",
"ProcessEWSPlotting" : "do_nothing",
"seasonStartString" : "20220201",
"Environment" : {
"SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"DataPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/input_csvs/",
"PlotPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
"PlotFilenameTemplates" : {
"stripe" : "${envPlotPath}/suitability_${SubRegionNameSpacedLower}_stripe_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
"stem" : "${envPlotPath}/suitability_${SubRegionNameSpacedLower}_stem_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
"leaf" : "${envPlotPath}/suitability_${SubRegionNameSpacedLower}_leaf_rust_total_${dateString}0000_${EnvEndString}0000_map.png"
},
"Aggregation" : {
"raster_path_template" : "${envDataPath}/suitability_${SubRegionNameSpacedLower}_${disease_name_snakecase}_total.csv",
"raster_name_template" : "RIE_${disease_name_camelcase}",
"shape_fn_entry" : "ShapeFilenameAdmin1",
"shape_coln" : "ZONENAME",
"func" : "mean",
"save_path_template" : "${jobPath}/images/suitability_${SubRegionNameSpacedLower}_${disease_name_snakecase}_mean_per_zone"
}
},
"Deposition" : {
"SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
"PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
"PlotFilenameTemplates" : {
"stripe": "${depPlotPath}/deposition_${SubRegionNameSpacedLower}_stripe_rust_total_${dateString}0000_${weekAheadString}0000_map.png",
"stem": "${depPlotPath}/deposition_${SubRegionNameSpacedLower}_stem_rust_total_${dateString}0000_${weekAheadString}0000_map.png",
"leaf": "${depPlotPath}/deposition_${SubRegionNameSpacedLower}_leaf_rust_total_${dateString}0000_${weekAheadString}0000_map.png"
},
"Aggregation" : {
"raster_path_template" : "${depPlotPath}/../../input_csvs/deposition_${SubRegionNameSpacedLowerShort}_${disease_name_snakecase}_total.csv",
"raster_name_template" : "spores_per_m2_per_week_${disease_name_camelcase}",
"shape_fn_entry" : "ShapeFilenameAdmin1",
"shape_coln" : "ADM1_EN",
"func" : "mean",
"save_path_template" : "${jobPath}/images/deposition_${SubRegionNameSpacedLower}_${disease_name_snakecase}_mean_per_zone"
}
},
"Surveys" : {
"EastAfrica" : {
"ShapeFilenameAdmin0" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/EthKen_admin0.shp",
"ShapeFilenameAdmin1" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/EthKen_admin1.shp",
"ShapeFilenameAdmin2" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/EthKen_admin2.shp"
},
"Ethiopia" : {
"ShapeFilenameAdmin0" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/admin-boundaries/Ethiopia_All/Eth_Region_2013.shp",
"ShapeFilenameAdmin1" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/admin-boundaries/Ethiopia_All/Eth_ADM1_EN.shp",
"ShapeFilenameAdmin2" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/admin-boundaries/Ethiopia_All/Eth_Woreda_2013.shp"
},
"Kenya" : {
"ShapeFilenameAdmin0" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/ken_adm_iebc_20191031_shp/ken_admbnda_adm0_iebc_20191031.shp",
"ShapeFilenameAdmin1" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/ken_adm_iebc_20191031_shp/ken_admbnda_adm1_iebc_20191031.shp",
"ShapeFilenameAdmin2" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/ken_adm_iebc_20191031_shp/ken_admbnda_adm2_iebc_20191031.shp"
}
},
"logos" : "/storage/app/EWS/Ethiopia/Documents/logos_Ethiopia_plotting.png"
}
}