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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_an_ewsdev.json 10.10 KiB
{
"RegionName" : "EastAfrica",
"SubRegionNames" : ["EastAfrica","Ethiopia","Kenya"],
"StartTime" : "?",
"StartString" : "?",
"WorkspacePathout" : "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_Ethiopia_analysis/",
"WorkspacePath" : "/storage/app/EWS/Ethiopia/Workspace/",
"ServerPath" : "/storage/home/ewsmanager/scratch_Ethiopia_analysis/",
"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}_an",
"TimeExpectedAvailable" : "1400",
"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/app/EWS/General/EWS-Coordinator-Dev/scratch_Ethiopia_analysis/",
"INPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_Ethiopia_analysis/",
"OUTPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_Ethiopia_analysis/",
"RUN_TYPE": "operational",
"EXTRACTION_DAYS": 7,
"FORECAST_DAYS": 6,
"STRAINS": ["LeafRust","StemRust", "StripeRust"],
"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
}
}
},
"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/app/EWS/General/EWS-Plotting-Dev/python/chart_areas/east_africa/ews_plotting_env_east_africa_main.py"
},
"Ethiopia" : {
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/chart/CHART_CONFIG_ETHIOPIA_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/chart_areas/ethiopia/ews_plotting_env_ethiopia_main.py"
},
"Kenya" : {
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/chart/CHART_CONFIG_KENYA_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/chart_areas/kenya/ews_plotting_env_kenya_main.py"
}
}
},
"Deposition" : {
"ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
"InputFileTemplate" : "WR_NAME_Ethiopia_${StartString}_fc",
"DataFileTemplate" : "deposition_srcs_allregions_${StartString}.nc",
"TimeExpectedAvailable" : "0800",
"ProcessPreJob" : "process_pre_job_server_download",
"ProcessInJob" : "process_in_job_dep",
"ProcessEWSPlotting" : "process_EWS_plotting_dep",
"EWS-Plotting" : {
"Path" : "/storage/app/EWS/General/EWS-Plotting-Dev/",
"SysConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/sys/SYS_CONFIG_PINE.json",
"NameExtractionConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/name_extraction/NAME_EXTRACTION_CONFIG.json",
"RunConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/deposition/RUN_CONFIG_DEPO.json",
"RunConfigNorm" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/deposition/RUN_CONFIG_DEPO_NORMALIZED.json",
"EastAfrica" : {
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/chart/CHART_CONFIG_EAST_AFRICA_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/chart_areas/east_africa/ews_plotting_depo_east_africa_main.py"
},
"Ethiopia" : {
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/chart/CHART_CONFIG_ETHIOPIA_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/chart_areas/ethiopia/ews_plotting_depo_ethiopia_main.py"
},
"Kenya" : {
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/chart/CHART_CONFIG_KENYA_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/chart_areas/kenya/ews_plotting_depo_kenya_main.py"
}
}
},
"Epidemiology" : {
"DiseaseNames" : ["StemRust","StripeRust","LeafRust"],
"CalculationSpanDays" : [0,5],
"TimeStep_hours": "3",
"ProcessPreJob" : "process_pre_job_epi",
"ProcessInJob" : "process_in_job_epi",
"ProcessEWSPlotting" : "process_EWS_plotting_epi",
"Deposition" : {
"PathTemplate" : "${WorkspacePathout}DEPOSITION_${StartString}/WR_NAME_Ethiopia_${StartString}_an/",
"SuccessFileTemplate" : "${WorkspacePathout}DEPOSITION_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "deposition_srcs_allregions_C1_T${tIndexPlusOneString}_${iTimeString}.txt",
"FileListerFunction" : "list_deposition_files_operational",
"FileNamePrepared" : "?"
},
"Environment" : {
"PathTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
"SuccessFileTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational", "FileNamePrepared" : "?"
},
"Host": {
"MaxFieldsPerCell": "1",
"HostRaster": "/storage/home/jws52/projects/EWS-EpiModel/input_Ethiopia/HOST/wheat_area_frac_MapSPAM2017SSA_Ethiopia.tif"
},
"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" : [32.5,48.0,3.3,15.0],
"UTMprojection" : 37
}
},{
"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" : [32.5,48.0,3.3,15.0],
"UTMprojection" : 37
}
},{
"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" : [32.5,48.0,3.3,15.0],
"UTMprojection" : 37
}
}
],
"EWS-Plotting" : {
"Path" : "/storage/app/EWS/General/EWS-Plotting-Dev/",
"RunConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/RUN_CONFIG_ETH_PINE.json",
"ChartConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/ews/chart/CHART_CONFIG_ETHIOPIA_PINE.json",
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/chart_areas/ethiopia/ews_plotting_epi_ethiopia_main.py",
"EpiCase" : "log10DepEnv"
}
}
}