From 7bd2135b0e60a86aa09278f04b105140acb7f415 Mon Sep 17 00:00:00 2001
From: Jake Smith <jws52@cam.ac.uk>
Date: Tue, 16 Mar 2021 12:00:19 +0000
Subject: [PATCH] fix: Distinct config files per run location
For now, one set for production, called 'live', and a second for development 'ewsdev'. Advise any clone of the repo creates its own set of these config files. This resolves the issue of having local uncommitted modifications to config files.
---
configs/config_Ethiopia_an_ewsdev.json | 158 +++++++++++++++++
.../config_Ethiopia_an_live.json | 0
configs/config_Ethiopia_fc_ewsdev.json | 158 +++++++++++++++++
.../config_Ethiopia_fc_live.json | 0
configs/config_SouthAsia_an_ewsdev.json | 164 ++++++++++++++++++
configs/config_SouthAsia_an_live.json | 164 ++++++++++++++++++
configs/config_SouthAsia_big_ewsdev.json | 154 ++++++++++++++++
.../config_SouthAsia_big_live.json | 0
configs/config_SouthAsia_fc_ewsdev.json | 164 ++++++++++++++++++
.../config_SouthAsia_fc_live.json | 0
crontab.txt | 24 +--
11 files changed, 974 insertions(+), 12 deletions(-)
create mode 100644 configs/config_Ethiopia_an_ewsdev.json
rename config_Ethiopia_an.json => configs/config_Ethiopia_an_live.json (100%)
create mode 100644 configs/config_Ethiopia_fc_ewsdev.json
rename config_Ethiopia.json => configs/config_Ethiopia_fc_live.json (100%)
create mode 100644 configs/config_SouthAsia_an_ewsdev.json
create mode 100644 configs/config_SouthAsia_an_live.json
create mode 100644 configs/config_SouthAsia_big_ewsdev.json
rename config_SouthAsia_big.json => configs/config_SouthAsia_big_live.json (100%)
create mode 100644 configs/config_SouthAsia_fc_ewsdev.json
rename config_SouthAsia.json => configs/config_SouthAsia_fc_live.json (100%)
diff --git a/configs/config_Ethiopia_an_ewsdev.json b/configs/config_Ethiopia_an_ewsdev.json
new file mode 100644
index 0000000..d97dd04
--- /dev/null
+++ b/configs/config_Ethiopia_an_ewsdev.json
@@ -0,0 +1,158 @@
+{
+ "RegionName" : "Ethiopia",
+ "SubRegionNames" : ["Ethiopia"],
+ "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/General/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/Workspace/Cred-ODK-EIAR.json",
+ "ServerPathExtra" : "/storage/sftp/metofficeupload/upload/Ethiopia/toMO/"
+ },
+ "Environment" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_EnvSuit_Met_Ethiopia_${StartString}_an",
+ "TimeExpectedAvailable" : "1400",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_env2_0",
+ "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
+ "TEMPLATE_PATH": "/storage/app/EWS/General/EWS-met_extractor/configs/",
+ "WORK_PATH": "/storage/app/EWS/General/EWS-met_extractor/",
+ "INPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_Ethiopia_analysis/",
+ "OUTPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_Ethiopia_analysis/",
+ "RUN_TYPE": "operational",
+ "EXTRACTION_DAYS": 7,
+ "FORECAST_DAYS": 6,
+ "STRAINS": ["LeafRust","StemRust", "StripeRust"],
+ "PARAMS": {
+ "LeafRust": {
+ "suitability_modules": ["semibool_dewperiod"],
+ "past_steps": 0,
+ "future_steps": 7,
+ "thresholds": {
+ "temperature": [2,15,20,30],
+ "precipitation": 0,
+ "relative_humidity": 90
+ }
+ },
+ "StemRust": {
+ "suitability_modules": ["semibool_dewperiod"],
+ "past_steps": 0,
+ "future_steps": 7,
+ "thresholds": {
+ "temperature": [2,15,24,30],
+ "precipitation": 0,
+ "relative_humidity": 90
+ }
+ },
+ "StripeRust": {
+ "suitability_modules": ["v1_dewperiod"],
+ "past_steps": 0,
+ "future_steps": 7,
+ "thresholds": {
+ "temperature": [2.37,19.8],
+ "precipitation": 0,
+ "relative_humidity": 90
+ }
+ }
+ },
+ "EWS-Plotting" : {
+ "Ethiopia" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_ETH_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/ethiopia/ews_plotting_env_ethiopia_main.py"
+ }
+ }
+ },
+ "Deposition" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/${RegionName}/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_NAME_${RegionName}_${StartString}_an",
+ "TimeExpectedAvailable" : "1400",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_dep",
+ "ProcessEWSPlotting" : "process_EWS_plotting_dep",
+ "EWS-Plotting" : {
+ "Ethiopia" : {
+ "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/ethiopia/ews_plotting_depo_ethiopia_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"
+ }
+ }
+}
\ No newline at end of file
diff --git a/config_Ethiopia_an.json b/configs/config_Ethiopia_an_live.json
similarity index 100%
rename from config_Ethiopia_an.json
rename to configs/config_Ethiopia_an_live.json
diff --git a/configs/config_Ethiopia_fc_ewsdev.json b/configs/config_Ethiopia_fc_ewsdev.json
new file mode 100644
index 0000000..64a2e2c
--- /dev/null
+++ b/configs/config_Ethiopia_fc_ewsdev.json
@@ -0,0 +1,158 @@
+{
+ "RegionName" : "Ethiopia",
+ "SubRegionNames" : ["Ethiopia"],
+ "StartTime" : "?",
+ "StartString" : "?",
+ "WorkspacePathout" : "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_Ethiopia/",
+ "WorkspacePath" : "/storage/app/EWS/Ethiopia/Workspace/",
+ "ServerPath" : "/storage/home/ewsmanager/scratch_Ethiopia/",
+ "ServerName" : "willow.csx.cam.ac.uk",
+ "ServerKey" : "/storage/app/EWS/General/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/Workspace/Cred-ODK-EIAR.json",
+ "ServerPathExtra" : "/storage/sftp/metofficeupload/upload/Ethiopia/toMO/"
+ },
+ "Environment" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_EnvSuit_Met_Ethiopia_${StartString}_fc",
+ "TimeExpectedAvailable" : "0800",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_env2_0",
+ "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
+ "TEMPLATE_PATH": "/storage/app/EWS/General/EWS-met_extractor/configs/",
+ "WORK_PATH": "/storage/app/EWS/General/EWS-met_extractor/",
+ "INPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_Ethiopia/",
+ "OUTPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_Ethiopia/",
+ "RUN_TYPE": "operational",
+ "EXTRACTION_DAYS": 7,
+ "FORECAST_DAYS": 6,
+ "STRAINS": ["LeafRust","StemRust", "StripeRust"],
+ "PARAMS": {
+ "LeafRust": {
+ "suitability_modules": ["semibool_dewperiod"],
+ "past_steps": 0,
+ "future_steps": 7,
+ "thresholds": {
+ "temperature": [2,15,20,30],
+ "precipitation": 0,
+ "relative_humidity": 90
+ }
+ },
+ "StemRust": {
+ "suitability_modules": ["semibool_dewperiod"],
+ "past_steps": 0,
+ "future_steps": 7,
+ "thresholds": {
+ "temperature": [2,15,24,30],
+ "precipitation": 0,
+ "relative_humidity": 90
+ }
+ },
+ "StripeRust": {
+ "suitability_modules": ["v1_dewperiod"],
+ "past_steps": 0,
+ "future_steps": 7,
+ "thresholds": {
+ "temperature": [2.37,19.8],
+ "precipitation": 0,
+ "relative_humidity": 90
+ }
+ }
+ },
+ "EWS-Plotting" : {
+ "Ethiopia" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_ETH_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/ethiopia/ews_plotting_env_ethiopia_main.py"
+ }
+ }
+ },
+ "Deposition" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/${RegionName}/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_NAME_${RegionName}_${StartString}_fc",
+ "TimeExpectedAvailable" : "0800",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_dep",
+ "ProcessEWSPlotting" : "process_EWS_plotting_dep",
+ "EWS-Plotting" : {
+ "Ethiopia" : {
+ "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/ethiopia/ews_plotting_depo_ethiopia_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"
+ }
+ }
+}
\ No newline at end of file
diff --git a/config_Ethiopia.json b/configs/config_Ethiopia_fc_live.json
similarity index 100%
rename from config_Ethiopia.json
rename to configs/config_Ethiopia_fc_live.json
diff --git a/configs/config_SouthAsia_an_ewsdev.json b/configs/config_SouthAsia_an_ewsdev.json
new file mode 100644
index 0000000..fdafb13
--- /dev/null
+++ b/configs/config_SouthAsia_an_ewsdev.json
@@ -0,0 +1,164 @@
+{
+ "RegionName" : "SouthAsia",
+ "SubRegionNames" : ["Bangladesh","Nepal"],
+ "StartTime" : "?",
+ "StartString" : "?",
+ "WorkspacePathout" : "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_SouthAsia_analysis/",
+ "WorkspacePath" : "/storage/app/EWS/SouthAsia/Workspace/",
+ "ServerPath" : "/storage/home/ewsmanager/scratch_SouthAsia_analysis/",
+ "ServerName" : "willow.csx.cam.ac.uk",
+ "ServerKey" : "/storage/app/EWS/General/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/SouthAsia/Workspace/Cred-ODK-CIMMYT-Bangladesh.json",
+ "ServerPathExtra" : "/storage/sftp/metofficeupload/upload/SouthAsia/toMO/"
+ },
+ "Environment" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_EnvSuit_Met_SouthAsia_${StartString}_an",
+ "TimeExpectedAvailable" : "1400",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_env2_0",
+ "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
+ "TEMPLATE_PATH": "/storage/app/EWS/General/EWS-met_extractor/configs/",
+ "WORK_PATH": "/storage/app/EWS/General/EWS-met_extractor/",
+ "INPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_SouthAsia_analysis/",
+ "OUTPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_SouthAsia_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" : {
+ "Bangladesh" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_BANG_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_env_bang_main.py"
+ },
+ "Nepal" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_NEPAL_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/nepal/ews_plotting_env_nepal_main.py"
+ }
+ }
+ },
+ "Deposition" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_an",
+ "TimeExpectedAvailable" : "1400",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_dep",
+ "ProcessEWSPlotting" : "process_EWS_plotting_dep",
+ "EWS-Plotting" : {
+ "Bangladesh" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_BANG_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_depo_bang_main.py"
+ },
+ "Nepal" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_NEPAL_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/nepal/ews_plotting_depo_nepal_main.py"
+ }
+ }
+ },
+ "Epidemiology" : {
+ "ProcessPreJob" : "process_pre_job_epi",
+ "ProcessInJob" : "process_in_job_epi",
+ "ProcessEWSPlotting" : "process_EWS_plotting_epi",
+ "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_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}Rust/",
+ "SuccessFileTemplate" : "${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_BANG_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_epi_bang_main.py",
+ "EpiCase" : "log10DepEnv"
+ }
+ }
+}
\ No newline at end of file
diff --git a/configs/config_SouthAsia_an_live.json b/configs/config_SouthAsia_an_live.json
new file mode 100644
index 0000000..34f86a0
--- /dev/null
+++ b/configs/config_SouthAsia_an_live.json
@@ -0,0 +1,164 @@
+{
+ "RegionName" : "SouthAsia",
+ "SubRegionNames" : ["Bangladesh","Nepal"],
+ "StartTime" : "?",
+ "StartString" : "?",
+ "WorkspacePathout" : "/storage/app/EWS/SouthAsia/Workspace_analysis/",
+ "WorkspacePath" : "/storage/app/EWS/SouthAsia/Workspace/",
+ "ServerPath" : "/storage/moved/SouthAsia/analysis/",
+ "ServerName" : "willow.csx.cam.ac.uk",
+ "ServerKey" : "/storage/app/EWS/General/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/SouthAsia/Workspace/Cred-ODK-CIMMYT-Bangladesh.json",
+ "ServerPathExtra" : "/storage/sftp/metofficeupload/upload/SouthAsia/toMO/"
+ },
+ "Environment" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_EnvSuit_Met_SouthAsia_${StartString}_an",
+ "TimeExpectedAvailable" : "1400",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_env2_0",
+ "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
+ "TEMPLATE_PATH": "/storage/app/EWS/General/EWS-met_extractor/configs/",
+ "WORK_PATH": "/storage/app/EWS/General/EWS-met_extractor/",
+ "INPUT_PATH": "/storage/app/EWS/SouthAsia/Workspace_analysis/",
+ "OUTPUT_PATH": "/storage/app/EWS/SouthAsia/Workspace_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" : {
+ "Bangladesh" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_BANG_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_env_bang_main.py"
+ },
+ "Nepal" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_NEPAL_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/nepal/ews_plotting_env_nepal_main.py"
+ }
+ }
+ },
+ "Deposition" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_an",
+ "TimeExpectedAvailable" : "1400",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_dep",
+ "ProcessEWSPlotting" : "process_EWS_plotting_dep",
+ "EWS-Plotting" : {
+ "Bangladesh" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_BANG_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_depo_bang_main.py"
+ },
+ "Nepal" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_NEPAL_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/nepal/ews_plotting_depo_nepal_main.py"
+ }
+ }
+ },
+ "Epidemiology" : {
+ "ProcessPreJob" : "process_pre_job_epi",
+ "ProcessInJob" : "process_in_job_epi",
+ "ProcessEWSPlotting" : "process_EWS_plotting_epi",
+ "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_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}Rust/",
+ "SuccessFileTemplate" : "${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_BANG_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_epi_bang_main.py",
+ "EpiCase" : "log10DepEnv"
+ }
+ }
+}
\ No newline at end of file
diff --git a/configs/config_SouthAsia_big_ewsdev.json b/configs/config_SouthAsia_big_ewsdev.json
new file mode 100644
index 0000000..13aa207
--- /dev/null
+++ b/configs/config_SouthAsia_big_ewsdev.json
@@ -0,0 +1,154 @@
+{
+ "RegionName" : "SouthAsia",
+ "SubRegionNames" : ["SouthAsia"],
+ "StartTime" : "?",
+ "StartString" : "?",
+ "WorkspacePathout" : "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_SouthAsia/",
+ "WorkspacePath" : "/storage/app/EWS/SouthAsia/Workspace/",
+ "ServerPath" : "/storage/home/ewsmanager/scratch_SouthAsia/",
+ "ServerName" : "willow.csx.cam.ac.uk",
+ "ServerKey" : "/storage/app/EWS/General/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/SouthAsia/Workspace/Cred-ODK-CIMMYT-Bangladesh.json",
+ "ServerPathExtra" : "/storage/sftp/metofficeupload/upload/SouthAsia/toMO/"
+ },
+ "Environment" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_EnvSuit_Met_SouthAsia_${StartString}_fc",
+ "TimeExpectedAvailable" : "0800",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_env2_0",
+ "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
+ "TEMPLATE_PATH": "/storage/app/EWS/General/EWS-met_extractor/configs/",
+ "WORK_PATH": "/storage/app/EWS/General/EWS-met_extractor/",
+ "INPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_SouthAsia/",
+ "OUTPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_SouthAsia/",
+ "RUN_TYPE": "operational",
+ "EXTRACTION_DAYS": 7,
+ "FORECAST_DAYS": 6,
+ "STRAINS": ["LeafRust","StemRust", "StripeRust"],
+ "PARAMS": {
+ "LeafRust": {
+ "suitability_modules": ["semibool_dewperiod"],
+ "past_steps": 0,
+ "future_steps": 7,
+ "thresholds": {
+ "temperature": [2,15,20,30],
+ "precipitation": 0,
+ "relative_humidity": 90
+ }
+ },
+ "StemRust": {
+ "suitability_modules": ["semibool_dewperiod"],
+ "past_steps": 0,
+ "future_steps": 7,
+ "thresholds": {
+ "temperature": [2,15,24,30],
+ "precipitation": 0,
+ "relative_humidity": 90
+ }
+ },
+ "StripeRust": {
+ "suitability_modules": ["v1_dewperiod"],
+ "past_steps": 0,
+ "future_steps": 7,
+ "thresholds": {
+ "temperature": [2.37,19.8],
+ "precipitation": 0,
+ "relative_humidity": 90
+ }
+ }
+ },
+ "EWS-Plotting" : {
+ "SouthAsia" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting-Dev/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/RUN_CONFIG_ASIA_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/south_asia/ews_plotting_env_asia_main.py"
+ }
+ }
+ },
+ "Deposition" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_fc",
+ "TimeExpectedAvailable" : "0800",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_dep",
+ "ProcessEWSPlotting" : "process_EWS_plotting_dep",
+ "EWS-Plotting" : {
+ "SouthAsia" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting-Dev/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/RUN_CONFIG_ASIA_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/south_asia/ews_plotting_depo_asia_main.py"
+ }
+ }
+ },
+ "Epidemiology" : {
+ "ProcessPreJob" : "process_pre_job_epi",
+ "ProcessInJob" : "process_in_job_epi",
+ "ProcessEWSPlotting" : "process_EWS_plotting_epi",
+ "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_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}Rust/",
+ "SuccessFileTemplate" : "${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-Dev/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/data/json_config/RUN_CONFIG_ASIA_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting-Dev/python/south_asia/ews_plotting_epi_asia_main.py",
+ "EpiCase" : "log10DepEnv"
+ }
+ }
+}
\ No newline at end of file
diff --git a/config_SouthAsia_big.json b/configs/config_SouthAsia_big_live.json
similarity index 100%
rename from config_SouthAsia_big.json
rename to configs/config_SouthAsia_big_live.json
diff --git a/configs/config_SouthAsia_fc_ewsdev.json b/configs/config_SouthAsia_fc_ewsdev.json
new file mode 100644
index 0000000..7590189
--- /dev/null
+++ b/configs/config_SouthAsia_fc_ewsdev.json
@@ -0,0 +1,164 @@
+{
+ "RegionName" : "SouthAsia",
+ "SubRegionNames" : ["Bangladesh","Nepal"],
+ "StartTime" : "?",
+ "StartString" : "?",
+ "WorkspacePathout" : "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_SouthAsia/",
+ "WorkspacePath" : "/storage/app/EWS/SouthAsia/Workspace/",
+ "ServerPath" : "/storage/home/ewsmanager/scratch_SouthAsia/",
+ "ServerName" : "willow.csx.cam.ac.uk",
+ "ServerKey" : "/storage/app/EWS/General/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/SouthAsia/Workspace/Cred-ODK-CIMMYT-Bangladesh-Dev.json",
+ "ServerPathExtra" : "/storage/sftp/metofficeupload/upload/SouthAsia/toMO/"
+ },
+ "Environment" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_EnvSuit_Met_SouthAsia_${StartString}_fc",
+ "TimeExpectedAvailable" : "0800",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_env2_0",
+ "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
+ "TEMPLATE_PATH": "/storage/app/EWS/General/EWS-met_extractor/configs/",
+ "WORK_PATH": "/storage/app/EWS/General/EWS-met_extractor/",
+ "INPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_SouthAsia/",
+ "OUTPUT_PATH": "/storage/app/EWS/General/EWS-Coordinator-Dev/scratch_SouthAsia/",
+ "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" : {
+ "Bangladesh" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_BANG_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_env_bang_main.py"
+ },
+ "Nepal" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_NEPAL_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/nepal/ews_plotting_env_nepal_main.py"
+ }
+ }
+ },
+ "Deposition" : {
+ "ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
+ "InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_fc",
+ "TimeExpectedAvailable" : "0800",
+ "ProcessPreJob" : "process_pre_job_server_download",
+ "ProcessInJob" : "process_in_job_dep",
+ "ProcessEWSPlotting" : "process_EWS_plotting_dep",
+ "EWS-Plotting" : {
+ "Bangladesh" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_BANG_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_depo_bang_main.py"
+ },
+ "Nepal" : {
+ "Path" : "/storage/app/EWS/General/EWS-Plotting/",
+ "RunConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/RUN_CONFIG_NEPAL_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/nepal/ews_plotting_depo_nepal_main.py"
+ }
+ }
+ },
+ "Epidemiology" : {
+ "ProcessPreJob" : "process_pre_job_epi",
+ "ProcessInJob" : "process_in_job_epi",
+ "ProcessEWSPlotting" : "process_EWS_plotting_epi",
+ "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_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}Rust/",
+ "SuccessFileTemplate" : "${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_BANG_PINE.json",
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/bangladesh/ews_plotting_epi_bang_main.py",
+ "EpiCase" : "log10DepEnv"
+ }
+ }
+}
\ No newline at end of file
diff --git a/config_SouthAsia.json b/configs/config_SouthAsia_fc_live.json
similarity index 100%
rename from config_SouthAsia.json
rename to configs/config_SouthAsia_fc_live.json
diff --git a/crontab.txt b/crontab.txt
index 97fc148..49ea095 100644
--- a/crontab.txt
+++ b/crontab.txt
@@ -3,38 +3,38 @@
### Ethiopia
# Source calculation from surveys
-00 23 * * * /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Survey -c /storage/app/EWS/General/EWS-Coordinator/config_Ethiopia.json --islive
+00 23 * * * /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Survey -c /storage/app/EWS/General/EWS-Coordinator/configs/config_Ethiopia_fc_live.json --islive
# NAME Deposition forecast
-15,45 09-22 * * * /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Deposition -c /storage/app/EWS/General/EWS-Coordinator/config_Ethiopia.json --islive
+15,45 09-22 * * * /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Deposition -c /storage/app/EWS/General/EWS-Coordinator/configs/config_Ethiopia_fc_live.json --islive
# Environmental suitability forecast (less frequent on Wednesday)
-30 9,11,13,15,17,19,21 * * 0-2,4-6 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/config_Ethiopia.json --islive
-30 9,11,13,15 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/config_Ethiopia.json --islive
+30 9,11,13,15,17,19,21 * * 0-2,4-6 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/configs/config_Ethiopia_fc_live.json --islive
+30 9,11,13,15 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/configs/config_Ethiopia_fc_live.json --islive
# NAME Deposition analysis (Wednesday only)
-25,55 14-22 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Deposition -c /storage/app/EWS/General/EWS-Coordinator/config_Ethiopia_an.json --islive
+25,55 14-22 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Deposition -c /storage/app/EWS/General/EWS-Coordinator/configs/config_Ethiopia_an_live.json --islive
# Environmental suitability analysis (Wednesday only)
-30 17,19,21 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/config_Ethiopia_an.json --islive
+30 17,19,21 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/configs/config_Ethiopia_an_live.json --islive
### South Asia
# Source calculation from surveys
-55 22 * * * /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Survey -c /storage/app/EWS/General/EWS-Coordinator/config_SouthAsia.json --islive
+55 22 * * * /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Survey -c /storage/app/EWS/General/EWS-Coordinator/configs/config_SouthAsia_fc_live.json --islive
# NAME Deposition forecast
-00,30 09-22 * * * /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Deposition -c /storage/app/EWS/General/EWS-Coordinator/config_SouthAsia.json --islive
+00,30 09-22 * * * /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Deposition -c /storage/app/EWS/General/EWS-Coordinator/configs/config_SouthAsia_fc_live.json --islive
# Environmental suitability forecast (less frequent on Wednesday)
-00 10,12,14,16,18,20,22 * * 0-2,4-6 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/config_SouthAsia.json --islive
-00 10,12,14,16 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/config_SouthAsia.json --islive
+00 10,12,14,16,18,20,22 * * 0-2,4-6 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/configs/config_SouthAsia_fc_live.json --islive
+00 10,12,14,16 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/configs/config_SouthAsia_fc_live.json --islive
# NAME Deposition analysis (Wednesday only)
-10,40 14-22 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Deposition -c /storage/app/EWS/General/EWS-Coordinator/config_SouthAsia_an.json --islive
+10,40 14-22 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Deposition -c /storage/app/EWS/General/EWS-Coordinator/configs/config_SouthAsia_an_live.json --islive
# Environmental suitability analysis (Wednesday only)
-00 18,20,22 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/config_SouthAsia_an.json --islive
+00 18,20,22 * * 3 /storage/app/EWS/General/EWS-Coordinator/run_Processor.sh -p Environment -c /storage/app/EWS/General/EWS-Coordinator/configs/config_SouthAsia_an_live.json --islive
# check for scraped media reports (Monday only)
00 12 * * 1 /storage/app/EWS/General/EWS-Coordinator/run_GatherScrapedMediaReports.sh
\ No newline at end of file
--
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