diff --git a/ProcessorComponents.py b/ProcessorComponents.py
index 6af63c112c084c7f072937a1320622d195269e9d..1912e8a9223b3efb401bdb1a1a8178a45f515d20 100644
--- a/ProcessorComponents.py
+++ b/ProcessorComponents.py
@@ -1530,8 +1530,10 @@ def process_EWS_plotting_dep(jobPath,config):
deposition_path = f"{jobPath}/{deposition_file_name}"
- # TODO: get the filename format part from the config
- name_file_wildcard = f"{deposition_path}/deposition_srcs_allregions_*.txt"
+ # get the file name from the config
+ # this file name can be a glob, as long as matches can all be loaded by iris
+ deposition_data_file_name = Template(config['Deposition']['DataFileTemplate']).substitute(**config)
+ name_file_wildcard = f"{deposition_path}/{deposition_data_file_name}"
EWSPlottingOutputGlobs = []
diff --git a/configs/config_EastAfrica_an_ewsdev.json b/configs/config_EastAfrica_an_ewsdev.json
index 2ff524745bc188231db0b263a3273d83f00270d7..7094604246a2f2507d0b1ce5c88e2f4979c39443 100644
--- a/configs/config_EastAfrica_an_ewsdev.json
+++ b/configs/config_EastAfrica_an_ewsdev.json
@@ -94,6 +94,7 @@
"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",
diff --git a/configs/config_EastAfrica_an_live.json b/configs/config_EastAfrica_an_live.json
index 400bdec2cbfd501c022276d0bd72fa85def6e8af..b1d86413fdc13e3a6ac96891f55d0810415a1443 100644
--- a/configs/config_EastAfrica_an_live.json
+++ b/configs/config_EastAfrica_an_live.json
@@ -94,6 +94,7 @@
"Deposition" : {
"ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
"InputFileTemplate" : "WR_NAME_Ethiopia_${StartString}_an",
+ "DataFileTemplate" : "deposition_srcs_allregions_${StartString}.nc",
"TimeExpectedAvailable" : "1500",
"ProcessPreJob" : "process_pre_job_server_download",
"ProcessInJob" : "process_in_job_dep",
diff --git a/configs/config_EastAfrica_fc_ewsdev.json b/configs/config_EastAfrica_fc_ewsdev.json
index 06a54241f21bcc445a22bfa196465e62f5bab25d..ea6c0f47a293c2219a179bf112fc755a9d023346 100644
--- a/configs/config_EastAfrica_fc_ewsdev.json
+++ b/configs/config_EastAfrica_fc_ewsdev.json
@@ -114,6 +114,7 @@
"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",
diff --git a/configs/config_EastAfrica_fc_live.json b/configs/config_EastAfrica_fc_live.json
index cbd454f7073cade4b4ac7e2e3210ea847efdf8c2..c074788fae4da0dd57e86e4a392b4c021d2c55f9 100644
--- a/configs/config_EastAfrica_fc_live.json
+++ b/configs/config_EastAfrica_fc_live.json
@@ -94,6 +94,7 @@
"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",
@@ -119,23 +120,28 @@
}
},
"Epidemiology" : {
+ "DiseaseNames" : ["StemRust"],
+ "CalculationSpanDays" : ["20210715",5],
+ "TimeStep_hours": "3",
"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"
+ "MaxFieldsPerCell" : "1",
+ "HostRaster" : "/storage/app/EWS/General/EWS-EpiModel/input_EastAfrica/wheat_area_frac_MapSPAM2010_EastAfrica.tif"
},
"Deposition" : {
- "VariableName" : "P_RECONDITA_DEPOSITION",
- "PathTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/WR_NAME_SouthAsia_${StartString}/",
- "SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/DEPOSITION_SUCCESS.txt",
+ "VariableName" : "P_GRAMINIS_DEPOSITION",
+ "PathTemplate" : "${WorkspacePath}DEPOSITION_${DateString}/WR_NAME_Ethiopia_${DateString}_fc/",
+ "SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
+ "FileListerFunction" : "list_deposition_files_historical",
"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",
+ "PathTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${DateString}/processed/${RegionName}/${DiseaseName}/",
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
+ "FileListerFunction" : "list_env_suit_files_historical",
"FileNameTemplate" : "RIE_value.csv",
"FileNamePrepared" : "?"
},
@@ -150,42 +156,37 @@
"vmax" : 1.5e+1,
"subplot_position" : [0,0],
"cmapString" : "CMRmap_r",
- "bounds" : [87.9, 92.7, 20.5, 26.7],
- "UTMprojection" : 45
+ "bounds": [32.5,48.0,3.3,15.0],
+ "UTMprojection" : 37
+
}
},{
- "model" : "log10Dep",
- "modelArguments" : {},
+ "model" : "ps",
+ "modelArguments": {
+ "beta": 4.0e-3,
+ "gamma": 6.3e-4,
+ "alpha": 1.0,
+ "infection": "previous"
+ },
"infectionRasterFileName" : "?",
- "description": "log(spore deposition)",
+ "description": "SE[beta*log10(alpha*D)+gamma*P]",
"analysis" : {
"vmin" : 0.0e+0,
- "vmax" : 3.0e+2,
+ "vmax" : 1,
"subplot_position" : [0,1],
"cmapString" : "CMRmap_r",
- "bounds" : [87.9, 92.7, 20.5, 26.7],
- "UTMprojection" : 45
+ "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" : [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"
+ "PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/chart_areas/east_africa/ews_plotting_epi_east_africa_main.py",
+ "ChartConfig" : "/storage/app/EWS/General/EWS-Plotting/python/data/json_config/ews/chart/CHART_CONFIG_EAST_AFRICA_PINE.json",
+ "RunConfig_seasonsofar" : "/storage/home/jws52/projects/EWS-plotting/python/data/json_config/ews/epi/RUN_CONFIG_EPI_seasonaccum.json",
+ "RunConfig_weekahead" : "/storage/home/jws52/projects/EWS-plotting/python/data/json_config/ews/epi/RUN_CONFIG_EPI_weekahead.json",
+ "EpiCase" : "ps"
}
},
"Advisory" :
@@ -252,4 +253,4 @@
},
"logos" : "/storage/app/EWS/Ethiopia/Documents/logos_Ethiopia_plotting.png"
}
-}
+}
\ No newline at end of file
diff --git a/configs/config_SouthAsia_an_ewsdev.json b/configs/config_SouthAsia_an_ewsdev.json
index 097c4c0a4674bbea06d73757c85e03176258ad2a..992e2835554702219bb305ef92210c70e2902998 100644
--- a/configs/config_SouthAsia_an_ewsdev.json
+++ b/configs/config_SouthAsia_an_ewsdev.json
@@ -93,6 +93,7 @@
"Deposition" : {
"ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
"InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_fc",
+ "DataFileTemplate" : "deposition_srcs_allregions_${StartString}.nc",
"TimeExpectedAvailable" : "0800",
"ProcessPreJob" : "process_pre_job_server_download",
"ProcessInJob" : "process_in_job_dep",
diff --git a/configs/config_SouthAsia_an_live.json b/configs/config_SouthAsia_an_live.json
index 876f6143d25af50b08e951ec063de38de16cbdb6..07b9b402b6a92e54a277bfe3dee70e0c7a06dfde 100644
--- a/configs/config_SouthAsia_an_live.json
+++ b/configs/config_SouthAsia_an_live.json
@@ -93,6 +93,7 @@
"Deposition" : {
"ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
"InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_fc",
+ "DataFileTemplate" : "deposition_srcs_allregions_${StartString}.nc",
"TimeExpectedAvailable" : "1500",
"ProcessPreJob" : "process_pre_job_server_download",
"ProcessInJob" : "process_in_job_dep",
diff --git a/configs/config_SouthAsia_fc_ewsdev.json b/configs/config_SouthAsia_fc_ewsdev.json
index 6bad040858f035b46b3c63b2db16826e6f3709c7..b384ecaa58e7e975f328569e87a8be01f0e0a90c 100644
--- a/configs/config_SouthAsia_fc_ewsdev.json
+++ b/configs/config_SouthAsia_fc_ewsdev.json
@@ -114,6 +114,7 @@
"Deposition" : {
"ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
"InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_fc",
+ "DataFileTemplate" : "deposition_srcs_allregions_${StartString}.nc",
"TimeExpectedAvailable" : "0800",
"ProcessPreJob" : "process_pre_job_server_download",
"ProcessInJob" : "process_in_job_dep",
diff --git a/configs/config_SouthAsia_fc_live.json b/configs/config_SouthAsia_fc_live.json
index 8c471390cb6e02253d7b8595d5dad516e2e38c75..386aadee9269020cc39598b4dec00ec41a158206 100644
--- a/configs/config_SouthAsia_fc_live.json
+++ b/configs/config_SouthAsia_fc_live.json
@@ -93,6 +93,7 @@
"Deposition" : {
"ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
"InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_fc",
+ "DataFileTemplate" : "deposition_srcs_allregions_${StartString}.nc",
"TimeExpectedAvailable" : "0800",
"ProcessPreJob" : "process_pre_job_server_download",
"ProcessInJob" : "process_in_job_dep",