From 80de8be1b925933a92ed1e1edec7ed60c1b00435 Mon Sep 17 00:00:00 2001
From: Jake Smith <jws52@cam.ac.uk>
Date: Mon, 17 May 2021 17:10:47 +0100
Subject: [PATCH] feat: Generate template advisories
The newly imported AdvisoryBuilder can be run separately, see
that project for more details.
Updated conda environment accordingly.
---
Processor.py | 3 +-
ProcessorComponents.py | 48 ++++++++++++++++++++----
configs/config_Ethiopia_an_ewsdev.json | 2 +-
configs/config_Ethiopia_an_live.json | 2 +-
configs/config_Ethiopia_fc_ewsdev.json | 36 +++++++++++++++++-
configs/config_Ethiopia_fc_live.json | 36 +++++++++++++++++-
configs/config_SouthAsia_an_ewsdev.json | 2 +-
configs/config_SouthAsia_an_live.json | 2 +-
configs/config_SouthAsia_big_ewsdev.json | 40 +++++++++++++++++++-
configs/config_SouthAsia_big_live.json | 40 +++++++++++++++++++-
configs/config_SouthAsia_fc_ewsdev.json | 40 +++++++++++++++++++-
configs/config_SouthAsia_fc_live.json | 40 +++++++++++++++++++-
run_Processor.sh | 3 +-
13 files changed, 274 insertions(+), 20 deletions(-)
diff --git a/Processor.py b/Processor.py
index a8d5d22..af2cacd 100755
--- a/Processor.py
+++ b/Processor.py
@@ -199,6 +199,7 @@ def move_default_logfile_handler(dstPathName,srcPathName=log_path_default,FileHa
return
def parse_and_check_args(todayString):
+
# define the command line arguments
my_parser = argparse.ArgumentParser(description='Command-line arguments for coordinator script of env suitability model')
@@ -209,7 +210,7 @@ def parse_and_check_args(todayString):
my_parser.add_argument(
'-p', '--component',
type = str,
- choices = ['Environment','Deposition','Epidemiology','Survey'],
+ choices = list(ProcessorComponents.short_name.keys()),
required = True,
dest = 'component',
help = '''Name of EWS component to process, which must be present
diff --git a/ProcessorComponents.py b/ProcessorComponents.py
index 4984223..180854c 100644
--- a/ProcessorComponents.py
+++ b/ProcessorComponents.py
@@ -25,6 +25,7 @@ from rasterio import open as rio_open
# gitlab projects
# TODO: Package these projects so they are robust for importing
+from AdvisoryBuilder import DataGatherer # created by jws52
from EpiModel import EpiModel, EpiPrep, EpiAnalysis, plotRaster # created by rs481
# submodules of this project
@@ -41,10 +42,12 @@ script_path = os.path.dirname(__file__)+'/'
coordinator_path = script_path
short_name = {
- 'Environment' : 'ENVIRONMENT_2.0',
+ 'Advisory' : 'SUMMARY',
'Deposition' : 'DEPOSITION',
+ 'Environment' : 'ENVIRONMENT_2.0',
'Epidemiology' : 'EPI',
- 'Survey' : 'SURVEYDATA'}
+ 'Survey' : 'SURVEYDATA',
+ }
def process_pre_job_survey(input_args):
'''Returns a boolean as to whether the job is ready for full processing.'''
@@ -218,6 +221,31 @@ def process_pre_job_epi(input_args):
return True
+def process_in_job_advisory(jobPath,status,config,component):
+ '''Generates a word processor file containing some basic survey statistics
+ and output figures from deposition, environmental suitability, and
+ eventually also the epi model. This template advisory is intended to speed
+ up the process of writing advisories. The intended user is a local expert
+ who edits the content of the document.
+ Uses the gitlab project EWS-advisory-builder.'''
+
+ config_advisory = config[component].copy()
+
+ # provide top-level arguments to advisory config
+ for k,v in config.items():
+ if k not in short_name.keys():
+ config_advisory[k]=v
+
+ dateString = config['StartString']
+
+ layout = 'tight'
+
+ report_names = DataGatherer.run_each_subregion(config_advisory, dateString, layout)
+
+ # pass the report filenames to upload to the remote server
+
+ return report_names
+
def get_ODK_form_as_csv(form_credentials: dict, jobPath: str, config: dict, status):
'''Given a dict with a single ODK form to download from an ODK Aggregate
server, obtains it and converts to csv.'''
@@ -1293,7 +1321,7 @@ def process_in_job_epi(jobPath,status,config,component):
# provide fundamental config elements to config_epi
for k,v in config.items():
- if k not in ['Survey','Environment','Deposition','Epidemiology']:
+ if k not in short_name.keys():
config_epi[k]=v
logger.info('Incremental configuration looks like:')
@@ -1376,7 +1404,7 @@ def process_in_job_epi(jobPath,status,config,component):
return
-def do_nothing(**kwargs):
+def do_nothing(*args, **kwargs):
'''Dummy function'''
logger.info('Called do_nothing(). Nothing to do here')
@@ -1652,12 +1680,16 @@ def process_EWS_plotting_epi(jobPath,config):
def upload(config,FilesToSend,component):
# TODO: replace subprocess ssh and scp commands with python-based paramiko
+
+ usual_path = f"{config['StartString']}_0000/"
component_path = {
- 'Environment':f"{config['StartString']}_0000/",
- 'Deposition':f"{config['StartString']}_0000/",
- 'Epidemiology':f"EPI_{config['StartString']}_0000/",
- 'Survey':f"SURVEYDATA_{config['StartString']}_0000/" }
+ 'Environment' : usual_path,
+ 'Deposition' : usual_path,
+ 'Epidemiology' : f"EPI_{config['StartString']}_0000/",
+ 'Survey' : f"SURVEYDATA_{config['StartString']}_0000/",
+ 'Advisory' : usual_path }
+
# TODO: make path discern Daily or Weekly sub-directory
diff --git a/configs/config_Ethiopia_an_ewsdev.json b/configs/config_Ethiopia_an_ewsdev.json
index 632d4ae..ac50e18 100644
--- a/configs/config_Ethiopia_an_ewsdev.json
+++ b/configs/config_Ethiopia_an_ewsdev.json
@@ -112,7 +112,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePathout}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
diff --git a/configs/config_Ethiopia_an_live.json b/configs/config_Ethiopia_an_live.json
index c325056..74109c5 100644
--- a/configs/config_Ethiopia_an_live.json
+++ b/configs/config_Ethiopia_an_live.json
@@ -112,7 +112,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePathout}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
diff --git a/configs/config_Ethiopia_fc_ewsdev.json b/configs/config_Ethiopia_fc_ewsdev.json
index 121087a..58b5ab0 100644
--- a/configs/config_Ethiopia_fc_ewsdev.json
+++ b/configs/config_Ethiopia_fc_ewsdev.json
@@ -112,7 +112,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
@@ -169,5 +169,39 @@
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/ethiopia/ews_plotting_epi_ethiopia_main.py",
"EpiCase" : "log10DepEnv"
}
+ },
+ "Advisory" :
+ {
+ "ProcessPreJob" : "query_past_successes",
+ "ProcessInJob" : "process_in_job_advisory",
+ "ProcessEWSPlotting" : "do_nothing",
+ "SubRegionNames" : ["Ethiopia"],
+ "seasonStartString" : "20200601",
+ "Environment" : {
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe" : "${envPlotPath}/suitability_${SubRegionNameLower}_stripe_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "stem" : "${envPlotPath}/suitability_${SubRegionNameLower}_stem_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "leaf" : "${envPlotPath}/suitability_${SubRegionNameLower}_leaf_rust_total_${dateString}0000_${EnvEndString}0000_map.png"
+ }
+ },
+ "Deposition" : {
+ "SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe": "${depPlotPath}/deposition_${SubRegionNameLower}_stripe_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "stem": "${depPlotPath}/deposition_${SubRegionNameLower}_stem_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "leaf": "${depPlotPath}/deposition_${SubRegionNameLower}_leaf_total_${dateString}0000_${weekAheadString}0000_map.png"
+ }
+ },
+ "Surveys" : {
+ "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_Zone_2013.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/admin-boundaries/Ethiopia_All/Eth_Woreda_2013.shp"
+ }
+ },
+ "logos" : "/storage/app/EWS/Ethiopia/Documents/logos_Ethiopia_plotting.png"
}
}
\ No newline at end of file
diff --git a/configs/config_Ethiopia_fc_live.json b/configs/config_Ethiopia_fc_live.json
index e728fee..5369921 100644
--- a/configs/config_Ethiopia_fc_live.json
+++ b/configs/config_Ethiopia_fc_live.json
@@ -112,7 +112,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
@@ -169,5 +169,39 @@
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/ethiopia/ews_plotting_epi_ethiopia_main.py",
"EpiCase" : "log10DepEnv"
}
+ },
+ "Advisory" :
+ {
+ "ProcessPreJob" : "query_past_successes",
+ "ProcessInJob" : "process_in_job_advisory",
+ "ProcessEWSPlotting" : "do_nothing",
+ "SubRegionNames" : ["Ethiopia"],
+ "seasonStartString" : "20200601",
+ "Environment" : {
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe" : "${envPlotPath}/suitability_${SubRegionNameLower}_stripe_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "stem" : "${envPlotPath}/suitability_${SubRegionNameLower}_stem_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "leaf" : "${envPlotPath}/suitability_${SubRegionNameLower}_leaf_rust_total_${dateString}0000_${EnvEndString}0000_map.png"
+ }
+ },
+ "Deposition" : {
+ "SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe": "${depPlotPath}/deposition_${SubRegionNameLower}_stripe_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "stem": "${depPlotPath}/deposition_${SubRegionNameLower}_stem_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "leaf": "${depPlotPath}/deposition_${SubRegionNameLower}_leaf_total_${dateString}0000_${weekAheadString}0000_map.png"
+ }
+ },
+ "Surveys" : {
+ "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_Zone_2013.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/Ethiopia/Documents/shapefiles/admin-boundaries/Ethiopia_All/Eth_Woreda_2013.shp"
+ }
+ },
+ "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 b821d86..7d754c5 100644
--- a/configs/config_SouthAsia_an_ewsdev.json
+++ b/configs/config_SouthAsia_an_ewsdev.json
@@ -121,7 +121,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePathout}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
diff --git a/configs/config_SouthAsia_an_live.json b/configs/config_SouthAsia_an_live.json
index d570960..e4a9a19 100644
--- a/configs/config_SouthAsia_an_live.json
+++ b/configs/config_SouthAsia_an_live.json
@@ -121,7 +121,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePathout}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePathout}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
diff --git a/configs/config_SouthAsia_big_ewsdev.json b/configs/config_SouthAsia_big_ewsdev.json
index 147839b..b379bc0 100644
--- a/configs/config_SouthAsia_big_ewsdev.json
+++ b/configs/config_SouthAsia_big_ewsdev.json
@@ -111,7 +111,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
@@ -168,5 +168,43 @@
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/south_asia/ews_plotting_epi_asia_main.py",
"EpiCase" : "log10DepEnv"
}
+ },
+ "Advisory" : {
+ "ProcessPreJob" : "query_past_successes",
+ "ProcessInJob" : "process_in_job_advisory",
+ "ProcessEWSPlotting" : "do_nothing",
+ "SubRegionNames" : ["Nepal","Bangladesh"],
+ "seasonStartString" : "20201201",
+ "Environment" : {
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe" : "${envPlotPath}/suitability_${SubRegionNameLower}_stripe_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "stem" : "${envPlotPath}/suitability_${SubRegionNameLower}_stem_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "leaf" : "${envPlotPath}/suitability_${SubRegionNameLower}_leaf_rust_total_${dateString}0000_${EnvEndString}0000_map.png"
+ }
+ },
+ "Deposition" : {
+ "SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe": "${depPlotPath}/deposition_${SubRegionNameLower}_stripe_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "stem": "${depPlotPath}/deposition_${SubRegionNameLower}_stem_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "leaf": "${depPlotPath}/deposition_${SubRegionNameLower}_leaf_total_${dateString}0000_${weekAheadString}0000_map.png"
+ }
+ },
+ "Surveys" : {
+ "Nepal" : {
+ "ShapeFilenameAdmin0" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin0.shp",
+ "ShapeFilenameAdmin1" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin1_withwheat_2017-19.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin2.shp"
+ },
+ "Bangladesh" : {
+ "ShapeFilenameAdmin0" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin0.shp",
+ "ShapeFilenameAdmin1" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin1.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin2.shp"
+ }
+ },
+ "logos" : "/storage/app/EWS/SouthAsia/Documents/logos_ARRCC.png"
}
}
\ No newline at end of file
diff --git a/configs/config_SouthAsia_big_live.json b/configs/config_SouthAsia_big_live.json
index 3b42306..b39a580 100644
--- a/configs/config_SouthAsia_big_live.json
+++ b/configs/config_SouthAsia_big_live.json
@@ -131,7 +131,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
@@ -188,5 +188,43 @@
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/south_asia/ews_plotting_epi_asia_main.py",
"EpiCase" : "log10DepEnv"
}
+ },
+ "Advisory" : {
+ "ProcessPreJob" : "query_past_successes",
+ "ProcessInJob" : "process_in_job_advisory",
+ "ProcessEWSPlotting" : "do_nothing",
+ "SubRegionNames" : ["Nepal","Bangladesh"],
+ "seasonStartString" : "20201201",
+ "Environment" : {
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe" : "${envPlotPath}/suitability_${SubRegionNameLower}_stripe_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "stem" : "${envPlotPath}/suitability_${SubRegionNameLower}_stem_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "leaf" : "${envPlotPath}/suitability_${SubRegionNameLower}_leaf_rust_total_${dateString}0000_${EnvEndString}0000_map.png"
+ }
+ },
+ "Deposition" : {
+ "SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe": "${depPlotPath}/deposition_${SubRegionNameLower}_stripe_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "stem": "${depPlotPath}/deposition_${SubRegionNameLower}_stem_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "leaf": "${depPlotPath}/deposition_${SubRegionNameLower}_leaf_total_${dateString}0000_${weekAheadString}0000_map.png"
+ }
+ },
+ "Surveys" : {
+ "Nepal" : {
+ "ShapeFilenameAdmin0" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin0.shp",
+ "ShapeFilenameAdmin1" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin1_withwheat_2017-19.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin2.shp"
+ },
+ "Bangladesh" : {
+ "ShapeFilenameAdmin0" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin0.shp",
+ "ShapeFilenameAdmin1" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin1.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin2.shp"
+ }
+ },
+ "logos" : "/storage/app/EWS/SouthAsia/Documents/logos_ARRCC.png"
}
}
\ No newline at end of file
diff --git a/configs/config_SouthAsia_fc_ewsdev.json b/configs/config_SouthAsia_fc_ewsdev.json
index 8c8347c..b52bbcf 100644
--- a/configs/config_SouthAsia_fc_ewsdev.json
+++ b/configs/config_SouthAsia_fc_ewsdev.json
@@ -120,7 +120,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
@@ -177,5 +177,43 @@
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/south_asia/ews_plotting_epi_asia_main.py",
"EpiCase" : "log10DepEnv"
}
+ },
+ "Advisory" : {
+ "ProcessPreJob" : "query_past_successes",
+ "ProcessInJob" : "process_in_job_advisory",
+ "ProcessEWSPlotting" : "do_nothing",
+ "SubRegionNames" : ["Nepal","Bangladesh"],
+ "seasonStartString" : "20201201",
+ "Environment" : {
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe" : "${envPlotPath}/suitability_${SubRegionNameLower}_stripe_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "stem" : "${envPlotPath}/suitability_${SubRegionNameLower}_stem_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "leaf" : "${envPlotPath}/suitability_${SubRegionNameLower}_leaf_rust_total_${dateString}0000_${EnvEndString}0000_map.png"
+ }
+ },
+ "Deposition" : {
+ "SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe": "${depPlotPath}/deposition_${SubRegionNameLower}_stripe_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "stem": "${depPlotPath}/deposition_${SubRegionNameLower}_stem_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "leaf": "${depPlotPath}/deposition_${SubRegionNameLower}_leaf_total_${dateString}0000_${weekAheadString}0000_map.png"
+ }
+ },
+ "Surveys" : {
+ "Nepal" : {
+ "ShapeFilenameAdmin0" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin0.shp",
+ "ShapeFilenameAdmin1" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin1_withwheat_2017-19.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin2.shp"
+ },
+ "Bangladesh" : {
+ "ShapeFilenameAdmin0" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin0.shp",
+ "ShapeFilenameAdmin1" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin1.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin2.shp"
+ }
+ },
+ "logos" : "/storage/app/EWS/SouthAsia/Documents/logos_ARRCC.png"
}
}
\ No newline at end of file
diff --git a/configs/config_SouthAsia_fc_live.json b/configs/config_SouthAsia_fc_live.json
index 87288ad..0d3a226 100644
--- a/configs/config_SouthAsia_fc_live.json
+++ b/configs/config_SouthAsia_fc_live.json
@@ -121,7 +121,7 @@
},
"Environment" : {
"PathTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/processed/${SubRegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_${StartString}/STATUS_SUCCESS",
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
"FileNameTemplate" : "RIE_value.csv",
"FileListerFunction" : "list_env_suit_files_operational",
"FileNamePrepared" : "?"
@@ -178,5 +178,43 @@
"PythonScript" : "/storage/app/EWS/General/EWS-Plotting/python/south_asia/ews_plotting_epi_asia_main.py",
"EpiCase" : "log10DepEnv"
}
+ },
+ "Advisory" : {
+ "ProcessPreJob" : "query_past_successes",
+ "ProcessInJob" : "process_in_job_advisory",
+ "ProcessEWSPlotting" : "do_nothing",
+ "SubRegionNames" : ["Nepal","Bangladesh"],
+ "seasonStartString" : "20201201",
+ "Environment" : {
+ "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe" : "${envPlotPath}/suitability_${SubRegionNameLower}_stripe_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "stem" : "${envPlotPath}/suitability_${SubRegionNameLower}_stem_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
+ "leaf" : "${envPlotPath}/suitability_${SubRegionNameLower}_leaf_rust_total_${dateString}0000_${EnvEndString}0000_map.png"
+ }
+ },
+ "Deposition" : {
+ "SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
+ "PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
+ "PlotFilenameTemplates" : {
+ "stripe": "${depPlotPath}/deposition_${SubRegionNameLower}_stripe_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "stem": "${depPlotPath}/deposition_${SubRegionNameLower}_stem_total_${dateString}0000_${weekAheadString}0000_map.png",
+ "leaf": "${depPlotPath}/deposition_${SubRegionNameLower}_leaf_total_${dateString}0000_${weekAheadString}0000_map.png"
+ }
+ },
+ "Surveys" : {
+ "Nepal" : {
+ "ShapeFilenameAdmin0" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin0.shp",
+ "ShapeFilenameAdmin1" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin1_withwheat_2017-19.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Nepal_admin2.shp"
+ },
+ "Bangladesh" : {
+ "ShapeFilenameAdmin0" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin0.shp",
+ "ShapeFilenameAdmin1" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin1.shp",
+ "ShapeFilenameAdmin2" : "/storage/app/EWS/SouthAsia/Documents/shapefiles/Bangladesh_admin2.shp"
+ }
+ },
+ "logos" : "/storage/app/EWS/SouthAsia/Documents/logos_ARRCC.png"
}
}
\ No newline at end of file
diff --git a/run_Processor.sh b/run_Processor.sh
index 918dc11..cf86948 100755
--- a/run_Processor.sh
+++ b/run_Processor.sh
@@ -3,7 +3,8 @@
# provide custom python packages so they can be imported
flagdir=/storage/app/EWS/General/EWS-python/custom_modules/flagdir/
epimodel=/storage/app/EWS/General/EWS-EpiModel/
-export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel
+advisory=/storage/app/EWS/General/EWS-advisory-builder/
+export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory
# activate conda environment of python modules so they can be imported
conda_env=/storage/app/EWS/General/EWS-python/py3EWSepi
--
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