From 2eff9e5fbd2b7e66216761f8f8ed9e079355b02c Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Wed, 26 Oct 2022 11:06:17 +0100
Subject: [PATCH] adding integration test for survey
---
coordinator/ProcessorEpidemiology.py | 7 +--
coordinator/ProcessorSurveys.py | 45 +++++++++-------
coordinator/ProcessorUtils.py | 9 ++--
tests/integration/test_survey.py | 47 ++++++++++++++++
.../LIVE_SURVEYDATA_TOUSE.csv | 2 +
.../SurveyDataErrorsToRemove.csv | 2 +
.../coordinator/configs/Cred-ODK-EIAR.json | 31 +++++++++++
.../configs/config_EastAfrica_fc_live.json | 51 ++++++++++++------
.../assets/approx_growth_timing_cleaned.csv | 11 ++++
.../boundaries/EastAfrica_clusters_small.cpg | 1 +
.../boundaries/EastAfrica_clusters_small.dbf | Bin 0 -> 893 bytes
.../boundaries/EastAfrica_clusters_small.prj | 1 +
.../boundaries/EastAfrica_clusters_small.qmd | 26 +++++++++
.../boundaries/EastAfrica_clusters_small.shp | Bin 0 -> 19516 bytes
.../boundaries/EastAfrica_clusters_small.shx | Bin 0 -> 124 bytes
.../boundaries/EastAfrica_regions_small.cpg | 1 +
.../boundaries/EastAfrica_regions_small.dbf | Bin 0 -> 628 bytes
.../boundaries/EastAfrica_regions_small.prj | 1 +
.../boundaries/EastAfrica_regions_small.qmd | 26 +++++++++
.../boundaries/EastAfrica_regions_small.shp | Bin 0 -> 14068 bytes
.../boundaries/EastAfrica_regions_small.shx | Bin 0 -> 116 bytes
...ica_clusters_with_wheat_ha_MAPSPAM2017.cpg | 1 +
...ica_clusters_with_wheat_ha_MAPSPAM2017.csv | 4 ++
...ica_clusters_with_wheat_ha_MAPSPAM2017.dbf | Bin 0 -> 313 bytes
...ica_clusters_with_wheat_ha_MAPSPAM2017.prj | 1 +
...ica_clusters_with_wheat_ha_MAPSPAM2017.shp | Bin 0 -> 19516 bytes
...ica_clusters_with_wheat_ha_MAPSPAM2017.shx | Bin 0 -> 124 bytes
...V1r1_SSA_gr_H_WHEA_A_rescaled_oneliner.tif | Bin 0 -> 1058 bytes
.../spam2017V1r1_SSA_gr_H_WHEA_A_small.tif | Bin 0 -> 1576 bytes
.../config_EastAfrica_mapspam2017.json | 14 +++++
30 files changed, 237 insertions(+), 44 deletions(-)
create mode 100644 tests/integration/test_survey.py
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/assets/SURVEYDATA_MANUAL/LIVE_SURVEYDATA_TOUSE.csv
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/assets/SURVEYDATA_MANUAL/SurveyDataErrorsToRemove.csv
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/Cred-ODK-EIAR.json
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/approx_growth_timing_cleaned.csv
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.cpg
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.dbf
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.prj
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.qmd
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.shp
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.shx
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_regions_small.cpg
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_regions_small.dbf
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_regions_small.prj
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_regions_small.qmd
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_regions_small.shp
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_regions_small.shx
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/preprocessed/EastAfrica_clusters_with_wheat_ha_MAPSPAM2017.cpg
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/preprocessed/EastAfrica_clusters_with_wheat_ha_MAPSPAM2017.csv
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/preprocessed/EastAfrica_clusters_with_wheat_ha_MAPSPAM2017.dbf
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/preprocessed/EastAfrica_clusters_with_wheat_ha_MAPSPAM2017.prj
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/preprocessed/EastAfrica_clusters_with_wheat_ha_MAPSPAM2017.shp
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/preprocessed/EastAfrica_clusters_with_wheat_ha_MAPSPAM2017.shx
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/preprocessed/spam2017V1r1_SSA_gr_H_WHEA_A_rescaled_oneliner.tif
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/spam2017V1r1_SSA_gr_H_WHEA_A_small.tif
create mode 100644 tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/configs/config_EastAfrica_mapspam2017.json
diff --git a/coordinator/ProcessorEpidemiology.py b/coordinator/ProcessorEpidemiology.py
index 76daa9f..baadb59 100644
--- a/coordinator/ProcessorEpidemiology.py
+++ b/coordinator/ProcessorEpidemiology.py
@@ -8,6 +8,7 @@ import logging
from pathlib import Path
import os
import shutil
+from typing import List
from numpy import argmax, unique
from pandas import read_csv, DataFrame, to_datetime
@@ -75,7 +76,7 @@ def calc_epi_date_range(init_str,span_days=[0,6]):
return start_date, end_date
-def process_pre_job_epi(input_args):
+def process_pre_job_epi(input_args: dict):
'''Returns a boolean as to whether the job is ready for full processing.'''
logger.info('started process_pre_job_epi()')
@@ -83,7 +84,7 @@ def process_pre_job_epi(input_args):
# check pre-requisite jobs are complete
query_past_successes(input_args)
- config_fns = input_args.config_paths
+ config_fns: List[str] = input_args['config_paths']
for configFile in config_fns:
@@ -91,7 +92,7 @@ def process_pre_job_epi(input_args):
config_i = open_and_check_config(configFile)
#determine end time, from config file
- arg_start_date = input_args.start_date
+ arg_start_date: str = input_args['start_date']
calc_span_days = config_i['Epidemiology']['CalculationSpanDays']
assert len(calc_span_days) == 2
diff --git a/coordinator/ProcessorSurveys.py b/coordinator/ProcessorSurveys.py
index c6ea0ea..064c40a 100644
--- a/coordinator/ProcessorSurveys.py
+++ b/coordinator/ProcessorSurveys.py
@@ -48,37 +48,41 @@ def get_ODK_form_as_csv(form_credentials: dict, jobPath: str, config: dict, stat
ODK_jar = form_credentials['ODK_jar']
assert os.path.exists(ODK_jar)
- ODK_download = ['java',
- '-jar', ODK_jar,
- '--pull_aggregate',
- '--form_id', form_credentials['form_id'],
- '--storage_directory', ODK_output_path,
- '--odk_url', form_credentials['url'],
- '--odk_username',form_credentials['user'],
- '--odk_password',form_credentials['pass']]
+ skip_download: bool = config['Survey'].get('SkipServerDownload', False)
ODK_download_success = True
- logger.debug('Performing ' + description_long)
+ if not skip_download:
+ try:
+ ODK_download = ['java',
+ '-jar', ODK_jar,
+ '--pull_aggregate',
+ '--form_id', form_credentials['form_id'],
+ '--storage_directory', ODK_output_path,
+ '--odk_url', form_credentials['url'],
+ '--odk_username', form_credentials['user'],
+ '--odk_password', form_credentials['pass']]
- try:
- # perform a pull from the ODK server, and if it fails write a warning message
+ logger.debug('Performing ' + description_long)
- subprocess_and_log(ODK_download,description_short,description_long,log_type='warning',check=True)
+ # perform a pull from the ODK server, and if it fails write a warning message
- except subprocess.CalledProcessError as e:
- status.reset('WARNING')
- ODK_download_success = False
+ subprocess_and_log(ODK_download,description_short,description_long,log_type='warning',check=True)
+
+ except subprocess.CalledProcessError as e:
+ status.reset('WARNING')
+ ODK_download_success = False
#TODO: Check it came down cleanly ($serverOutputDir is created whether cleanly or not, so test more explicitly):
ODK_csv_path = f"{jobPath}/ExportCSV/"
- Path(ODK_csv_path).mkdir(parents=True, exist_ok=True)
+ Path(ODK_csv_path).mkdir(parents = True, exist_ok = True)
ODK_csv_filename = f"SurveyData_{form_credentials['form_id']}.csv"
- if ODK_download_success:
+ if ODK_download_success and not skip_download:
+
description_short = 'ODK export'
description_long = 'converting ODK download to csv'
logger.debug(description_long)
@@ -100,9 +104,9 @@ def get_ODK_form_as_csv(form_credentials: dict, jobPath: str, config: dict, stat
status.reset('WARNING')
ODK_download_success = False
- if not ODK_download_success:
+ if not ODK_download_success or skip_download:
- logger.info("Because ODK server download failed somewhere, trying to recover by copying recent download")
+ logger.info("Because ODK server download failed somewhere (or we are skipping downloads), trying to recover by copying recent download")
ODK_copy_success = False
@@ -131,6 +135,7 @@ def get_ODK_form_as_csv(form_credentials: dict, jobPath: str, config: dict, stat
past_ODK_csv_filename = ODK_csv_filename
logger.info(f"Looking for {past_ODK_csv_path+past_ODK_csv_filename}")
+ print(f"Looking for {past_ODK_csv_path+past_ODK_csv_filename}")
copyfile(past_ODK_csv_path+past_ODK_csv_filename,ODK_csv_path+ODK_csv_filename)
@@ -775,7 +780,7 @@ def process_in_job_survey(jobPath,status,config,component):
credentials_filename = config['Survey']['ServerCredentialsFile']
with open(credentials_filename) as credentials_file:
- cred = json.load(credentials_file)
+ cred: dict = json.load(credentials_file)
assert 'forms' in cred.keys()
diff --git a/coordinator/ProcessorUtils.py b/coordinator/ProcessorUtils.py
index 9dddef9..e8ce959 100644
--- a/coordinator/ProcessorUtils.py
+++ b/coordinator/ProcessorUtils.py
@@ -10,6 +10,7 @@ from string import Template
import subprocess
import sys
import tarfile
+from typing import List
short_name = {
@@ -214,14 +215,14 @@ def query_proceed(necessary_file,description):
return True
-def query_past_successes(input_args):
+def query_past_successes(input_args: dict):
'''Checks if deposition and environment jobs are already completed
successfully. If not, it raises an error.'''
- component = input_args.component
+ component: str = input_args['component']
# check configs can be loaded
- config_fns = input_args.config_paths
+ config_fns: List[str] = input_args['config_paths']
for configFile in config_fns:
try:
config_i = open_and_check_config(configFile)
@@ -230,7 +231,7 @@ def query_past_successes(input_args):
endScript(premature=True)
# some config initialisation is necessary
- config_i['StartString'] = input_args.start_date
+ config_i['StartString'] = input_args['start_date']
# check if deposition data is readily available
dep_success_file = Template(config_i[component]['Deposition']['SuccessFileTemplate']).substitute(**config_i)
diff --git a/tests/integration/test_survey.py b/tests/integration/test_survey.py
new file mode 100644
index 0000000..dd5d042
--- /dev/null
+++ b/tests/integration/test_survey.py
@@ -0,0 +1,47 @@
+import copy
+import os
+import unittest
+
+from integration.integration_test_utils import IntegrationTestUtils
+
+
+class TestEnvSuit(unittest.TestCase):
+
+ def setUp(self) -> None:
+ super().setUp()
+ default_config = '../test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json'
+ self.default_config_dict: dict = IntegrationTestUtils.load_json_file(default_config)
+
+ def test_env_suit_standard_inputs_expected_results1(self):
+
+ # nowstring: str = IntegrationTestUtils.get_now_string()
+ nowstring: str = ""
+
+ os.environ["EMAIL_CRED"] = "../test_data/test_deployment/envs/Cred_gmail.json"
+ from Processor import run_Process, set_log_level
+ args_dict: dict = {}
+ args_dict['component'] = 'Survey'
+ args_dict['config_paths'] = [IntegrationTestUtils.TEMP_CONFIG_FILE_PATH]
+ args_dict['log_level'] = 'info'
+ args_dict['live'] = False
+ args_dict['start_date'] = '20221001'
+ args_dict['noupload'] = True
+ set_log_level(args_dict['log_level'])
+
+ run_dict: dict = copy.deepcopy(self.default_config_dict)
+ test_out_path = run_dict['WorkspacePathout'] + nowstring + os.sep
+ run_dict['WorkspacePathout'] = test_out_path
+ run_dict['WorkspacePath'] = test_out_path
+ run_dict['Survey']['SkipServerDownload'] = True
+ run_dict['ServerName'] = '' # nothing, as local machine
+
+ # run_dict['SubRegionNames'].remove('Kenya')
+
+ IntegrationTestUtils.write_json_file(run_dict, IntegrationTestUtils.TEMP_CONFIG_FILE_PATH)
+
+ run_Process(args_dict)
+ self.assertTrue(True)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/assets/SURVEYDATA_MANUAL/LIVE_SURVEYDATA_TOUSE.csv b/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/assets/SURVEYDATA_MANUAL/LIVE_SURVEYDATA_TOUSE.csv
new file mode 100644
index 0000000..d4e06f7
--- /dev/null
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/assets/SURVEYDATA_MANUAL/LIVE_SURVEYDATA_TOUSE.csv
@@ -0,0 +1,2 @@
+SubmissionDate,start,end,today,deviceid,subscriberid,imei,phonenumber,username,surveyor_infromation-country,surveyor_infromation-surveyor_name,surveyor_infromation-institution,survey_infromation-location_name,survey_infromation-location-Latitude,survey_infromation-location-Longitude,survey_infromation-location-Altitude,survey_infromation-location-Accuracy,survey_infromation-survey_date,site_information-survey_site,site_information-crop,site_information-field_area,site_information-variety,site_information-growth_stage,other_crop,stem_rust-stemrust_incidence,stem_rust-Stemrust_severity,stem_rust-stemrust_host_plant_reaction,leaf_rust-leafrust_incidence,leaf_rust-leafrust_severity,leaf_rust-leafrust_host_plant_reaction,yellow_rust-yellowrust_incidence,yellow_rust-yellowrust_severity,yellow_rust-yellowrust_host_plant_reaction,septoria-septoria_incidence,septoria-septoria_severity,other_diseases_group-other_diseases,score_diseases_count,SET-OF-score_diseases,samples_collected,samples_type,sample_size-number_stemrust_live,sample_size-number_stemrust_dead_dna,sample_size-number_yellowrust_live,sample_size-number_yellowrust_dead,sample_size-number_leafrust_live,sample_size-using_barcode,live_stemrust_samples_count,SET-OF-live_stemrust_samples,dead_stemrust_samples_count,SET-OF-dead_stemrust_samples,live_yellowrust_samples_count,SET-OF-live_yellowrust_samples,dead_yellowrust_samples_count,SET-OF-dead_yellowrust_samples,live_leafrust_samples_count,SET-OF-live_leafrust_samples,comment,meta-instanceID,KEY
+17-09-21 8:00,10-09-21 9:00,10-09-21 9:03,10-Sep-21,collect:1qNmuTci1M7xyjou,,collect:1qNmuTci1M7xyjou,,debrebirhan,Ethiopia,Kalkidan Yalew,Debre Birhan,Hagere Mariyam,9.2610515,39.4485883,2841.798221,3.95,10-Sep-21,farmer_field,bread_wheat,0.25,Kekeba,tillering,,none,9,na,none,9,na,none,9,na,low,11,,0,uuid:f3896fd5-741c-4ef7-8497-cce9f395a931/score_diseases,no,,,,,,,,,,,,,,,,,,A wheat field is found in less than 20m distance far from the inspected field,uuid:f3896fd5-741c-4ef7-8497-cce9f395a931,uuid:f3896fd5-741c-4ef7-8497-cce9f395a931
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/assets/SURVEYDATA_MANUAL/SurveyDataErrorsToRemove.csv b/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/assets/SURVEYDATA_MANUAL/SurveyDataErrorsToRemove.csv
new file mode 100644
index 0000000..41e8e7f
--- /dev/null
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/assets/SURVEYDATA_MANUAL/SurveyDataErrorsToRemove.csv
@@ -0,0 +1,2 @@
+SubmissionDate,start,end,today,deviceid,subscriberid,imei,phonenumber,username,surveyor_infromation-country,surveyor_infromation-surveyor_name,surveyor_infromation-institution,survey_infromation-location_name,survey_infromation-location-Latitude,survey_infromation-location-Longitude,survey_infromation-location-Altitude,survey_infromation-location-Accuracy,survey_infromation-survey_date,site_information-survey_site,site_information-crop,site_information-field_area,site_information-variety,site_information-growth_stage,other_crop,stem_rust-stemrust_incidence,stem_rust-Stemrust_severity,stem_rust-stemrust_host_plant_reaction,leaf_rust-leafrust_incidence,leaf_rust-leafrust_severity,leaf_rust-leafrust_host_plant_reaction,yellow_rust-yellowrust_incidence,yellow_rust-yellowrust_severity,yellow_rust-yellowrust_host_plant_reaction,septoria-septoria_incidence,septoria-septoria_severity,other_diseases_group-other_diseases,score_diseases_count,SET-OF-score_diseases,samples_collected,samples_type,sample_size-number_stemrust_live,sample_size-number_stemrust_dead_dna,sample_size-number_yellowrust_live,sample_size-number_yellowrust_dead,sample_size-number_leafrust_live,sample_size-using_barcode,live_stemrust_samples_count,SET-OF-live_stemrust_samples,dead_stemrust_samples_count,SET-OF-dead_stemrust_samples,live_yellowrust_samples_count,SET-OF-live_yellowrust_samples,dead_yellowrust_samples_count,SET-OF-dead_yellowrust_samples,live_leafrust_samples_count,SET-OF-live_leafrust_samples,comment,meta-instanceID,KEY
+"Aug 6, 2018 12:43:06 PM","Jun 13, 2018 11:26:53 AM","Aug 6, 2018 12:42:21 PM","Jun 13, 2018",FC:19:10:89:E2:6B,"",FC:19:10:89:E2:6B,"",mekele,Ethiopia,tesfay gebrekirstos,Tigray Agricultural Research Institute,Ilala,13.5235519900,39.5033560800,1991.0000000000,5.0000000000,"Aug 6, 2018",farmer_field,bread_wheat,2.0000000000,mekele-1,tillering,"",high,20,mr,low,10,mr,high,50,s,medium,55,glume_blotch loose_smut pythium_root_rot scab_fusarium_head_blight take_all tan_spot,6,uuid:58cb6a0f-8e47-4339-8080-0e320234415c/score_diseases,no,"","","","","","","","","","","","","","","","","",There is potential inoculum for the future.,uuid:58cb6a0f-8e47-4339-8080-0e320234415c,uuid:58cb6a0f-8e47-4339-8080-0e320234415c
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/Cred-ODK-EIAR.json b/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/Cred-ODK-EIAR.json
new file mode 100644
index 0000000..00d5287
--- /dev/null
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/Cred-ODK-EIAR.json
@@ -0,0 +1,31 @@
+{
+ "forms" : [
+ {
+ "type" : "ODK",
+ "ODK_jar" : "./test_survey.py",
+ "url" : "not_needed",
+ "user" : "not_needed",
+ "pass" : "not_needed",
+ "form_id" : "wheat_rust_survey_1_0",
+ "form_name" : "Wheat rust survey 1_0"
+ },
+ {
+ "type" : "kobotoolbox",
+ "url" : "not_needed",
+ "user" : "not_needed",
+ "pass" : "not_needed",
+ "form_token" : "not_needed",
+ "form_id" : "akpyJHvYxkLKPkxFJnPyTW",
+ "form_name" : "Wheat rust survey 1.0"
+ },
+ {
+ "type" : "WRSIS",
+ "url" : "not_needed",
+ "user" : "not_needed",
+ "pass" : "not_needed",
+ "form_id" : "WRSIS",
+ "form_name" : "WRSIS"
+ }
+
+ ]
+}
\ No newline at end of file
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json b/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json
index 702d9bb..72b7d01 100644
--- a/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json
@@ -12,19 +12,24 @@
"Survey" : {
"ProcessPreJob" : "process_pre_job_survey",
"ProcessInJob" : "process_in_job_survey",
- "ProcessEWSPlotting" : "process_EWS_plotting_survey",
+ "ProcessEWSPlotting": "process_EWS_plotting_survey",
+ "AcceptableDowntimeDays": 35,
+ "SeasonStartString" : "20220930",
+ "SkipServerDownload" : true,
"ServerCredentialsFile" : "../test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/Cred-ODK-EIAR.json",
"ServerPathExtra" : "/storage/sftp/metofficeupload/upload/Ethiopia/toMO/",
"FormEdits" : {
"wheat_rust_survey_1_0" : {},
"akpyJHvYxkLKPkxFJnPyTW" : {
- "filter": {
- "surveyor_infromation-country" : "Kenya"
+ "filter_by_list": {
+ "surveyor_infromation-country" : ["Kenya", "Ethiopia"]
}
- }
+ },
+ "WRSIS" : {}
},
"SourcesConfigFilename" : "../test_data/test_deployment/regions/EastAfrica/resources/wheat_source_generation/configs/config_EastAfrica_mapspam2017.R",
- "SourcesRegionName" : "EastAfrica"
+ "SourcesRegionName" : "EastAfrica",
+ "pySourcesConfigFilename" : "../test_data/test_deployment/regions/EastAfrica/resources/source_gen/configs/config_EastAfrica_mapspam2017.json"
},
"Environment" : {
"ServerPathTemplate" : "/storage/sftp/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
@@ -164,14 +169,14 @@
"VariableNames" : ["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",
+ "FileListerFunction" : "list_files_split_historical_operational",
+ "FileNameTemplate" : "deposition_srcs_allregions_${DateString}.nc",
"FileNamePrepared" : "?"
},
"Environment" : {
"PathTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${DateString}/processed/${RegionName}/${DiseaseName}/",
"SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
- "FileListerFunction" : "list_env_suit_files_historical",
+ "FileListerFunction" : "list_files_split_historical_operational",
"FileNameTemplate" : "RIE_value.csv",
"FileNamePrepared" : "?"
},
@@ -214,6 +219,7 @@
"RunConfig_seasonsofar" : "/../test_data/test_deployment/regions/EastAfrica/resources/plotting/configs/epi/RUN_CONFIG_EPI.json",
"RunConfig_seasonplusforecast" : "../test_data/test_deployment/regions/EastAfrica/resources/plotting/configs/epi/RUN_CONFIG_EPI.json",
"ChartConfig" : "../test_data/test_deployment/regions/EastAfrica/resources/plotting/configs/chart/CHART_CONFIG_ETHIOPIA_PINE.json",
+ "PlottingRegionName" : "Ethiopia",
"EpiCase" : "ps"
}
},
@@ -234,15 +240,22 @@
},
"Aggregation" : {
"raster_path_template" : "${envDataPath}/suitability_${SubRegionNameLower}_${disease_name_snakecase}_total.csv",
- "raster_name_template" : "RIE_${disease_name_camelcase}",
- "shape_fn_entry" : "ShapeFilenameAdmin1",
- "shape_coln" : "ZONENAME",
+ "raster_name_template" : "RIE_${disease_name_camelcase}_%",
+ "shape_fn_entry" : "ShapeFilenameAdmin2",
+ "shape_coln" : "ADM2_EN",
+ "show_columns" : ["ADM0_EN","ADM1_EN"],
+ "separate_rows_for_coln":"ADM0_EN",
"func" : "mean",
- "save_path_template" : "${jobPath}/images/suitability_${SubRegionNameLower}_${disease_name_snakecase}_mean_per_zone"
+ "multiply_by" : 100,
+ "float_format" : ".0f",
+ "display_format" : ".0f",
+ "save_path_template" : "${jobPath}/images/suitability_${SubRegionNameLower}_${disease_name_snakecase}_mean_per_zone",
+ "max_entries" : 20
}
},
"Deposition" : {
"SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
+ "DataPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/input_csvs/",
"PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
"PlotFilenameTemplates" : {
"stripe": "${depPlotPath}/deposition_${SubRegionNameLower}_stripe_rust_total_${dateString}0000_${weekAheadString}0000_map.png",
@@ -250,14 +263,18 @@
"leaf": "${depPlotPath}/deposition_${SubRegionNameLower}_leaf_rust_total_${dateString}0000_${weekAheadString}0000_map.png"
},
"Aggregation" : {
- "raster_path_template" : "${depPlotPath}/../../input_csvs/deposition_${SubRegionNameLowerShort}_${disease_name_snakecase}_total.csv",
+ "raster_path_template" : "${depDataPath}/deposition_${SubRegionNameLower}_${disease_name_snakecase}_total.csv",
"raster_name_template" : "spores_per_m2_per_week_${disease_name_camelcase}",
- "shape_fn_entry" : "ShapeFilenameAdmin1",
- "shape_coln" : "ADM1_EN",
- "show_columns" : ["ADM0_EN","REGIONNAME"],
+ "shape_fn_entry" : "ShapeFilenameAdmin2",
+ "shape_coln" : "ADM2_EN",
+ "show_columns" : ["ADM0_EN","ADM1_EN"],
"separate_rows_for_coln":"ADM0_EN",
"func" : "mean",
- "save_path_template" : "${jobPath}/images/deposition_${SubRegionNameLower}_${disease_name_snakecase}_mean_per_zone"
+ "multiply_by" : 1,
+ "float_format" : ".1e",
+ "display_format" : ".0f",
+ "save_path_template" : "${jobPath}/images/deposition_${SubRegionNameLower}_${disease_name_snakecase}_mean_per_zone",
+ "max_entries" : 20
}
},
"Surveys" : {
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/approx_growth_timing_cleaned.csv b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/approx_growth_timing_cleaned.csv
new file mode 100644
index 0000000..5a6c122
--- /dev/null
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/approx_growth_timing_cleaned.csv
@@ -0,0 +1,11 @@
+Remaining_days_Spring,Remaining_days_Winter,GrowthStageName
+110,130,tillering
+60,90,boot
+50,50,heading
+40,40,flowering
+30,40,milk
+20,40,dough
+7,7,maturity
+40,40,NA
+40,40,na
+40,40,n/a
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.cpg b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.cpg
new file mode 100644
index 0000000..3ad133c
--- /dev/null
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.cpg
@@ -0,0 +1 @@
+UTF-8
\ No newline at end of file
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.dbf b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.dbf
new file mode 100644
index 0000000000000000000000000000000000000000..0fa734a5cf756be7097af5ae67a91bcc45b0e9f0
GIT binary patch
literal 893
zcmZRs;*euzU|>jO;A8|+7$7qRF60bi{eyEMj38HcPk+C7PZtITKadC)nmn(9p~5Ht
YhJc}h(P%h;LcmDDcr+kDAz&y400{hQ82|tP
literal 0
HcmV?d00001
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.prj b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.prj
new file mode 100644
index 0000000..f45cbad
--- /dev/null
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.prj
@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]
\ No newline at end of file
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.qmd b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.qmd
new file mode 100644
index 0000000..ba33e81
--- /dev/null
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.qmd
@@ -0,0 +1,26 @@
+<!DOCTYPE qgis PUBLIC 'http://mrcc.com/qgis.dtd' 'SYSTEM'>
+<qgis version="3.22.9-Bia?owie?a">
+ <identifier></identifier>
+ <parentidentifier></parentidentifier>
+ <language></language>
+ <type>dataset</type>
+ <title></title>
+ <abstract></abstract>
+ <links/>
+ <fees></fees>
+ <encoding></encoding>
+ <crs>
+ <spatialrefsys>
+ <wkt></wkt>
+ <proj4></proj4>
+ <srsid>0</srsid>
+ <srid>0</srid>
+ <authid></authid>
+ <description></description>
+ <projectionacronym></projectionacronym>
+ <ellipsoidacronym></ellipsoidacronym>
+ <geographicflag>false</geographicflag>
+ </spatialrefsys>
+ </crs>
+ <extent/>
+</qgis>
diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.shp b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters_small.shp
new file mode 100644
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diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_regions_small.prj b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_regions_small.prj
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diff --git a/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/configs/config_EastAfrica_mapspam2017.json b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/configs/config_EastAfrica_mapspam2017.json
new file mode 100644
index 0000000..b5106eb
--- /dev/null
+++ b/tests/test_data/test_deployment/regions/EastAfrica/resources/source_gen/configs/config_EastAfrica_mapspam2017.json
@@ -0,0 +1,14 @@
+{
+ "config_name" : "EastAfrica",
+ "region_file" : "/media/scratch/lb584_scratch/projects/ews_local_prod/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_9regions.shp",
+ "wheat_source_name" : "MAPSPAM2017",
+ "wheat_file" : "/media/scratch/lb584_scratch/projects/ews_local_prod/regions/EastAfrica/resources/source_gen/assets/spam2017V1r1_SSA_gr_H_WHEA_A.tif",
+ "wheat_file_rescaled" : "/media/scratch/lb584_scratch/projects/ews_local_prod/regions/EastAfrica/resources/source_gen/assets/preprocessed/spam2017V1r1_SSA_gr_H_WHEA_A_rescaled_oneliner.tif",
+ "cluster_poly_file_no_wheat" : "/media/scratch/lb584_scratch/projects/ews_local_prod/regions/EastAfrica/resources/source_gen/assets/boundaries/EastAfrica_clusters.shp",
+ "cluster_poly_file" : "//media/scratch/lb584_scratch/projects/ews_local_prod/regions/EastAfrica/resources/source_gen/assets/preprocessed/EastAfrica_clusters_with_wheat_ha_MAPSPAM2017.shp",
+ "surveyor_name_col" : "surveyor_infromation-surveyor_name",
+ "id_col" : "id",
+ "region_id_col" : "REGION_ID",
+ "wheat_stages_file" : "/media/scratch/lb584_scratch/projects/ews_local_prod/regions/EastAfrica/resources/source_gen/assets/approx_growth_timing_cleaned.csv"
+}
+
--
GitLab