From d6b9d7e4436502a5da070a76de6f63dda1751057 Mon Sep 17 00:00:00 2001
From: jws52 <jws52@cam.ac.uk>
Date: Mon, 19 Jun 2023 10:18:07 +0100
Subject: [PATCH] refactor: Update epi processor imports
So that coordinator tests work with ews-epidemiology commit d344567 .
---
coordinator/ProcessorEpidemiology.py | 16 +++++++---------
1 file changed, 7 insertions(+), 9 deletions(-)
diff --git a/coordinator/ProcessorEpidemiology.py b/coordinator/ProcessorEpidemiology.py
index 3dbd1d9..7dad3c3 100644
--- a/coordinator/ProcessorEpidemiology.py
+++ b/coordinator/ProcessorEpidemiology.py
@@ -19,11 +19,9 @@ from rasterio import open as rio_open
from EpiModel import ( # created by rs481
EpiAnalysis,
EpiModel,
- EpiPrep,
- EpiPrepLister,
- EpiPrepLoader,
plotRaster
)
+from EpiModel.EpiPrep import lister, loader, prep
from ews_postprocessing.epi.epi_post_processor import EPIPostPostProcessor
from ProcessorUtils import (
@@ -272,7 +270,7 @@ def process_in_job_epi(jobPath,status,config,component):
# Use config-defined file lister
file_lister_dep_name = config_epi['Deposition']['FileListerFunction']
- file_lister_dep = getattr(EpiPrepLister,file_lister_dep_name)
+ file_lister_dep = getattr(lister,file_lister_dep_name)
config_for_lister = config.copy()
config_for_lister.update(config_epi)
@@ -286,10 +284,10 @@ def process_in_job_epi(jobPath,status,config,component):
try:
- EpiPrep.prep_input(config_for_lister,start_date,end_date,
+ prep.prep_input(config_for_lister,start_date,end_date,
component='Deposition',
file_lister=file_lister_dep,
- file_loader=EpiPrepLoader.load_NAME_file,
+ file_loader=loader.load_NAME_file,
lister_kwargs=lister_kwargs,
**loader_kwargs)
@@ -363,16 +361,16 @@ def process_in_job_epi(jobPath,status,config,component):
# Use config-defined file lister
file_lister_env_name = config_epi['Environment']['FileListerFunction']
- file_lister_env = getattr(EpiPrepLister,file_lister_env_name)
+ file_lister_env = getattr(lister,file_lister_env_name)
config_for_lister = config.copy()
config_for_lister.update(config_epi)
try:
- EpiPrep.prep_input(config_for_lister,start_date,end_date,
+ prep.prep_input(config_for_lister,start_date,end_date,
component='Environment',
- file_loader=EpiPrepLoader.load_env_file,
+ file_loader=loader.load_env_file,
file_lister=file_lister_env)
assert os.path.isfile(config_epi['Environment']['FileNamePrepared'])
--
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