From d74904ddc5285b84ab7c4a29b7bbaad088371522 Mon Sep 17 00:00:00 2001
From: Tamas Mona <tm689@cam.ac.uk>
Date: Wed, 27 Jul 2022 16:50:22 +0100
Subject: [PATCH] Updated paths
---
EnvSuitPipeline.py | 6 +++---
ProcessorComponents.py | 2 +-
run_Processor.sh | 14 +++++++-------
3 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/EnvSuitPipeline.py b/EnvSuitPipeline.py
index 666b95e..21a30cc 100644
--- a/EnvSuitPipeline.py
+++ b/EnvSuitPipeline.py
@@ -163,7 +163,7 @@ def run_merger(workPath):
def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent_overwrite = True):
'''
- The prevent_overwrite parameter can be set to False if you want to re-run
+ The prevent_overwrite parameter can be set to False if you want to re-run
a job in-place.
'''
# Get parameters from the config
@@ -183,7 +183,7 @@ def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent
sys_config = loadConfig(sys_config_file)
templateName = 'template_' + runType + '_config.json'
- template_configFile = resourcesPath + templateName
+ template_configFile = resourcesPath + 'configs/' + templateName
config = loadConfig(template_configFile)
# Before writing any files, check the output path doesn't exist already
@@ -192,7 +192,7 @@ def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent
if prevent_overwrite: assert not os.path.exists(region_outPath)
# Get spatial points file for the region
- region_spatial_points_file = resourcesPath + 'input_spatial_points_' + region + '.csv'
+ region_spatial_points_file = resourcesPath + 'assets/' + 'input_spatial_points_' + region + '.csv'
input_spatial_points_file = workPath + 'input_spatial_points.csv'
if prevent_overwrite: assert not os.path.exists(input_spatial_points_file)
shutil.copy(region_spatial_points_file,input_spatial_points_file)
diff --git a/ProcessorComponents.py b/ProcessorComponents.py
index 0b975d1..75f7b81 100644
--- a/ProcessorComponents.py
+++ b/ProcessorComponents.py
@@ -1171,7 +1171,7 @@ def process_in_job_survey(jobPath,status,config,component):
date = datetime.datetime.now()
- cluster_calc_path = "/storage/app/EWS/General/wheat-source-generation/"
+ cluster_calc_path = "/storage/app/EWS_prod/code/wheat_source_generation/"
# clear old output
old_clustering_output_glob = f"{cluster_calc_path}/output/sources_*"
diff --git a/run_Processor.sh b/run_Processor.sh
index ef384aa..5f173fe 100755
--- a/run_Processor.sh
+++ b/run_Processor.sh
@@ -1,17 +1,17 @@
#!/bin/bash
# directory containing all environment
-envs=/storage/app/EWS/envs/
+envs=/storage/app/EWS_prod/envs/
# directory containing all custom python packages
-bin=/storage/app/EWS/General
+bin=/storage/app/EWS_prod/code/
# provide custom python packages so they can be imported
flagdir=${bin}/flagdir/
-epimodel=${bin}/EWS-EpiModel/
-advisory=${bin}/EWS-advisory-builder/
-met_extractor=${bin}/EWS-met_extractor/era5_met_data_extraction/python/
-plotting=${bin}/EWS-Plotting/
+epimodel=${bin}/epimodel/
+advisory=${bin}/advisory_builder/
+met_extractor=${bin}/met_extractor/python/
+plotting=${bin}/plotting/
export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_extractor:$plotting
@@ -21,7 +21,7 @@ export EMAIL_CRED=${envs}/Cred_gmail.json
# activate conda environment of python modules so they can be imported
#TODO: Move conda_env from bin to envs
-conda_env=${bin}/EWS-python/py3EWS
+conda_env=${envs}/conda/py3EWS
source /storage/app/miniconda3/bin/activate ${conda_env}
# get path of this script (to point to files within the same git repo)
--
GitLab