From 5c534c3a5f84de94fdf5209f4dbaf164f2363b02 Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Mon, 3 Oct 2022 13:59:24 +0100
Subject: [PATCH] repackaging (phase 1)
---
.../BufferingSMTPHandler.py | 0
.../ENVDataPostProcessor.py | 0
EnvSuitPipeline.py => coordinator/EnvSuitPipeline.py | 0
.../GatherScrapedMediaReports.py | 0
NAMEPreProcessor.py => coordinator/NAMEPreProcessor.py | 0
Processor.py => coordinator/Processor.py | 8 ++++----
ProcessorAdvisory.py => coordinator/ProcessorAdvisory.py | 0
.../ProcessorComponents.py | 0
.../ProcessorDeposition.py | 0
.../ProcessorEnvironment.py | 0
.../ProcessorEpidemiology.py | 0
ProcessorServer.py => coordinator/ProcessorServer.py | 0
ProcessorSurveys.py => coordinator/ProcessorSurveys.py | 0
ProcessorUtils.py => coordinator/ProcessorUtils.py | 0
coordinator/__init__.py | 0
{logs => coordinator/logs}/.gitignore | 2 +-
run_Processor.sh | 2 +-
tests/integration/__init__.py | 0
tests/unit/__init__.py | 0
19 files changed, 6 insertions(+), 6 deletions(-)
rename BufferingSMTPHandler.py => coordinator/BufferingSMTPHandler.py (100%)
rename ENVDataPostProcessor.py => coordinator/ENVDataPostProcessor.py (100%)
rename EnvSuitPipeline.py => coordinator/EnvSuitPipeline.py (100%)
rename GatherScrapedMediaReports.py => coordinator/GatherScrapedMediaReports.py (100%)
rename NAMEPreProcessor.py => coordinator/NAMEPreProcessor.py (100%)
rename Processor.py => coordinator/Processor.py (98%)
rename ProcessorAdvisory.py => coordinator/ProcessorAdvisory.py (100%)
rename ProcessorComponents.py => coordinator/ProcessorComponents.py (100%)
rename ProcessorDeposition.py => coordinator/ProcessorDeposition.py (100%)
rename ProcessorEnvironment.py => coordinator/ProcessorEnvironment.py (100%)
rename ProcessorEpidemiology.py => coordinator/ProcessorEpidemiology.py (100%)
rename ProcessorServer.py => coordinator/ProcessorServer.py (100%)
rename ProcessorSurveys.py => coordinator/ProcessorSurveys.py (100%)
rename ProcessorUtils.py => coordinator/ProcessorUtils.py (100%)
create mode 100644 coordinator/__init__.py
rename {logs => coordinator/logs}/.gitignore (86%)
create mode 100644 tests/integration/__init__.py
create mode 100644 tests/unit/__init__.py
diff --git a/BufferingSMTPHandler.py b/coordinator/BufferingSMTPHandler.py
similarity index 100%
rename from BufferingSMTPHandler.py
rename to coordinator/BufferingSMTPHandler.py
diff --git a/ENVDataPostProcessor.py b/coordinator/ENVDataPostProcessor.py
similarity index 100%
rename from ENVDataPostProcessor.py
rename to coordinator/ENVDataPostProcessor.py
diff --git a/EnvSuitPipeline.py b/coordinator/EnvSuitPipeline.py
similarity index 100%
rename from EnvSuitPipeline.py
rename to coordinator/EnvSuitPipeline.py
diff --git a/GatherScrapedMediaReports.py b/coordinator/GatherScrapedMediaReports.py
similarity index 100%
rename from GatherScrapedMediaReports.py
rename to coordinator/GatherScrapedMediaReports.py
diff --git a/NAMEPreProcessor.py b/coordinator/NAMEPreProcessor.py
similarity index 100%
rename from NAMEPreProcessor.py
rename to coordinator/NAMEPreProcessor.py
diff --git a/Processor.py b/coordinator/Processor.py
similarity index 98%
rename from Processor.py
rename to coordinator/Processor.py
index 99268c1..e1845a6 100755
--- a/Processor.py
+++ b/coordinator/Processor.py
@@ -289,7 +289,7 @@ def parse_and_check_args(todayString):
if not args.live:
# remove the log handler that would send emails
- logger.handlers = [h for h in logger.handlers if not isinstance(h,BufferingSMTPHandler.BufferingSMTPHandler)]
+ logger.handlers = [h for h in logger.handlers if not isinstance(h, BufferingSMTPHandler.BufferingSMTPHandler)]
if not isinstance(args.config_paths,list):
logger.error('Expecting a list of config paths')
@@ -391,11 +391,11 @@ def run_Process():
workspacePath = universal_config['WorkspacePathout']
- process_pre_job = getattr(ProcessorComponents,universal_config['ProcessPreJob'])
+ process_pre_job = getattr(ProcessorComponents, universal_config['ProcessPreJob'])
- process_in_job = getattr(ProcessorComponents,universal_config['ProcessInJob'])
+ process_in_job = getattr(ProcessorComponents, universal_config['ProcessInJob'])
- process_EWS_plotting = getattr(ProcessorComponents,universal_config['ProcessEWSPlotting'])
+ process_EWS_plotting = getattr(ProcessorComponents, universal_config['ProcessEWSPlotting'])
# determine job directory
jobPath = f'{workspacePath}{short_name[args.component]}_{args.start_date}'
diff --git a/ProcessorAdvisory.py b/coordinator/ProcessorAdvisory.py
similarity index 100%
rename from ProcessorAdvisory.py
rename to coordinator/ProcessorAdvisory.py
diff --git a/ProcessorComponents.py b/coordinator/ProcessorComponents.py
similarity index 100%
rename from ProcessorComponents.py
rename to coordinator/ProcessorComponents.py
diff --git a/ProcessorDeposition.py b/coordinator/ProcessorDeposition.py
similarity index 100%
rename from ProcessorDeposition.py
rename to coordinator/ProcessorDeposition.py
diff --git a/ProcessorEnvironment.py b/coordinator/ProcessorEnvironment.py
similarity index 100%
rename from ProcessorEnvironment.py
rename to coordinator/ProcessorEnvironment.py
diff --git a/ProcessorEpidemiology.py b/coordinator/ProcessorEpidemiology.py
similarity index 100%
rename from ProcessorEpidemiology.py
rename to coordinator/ProcessorEpidemiology.py
diff --git a/ProcessorServer.py b/coordinator/ProcessorServer.py
similarity index 100%
rename from ProcessorServer.py
rename to coordinator/ProcessorServer.py
diff --git a/ProcessorSurveys.py b/coordinator/ProcessorSurveys.py
similarity index 100%
rename from ProcessorSurveys.py
rename to coordinator/ProcessorSurveys.py
diff --git a/ProcessorUtils.py b/coordinator/ProcessorUtils.py
similarity index 100%
rename from ProcessorUtils.py
rename to coordinator/ProcessorUtils.py
diff --git a/coordinator/__init__.py b/coordinator/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/logs/.gitignore b/coordinator/logs/.gitignore
similarity index 86%
rename from logs/.gitignore
rename to coordinator/logs/.gitignore
index 5e7d273..28db78b 100644
--- a/logs/.gitignore
+++ b/coordinator/logs/.gitignore
@@ -1,4 +1,4 @@
# Ignore everything in this directory
-*
+.gitignore
# Except this file
!.gitignore
diff --git a/run_Processor.sh b/run_Processor.sh
index 9cf6064..63483bd 100755
--- a/run_Processor.sh
+++ b/run_Processor.sh
@@ -31,7 +31,7 @@ source /storage/app/miniconda3/bin/activate ${conda_env}
proc_path="$( dirname "$(readlink -f "$0" )" )"
# run the processor with all arguments
-python ${proc_path}/Processor.py "$@"
+python ${proc_path}/coordinator/Processor.py "$@"
# deactivate conda environment
source /storage/app/miniconda3/bin/deactivate ${conda_env}
diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py
new file mode 100644
index 0000000..e69de29
--
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