From 8c32ad24b6ec547eddb8fcd2900a928703cffb11 Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Mon, 24 Apr 2023 13:36:45 +0100
Subject: [PATCH] test commit
---
configs/docker/run/launchDockerRunnerIaas.sh~ | 13 ++
configs/docker/run/runDockerEWS.sh~ | 57 ++++++++
configs/docker/run/runDockerEWS2.sh | 1 +
tests/integration/full/full_test_env_suit.py~ | 129 ++++++++++++++++++
tests/integration/full/run_tests.sh~ | 26 ++++
..._test.ExampleTest_2023-02-02_18-38-27.html | 68 +++++++++
tests/integration/partial/example_test.py | 16 +++
tests/integration/partial/run_tests.sh~ | 24 ++++
tests/integration/partial/runreport.py | 11 ++
tests/integration/partial/runreport.py~ | 11 ++
tests/unit/coordinator/.coverage | Bin 0 -> 53248 bytes
tests/unit/coordinator/run_tests.sh | 28 ++++
12 files changed, 384 insertions(+)
create mode 100755 configs/docker/run/launchDockerRunnerIaas.sh~
create mode 100755 configs/docker/run/runDockerEWS.sh~
create mode 100755 configs/docker/run/runDockerEWS2.sh
create mode 100644 tests/integration/full/full_test_env_suit.py~
create mode 100755 tests/integration/full/run_tests.sh~
create mode 100644 tests/integration/partial/example_suite/TestResults_unit.coordinator.example_test.ExampleTest_2023-02-02_18-38-27.html
create mode 100644 tests/integration/partial/example_test.py
create mode 100755 tests/integration/partial/run_tests.sh~
create mode 100644 tests/integration/partial/runreport.py
create mode 100644 tests/integration/partial/runreport.py~
create mode 100644 tests/unit/coordinator/.coverage
create mode 100755 tests/unit/coordinator/run_tests.sh
diff --git a/configs/docker/run/launchDockerRunnerIaas.sh~ b/configs/docker/run/launchDockerRunnerIaas.sh~
new file mode 100755
index 0000000..87979f8
--- /dev/null
+++ b/configs/docker/run/launchDockerRunnerIaas.sh~
@@ -0,0 +1,13 @@
+#!/bin/bash
+set -e
+
+docker run -it -v "/storage/app/EWS_prod/code:/storage/app/EWS_prod/code" \
+ -v "/storage/app/EWS_prod/regions:/storage/app/EWS_prod/regions" \
+ -v "/storage/app/EWS_prod/envs/credentials:/storage/app/EWS_prod/envs/credentials" \
+ -v "/storage/sftp:/storage/sftp" \
+ -v "/mnt/ewsmanager/RDS/webdata:/storage/moved" \
+ -w "/storage/app/EWS_prod/code" \
+ --name ews_runner \
+ lb584/ews_coordinator
+
+echo "launched"
diff --git a/configs/docker/run/runDockerEWS.sh~ b/configs/docker/run/runDockerEWS.sh~
new file mode 100755
index 0000000..d63eec6
--- /dev/null
+++ b/configs/docker/run/runDockerEWS.sh~
@@ -0,0 +1,57 @@
+#!/bin/bash
+set -e
+
+upload='--noupload' # default
+config='/storage/app/EWS_prod/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json' # default
+rundate=$(date '+%Y%m%d') # default today
+
+SHORT=p:,c:,s:,h
+LONG=component:,config:,rundate::,help
+OPTS=$(getopt -a -n weather --options $SHORT --longoptions $LONG -- "$@")
+
+eval set -- "$OPTS"
+
+while :
+do
+ case "$1" in
+ -p | --component )
+ component="$2"
+ shift 2
+ ;;
+ -c | --config )
+ config="$2"
+ shift 2
+ ;;
+ -s | --rundate )
+ rundate="$2"
+ shift 2
+ ;;
+ -h | --help)
+ "This is a launch script, example usage: runDockerEWS.sh -p Deposition -c -c /<path>/config_EastAfrica_fc_live.json -s 20220808"
+ exit 2
+ ;;
+ --)
+ shift;
+ break
+ ;;
+ *)
+ echo "Unexpected option: $1"
+ ;;
+ esac
+done
+
+
+
+function run_coordinator() {
+ printf "component: %s\nconfig: %s\nrundate: %s\nupload: %s\n" $component $config $rundate $upload;
+ docker container ls;
+ docker exec -it \
+ ews_runner \
+ /storage/app/EWS_prod/code/coordinator/run_Processor.sh \
+ -p $component \
+ -c $config \
+ -s $rundate \
+ $upload
+}
+
+run_coordinator
diff --git a/configs/docker/run/runDockerEWS2.sh b/configs/docker/run/runDockerEWS2.sh
new file mode 100755
index 0000000..414ff69
--- /dev/null
+++ b/configs/docker/run/runDockerEWS2.sh
@@ -0,0 +1 @@
+echo "where does this go?"
diff --git a/tests/integration/full/full_test_env_suit.py~ b/tests/integration/full/full_test_env_suit.py~
new file mode 100644
index 0000000..58c58b9
--- /dev/null
+++ b/tests/integration/full/full_test_env_suit.py~
@@ -0,0 +1,129 @@
+import argparse
+import copy
+import glob
+import os
+import sys
+import unittest
+
+from integration.partial.integration_test_utils import IntegrationTestUtils
+
+
+class FullTestEnvSuit(unittest.TestCase):
+
+ TEST_OUT_PATH: str = "NOT_SET"
+ TEST_START_DATE: str = 'NOT_SET'
+ TEST_JOB_DIR: str = "NOT_SET"
+
+ @classmethod
+ def setUpClass(cls) -> None:
+ # FullTestEnvSuit.write_temp_run_config_file()
+ # FullTestEnvSuit.run_env_pipeline()
+ status_file_path = os.path.join(FullTestEnvSuit.TEST_OUT_PATH, FullTestEnvSuit.TEST_JOB_DIR)
+ status_file = os.path.join(FullTestEnvSuit.TEST_OUT_PATH, FullTestEnvSuit.TEST_JOB_DIR, "STATUS_SUCCESS")
+ #os.makedirs(status_file_path, exist_ok = True)
+ #os.mknod(status_file)
+ pass
+
+
+ @staticmethod
+ def write_temp_run_config_file():
+ default_config = IntegrationTestUtils.DEFAULT_CONFIG_FILE_PATH
+ default_config_dict: dict = IntegrationTestUtils.load_json_file(default_config)
+ run_dict: dict = copy.deepcopy(default_config_dict)
+ run_dict['WorkspacePathout'] = FullTestEnvSuit.TEST_OUT_PATH
+ run_dict['WorkspacePath'] = FullTestEnvSuit.TEST_OUT_PATH
+ run_dict['Environment']['WORK_PATH'] = FullTestEnvSuit.TEST_OUT_PATH
+ run_dict['Environment']['INPUT_PATH'] = FullTestEnvSuit.TEST_OUT_PATH
+ run_dict['Environment']['OUTPUT_PATH'] = FullTestEnvSuit.TEST_OUT_PATH
+
+ IntegrationTestUtils.TEMP_CONFIG_FILE_PATH = FullTestEnvSuit.TEST_OUT_PATH + "temp_config.json"
+ IntegrationTestUtils.write_json_file(run_dict, IntegrationTestUtils.TEMP_CONFIG_FILE_PATH)
+
+
+ @staticmethod
+ def run_env_pipeline():
+ component = 'Environment'
+ IntegrationTestUtils.run_external_pipeline(component,
+ FullTestEnvSuit.TEST_START_DATE,
+ IntegrationTestUtils.EMAIL_CRED_PATH)
+
+
+ def test_standard_run_input_status_success(self):
+ status_file_path = os.path.join(FullTestEnvSuit.TEST_OUT_PATH, FullTestEnvSuit.TEST_JOB_DIR, "STATUS_SUCCESS")
+ print(f"looking for {status_file_path}")
+ success_file_exists: bool = os.path.isfile(status_file_path)
+ self.assertTrue(success_file_exists)
+
+
+ def test_standard_run_input_all_regions_ran(self):
+ """
+ working on the assumption that if there are images for each region, it must have run through
+ (at least past the region iteration)
+ """
+
+ east_africa_image_path = os.path.join(FullTestEnvSuit.TEST_OUT_PATH, FullTestEnvSuit.TEST_JOB_DIR,
+ "plotting", "eastafrica", "images", "Weekly",
+ "suitability_eastafrica_leaf_rust_total_*_map.png")
+ ethiopia_image_path = os.path.join(FullTestEnvSuit.TEST_OUT_PATH, FullTestEnvSuit.TEST_JOB_DIR,
+ "plotting", "ethiopia", "images", "Weekly",
+ "suitability_ethiopia_leaf_rust_total_*_map.png")
+
+ ea_file_exists: bool = len(glob.glob(east_africa_image_path)) > 0
+ eth_file_exists: bool = len(glob.glob(ethiopia_image_path)) > 0
+ self.assertTrue(ea_file_exists)
+ self.assertTrue(eth_file_exists)
+
+
+ def test_standard_run_all_input_csvs_produced(self):
+ east_africa_csv_path = os.path.join(FullTestEnvSuit.TEST_OUT_PATH, FullTestEnvSuit.TEST_JOB_DIR,
+ "plotting", "eastafrica", "input_csvs", "*.csv")
+ ethiopia_csv_path = os.path.join(FullTestEnvSuit.TEST_OUT_PATH, FullTestEnvSuit.TEST_JOB_DIR,
+ "plotting", "ethiopia", "input_csvs", "*.csv")
+
+ ea_csv_count: int = IntegrationTestUtils.count_files_in_wildcard(east_africa_csv_path)
+ eth_csv_count: int = IntegrationTestUtils.count_files_in_wildcard(ethiopia_csv_path)
+ self.assertEqual(18, ea_csv_count)
+ self.assertEqual(18, eth_csv_count)
+
+
+ def test_standard_run_all_images_produced(self):
+ east_africa_image_path = os.path.join(FullTestEnvSuit.TEST_OUT_PATH, FullTestEnvSuit.TEST_JOB_DIR,
+ "plotting", "eastafrica", "images", "Weekly", "*.png")
+ ethiopia_image_path = os.path.join(FullTestEnvSuit.TEST_OUT_PATH, FullTestEnvSuit.TEST_JOB_DIR,
+ "plotting", "ethiopia", "images", "Weekly", "*.png")
+
+ ea_csv_count: int = IntegrationTestUtils.count_files_in_wildcard(east_africa_image_path)
+ eth_csv_count: int = IntegrationTestUtils.count_files_in_wildcard(ethiopia_image_path)
+ self.assertEqual(6, ea_csv_count)
+ self.assertEqual(6, eth_csv_count)
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--config', required = True)
+ parser.add_argument('--outdir', required = True)
+ parser.add_argument('--email_cred', required = True)
+ parser.add_argument('--run_date_type', required = False)
+ parser.add_argument('--custom_run_date', required = False)
+ parser.add_argument('unittest_args', nargs='*')
+
+ _args = parser.parse_args()
+ _config_file: str = _args.config
+ _outdir: str = _args.outdir
+ _email_cred_path: str = _args.email_cred
+ _run_date_type: str = _args.run_date_type
+ _custom_run_date: str = _args.custom_run_date
+
+ IntegrationTestUtils.DEFAULT_CONFIG_FILE_PATH = _config_file
+
+ FullTestEnvSuit.TEST_OUT_PATH = _outdir
+ IntegrationTestUtils.EMAIL_CRED_PATH = _email_cred_path
+
+ FullTestEnvSuit.TEST_START_DATE = "20230227"
+
+ FullTestEnvSuit.TEST_JOB_DIR = "ENVIRONMENT_2.0" \
+ "_" + FullTestEnvSuit.TEST_START_DATE
+
+ # Now set the sys.argv to the unittest_args (leaving sys.argv[0] alone)
+ sys.argv[1:] = _args.unittest_args
+ unittest.main()
diff --git a/tests/integration/full/run_tests.sh~ b/tests/integration/full/run_tests.sh~
new file mode 100755
index 0000000..227fecc
--- /dev/null
+++ b/tests/integration/full/run_tests.sh~
@@ -0,0 +1,26 @@
+
+#note this script only works if run in the project docker image, or an environment with the necessary paths and
+# software installed
+
+source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
+
+PACKAGES_DIR="../../../../" # assumes run from the tests/integration/partial dir
+
+flagdir=$PACKAGES_DIR/flagdir
+epimodel=$PACKAGES_DIR/epimodel
+advisory=$PACKAGES_DIR/advisory_builder
+met_processing=$PACKAGES_DIR/met_extractor_v2/met_data_extraction
+met_processor=$PACKAGES_DIR/environmental_suitability/environmental_suitability
+plotting=$PACKAGES_DIR/plotting/plotting
+post_processing=$PACKAGES_DIR/post_processing/ews_postprocessing
+source_gen=$PACKAGES_DIR/source_gen
+coordinator=$PACKAGES_DIR/coordinator/coordinator
+coordinator_tests=$PACKAGES_DIR/coordinator/tests
+
+export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests
+
+echo $PYTHONPATH
+
+python full_test_deposition.py --config /storage/app/EWS_prod/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json \
+--outdir /storage/app/EWS_prod/regions/EastAfrica/workspace/ \
+--email_cred /storage/app/EWS_prod/envs/credentials/Cred_gmail.json
\ No newline at end of file
diff --git a/tests/integration/partial/example_suite/TestResults_unit.coordinator.example_test.ExampleTest_2023-02-02_18-38-27.html b/tests/integration/partial/example_suite/TestResults_unit.coordinator.example_test.ExampleTest_2023-02-02_18-38-27.html
new file mode 100644
index 0000000..a041e2a
--- /dev/null
+++ b/tests/integration/partial/example_suite/TestResults_unit.coordinator.example_test.ExampleTest_2023-02-02_18-38-27.html
@@ -0,0 +1,68 @@
+<!DOCTYPE html>
+<html>
+<head>
+ <title>Unittest Results</title>
+ <meta charset="utf-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+ <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" integrity="sha384-1q8mTJOASx8j1Au+a5WDVnPi2lkFfwwEAa8hDDdjZlpLegxhjVME1fgjWPGmkzs7" crossorigin="anonymous">
+</head>
+<body>
+ <div class="container">
+ <div class="row">
+ <div class="col-xs-12">
+ <h2 class="text-capitalize">Unittest Results</h2>
+ <p class='attribute'><strong>Start Time: </strong>2023-02-02 18:38:27</p>
+ <p class='attribute'><strong>Duration: </strong>0 ms</p>
+ <p class='attribute'><strong>Summary: </strong>Total: 1, Pass: 1</p>
+ </div>
+ </div>
+ <div class="row">
+ <div class="col-xs-12 col-sm-10 col-md-10">
+ <table class='table table-hover table-responsive'>
+ <thead>
+ <tr>
+ <th>unit.coordinator.example_test.ExampleTest</th>
+ <th>Status</th>
+ <th></th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr class='success'>
+ <td class="col-xs-10">test_v1_dewperiod_expected_results1</td>
+ <td class="col-xs-1">
+ <span class="label label-success" style="display:block;width:40px;">Pass</span>
+ </td>
+ <td class="col-xs-1">
+ </td>
+ </tr>
+ <tr>
+ <td colspan="3">
+ Total: 1, Pass: 1 -- Duration: 0 ms
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </div>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.2.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ $(document).ready(function(){
+ $('td').on('click', '.btn', function(e){
+ e.preventDefault();
+ e.stopImmediatePropagation();
+ var $this = $(this);
+ var $nextRow = $this.closest('tr').next('tr');
+ $nextRow.slideToggle("fast");
+ $this.text(function(i, text){
+ if (text === 'View') {
+ return 'Hide';
+ } else {
+ return 'View';
+ };
+ });
+ });
+ });
+ </script>
+</body>
+</html
\ No newline at end of file
diff --git a/tests/integration/partial/example_test.py b/tests/integration/partial/example_test.py
new file mode 100644
index 0000000..b5bc92e
--- /dev/null
+++ b/tests/integration/partial/example_test.py
@@ -0,0 +1,16 @@
+import unittest
+
+
+class ExampleTest(unittest.TestCase):
+
+ def setUp(self) -> None:
+ super().setUp()
+
+
+ def test_v1_dewperiod_expected_results1(self):
+ self.assertTrue(True)
+
+
+if __name__ == '__main__':
+ print("hello")
+ unittest.main()
diff --git a/tests/integration/partial/run_tests.sh~ b/tests/integration/partial/run_tests.sh~
new file mode 100755
index 0000000..81cfad5
--- /dev/null
+++ b/tests/integration/partial/run_tests.sh~
@@ -0,0 +1,24 @@
+
+#note this script only works if run in the project docker image, or an environment with the necessary paths and
+# software installed
+
+source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
+
+PACKAGES_DIR="../../../../" # assumes run from the tests/integration/partial dir
+
+flagdir=$PACKAGES_DIR/flagdir
+epimodel=$PACKAGES_DIR/epimodel
+advisory=$PACKAGES_DIR/advisory_builder
+met_processing=$PACKAGES_DIR/met_extractor_v2/met_data_extraction
+met_processor=$PACKAGES_DIR/environmental_suitability/environmental_suitability
+plotting=$PACKAGES_DIR/plotting/plotting
+post_processing=$PACKAGES_DIR/post_processing/ews_postprocessing
+source_gen=$PACKAGES_DIR/source_gen
+coordinator=$PACKAGES_DIR/coordinator/coordinator
+coordinator_tests=$PACKAGES_DIR/coordinator/tests
+
+export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests
+
+echo $PYTHONPATH
+
+python3 runreport.py
diff --git a/tests/integration/partial/runreport.py b/tests/integration/partial/runreport.py
new file mode 100644
index 0000000..faa2034
--- /dev/null
+++ b/tests/integration/partial/runreport.py
@@ -0,0 +1,11 @@
+from unittest import TestLoader, TestSuite
+from HtmlTestRunner import HTMLTestRunner
+from unit.coordinator.example_test import ExampleTest
+
+example_tests = TestLoader().loadTestsFromTestCase(ExampleTest)
+
+suite = TestSuite([example_tests])
+
+runner = HTMLTestRunner(output='example_suite')
+
+runner.run(suite)
diff --git a/tests/integration/partial/runreport.py~ b/tests/integration/partial/runreport.py~
new file mode 100644
index 0000000..e674836
--- /dev/null
+++ b/tests/integration/partial/runreport.py~
@@ -0,0 +1,11 @@
+from unittest import TestLoader, TestSuite
+from HtmlTestRunner import HTMLTestRunner
+import unit.coordinator.example_test.ExampleTest
+
+example_tests = TestLoader().loadTestsFromTestCase(ExampleTest)
+
+suite = TestSuite([example_tests])
+
+runner = HTMLTestRunner(output='example_suite')
+
+runner.run(suite)
diff --git a/tests/unit/coordinator/.coverage b/tests/unit/coordinator/.coverage
new file mode 100644
index 0000000000000000000000000000000000000000..83a6bedd12acaf9faa978b84c5d6f9ee1c527fbe
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diff --git a/tests/unit/coordinator/run_tests.sh b/tests/unit/coordinator/run_tests.sh
new file mode 100755
index 0000000..d0980bf
--- /dev/null
+++ b/tests/unit/coordinator/run_tests.sh
@@ -0,0 +1,28 @@
+
+#note this script only works if run in the project docker image, or an environment with the necessary paths and
+# software installed
+
+source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
+
+PACKAGES_DIR="../../../../" # assumes run from the tests/integration/partial dir
+
+flagdir=$PACKAGES_DIR/flagdir
+epimodel=$PACKAGES_DIR/epimodel
+advisory=$PACKAGES_DIR/advisory_builder
+met_processing=$PACKAGES_DIR/met_extractor_v2/met_data_extraction
+met_processor=$PACKAGES_DIR/environmental_suitability/environmental_suitability
+plotting=$PACKAGES_DIR/plotting/plotting
+post_processing=$PACKAGES_DIR/post_processing/ews_postprocessing
+source_gen=$PACKAGES_DIR/source_gen
+coordinator=$PACKAGES_DIR/coordinator/coordinator
+coordinator_tests=$PACKAGES_DIR/coordinator/tests
+
+export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests
+
+echo $PYTHONPATH
+
+python3 -m unittest test_advisory.py
+python3 -m unittest test_deposition.py
+python3 -m unittest test_env_suit.py
+python3 -m unittest test_epi.py
+python3 -m unittest test_survey.py
\ No newline at end of file
--
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