diff --git a/tests/integration/integration_test_utils.py b/tests/integration/integration_test_utils.py
index 03a616b393bf770b168230ce14a0f3aaff197741..bf5e5e86f16eb4b0321968f3a4d0036fb9214f2d 100644
--- a/tests/integration/integration_test_utils.py
+++ b/tests/integration/integration_test_utils.py
@@ -2,6 +2,7 @@ import glob
import json
import os
from datetime import datetime
+from typing import List
from zipfile import ZipFile
@@ -46,9 +47,32 @@ class IntegrationTestUtils:
@staticmethod
- def check_file_not_empty(file_path: str):
+ def check_file_not_empty(file_path: str) -> bool:
return os.stat(file_path).st_size != 0
+ @staticmethod
+ def check_file_exists(file_path: str) -> bool:
+ return os.path.isfile(file_path)
+
+ @staticmethod
+ def check_wildcard_exists_and_not_empty(wildcard: str) -> bool:
+
+ """
+ requires at least one file matching the wildcard to exist and not be empty
+ """
+ result = False
+ files: List[str] = glob.glob(wildcard)
+ for file in files:
+ result = IntegrationTestUtils.check_file_not_empty(file)
+ if result is False:
+ break
+ return result
+
+ @staticmethod
+ def check_file_exists_and_not_empty(file_path: str) -> bool:
+ file_exists = IntegrationTestUtils.check_file_exists(file_path)
+ file_not_empty = IntegrationTestUtils.check_file_not_empty(file_path)
+ return file_exists and file_not_empty
@staticmethod
def run_pipeline(component: str,
diff --git a/tests/integration/test_epi.py b/tests/integration/test_epi.py
index 18d406d9c5879288bd4f2cc864b5a10743efac48..58686e90e24418f1a5d9de9c4548b1b35196c450 100644
--- a/tests/integration/test_epi.py
+++ b/tests/integration/test_epi.py
@@ -9,19 +9,20 @@ class TestEpi(unittest.TestCase):
TEST_OUT_PATH: str = "not_set"
TEST_START_DATE: str = '20221001'
- TEST_JOB_DIR: str = "SUMMARY_" + TEST_START_DATE
+ TEST_JOB_DIR: str = "EPI_" + TEST_START_DATE
@classmethod
def setUpClass(cls) -> None:
TestEpi.write_temp_run_config_files()
- TestEpi.unpack_dependencies()
- TestEpi.run_advisory_pipeline()
+ # TestEpi.unpack_dependencies()
+ # TestEpi.run_epi_pipeline()
@staticmethod
def write_temp_run_config_files():
nowstring: str = IntegrationTestUtils.get_now_string()
- prefix: str = "temp_epi_" + nowstring
+ # prefix: str = "temp_epi_" + nowstring
+ prefix: str = "temp_epi_2022-11-23_164339"
# prefix: str = ""
default_config = IntegrationTestUtils.DEFAULT_CONFIG_FILE_PATH
@@ -43,7 +44,7 @@ class TestEpi(unittest.TestCase):
@staticmethod
- def run_advisory_pipeline():
+ def run_epi_pipeline():
component = 'Epidemiology'
IntegrationTestUtils.run_pipeline(component, TestEpi.TEST_START_DATE)
@@ -53,19 +54,65 @@ class TestEpi(unittest.TestCase):
success_file_exists: bool = os.path.isfile(status_file_path)
self.assertTrue(success_file_exists)
- def test_standard_run_input_all_docs_produced(self):
+ def test_standard_run_input_all_stem_rust_files_produced(self):
- east_africa_image_path = os.path.join(TestEpi.TEST_OUT_PATH, TestEpi.TEST_JOB_DIR,
- "tight-layout",
- "wheat_rust_advisory_template_EastAfrica_20221001.docx")
- ethiopia_image_path = os.path.join(TestEpi.TEST_OUT_PATH, TestEpi.TEST_JOB_DIR,
- "tight-layout",
- "wheat_rust_advisory_template_Ethiopia_20221001.docx")
+ alpha_beta_gamma_root = os.path.join(TestEpi.TEST_OUT_PATH, TestEpi.TEST_JOB_DIR,
+ "EastAfrica",
+ "StemRust",
+ "*psbeta0.004gamma0.00025alpha1.0")
- ea_file_exists: bool = os.path.isfile(east_africa_image_path)
- eth_file_exists: bool = os.path.isfile(ethiopia_image_path)
- self.assertTrue(ea_file_exists)
- self.assertTrue(eth_file_exists)
+ self.check_wildcard_exists_and_not_empty(alpha_beta_gamma_root, ".csv")
+ self.check_wildcard_exists_and_not_empty(alpha_beta_gamma_root, "*comparison.png")
+ self.check_wildcard_exists_and_not_empty(alpha_beta_gamma_root, "*progression.csv")
+ self.check_wildcard_exists_and_not_empty(alpha_beta_gamma_root, ".png")
+ self.check_wildcard_exists_and_not_empty(alpha_beta_gamma_root, ".tif")
+
+ env_root = os.path.join(TestEpi.TEST_OUT_PATH, TestEpi.TEST_JOB_DIR,
+ "EastAfrica",
+ "StemRust",
+ "infections_temp_config_Epidemiology")
+
+ self.check_wildcard_exists_and_not_empty(env_root, "*env.csv")
+ self.check_wildcard_exists_and_not_empty(env_root, "*env.png")
+ self.check_wildcard_exists_and_not_empty(env_root, "*env.tif")
+
+ data_input_root = os.path.join(TestEpi.TEST_OUT_PATH, TestEpi.TEST_JOB_DIR,
+ "EastAfrica",
+ "StemRust",
+ "input_data",
+ "data_input*")
+
+ self.check_wildcard_exists_and_not_empty(data_input_root, "*deposition.csv")
+ self.check_wildcard_exists_and_not_empty(data_input_root, "*environment.csv")
+
+ map_spam_root = os.path.join(TestEpi.TEST_OUT_PATH, TestEpi.TEST_JOB_DIR,
+ "EastAfrica",
+ "StemRust",
+ "input_data",
+ "wheat_area_frac_MapSPAM2010_EastAfrica*")
+
+ self.check_wildcard_exists_and_not_empty(map_spam_root, ".csv")
+ self.check_wildcard_exists_and_not_empty(map_spam_root, ".csv")
+
+ def test_standard_run_input_all_plotting_files_produced(self):
+
+ input_csvs_root = os.path.join(TestEpi.TEST_OUT_PATH, TestEpi.TEST_JOB_DIR,
+ "plotting",
+ "input_csvs",
+ "*stem*")
+
+ self.check_wildcard_exists_and_not_empty(input_csvs_root, ".csv")
+
+ images_root = os.path.join(TestEpi.TEST_OUT_PATH, TestEpi.TEST_JOB_DIR,
+ "plotting",
+ "images",
+ "*stem*")
+
+ self.check_wildcard_exists_and_not_empty(images_root, "png")
+
+ def check_wildcard_exists_and_not_empty(self, root: str, extension: str):
+ file_exists: bool = IntegrationTestUtils.check_wildcard_exists_and_not_empty(root + extension)
+ self.assertTrue(file_exists)
if __name__ == '__main__':