adding asserts for the epi test

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,

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__':