groundwork for using tifs/netcdf throughout the pipeline.

splitting out some csv parsing functions

coordinator/ProcessorEnvironment.py

@@ -180,7 +180,6 @@ class ProcessorEnvironment(Processor):
         for region in subregions:
     
             output_dir = f"{jobPath}/plotting/{region.lower()}"
-            # csv_template_dir = input_dir + "/{DISEASE_DIR}/RIE_value.csv"
             csv_template_dir = input_dir + "/{DISEASE_DIR}/RIE_value.tif"
 
             Path(output_dir).mkdir(parents=True, exist_ok=True)

tests/integration/partial/test_env_suit.py

@@ -42,8 +42,8 @@ class TestEnvSuit(BaseEnvSuitTestSuite.EnvSuitTestSuite):
     @staticmethod
     def write_temp_run_config_file():
         nowstring: str = IntegrationTestUtils.get_now_string()
-        # prefix: str = "temp_env_" + nowstring
-        prefix: str = "temp_env"
+        prefix: str = "temp_env_" + nowstring
+        # prefix: str = "temp_env"
 
         default_config = IntegrationTestUtils.DEFAULT_CONFIG_FILE_PATH
         default_config_dict: dict = IntegrationTestUtils.load_json_file(default_config)

tests/integration/test_suites/depo_test_suite.py

@@ -61,10 +61,10 @@ class BaseDepoTestSuite:
         def test_standard_run_all_input_csvs_produced(self):
             east_africa_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                                 IntegrationTestUtils.TEST_JOB_DIR,
-                                                "plotting", "eastafrica", "input_csvs", "*.csv")
+                                                "plotting", "eastafrica", "input_csvs", "*.tif")
             ethiopia_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                              IntegrationTestUtils.TEST_JOB_DIR,
-                                             "plotting", "ethiopia", "input_csvs", "*.csv")
+                                             "plotting", "ethiopia", "input_csvs", "*.tif")
 
             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)

tests/integration/test_suites/env_suit_test_suite.py

@@ -62,10 +62,10 @@ class BaseEnvSuitTestSuite:
         def test_standard_run_all_input_csvs_produced(self):
             east_africa_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                                 IntegrationTestUtils.TEST_JOB_DIR,
-                                                "plotting", "eastafrica", "input_csvs", "*.csv")
+                                                "plotting", "eastafrica", "input_csvs", "*.tif")
             ethiopia_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                              IntegrationTestUtils.TEST_JOB_DIR,
-                                             "plotting", "ethiopia", "input_csvs", "*.csv")
+                                             "plotting", "ethiopia", "input_csvs", "*.tif")
 
             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)