more work wiring in nc files as output

coordinator/EnvSuitPipeline.py

@@ -261,9 +261,9 @@ def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent
 
                 # run_merger(config, sys_config, processor_name)
 
-                resultFile = envSuitPath + 'RIE.tif'
+                resultFile = envSuitPath + 'RIE.nc'
                 strain_outPath = os.path.join(region_outPath,strain)
-                strain_outFile = strain_outPath + '/RIE_value.tif'
+                strain_outFile = strain_outPath + '/RIE_value.nc'
 
                 # Check results dimension
                 # result = pd.read_csv(resultFile)

coordinator/ProcessorEnvironment.py

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

tests/integration/full/full_test_epi.py

@@ -20,10 +20,10 @@ class FullTestEpi(BaseEpiTestSuite.EpiTestSuite):
 
         self.set_expected_values()
 
-        if IntegrationTestUtils.TEST_OUT_PATH is None or not os.path.isdir(IntegrationTestUtils.TEST_OUT_PATH):
-        # if True:
+        # if IntegrationTestUtils.TEST_OUT_PATH is None or not os.path.isdir(IntegrationTestUtils.TEST_OUT_PATH):
+        if True:
             FullTestEpi.write_temp_run_config_files()
-            FullTestEpi.run_dependent_pipelines()
+            # FullTestEpi.run_dependent_pipelines()
             FullTestEpi.run_epi_pipeline()
         else:
             print(f"output in {IntegrationTestUtils.TEST_OUT_PATH} already written, skipping rerun")

tests/integration/partial/integration_test_utils.py

@@ -83,8 +83,8 @@ class IntegrationTestUtils:
         IntegrationTestUtils.DEFAULT_CONFIG_FILE_PATH = _config_file
 
         nowstring: str = IntegrationTestUtils.get_now_string()
-        prefix: str = f"temp_{test_prefix}_" + nowstring
-        # prefix: str = f"temp_{test_prefix}"
+        # prefix: str = f"temp_{test_prefix}_" + nowstring
+        prefix: str = f"temp_{test_prefix}"
         IntegrationTestUtils.TEST_OUT_PATH = _outdir + prefix + os.sep
         IntegrationTestUtils.EMAIL_CRED_PATH = _email_cred_path
 
@@ -264,6 +264,6 @@ class IntegrationTestUtils:
             result = custom_run_date
         else:
             print("default")
-            result = "20230126"
+            result = "20231127"
 
         return result

tests/integration/partial/test_advisory.py

@@ -18,7 +18,7 @@ class TestAdvisory(BaseAdvisoryTestSuite.AdvisoryTestSuite):
         IntegrationTestUtils.TEST_OUT_PATH = None
 
     def set_expected_values(self):
-        IntegrationTestUtils.TEST_START_DATE = '20221001'
+        IntegrationTestUtils.TEST_START_DATE = '20231127'
         IntegrationTestUtils.TEST_JOB_DIR = "ADVISORY_" + IntegrationTestUtils.TEST_START_DATE
         self.EXPECTED_EA_IMAGE_COUNT = 6
         self.EXPECTED_ETH_IMAGE_COUNT = 6

tests/integration/partial/test_deposition.py

@@ -19,7 +19,7 @@ class TestDeposition(BaseDepoTestSuite.DepoTestSuite):
 
     def set_expected_values(self):
 
-        IntegrationTestUtils.TEST_START_DATE = "20221001"
+        IntegrationTestUtils.TEST_START_DATE = "20231127"
         IntegrationTestUtils.TEST_JOB_DIR = "DEPOSITION_" + IntegrationTestUtils.TEST_START_DATE
 
         self.EA_CSV_COUNT = 9

tests/integration/partial/test_env_suit.py

@@ -18,7 +18,7 @@ class TestEnvSuit(BaseEnvSuitTestSuite.EnvSuitTestSuite):
         IntegrationTestUtils.TEST_OUT_PATH = None
 
     def set_expected_values(self):
-        IntegrationTestUtils.TEST_START_DATE = "20221001"
+        IntegrationTestUtils.TEST_START_DATE = "20231127"
         IntegrationTestUtils.TEST_JOB_DIR = "ENVIRONMENT_2.0_" + IntegrationTestUtils.TEST_START_DATE
 
         self.EA_CSV_COUNT = 18

tests/integration/partial/test_epi.py

@@ -18,7 +18,7 @@ class TestEpi(BaseEpiTestSuite.EpiTestSuite):
 
     def set_expected_values(self):
         super().set_expected_values()
-        IntegrationTestUtils.TEST_START_DATE = '20221001'
+        IntegrationTestUtils.TEST_START_DATE = '20231127'
         IntegrationTestUtils.TEST_JOB_DIR = "EPI_" + IntegrationTestUtils.TEST_START_DATE
 
 

tests/integration/partial/test_survey.py

@@ -18,7 +18,7 @@ class TestSurvey(BaseSurveyTestSuite.SurveyTestSuite):
         IntegrationTestUtils.TEST_OUT_PATH = None
 
     def set_expected_values(self):
-        IntegrationTestUtils.TEST_START_DATE = '20221001'
+        IntegrationTestUtils.TEST_START_DATE = '20231127'
         IntegrationTestUtils.TEST_JOB_DIR = "SURVEYDATA_" + IntegrationTestUtils.TEST_START_DATE
 
 

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", "*.tif")
+                                                "plotting", "eastafrica", "input_csvs", "*.nc")
             ethiopia_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                              IntegrationTestUtils.TEST_JOB_DIR,
-                                             "plotting", "ethiopia", "input_csvs", "*.tif")
+                                             "plotting", "ethiopia", "input_csvs", "*.nc")
 
             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", "*.tif")
+                                                "plotting", "eastafrica", "input_csvs", "*.nc")
             ethiopia_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                              IntegrationTestUtils.TEST_JOB_DIR,
-                                             "plotting", "ethiopia", "input_csvs", "*.tif")
+                                             "plotting", "ethiopia", "input_csvs", "*.nc")
 
             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)