diff --git a/coordinator/EnvSuitPipeline.py b/coordinator/EnvSuitPipeline.py index daf5e3a3a90c653b11dd5a2bf6c68378ddc00d4a..20e570c91e24027726efee3ad469c62e9d764dc0 100644 --- a/coordinator/EnvSuitPipeline.py +++ b/coordinator/EnvSuitPipeline.py @@ -261,13 +261,13 @@ def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent # run_merger(config, sys_config, processor_name) - resultFile = envSuitPath + 'RIE.csv' + resultFile = envSuitPath + 'RIE.tif' strain_outPath = os.path.join(region_outPath,strain) - strain_outFile = strain_outPath + '/RIE_value.csv' + strain_outFile = strain_outPath + '/RIE_value.tif' # Check results dimension - result = pd.read_csv(resultFile) - result_dims = result.shape + # result = pd.read_csv(resultFile) + # result_dims = result.shape """ read in the input_spatial_points.csv file and get the number of spatial points - this is used for @@ -278,9 +278,9 @@ def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent spatial_points = pd.read_csv(region_spatial_points_file) spatial_dim = spatial_points.shape[0] - if ((result_dims[0] != spatial_dim) or (result_dims[1] != (temporal_dim + 4))): # + 4 required because there are extra columns in the result file - logger.error(f"Result dimension {result_dims} does not match with the expected: ({spatial_dim}, {temporal_dim + 4})") - raise IndexError + # if ((result_dims[0] != spatial_dim) or (result_dims[1] != (temporal_dim + 4))): # + 4 required because there are extra columns in the result file + # logger.error(f"Result dimension {result_dims} does not match with the expected: ({spatial_dim}, {temporal_dim + 4})") + # raise IndexError if not os.path.exists(strain_outPath): os.makedirs(strain_outPath) diff --git a/coordinator/ProcessorEnvironment.py b/coordinator/ProcessorEnvironment.py index df64fc01a2216e1b7141c9e0951db5424c3e9438..c90530bf4465440baae3ad8f0c75c70bd619b77c 100644 --- a/coordinator/ProcessorEnvironment.py +++ b/coordinator/ProcessorEnvironment.py @@ -180,8 +180,9 @@ 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.csv" + csv_template_dir = input_dir + "/{DISEASE_DIR}/RIE_value.tif" + Path(output_dir).mkdir(parents=True, exist_ok=True) sys_config = config['Environment']['EWS-Plotting']['SysConfig'] diff --git a/tests/integration/partial/test_env_suit.py b/tests/integration/partial/test_env_suit.py index 11169a6601406b1bb4c8a193dd9f2ce72097f47f..0c5c44e95f76aff48a99304f4af62f18e16c098e 100644 --- a/tests/integration/partial/test_env_suit.py +++ b/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)