From 360ee339fe435723f1cf3571323327bebc1053cf Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Tue, 12 Dec 2023 14:50:07 +0000
Subject: [PATCH] groundwork for using tifs/netcdf throughout the pipeline.
splitting out some csv parsing functions
---
coordinator/ProcessorEnvironment.py | 1 -
tests/integration/partial/test_env_suit.py | 4 ++--
tests/integration/test_suites/depo_test_suite.py | 4 ++--
tests/integration/test_suites/env_suit_test_suite.py | 4 ++--
4 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/coordinator/ProcessorEnvironment.py b/coordinator/ProcessorEnvironment.py
index c90530b..d3b70db 100644
--- a/coordinator/ProcessorEnvironment.py
+++ b/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)
diff --git a/tests/integration/partial/test_env_suit.py b/tests/integration/partial/test_env_suit.py
index 0c5c44e..843556a 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)
diff --git a/tests/integration/test_suites/depo_test_suite.py b/tests/integration/test_suites/depo_test_suite.py
index 15f88ea..2b7c831 100644
--- a/tests/integration/test_suites/depo_test_suite.py
+++ b/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)
diff --git a/tests/integration/test_suites/env_suit_test_suite.py b/tests/integration/test_suites/env_suit_test_suite.py
index e21de97..0030bfc 100644
--- a/tests/integration/test_suites/env_suit_test_suite.py
+++ b/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)
--
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