From 8c7b0aef219058305f7d915b6c4b2502a43d972b Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Thu, 25 Jan 2024 17:27:47 +0000
Subject: [PATCH] more work getting rid of csv references
---
coordinator/ProcessorEnvironment.py | 10 +++++-----
tests/integration/test_suites/env_suit_test_suite.py | 6 +++---
tests/integration/test_suites/epi_test_suite.py | 2 +-
3 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/coordinator/ProcessorEnvironment.py b/coordinator/ProcessorEnvironment.py
index 5780126..36082c8 100644
--- a/coordinator/ProcessorEnvironment.py
+++ b/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.nc"
+ rie_template_dir = input_dir + "/{DISEASE_DIR}/RIE_value.nc"
Path(output_dir).mkdir(parents=True, exist_ok=True)
@@ -199,16 +199,16 @@ class ProcessorEnvironment(Processor):
run_params_file_arg = run_config,
es_output_dir_arg = output_dir,
issue_date_arg = config['StartString'],
- disease_csv_template_arg = csv_template_dir)
+ disease_nc_template_arg = rie_template_dir)
env_suit_processor.run_params.FILTER_FOR_COUNTRY = (filter_for_country.upper() == "TRUE")
# Include further diseases in plotting. In this case the irrigated suitabilite for the rusts.
# TODO: move this part out into a config
extra_diseases = [
- EnvSuitDiseaseInfo("Stem rust temp-only", "stem_rust_temponly", config['StartString'], "StemRust_TempOnly", csv_template_dir),
- EnvSuitDiseaseInfo("Leaf rust temp-only", "leaf_rust_temponly", config['StartString'], "LeafRust_TempOnly", csv_template_dir),
- EnvSuitDiseaseInfo("Stripe rust temp-only", "stripe_temponly", config['StartString'], "StripeRust_TempOnly", csv_template_dir),
+ EnvSuitDiseaseInfo("Stem rust temp-only", "stem_rust_temponly", config['StartString'], "StemRust_TempOnly", rie_template_dir),
+ EnvSuitDiseaseInfo("Leaf rust temp-only", "leaf_rust_temponly", config['StartString'], "LeafRust_TempOnly", rie_template_dir),
+ EnvSuitDiseaseInfo("Stripe rust temp-only", "stripe_temponly", config['StartString'], "StripeRust_TempOnly", rie_template_dir),
]
env_suit_processor.add_diseases(diseases=extra_diseases)
diff --git a/tests/integration/test_suites/env_suit_test_suite.py b/tests/integration/test_suites/env_suit_test_suite.py
index 95cdca5..8981a64 100644
--- a/tests/integration/test_suites/env_suit_test_suite.py
+++ b/tests/integration/test_suites/env_suit_test_suite.py
@@ -59,13 +59,13 @@ class BaseEnvSuitTestSuite:
self.assertTrue(eth_file_exists)
- def test_standard_run_all_input_csvs_produced(self):
+ def test_standard_run_all_input_ncs_produced(self):
east_africa_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
IntegrationTestUtils.TEST_JOB_DIR,
- "plotting", "eastafrica", "input_csvs", "*.nc")
+ "plotting", "eastafrica", "input_nc", "*.nc")
ethiopia_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
IntegrationTestUtils.TEST_JOB_DIR,
- "plotting", "ethiopia", "input_csvs", "*.nc")
+ "plotting", "ethiopia", "input_nc", "*.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)
diff --git a/tests/integration/test_suites/epi_test_suite.py b/tests/integration/test_suites/epi_test_suite.py
index 30c46dd..c2b08dd 100644
--- a/tests/integration/test_suites/epi_test_suite.py
+++ b/tests/integration/test_suites/epi_test_suite.py
@@ -67,7 +67,7 @@ class BaseEpiTestSuite:
input_csvs_root = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
IntegrationTestUtils.TEST_JOB_DIR,
"plotting",
- "input_csvs",
+ "input_nc",
"*stem*")
self.check_wildcard_exists_and_not_empty(input_csvs_root, ".nc")
--
GitLab