From 6fd5efe1424393f8100c7de8c65fc568c4759287 Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Thu, 21 Dec 2023 14:02:45 +0000
Subject: [PATCH] more work wiring in nc files as output
---
coordinator/EnvSuitPipeline.py | 4 ++--
coordinator/ProcessorEnvironment.py | 2 +-
tests/integration/full/full_test_epi.py | 6 +++---
tests/integration/partial/integration_test_utils.py | 6 +++---
tests/integration/partial/test_advisory.py | 2 +-
tests/integration/partial/test_deposition.py | 2 +-
tests/integration/partial/test_env_suit.py | 2 +-
tests/integration/partial/test_epi.py | 2 +-
tests/integration/partial/test_survey.py | 2 +-
tests/integration/test_suites/depo_test_suite.py | 4 ++--
tests/integration/test_suites/env_suit_test_suite.py | 4 ++--
11 files changed, 18 insertions(+), 18 deletions(-)
diff --git a/coordinator/EnvSuitPipeline.py b/coordinator/EnvSuitPipeline.py
index 20e570c..5fb07ec 100644
--- a/coordinator/EnvSuitPipeline.py
+++ b/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)
diff --git a/coordinator/ProcessorEnvironment.py b/coordinator/ProcessorEnvironment.py
index d3b70db..5780126 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.tif"
+ csv_template_dir = input_dir + "/{DISEASE_DIR}/RIE_value.nc"
Path(output_dir).mkdir(parents=True, exist_ok=True)
diff --git a/tests/integration/full/full_test_epi.py b/tests/integration/full/full_test_epi.py
index 33fb8ed..1c96b33 100644
--- a/tests/integration/full/full_test_epi.py
+++ b/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")
diff --git a/tests/integration/partial/integration_test_utils.py b/tests/integration/partial/integration_test_utils.py
index 9903274..2003841 100644
--- a/tests/integration/partial/integration_test_utils.py
+++ b/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
diff --git a/tests/integration/partial/test_advisory.py b/tests/integration/partial/test_advisory.py
index d8558cd..bdfe984 100644
--- a/tests/integration/partial/test_advisory.py
+++ b/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
diff --git a/tests/integration/partial/test_deposition.py b/tests/integration/partial/test_deposition.py
index 96268cb..8e665e4 100644
--- a/tests/integration/partial/test_deposition.py
+++ b/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
diff --git a/tests/integration/partial/test_env_suit.py b/tests/integration/partial/test_env_suit.py
index 843556a..55c7d82 100644
--- a/tests/integration/partial/test_env_suit.py
+++ b/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
diff --git a/tests/integration/partial/test_epi.py b/tests/integration/partial/test_epi.py
index a5433b9..5922cf2 100644
--- a/tests/integration/partial/test_epi.py
+++ b/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
diff --git a/tests/integration/partial/test_survey.py b/tests/integration/partial/test_survey.py
index 0026f52..1c33aff 100644
--- a/tests/integration/partial/test_survey.py
+++ b/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
diff --git a/tests/integration/test_suites/depo_test_suite.py b/tests/integration/test_suites/depo_test_suite.py
index 2b7c831..897462b 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", "*.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)
diff --git a/tests/integration/test_suites/env_suit_test_suite.py b/tests/integration/test_suites/env_suit_test_suite.py
index 0030bfc..95cdca5 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", "*.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)
--
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