From bccc72d15c0f52a07c313b7f63a6579bb1308ce4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Fri, 17 Mar 2023 12:38:12 +0000
Subject: [PATCH] fix(dataset): check valid suffixes properly.
---
src/aliby/io/dataset.py | 2 +-
.../pipeline/test_pipeline_local_nometa.py | 31 ++++++++++++-------
2 files changed, 20 insertions(+), 13 deletions(-)
diff --git a/src/aliby/io/dataset.py b/src/aliby/io/dataset.py
index fbedf23c..187e5302 100644
--- a/src/aliby/io/dataset.py
+++ b/src/aliby/io/dataset.py
@@ -147,7 +147,7 @@ class DatasetLocalOME(DatasetLocalABC):
super().__init__(dpath)
assert len(
self.get_images()
- ), f"No valid files found. Formats are {suffixes}"
+ ), f"No valid files found. Formats are {self._valid_suffixes}"
@property
def date(self):
diff --git a/tests/aliby/pipeline/test_pipeline_local_nometa.py b/tests/aliby/pipeline/test_pipeline_local_nometa.py
index 5fd397ac..095fb75b 100644
--- a/tests/aliby/pipeline/test_pipeline_local_nometa.py
+++ b/tests/aliby/pipeline/test_pipeline_local_nometa.py
@@ -1,18 +1,25 @@
#!/usr/bin/env jupyter
-from aliby.pipeline import PipelineParameters, Pipeline
+from pathlib import Path
+
+import pytest
+
+from aliby.pipeline import Pipeline, PipelineParameters
def test_local_pipeline(file: str):
- params = PipelineParameters.default(
- general={
- "expt_id": file,
- "distributed": 0,
- "directory": "test_output/",
- "overwrite": True,
- },
- tiler={"ref_channel": 0},
- )
- p = Pipeline(params)
+ if Path(file).exists():
+ params = PipelineParameters.default(
+ general={
+ "expt_id": file,
+ "distributed": 0,
+ "directory": "test_output/",
+ "overwrite": True,
+ },
+ tiler={"ref_channel": 0},
+ )
+ p = Pipeline(params)
- p.run()
+ p.run()
+ else:
+ print("Test dataset not downloaded")
--
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