Merge pull request #1122 from TeamCOMPAS/fix_h5sample_dimension_error

add try-catch for h5sample if there are issues parsing the file

compas_python_utils/h5sample.py

@@ -9,6 +9,7 @@
 
 import h5py
 import numpy as np
+import os
 
 from compas_python_utils.h5view import printSummary
 from compas_python_utils.h5copy import copyHDF5File
@@ -86,10 +87,17 @@ def sample_h5(
     with h5py.File(compas_h5_filepath, "r") as compas_h5_file:
         printSummary(compas_h5_filepath, compas_h5_file)
 
-    with h5py.File(output_filepath, 'w') as out_h5_file:
-        copyHDF5File(compas_h5_filepath, out_h5_file)
-        sampled_binary_seeds = np.random.choice(binary_seeds, size=n, replace=replace)
-        _sample(out_h5_file, seed_key, sampled_binary_seeds)
+    try:
+        with h5py.File(output_filepath, 'w') as out_h5_file:
+            copyHDF5File(compas_h5_filepath, out_h5_file)
+            sampled_binary_seeds = np.random.choice(binary_seeds, size=n, replace=replace)
+            _sample(out_h5_file, seed_key, sampled_binary_seeds)
+    except Exception as e:
+        print(f"Error sampling COMPAS h5 file: {e}")
+        # remove the output file if it was created
+        if os.path.exists(output_filepath):
+            os.remove(output_filepath)
+        return
 
     print("Sampled file summary:")
     with h5py.File(output_filepath, "r") as output_h5_file:
@@ -187,4 +195,4 @@ def main():  # pragma: no cover
 
 
 if __name__ == "__main__":  # pragma: no cover
-    main()
+    main()

py_tests/test_h5sample.py

@@ -1,38 +1,38 @@
 import os
 
 import numpy as np
-import pytest
 from conftest import get_compas_data
 from deepdiff import DeepDiff
 
 from compas_python_utils import h5sample
+import pytest
 
 
-def test_sample(tmp_path, example_compas_output_path):
+@pytest.mark.parametrize(
+"test_kwargs",
+[
+    dict(n=100, replace=True),
+    dict(frac=0.5, replace=False),
+    dict(frac=1.2, replace=True),
+    dict(seed_group="BSE_Double_Compact_Objects", frac=2.0, replace=True),
+],
+)
+def test_sample(test_kwargs, tmp_path, fake_compas_output):
     """Test that h5sample can sample a file"""
     np.random.seed(0)
-    init_file = example_compas_output_path
-
-    test_kwargs = [
-        dict(n=100, replace=True),
-        dict(frac=0.5, replace=False),
-        dict(frac=1.2, replace=True),
-        dict(seed_group="BSE_Double_Compact_Objects", frac=2.0, replace=True),
-    ]
-
-    for kwg in test_kwargs:
-        # creating new h5 file to copy contents to
-        new_file = f"{tmp_path}/sampled_compas_out.h5"
-        if os.path.exists(new_file):
-            os.remove(new_file)
-        h5sample.sample_h5(init_file, new_file, **kwg)
-        assert os.path.exists(new_file), f"File {new_file} does not exist"
-        init_data = get_compas_data(init_file)
-        new_data = get_compas_data(new_file)
-        diff = DeepDiff(init_data, new_data)
-        assert (
-            len(diff) > 0
-        ), f"The sampled file is the same as the original when using kwgs: {kwg}"
+    init_file = fake_compas_output
+
+    new_file = f"{tmp_path}/sampled_compas_out.h5"
+    if os.path.exists(new_file):
+        os.remove(new_file)
+    h5sample.sample_h5(init_file, new_file, **test_kwargs)
+    assert os.path.exists(new_file), f"File {new_file} does not exist"
+    init_data = get_compas_data(init_file)
+    new_data = get_compas_data(new_file)
+    diff = DeepDiff(init_data, new_data)
+    assert (
+        len(diff) > 0
+    ), f"The sampled file is the same as the original when using kwgs: {test_kwargs}"
 
 
 def test_argparser(capsys):