Skip to content

Commit

Permalink
add tests for biodata
Browse files Browse the repository at this point in the history
  • Loading branch information
@psmyth94
psmyth94 committed Oct 18, 2024
1 parent cb60264 commit 122f5fa
Showing 1 changed file with 111 additions and 45 deletions.
156 changes: 111 additions & 45 deletions tests/packaged_modules/test_biodata.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
DataFilesList,
_get_origin_metadata,
)
from datasets.exceptions import DatasetGenerationError
from datasets.features import Features, Value
from datasets.packaged_modules.json.json import Json

Expand Down Expand Up @@ -217,9 +218,9 @@ def data_with_metadata(tmp_path):
filename = tmp_path / "data_with_metadata.csv"
data = textwrap.dedent(
"""
sample,metadata1,metadata2,header1,header2
sample1,1,2,1,2
sample2,10,20,10,20
sample,metadata1,metadata2,header1,header2,target
sample1,1,2,1,2,a
sample2,10,20,10,20,b
"""
)
with open(filename, "w") as f:
Expand Down Expand Up @@ -541,15 +542,17 @@ def test_generate_tables_csv(self):
with self.assertLogs(
"biosets.packaged_modules.biodata.biodata", level="WARNING"
) as log:
generator = biodata._generate_tables(reader, [[self.csv_file]])
generator = biodata._generate_tables(
reader, [[self.csv_file]], split_name="train"
)
pa_table = pa.concat_tables([table for _, table in generator])
self.assertIn(
"Could not find the samples column in metadata table\nAvailable "
"Could not find the samples column in data table. Available "
"columns in data table: ['header1', 'header2']",
log.output[0],
)
self.assertIn(
"Could not find the batches column in metadata table\nAvailable "
"Could not find the batches column in data table. Available "
"columns in data table: ['header1', 'header2']",
log.output[1],
)
Expand All @@ -572,15 +575,15 @@ def test_generate_tables_jsonl(self):
with self.assertLogs(
"biosets.packaged_modules.biodata.biodata", level="WARNING"
) as log:
generator = biodata._generate_tables(reader, [[file]])
generator = biodata._generate_tables(reader, [[file]], split_name="train")
pa_table = pa.concat_tables([table for _, table in generator])
self.assertIn(
"Could not find the samples column in metadata table\nAvailable "
"Could not find the samples column in data table. Available "
"columns in data table: ['header1', 'header2']",
log.output[0],
)
self.assertIn(
"Could not find the batches column in metadata table\nAvailable "
"Could not find the batches column in data table. Available "
"columns in data table: ['header1', 'header2']",
log.output[1],
)
Expand All @@ -603,15 +606,15 @@ def test_generate_tables_txt(self):
with self.assertLogs(
"biosets.packaged_modules.biodata.biodata", level="WARNING"
) as log:
generator = biodata._generate_tables(reader, [[file]])
generator = biodata._generate_tables(reader, [[file]], split_name="train")
pa_table = pa.concat_tables([table for _, table in generator])
self.assertIn(
"Could not find the samples column in metadata table\nAvailable "
"Could not find the samples column in data table. Available "
"columns in data table: ['header1', 'header2']",
log.output[0],
)
self.assertIn(
"Could not find the batches column in metadata table\nAvailable "
"Could not find the batches column in data table. Available "
"columns in data table: ['header1', 'header2']",
log.output[1],
)
Expand All @@ -634,20 +637,20 @@ def test_generate_tables_npz(self):
with self.assertLogs(
"biosets.packaged_modules.biodata.biodata", level="WARNING"
) as log:
generator = biodata._generate_tables(reader, [[file]])
generator = biodata._generate_tables(reader, [[file]], split_name="train")
pa_table = pa.concat_tables([table for _, table in generator])
self.assertIn(
"Could not find the samples column in metadata table\nAvailable "
"columns in data table: ['0', '1', '2', '3', '4']",
"Could not find the samples column in data table. Available "
"columns in data table: ['0', '1']",
log.output[0],
)
self.assertIn(
"Could not find the batches column in metadata table\nAvailable "
"columns in data table: ['0', '1', '2', '3', '4']",
"Could not find the batches column in data table. Available "
"columns in data table: ['0', '1']",
log.output[1],
)

self.assertEqual(pa_table.num_columns, 5)
self.assertEqual(pa_table.num_columns, 2)
self.assertEqual(pa_table.num_rows, 2)

def test_generate_tables_multiclass_labels(self):
Expand All @@ -658,7 +661,9 @@ def test_generate_tables_multiclass_labels(self):
biodata = BioData(data_files=data_files)
biodata.INPUT_FEATURE = Abundance
reader = Csv()
generator = biodata._generate_tables(reader, [[self.multiclass]])
generator = biodata._generate_tables(
reader, [[self.multiclass]], split_name="train"
)
pa_table = pa.concat_tables([table for _, table in generator])

self.assertEqual(pa_table.num_columns, 4)
Expand Down Expand Up @@ -691,7 +696,9 @@ def test_generate_tables_missing_sample_column(self):
"biosets.packaged_modules.biodata.biodata", level="WARNING"
) as log:
generator = biodata._generate_tables(
reader, [[self.data_with_index_missing_sample_column]]
reader,
[[self.data_with_index_missing_sample_column]],
split_name="train",
)
pa.concat_tables([table for _, table in generator])

Expand Down Expand Up @@ -722,7 +729,9 @@ def test_generate_tables_matching_sample_column_name(self):
biodata.INPUT_FEATURE = Abundance
biodata.config.sample_column = "sample"
reader = Csv()
generator = biodata._generate_tables(reader, [[self.data_with_samples]])
generator = biodata._generate_tables(
reader, [[self.data_with_samples]], split_name="train"
)
pa_table = pa.concat_tables([table for _, table in generator])

self.assertIn("sample", pa_table.column_names)
Expand All @@ -744,7 +753,9 @@ def test_generate_tables_feature_metadata_missing_header(self):
with self.assertLogs(
"biosets.packaged_modules.biodata.biodata", level="WARNING"
) as log:
generator = biodata._generate_tables(reader, [[self.data_with_samples]])
generator = biodata._generate_tables(
reader, [[self.data_with_samples]], split_name="train"
)
pa.concat_tables([table for _, table in generator])
self.assertIn(
"Could not find the following columns in the data table: {'header3'}",
Expand All @@ -764,7 +775,9 @@ def test_generate_tables_feature_metadata_matching_sample_column_name(self):
biodata.config.feature_metadata_files = [self.feature_metadata_file]
biodata.config.feature_column = "feature"
reader = Csv()
generator = biodata._generate_tables(reader, [[self.data_with_samples]])
generator = biodata._generate_tables(
reader, [[self.data_with_samples]], split_name="train"
)
pa.concat_tables([table for _, table in generator])

self.assertIn("header1", biodata.info.features)
Expand All @@ -784,7 +797,9 @@ def test_generate_tables_with_all_data_in_one_file(self):
]
biodata.config.sample_column = "sample"
reader = Csv()
generator = biodata._generate_tables(reader, [[self.data_with_metadata]])
generator = biodata._generate_tables(
reader, [[self.data_with_metadata]], split_name="train"
)
pa_table = pa.concat_tables([table for _, table in generator])

self.assertIn("metadata1", pa_table.column_names)
Expand All @@ -810,7 +825,7 @@ def test_generate_tables_unmatched_sample_column(self):
"biosets.packaged_modules.biodata.biodata", level="WARNING"
) as log:
generator = biodata._generate_tables(
reader, [[self.data_with_unmatched_sample_column]]
reader, [[self.data_with_unmatched_sample_column]], split_name="train"
)
pa_table = pa.concat_tables([table for _, table in generator])

Check failure on line 830 in tests/packaged_modules/test_biodata.py

View workflow job for this annotation

GitHub Actions / Check Code Quality

Ruff (F841) 

tests/packaged_modules/test_biodata.py:830:13: F841 Local variable `pa_table` is assigned to but never used
self.assertIn(
Expand All @@ -833,7 +848,9 @@ def test_generate_tables_feature_metadata_with_missing_header(self):
self.feature_metadata_with_missing_header
]
reader = Csv()
generator = biodata._generate_tables(reader, [[self.data_with_samples]])
generator = biodata._generate_tables(
reader, [[self.data_with_samples]], split_name="train"
)
pa_table = pa.concat_tables([table for _, table in generator])

Check failure on line 854 in tests/packaged_modules/test_biodata.py

View workflow job for this annotation

GitHub Actions / Check Code Quality

Ruff (F841) 

tests/packaged_modules/test_biodata.py:854:9: F841 Local variable `pa_table` is assigned to but never used

def test_generate_tables_feature_metadata_with_missing_feature_column(self):
Expand All @@ -854,7 +871,9 @@ def test_generate_tables_feature_metadata_with_missing_feature_column(self):
with self.assertLogs(
"biosets.packaged_modules.biodata.biodata", level="WARNING"
) as log:
generator = biodata._generate_tables(reader, [[self.data_with_samples]])
generator = biodata._generate_tables(
reader, [[self.data_with_samples]], split_name="train"
)
pa_table = pa.concat_tables([table for _, table in generator])

Check failure on line 877 in tests/packaged_modules/test_biodata.py

View workflow job for this annotation

GitHub Actions / Check Code Quality

Ruff (F841) 

tests/packaged_modules/test_biodata.py:877:13: F841 Local variable `pa_table` is assigned to but never used
self.assertIn(
"Could not find the features column in metadata table", log.output[0]
Expand All @@ -874,7 +893,9 @@ def test_abundance_data_loading_binarized(self):
)
biodata.INPUT_FEATURE = Abundance
reader = Csv()
generator = biodata._generate_tables(reader, [[self.multiclass]])
generator = biodata._generate_tables(
reader, [[self.multiclass]], split_name="train"
)
pa_table = pa.concat_tables([table for _, table in generator])

assert pa_table.num_columns == 4
Expand Down Expand Up @@ -907,7 +928,9 @@ def test_abundance_data_loading_binarized_with_missing_labels(self):
)
biodata.INPUT_FEATURE = Abundance
reader = Csv()
generator = biodata._generate_tables(reader, [[self.multiclass]])
generator = biodata._generate_tables(
reader, [[self.multiclass]], split_name="train"
)
pa_table = pa.concat_tables([table for _, table in generator])

assert pa_table.num_columns == 4
Expand Down Expand Up @@ -955,7 +978,7 @@ def test_read_metadata_invalid_paths(self):

def test_create_features_valid(self):
schema = pa.schema([("sample", pa.int64()), ("target", pa.float64())])
features = self.data._create_features(schema)
features = self.data._create_features(schema, column_names=["sample", "target"])
self.assertIsInstance(features, Features)
self.assertIn("sample", features)

Expand Down Expand Up @@ -1009,21 +1032,64 @@ def test_biodata_load_dataset_with_sparse_reader(self):
data_files=self.npz_file,
sample_metadata_files=self.sample_metadata_file,
feature_metadata_files=self.feature_metadata_file,
target_column="metadata1",
target_column="target",
)["train"]
pd_data = data.to_pandas()
assert len(pd_data) == 2
assert pd_data["sample"].tolist() == ["sample1", "sample2"]
assert pd_data["target"].tolist() == ["a", "b"]
assert pd_data["labels"].tolist() == [0, 1]

def test_biodata_load_dataset_with_multiple_files_and_without_labels(self):
with self.assertRaises(DatasetGenerationError) as context:
load_dataset(
"snp",
data_files=[self.npz_file, self.npz_file],
sample_metadata_files=[
self.sample_metadata_file,
self.sample_metadata_file_2,
],
feature_metadata_files=self.feature_metadata_file,
target_column="target",
)["train"]

def test_biodata_load_dataset_with_multiple_sparse_reader(self):
data = load_dataset(
"snp",
data_files=[self.npz_file, self.npz_file],
sample_metadata_files=[
self.sample_metadata_file,
self.sample_metadata_file_2,
],
feature_metadata_files=self.feature_metadata_file,
target_column="metadata1",
)["train"]
pd_data = data.to_pandas()
assert len(pd_data) == 2
self.assertIn(
"Labels must be provided if multiple sample metadata files "
"are provided. Either set `labels`, `positive_labels` "
"and/or `negative_labels` in `load_dataset`.",
str(context.exception),
)

with self.assertRaises(DatasetGenerationError) as context:
load_dataset(
"snp",
data_files=[self.data_with_metadata, self.data_with_metadata],
feature_metadata_files=self.feature_metadata_file,
target_column="target",
)["train"]

self.assertIn(
"Labels must be provided if multiple data files "
"are provided and the target column is found in the "
"data table. Either set `labels`, `positive_labels` "
"and/or `negative_labels` in `load_dataset`.",
str(context.exception),
)

# def test_biodata_load_dataset_with_multiple_files_and_with_labels(self):
# data = load_dataset(
# "snp",
# data_files=[self.data_with_metadata, self.data_with_metadata],
# feature_metadata_files=self.feature_metadata_file,
# labels=["a", "b"],
# target_column="target",
# )["train"]
# pd_data = data.to_pandas()
# assert len(pd_data) == 4
# assert pd_data["sample"].tolist() == [
# "sample1",
# "sample2",
# "sample3",
# "sample4",
# ]
# assert pd_data["target"].tolist() == ["a", "b", "c", "d"]
# assert pd_data["labels"].tolist() == [0, 1, 2, 4]

0 comments on commit 122f5fa

Please sign in to comment.