def test_get_av_cluster_expression(self):
file_dir = os.path.join(os.path.dirname(__file__), "testfiles")
class TmpClass:
pass
file_dir_obj = TmpClass()
file_dir_obj.name = file_dir
fetcher = ScExpressionAtlasFetcher()
(exp, rows, cols) = fetcher._get_av_cluster_expression(
matrix_file_dir=file_dir_obj,
cell_clusterings={
"c1": ["Sample 1"],
"c2": ["Sample 2"],
"c3": ["Sample 3"]
})
self.assertIsNotNone(exp)
self.assertIsNotNone(rows)
self.assertIsNotNone(cols)
# also test the creation of the final table
exp_table = fetcher._create_expression_table(exp, rows, cols)
self.assertEqual(
"\tc1\tc2\tc3\nGene 1\t1.0\t5.0\t9.0\nGene 2\t2.0\t6.0\t10.0\nGene 3\t3.0\t7.0\t1.1\nGene 4\t4.0\t8.0\t1.2",
exp_table)
def test_get_dataset_id(self):
fetcher = ScExpressionAtlasFetcher()
dataset_id = fetcher.get_dataset_id(self.default_parameters)
self.assertIsNotNone(dataset_id)
self.assertEqual("E-CURD-11_3", dataset_id)
def test_extract_factor_values(self):
test_file = os.path.join(os.path.dirname(__file__), "testfiles",
"E-CURD-11.sdrf.txt")
fetcher = ScExpressionAtlasFetcher()
cell_factors = fetcher._extract_factor_values_from_sdrf(test_file)
self.assertEqual(176, len(cell_factors))
def test_load_expr_data(self):
fetcher = ScExpressionAtlasFetcher()
failed_experiment = [
DatasetRequestParameter(name="dataset_id", value="E-MTAB-7078"),
DatasetRequestParameter(name="k", value="3")
]
fetcher.load_dataset(failed_experiment, MockMQ())
def test_failed_loading(self):
fetcher = ScExpressionAtlasFetcher()
failed_experiment = [
DatasetRequestParameter(name="dataset_id", value="E-HCAD-13"),
DatasetRequestParameter(name="k", value="12")
]
fetcher.load_dataset(failed_experiment, MockMQ())
def test_get_cell_clustering(self):
fetcher = ScExpressionAtlasFetcher()
cell_clustering = fetcher._get_cell_clusterings(dataset_id="E-CURD-11",
k=3)
self.assertIsNotNone(cell_clustering)
self.assertEqual(3, len(cell_clustering))
self.assertTrue("SRR2049340" in cell_clustering["Cluster 2"])
self.assertTrue("SRR2049535" in cell_clustering["Cluster 3"])
def test_load_exp_design(self):
dataset_id = "E-HCAD-13"
fetcher = ScExpressionAtlasFetcher()
exp_design = fetcher._load_experiment_design_factors(dataset_id)
self.assertIsNotNone(exp_design)
self.assertEqual(6263, len(exp_design))
self.assertTrue("age" in exp_design[list(exp_design.keys())[0]])
def test_download_zip_file(self):
fetcher = ScExpressionAtlasFetcher()
file_url = "https://www.ebi.ac.uk/gxa/sc/experiment/E-CURD-11/download/zip?fileType=normalised&accessKey="
tmp_dir = fetcher._download_zip_file(file_url=file_url)
self.assertIsNotNone(tmp_dir)
self.assertTrue(os.path.isdir(tmp_dir.name))
self.assertTrue(
os.path.isfile(
os.path.join(
tmp_dir.name,
"E-CURD-11.aggregated_filtered_normalised_counts.mtx")))
def _get_dataset_fetcher_for_identifier(self, resource_id: str) -> DatasetFetcher:
"""
Returns the matching DatasetFetcher for the passed resource id or None
in case the identifier does not match any known format.
:param resource_id: The identifier to get the DatasetFetcher for.
:return: The matching DatasetFetcher or None if it does not match any known format.
"""
if resource_id == "example_datasets":
return ExampleDatasetFetcher()
if resource_id == "ebi_gxa":
return ExpressionAtlasFetcher()
if resource_id == "ebi_sc_gxa":
return ScExpressionAtlasFetcher()
return None
def test_create_summary(self):
fetcher = ScExpressionAtlasFetcher()
# get the data
file_url = "https://www.ebi.ac.uk/gxa/sc/experiment/E-CURD-11/download/zip?fileType=normalised&accessKey="
tmp_dir = fetcher._download_zip_file(file_url=file_url)
# get the cell clustering
cell_clustering = fetcher._get_cell_clusterings(dataset_id="E-CURD-11",
k=3)
(exp, rows, cols) = fetcher._get_av_cluster_expression(
matrix_file_dir=tmp_dir, cell_clusterings=cell_clustering)
# create the summary
summary = fetcher._create_summary(dataset_id="E-CURD-11",
k=3,
sample_ids=cols,
cell_clusterings=cell_clustering)
self.assertIsNotNone(summary)
self.assertEqual(1, len(summary.default_parameters))