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‎tests/test_ingest.py‎

Lines changed: 66 additions & 70 deletions
Original file line numberDiff line numberDiff line change
@@ -86,7 +86,7 @@ def get_nth_gene_models(n, models, mock_dir):
8686
class IngestTestCase(unittest.TestCase):
8787
@patch('google.cloud.storage.Blob', side_effect=mock_storage_blob)
8888
@patch('google.cloud.storage.Client', side_effect=mock_storage_client)
89-
@patch("google.cloud.firestore.Client", side_effect=mock_firestore_client)
89+
@patch('google.cloud.firestore.Client', side_effect=mock_firestore_client)
9090
def setup_ingest(
9191
self, args, mock_storage_client, mock_storage_blob, mock_firestore_client
9292
):
@@ -145,7 +145,7 @@ def test_ingest_dense_matrix(self):
145145
expected_num_models = 19
146146
self.assertEqual(num_models, expected_num_models)
147147
# Verify that the first gene model looks as expected
148-
mock_dir = "dense_matrix_19_genes_100k_cells_txt"
148+
mock_dir = 'dense_matrix_19_genes_100k_cells_txt'
149149
model, expected_model = get_nth_gene_models(0, models, mock_dir)
150150

151151
self.assertEqual(model, expected_model)
@@ -183,25 +183,25 @@ def test_ingest_local_dense_matrix(self):
183183
"""
184184

185185
args = [
186-
"--study-accession",
187-
"SCP1",
188-
"--file-id",
189-
"1234abc",
190-
"ingest_expression",
191-
"--taxon-name",
192-
"Homo sapiens",
193-
"--taxon-common-name",
194-
"human",
195-
"--ncbi-taxid",
196-
"9606",
197-
"--genome-assembly-accession",
198-
"GCA_000001405.15",
199-
"--genome-annotation",
200-
"Ensembl 94",
201-
"--matrix-file",
202-
"../tests/data/dense_matrix_19_genes_100k_cells.txt",
203-
"--matrix-file-type",
204-
"dense",
186+
'--study-accession',
187+
'SCP1',
188+
'--file-id',
189+
'1234abc',
190+
'ingest_expression',
191+
'--taxon-name',
192+
'Homo sapiens',
193+
'--taxon-common-name',
194+
'human',
195+
'--ncbi-taxid',
196+
'9606',
197+
'--genome-assembly-accession',
198+
'GCA_000001405.15',
199+
'--genome-annotation',
200+
'Ensembl 94',
201+
'--matrix-file',
202+
'../tests/data/dense_matrix_19_genes_100k_cells.txt',
203+
'--matrix-file-type',
204+
'dense',
205205
]
206206
ingest = self.setup_ingest(args)
207207

@@ -213,7 +213,7 @@ def test_ingest_local_dense_matrix(self):
213213
self.assertEqual(num_models, expected_num_models)
214214

215215
# Verify that the first gene model looks as expected
216-
mock_dir = "dense_matrix_19_genes_100k_cells_txt"
216+
mock_dir = 'dense_matrix_19_genes_100k_cells_txt'
217217
model, expected_model = get_nth_gene_models(0, models, mock_dir)
218218

219219
self.assertEqual(model, expected_model)
@@ -251,29 +251,29 @@ def test_ingest_mtx_matrix(self):
251251
"""
252252

253253
args = [
254-
"--study-accession",
255-
"SCP1",
256-
"--file-id",
257-
"1234abc",
258-
"ingest_expression",
259-
"--taxon-name",
260-
"Homo sapiens",
261-
"--taxon-common-name",
262-
"human",
263-
"--ncbi-taxid",
264-
"9606",
265-
"--genome-assembly-accession",
266-
"GCA_000001405.15",
267-
"--genome-annotation",
268-
"Ensembl 94",
269-
"--matrix-file",
270-
"../tests/data/matrix.mtx",
271-
"--matrix-file-type",
272-
"mtx",
273-
"--gene-file",
274-
"../tests/data/genes.tsv",
275-
"--barcode-file",
276-
"../tests/data/barcodes.tsv",
254+
'--study-accession',
255+
'SCP1',
256+
'--file-id',
257+
'1234abc',
258+
'ingest_expression',
259+
'--taxon-name',
260+
'Homo sapiens',
261+
'--taxon-common-name',
262+
'human',
263+
'--ncbi-taxid',
264+
'9606',
265+
'--genome-assembly-accession',
266+
'GCA_000001405.15',
267+
'--genome-annotation',
268+
'Ensembl 94',
269+
'--matrix-file',
270+
'../tests/data/matrix.mtx',
271+
'--matrix-file-type',
272+
'mtx',
273+
'--gene-file',
274+
'../tests/data/genes.tsv',
275+
'--barcode-file',
276+
'../tests/data/barcodes.tsv',
277277
]
278278
ingest = self.setup_ingest(args)
279279

@@ -285,10 +285,8 @@ def test_ingest_mtx_matrix(self):
285285
self.assertEqual(num_models, expected_num_models)
286286

287287
# Verify that the first gene model looks as expected
288-
mock_dir = "matrix_mtx"
288+
mock_dir = 'matrix_mtx'
289289
model, expected_model = get_nth_gene_models(0, models, mock_dir)
290-
print(f"\n\n\n{model}\n\n\n")
291-
print(f"\n\n\n{expected_model}\n\n\n")
292290
self.assertEqual(model, expected_model)
293291

294292
def test_mtx_bundle_argument_validation(self):
@@ -324,25 +322,25 @@ def test_ingest_loom(self):
324322
"""
325323

326324
args = [
327-
"--study-accession",
328-
"SCP1",
329-
"--file-id",
330-
"1234abc",
331-
"ingest_expression",
332-
"--taxon-name",
333-
"Homo Sapiens",
334-
"--taxon-common-name",
335-
"human",
336-
"--ncbi-taxid",
337-
"9606",
338-
"--genome-assembly-accession",
339-
"GCA_000001405.15",
340-
"--genome-annotation",
341-
"Ensemble 94",
342-
"--matrix-file",
343-
"../tests/data/test_loom.loom",
344-
"--matrix-file-type",
345-
"loom",
325+
'--study-accession',
326+
'SCP1',
327+
'--file-id',
328+
'1234abc',
329+
'ingest_expression',
330+
'--taxon-name',
331+
'Homo Sapiens',
332+
'--taxon-common-name',
333+
'human',
334+
'--ncbi-taxid',
335+
'9606',
336+
'--genome-assembly-accession',
337+
'GCA_000001405.15',
338+
'--genome-annotation',
339+
'Ensemble 94',
340+
'--matrix-file',
341+
'../tests/data/test_loom.loom',
342+
'--matrix-file-type',
343+
'loom',
346344
]
347345

348346
ingest = self.setup_ingest(args)
@@ -355,10 +353,8 @@ def test_ingest_loom(self):
355353
self.assertEqual(num_models, expected_num_models)
356354

357355
# Verify that the first gene model looks as expected
358-
mock_dir = "loom"
356+
mock_dir = 'loom'
359357
model, expected_model = get_nth_gene_models(0, models, mock_dir)
360-
print(f"\n\n\n{model}\n\n\n")
361-
print(f"\n\n\n{expected_model}\n\n\n")
362358
self.assertEqual(model, expected_model)
363359

364360

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