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gene sets summary route (#2099)

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* gene sets summary route

* lint

* clarify return type

* style
This commit is contained in:
Bruce Martin
2021-03-10 16:02:05 -08:00
committed by GitHub
parent 1d3d9237e7
commit 31e0326ded
10 changed files with 228 additions and 38 deletions
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local_server/test/unit/common/test_api.py
+97 -5
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@@ -509,6 +509,16 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints):
{"genes": [], "geneset_description": "", "geneset_name": "third gene set"},
{"genes": [], "geneset_description": "fourth description", "geneset_name": "fourth_gene_set"},
{"genes": [], "geneset_description": "", "geneset_name": "fifth_dataset"},
{
"genes": [
{"gene_description": "", "gene_symbol": "ACD"},
{"gene_description": "", "gene_symbol": "AATF"},
{"gene_description": "", "gene_symbol": "F5"},
{"gene_description": "", "gene_symbol": "PIGU"},
],
"geneset_description": "",
"geneset_name": "summary test",
},
],
"tid": 0,
},
@@ -531,6 +541,10 @@ second gene set,,SIK1,\r
third gene set,,,\r
fourth_gene_set,fourth description,,\r
fifth_dataset,,,\r
summary test,,ACD,\r
summary test,,AATF,\r
summary test,,F5,\r
summary test,,PIGU,\r
""",
)
@@ -677,8 +691,86 @@ fifth_dataset,,,\r
original_data,
)
"""
TODO once we have some code to support it:
1. GET genesets_summary
2. genesets_summary obeys tid
"""
def test_get_geneset_summary(self):
endpoint = "geneset_summary?geneset_name=summary%20test&method=mean"
url = f"{self.URL_BASE}{endpoint}"
header = {"Accept": "application/octet-stream"}
result = self.session.get(url, headers=header)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df["n_rows"], 2638)
self.assertEqual(df["n_cols"], 1)
self.assertEqual(df["col_idx"], ["summary test"])
self.assertAlmostEqual(df["columns"][0][0], -0.19863907)
def test_get_geneset_summary_default_method(self):
endpoint = "geneset_summary?geneset_name=summary%20test"
url = f"{self.URL_BASE}{endpoint}"
header = {"Accept": "application/octet-stream"}
result = self.session.get(url, headers=header)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df["n_rows"], 2638)
self.assertEqual(df["n_cols"], 1)
self.assertEqual(df["col_idx"], ["summary test"])
self.assertAlmostEqual(df["columns"][0][0], -0.19863907)
def test_get_geneset_summary_check_tid(self):
# get the TID
result = self.session.get(f"{self.URL_BASE}genesets", headers={"Accept": "application/json"})
self.assertEqual(result.status_code, HTTPStatus.OK)
tid = result.json()["tid"]
# current tid
endpoint = f"geneset_summary?geneset_name=summary%20test&tid={tid}"
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
self.assertEqual(result.status_code, HTTPStatus.OK)
# future tid
endpoint = f"geneset_summary?geneset_name=summary%20test&tid={tid+1}"
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
self.assertEqual(result.status_code, HTTPStatus.NOT_FOUND)
# past tid
endpoint = f"geneset_summary?geneset_name=summary%20test&tid={tid-1}"
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
self.assertEqual(result.status_code, HTTPStatus.NOT_FOUND)
# No tid - ie, skip check
endpoint = "geneset_summary?geneset_name=summary%20test"
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
self.assertEqual(result.status_code, HTTPStatus.OK)
def test_get_geneset_summary_edge_cases(self):
# attempt to summarize _all_ genesets, including edge cases with zero or one gene
result = self.session.get(f"{self.URL_BASE}genesets", headers={"Accept": "application/json"})
self.assertEqual(result.status_code, HTTPStatus.OK)
geneset_names = [gs["geneset_name"] for gs in result.json()["genesets"]]
for gs in geneset_names:
endpoint = f"geneset_summary?geneset_name={gs}"
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
df = decode_fbs.decode_matrix_FBS(result.content)
self.assertEqual(df["n_rows"], 2638)
self.assertEqual(df["n_cols"], 1)
self.assertEqual(df["col_idx"], [gs])
def test_get_geneset_error_handling(self):
# no geneset
endpoint = "geneset_summary"
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
# unknown geneset
endpoint = "geneset_summary?geneset_name=NO_SUCH_GENE_SET"
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
# unknown method
endpoint = "geneset_summary?geneset_name=summary%20test&method=NO_SUCH_METHOD"
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)