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Upgraded to ATTED-II API v5 #257

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Feb 8, 2025
Merged

Upgraded to ATTED-II API v5 #257

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8 changes: 4 additions & 4 deletions api/resources/proxy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,12 @@
request_headers = {"user-agent": "BAR API", "accept": "application/json"}


@bar_proxy.route("/atted_api4/<string:gene_id>/<int:top_n>")
class ATTEDApi4(Resource):
@bar_proxy.route("/atted_api5/<string:gene_id>/<int:top_n>")
class ATTEDApi5(Resource):
@bar_proxy.param("gene_id", _in="path", default="At1g01010")
@bar_proxy.param("top_n", _in="path", default=5)
def get(self, gene_id="", top_n=""):
"""This end point is a proxy for ATTED-II api version 4.
"""This end point is a proxy for ATTED-II api version 5.
This is used by ThaleMine.
This end point is currently not cached.
"""
Expand All @@ -30,7 +30,7 @@ def get(self, gene_id="", top_n=""):

# Now query the web service
payload = {"gene": gene_id, "topN": top_n}
resp = requests.get("https://atted.jp/cgi-bin/api4.cgi", params=payload, headers=request_headers)
resp = requests.get("https://atted.jp/api5/", params=payload, headers=request_headers)

# I think the remote API always returns status 200, so skip status checking
return resp.json()
17 changes: 6 additions & 11 deletions tests/data/get_atted_api4.json → tests/data/get_atted_api5.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@
"entrez_gene_id": [
839580
],
"type": null,
"value": null,
"topN": 5,
"database": "Ath-u.c4-0",
Expand All @@ -14,36 +13,32 @@
"result_set": [
{
"entrez_gene_id": 839580,
"type": "z",
"results": [
{
"gene": 842367,
"other_id": "At1g60730",
"mutual_rank": 793.88,
"logit_score": 4.5801
"z": 4.5801
},
{
"gene": 838288,
"other_id": "At1g17170",
"mutual_rank": 968.79,
"logit_score": 4.2795
"z": 4.2795
},
{
"gene": 817498,
"other_id": "At2g29490",
"mutual_rank": 1006.44,
"logit_score": 4.2216
"z": 4.2216
},
{
"gene": 829559,
"other_id": "At4g34131",
"mutual_rank": 1014.08,
"logit_score": 4.2101
"z": 4.2101
},
{
"gene": 825091,
"other_id": "At3g59220",
"mutual_rank": 1119.2,
"logit_score": 4.0597
"z": 4.0597
}
],
"other_id": "At1g01010"
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12 changes: 6 additions & 6 deletions tests/resources/test_proxy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,29 +7,29 @@ class TestIntegrations(TestCase):
def setUp(self):
self.app_client = app.test_client()

def test_get_atted_api4(self):
def test_get_atted_api5(self):
"""This tests the data returned by the Atted proxy
:return:
"""
# Valid data
response = self.app_client.get("/proxy/atted_api4/At1g01010/5")
response = self.app_client.get("/proxy/atted_api5/At1g01010/5")
# Note: pytest is running from project root. So path is relative to project root
with open("tests/data/get_atted_api4.json") as json_file:
with open("tests/data/get_atted_api5.json") as json_file:
expected = load(json_file)
self.assertEqual(response.json, expected)

# Invalid gene
response = self.app_client.get("/proxy/atted_api4/At1g0101x/5")
response = self.app_client.get("/proxy/atted_api5/At1g0101x/5")
expected = {"wasSuccessful": False, "error": "Invalid gene id"}
self.assertEqual(response.json, expected)

# If no data, the service should return this response
response = self.app_client.get("/proxy/atted_api4/At1g01011/5")
response = self.app_client.get("/proxy/atted_api5/At1g01011/5")

expected = {"error": "No gene ID specified.", "status_code": 400}
self.assertEqual(response.json, expected)

# Invalid topN count
response = self.app_client.get("proxy/atted_api4/At1g01010/9999999999999999999")
response = self.app_client.get("proxy/atted_api5/At1g01010/9999999999999999999")
expected = {"wasSuccessful": False, "error": "Invalid count"}
self.assertEqual(response.json, expected)
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