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Merged
costero-e merged 4 commits into from
Mar 20, 2026
Merged

Upate hotfixes branch #171

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c45d5b1
unit test for alternateBases bug
costero-e Mar 10, 2026
30e218e
Merge pull request #163 from EGA-archive/debug
costero-e Mar 10, 2026
425f929
updating version
costero-e Mar 12, 2026
b530d3b
Merge pull request #167 from EGA-archive/debug
costero-e Mar 12, 2026
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2 changes: 1 addition & 1 deletion beacon/auth/tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
from beacon.logs.logs import LOG

# for keycloak, create aud in mappers, with custom, aud and beacon for audience
mock_access_token = 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJreS1tUXNxZ0ZYeHdSUVRfRUhuQlJJUGpmbVhfRXZuUTVEbzZWUTJCazdZIn0.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.Sk9XwP3aPC8WLV_a_-ekJbsNmdN9IIvIPyKaHdb_VwbHO1FtqDmjpSZ80S8jnuZEPkLgiBGMUupJdVAKHlMw77SEWt1ka8KInHJbIY3bMBqxHu13_qzsQnw1_Y-nQbAp5C0Q-Hwr1tFnzjoQho0jVhIvi0b3GdTczzWbVZFgIHX_ESoD8bgKfQQGZChFvPkPycKYFqwmC2-YuMPTgK_iKSWtUqe4WwoL7P1NNgo0yho0HxVymzm2vKDf2bww0-Qa_40IsNJUcFJ5IYBtZ3YUNUE2TeX7S97A7HLN0S-iIg6KY9niOY0mElj_-bcbvNDI3r1Xs0_4VfJ9it72YuJd2A'
mock_access_token = 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJreS1tUXNxZ0ZYeHdSUVRfRUhuQlJJUGpmbVhfRXZuUTVEbzZWUTJCazdZIn0.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.kFp3W53979Ib3Z17miTlWCqP-hoDJYo3aYLGfZOgRJI0HM08ngPi87fItWPBurx9Fb1fiHTZqeTMZ-XBuIK1bIRszq9E9Dg9Hem2nxgr_b8OMlmns1S6aE3p8kxWm3-Csmpmelt01HJlNxlYysTMK5mH6QOU2sANL1iCa0z9n-FX8H9IPQ9dKFdRGCvGU0vwUw4LwHW2SVk5DDGYBIy-z5hSjkdqLZ72OTRQWb_ZZEJlsT7gv-xPkjEW3AJW2vgRyZILqiUtAkrfapIPA42Iva2PsFzp1PnJeis_UksBOh1yH_BR6C9ycxfi__251JoaPrIqb4G3YidarYOcMCQSzA'
mock_access_token_false = 'public'
#dummy test anonymous
#dummy test login
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2 changes: 1 addition & 1 deletion beacon/conf/api_version.yml
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@@ -1 +1 @@
api_version: v2.1.0
api_version: v2.1.1
4 changes: 4 additions & 0 deletions ...a4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/alphanumeric.py
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Expand Up @@ -144,6 +144,10 @@ def parse_request_parameters(self, query, filter):
dict_expr['$expr']=dict_gt
andquery["$and"].append(dict_expr)
query=andquery
else:
formatted_value = format_value(self, filter.value)
formatted_operator = format_operator(self, filter.operator)
query[filter.id] = { formatted_operator: formatted_value }

elif filter.id == 'assemblyId':
pass
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13 changes: 13 additions & 0 deletions beacon/tests/__main__.py
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Expand Up @@ -1310,6 +1310,19 @@ async def test_check_g_variants_endpoint_with_parameters_is_working():
assert responsedict["responseSummary"]["numTotalResults"] == 1
loop.run_until_complete(test_check_g_variants_endpoint_with_parameters_is_working())
loop.run_until_complete(client.close())
def test_main_check_g_variants_sequence_query_gives_0_results(self):
with loop_context() as loop:
app = create_app()
client = TestClient(TestServer(app), loop=loop)
loop.run_until_complete(client.start_server())
async def test_check_g_variants_endpoint_with_parameters_is_working():
resp = await client.get(conf_override.config.uri_subpath+"/"+genomicVariant["genomicVariant"]["endpoint_name"]+"?start=43045703&referenceName=17&assemblyId=GRCh37&referenceBases=G&alternateBases=C&testMode=True")
assert resp.status == 200
responsetext=await resp.text()
responsedict=json.loads(responsetext)
assert responsedict["responseSummary"]["exists"] == False
loop.run_until_complete(test_check_g_variants_endpoint_with_parameters_is_working())
loop.run_until_complete(client.close())
def test_main_check_g_variants_range_query(self):
with loop_context() as loop:
app = create_app()
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