From 5602eddf63f6b181e742d45d64c5ae65c80d4fcd Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 27 Jan 2025 14:25:40 +0100 Subject: [PATCH 1/3] improving unit tests --- beacon/connections/mongo/Makefile | 18 +++++++++--------- beacon/tests/__main__.py | 3 +++ 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/beacon/connections/mongo/Makefile b/beacon/connections/mongo/Makefile index 107c5b5..da12bcf 100644 --- a/beacon/connections/mongo/Makefile +++ b/beacon/connections/mongo/Makefile @@ -1,10 +1,10 @@ build: - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/datasets.json --collection datasets - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/individuals.json --collection individuals - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/cohorts.json --collection cohorts - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/analyses.json --collection analyses - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/biosamples.json --collection biosamples - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/genomicVariations.json --collection genomicVariations - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/runs.json --collection runs - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/targets.json --collection targets - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/caseLevelData.json --collection caseLevelData \ No newline at end of file + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/test/datasets.json --collection datasets + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/test/individuals.json --collection individuals + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/test/cohorts.json --collection cohorts + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/test/analyses.json --collection analyses + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/test/biosamples.json --collection biosamples + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/test/genomicVariations.json --collection genomicVariations + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/test/runs.json --collection runs + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/test/targets.json --collection targets + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /data/test/caseLevelData.json --collection caseLevelData \ No newline at end of file diff --git a/beacon/tests/__main__.py b/beacon/tests/__main__.py index 28bb7eb..c1d983b 100644 --- a/beacon/tests/__main__.py +++ b/beacon/tests/__main__.py @@ -1275,6 +1275,9 @@ async def test_check_heterozygosity(): } } ) + responsetext=await resp.text() + responsedict=json.loads(responsetext) + assert responsedict["responseSummary"]["numTotalResults"] == 4 assert resp.status == 200 loop.run_until_complete(test_check_heterozygosity()) loop.run_until_complete(client.close()) From 570cbf0285b7fa3a6e28d47a260936f7484d6e4d Mon Sep 17 00:00:00 2001 From: API version update Date: Mon, 27 Jan 2025 13:26:12 +0000 Subject: [PATCH 2/3] api version automatically generated --- beacon/conf/api_version.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beacon/conf/api_version.yml b/beacon/conf/api_version.yml index d34da88..172db20 100644 --- a/beacon/conf/api_version.yml +++ b/beacon/conf/api_version.yml @@ -1 +1 @@ -api_version: v2.0-495e58f +api_version: v2.0-832394a From d353a685ebac0224098a5e314e038044c79219aa Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 27 Jan 2025 14:28:13 +0100 Subject: [PATCH 3/3] improving range query unit test --- beacon/tests/__main__.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/beacon/tests/__main__.py b/beacon/tests/__main__.py index c1d983b..802f60a 100644 --- a/beacon/tests/__main__.py +++ b/beacon/tests/__main__.py @@ -694,6 +694,9 @@ def test_main_check_g_variants_range_query(self): loop.run_until_complete(client.start_server()) async def test_check_g_variants_endpoint_with_parameters_is_working(): resp = await client.get("/api/g_variants?start=345675&referenceName=2&assemblyId=GRCh38&end=345681") + responsetext=await resp.text() + responsedict=json.loads(responsetext) + assert responsedict["responseSummary"]["numTotalResults"] == 6 assert resp.status == 200 loop.run_until_complete(test_check_g_variants_endpoint_with_parameters_is_working()) loop.run_until_complete(client.close())