From 45c6572dc2cd782be4253d6d5579dc303274617e Mon Sep 17 00:00:00 2001 From: costero-e Date: Sun, 3 Nov 2024 17:24:58 +0000 Subject: [PATCH] updating unit tests --- beacon/connections/mongo/Makefile | 8 +- beacon/connections/mongo/analyses.py | 3 +- beacon/connections/mongo/biosamples.py | 3 +- .../connections/mongo/data/caseLevelData.json | 1 + .../mongo/data/genomicVariations.json | 751406 +-------------- beacon/connections/mongo/data/targets.json | 1 + beacon/connections/mongo/reindex.py | 8 + beacon/connections/mongo/runs.py | 3 +- beacon/tests/__main__.py | 10 +- 9 files changed, 29 insertions(+), 751414 deletions(-) create mode 100644 beacon/connections/mongo/data/caseLevelData.json create mode 100644 beacon/connections/mongo/data/targets.json diff --git a/beacon/connections/mongo/Makefile b/beacon/connections/mongo/Makefile index 5e80856..53d796a 100644 --- a/beacon/connections/mongo/Makefile +++ b/beacon/connections/mongo/Makefile @@ -5,9 +5,15 @@ build: docker cp data/datasets.json mongoprod:tmp/datasets.json docker cp data/genomicVariations.json mongoprod:tmp/genomicVariations.json docker cp data/individuals.json mongoprod:tmp/individuals.json + docker cp data/runs.json mongoprod:tmp/runs.json + docker cp data/targets.json mongoprod:tmp/targets.json + docker cp data/caseLevelData.json mongoprod:tmp/caseLevelData.json docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples - docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations \ No newline at end of file + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/targets.json --collection targets + docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/caseLevelData.json --collection caseLevelData \ No newline at end of file diff --git a/beacon/connections/mongo/analyses.py b/beacon/connections/mongo/analyses.py index 571661b..2389640 100644 --- a/beacon/connections/mongo/analyses.py +++ b/beacon/connections/mongo/analyses.py @@ -95,4 +95,5 @@ def get_variants_of_analysis(self, entry_id: Optional[str], qparams: RequestPara if limit > 100 or limit == 0: limit = 100# pragma: no cover idq="caseLevelData.biosampleId" - count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq) \ No newline at end of file + count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq) + return schema, count, dataset_count, docs, dataset \ No newline at end of file diff --git a/beacon/connections/mongo/biosamples.py b/beacon/connections/mongo/biosamples.py index e3f5c88..d6530a7 100644 --- a/beacon/connections/mongo/biosamples.py +++ b/beacon/connections/mongo/biosamples.py @@ -122,4 +122,5 @@ def get_runs_of_biosample(self, entry_id: Optional[str], qparams: RequestParams, if limit > 100 or limit == 0: limit = 100# pragma: no cover idq="biosampleId" - count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq) \ No newline at end of file + count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq) + return schema, count, dataset_count, docs, dataset \ No newline at end of file diff --git a/beacon/connections/mongo/data/caseLevelData.json b/beacon/connections/mongo/data/caseLevelData.json new file mode 100644 index 0000000..1ac4197 --- /dev/null +++ b/beacon/connections/mongo/data/caseLevelData.json @@ -0,0 +1 @@ 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diff --git a/beacon/connections/mongo/reindex.py b/beacon/connections/mongo/reindex.py index c63cf9a..4628952 100644 --- a/beacon/connections/mongo/reindex.py +++ b/beacon/connections/mongo/reindex.py @@ -33,6 +33,14 @@ client.beacon.validate_collection("synonyms") except Exception: db=client.beacon.create_collection(name="synonyms") +try: + client.beacon.validate_collection("targets") +except Exception: + db=client.beacon.create_collection(name="targets") +try: + client.beacon.validate_collection("caseLevelData") +except Exception: + db=client.beacon.create_collection(name="caseLevelData") try: client.beacon.drop_collection("counts") except Exception: diff --git a/beacon/connections/mongo/runs.py b/beacon/connections/mongo/runs.py index ba9fa9d..14151b9 100644 --- a/beacon/connections/mongo/runs.py +++ b/beacon/connections/mongo/runs.py @@ -107,4 +107,5 @@ def get_analyses_of_run(self, entry_id: Optional[str], qparams: RequestParams, d if limit > 100 or limit == 0: limit = 100# pragma: no cover idq="biosampleId" - count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq) \ No newline at end of file + count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq) + return schema, count, dataset_count, docs, dataset \ No newline at end of file diff --git a/beacon/tests/__main__.py b/beacon/tests/__main__.py index 9936d4b..e2047e3 100644 --- a/beacon/tests/__main__.py +++ b/beacon/tests/__main__.py @@ -601,7 +601,7 @@ def test_main_check_g_variants_with_id_endpoint_is_working(self): client = TestClient(TestServer(app), loop=loop) loop.run_until_complete(client.start_server()) async def test_check_g_variants_with_id_endpoint_is_working(): - resp = await client.get("/api/g_variants/da5a95e4-bc26-11ee-b6b0-0242ac170002:A:G") + resp = await client.get("/api/g_variants/24070fa2-9a01-11ef-907f-0242ac160002:A:G") assert resp.status == 200 loop.run_until_complete(test_check_g_variants_with_id_endpoint_is_working()) loop.run_until_complete(client.close()) @@ -611,7 +611,7 @@ def test_main_check_g_variants_runs_endpoint_is_working(self): client = TestClient(TestServer(app), loop=loop) loop.run_until_complete(client.start_server()) async def test_check_g_variants_runs_endpoint_is_working(): - resp = await client.get("/api/g_variants/da5a95e4-bc26-11ee-b6b0-0242ac170002:A:G/runs") + resp = await client.get("/api/g_variants/24070fa2-9a01-11ef-907f-0242ac160002:A:G/runs") assert resp.status == 200 loop.run_until_complete(test_check_g_variants_runs_endpoint_is_working()) loop.run_until_complete(client.close()) @@ -621,7 +621,7 @@ def test_main_check_g_variants_biosamples_endpoint_is_working(self): client = TestClient(TestServer(app), loop=loop) loop.run_until_complete(client.start_server()) async def test_check_g_variants_biosamples_endpoint_is_working(): - resp = await client.get("/api/g_variants/da5a95e4-bc26-11ee-b6b0-0242ac170002:A:G/biosamples") + resp = await client.get("/api/g_variants/24070fa2-9a01-11ef-907f-0242ac160002:A:G/biosamples") assert resp.status == 200 loop.run_until_complete(test_check_g_variants_biosamples_endpoint_is_working()) loop.run_until_complete(client.close()) @@ -631,7 +631,7 @@ def test_main_check_g_variants_analyses_endpoint_is_working(self): client = TestClient(TestServer(app), loop=loop) loop.run_until_complete(client.start_server()) async def test_check_g_variants_analyses_endpoint_is_working(): - resp = await client.get("/api/g_variants/da5a95e4-bc26-11ee-b6b0-0242ac170002:A:G/analyses") + resp = await client.get("/api/g_variants/24070fa2-9a01-11ef-907f-0242ac160002:A:G/analyses") assert resp.status == 200 loop.run_until_complete(test_check_g_variants_analyses_endpoint_is_working()) loop.run_until_complete(client.close()) @@ -641,7 +641,7 @@ def test_main_check_g_variants_individuals_endpoint_is_working(self): client = TestClient(TestServer(app), loop=loop) loop.run_until_complete(client.start_server()) async def test_check_g_variants_inividuals_endpoint_is_working(): - resp = await client.get("/api/g_variants/da5a95e4-bc26-11ee-b6b0-0242ac170002:A:G/individuals") + resp = await client.get("/api/g_variants/24070fa2-9a01-11ef-907f-0242ac160002:A:G/individuals") assert resp.status == 200 loop.run_until_complete(test_check_g_variants_inividuals_endpoint_is_working()) loop.run_until_complete(client.close())