test(streaming): some http/DRS streaming tests

tests/conftest.py

@@ -1,9 +1,9 @@
-import asyncio
 import asyncpg
 import pytest
 import pytest_asyncio
 
 from aioresponses import aioresponses
+from bento_lib.drs.resolver import DrsResolver
 from fastapi.testclient import TestClient
 from typing import AsyncGenerator
 
@@ -14,12 +14,26 @@
 os.environ["CORS_ORIGINS"] = "*"
 os.environ["BENTO_AUTHZ_SERVICE_URL"] = "https://authz.local"
 
-from bento_reference_service.config import get_config
+from bento_reference_service.config import Config, get_config
 from bento_reference_service.db import Database, get_db
+from bento_reference_service.drs import get_drs_resolver
 from bento_reference_service.logger import get_logger
 from bento_reference_service.main import app
 
 
+@pytest.fixture()
+def config() -> Config:
+    return get_config()
+
+
+@pytest.fixture()
+def drs_resolver(config: Config) -> DrsResolver:
+    drs = get_drs_resolver(config)
+    drs._cache_ttl = 0
+    drs._drs_record_cache = {}
+    return drs
+
+
 async def get_test_db() -> AsyncGenerator[Database, None]:
     config = get_config()
     db_instance = Database(config, get_logger(config))

tests/shared_data.py

@@ -15,6 +15,9 @@
     "TEST_GENOME_HG38_CHR1_F100K",
     "TEST_GENOME_HG38_CHR1_F100K_OBJ",
     "AUTHORIZATION_HEADER",
+    "TEST_DRS_ID",
+    "TEST_DRS_REPLY_NO_ACCESS",
+    "TEST_DRS_REPLY",
 ]
 
 DATA_DIR = (pathlib.Path(__file__).parent / "data").absolute()
@@ -75,3 +78,37 @@
 TEST_GENOME_HG38_CHR1_F100K_OBJ = Genome(**TEST_GENOME_HG38_CHR1_F100K)
 
 AUTHORIZATION_HEADER = {"Authorization": "Token bearer"}
+
+
+# Test DRS responses
+
+TEST_DRS_ID = "dd11912c-3433-4a0a-8a01-3c0699288bef"
+
+TEST_DRS_REPLY_NO_ACCESS = {
+    "checksums": [
+        {
+            "checksum": "9f86d081884c7d659a2feaa0c55ad015a3bf4f1b2b0b822cd15d6c15b0f00a08",
+            "type": "sha-256",
+        }
+    ],
+    "created_time": "2021-03-17T21:29:15+00:00",
+    "updated_time": "2021-03-17T21:29:15+00:00",
+    "id": TEST_DRS_ID,
+    "mime_type": "text/plain",
+    "self_uri": f"drs://localhost/{TEST_DRS_ID}",
+    "size": 4,
+}
+
+TEST_DRS_REPLY = {
+    **TEST_DRS_REPLY_NO_ACCESS,
+    "access_methods": [
+        {
+            "type": "file",
+            "access_url": {"url": "file:///test.txt"},
+        },
+        {
+            "type": "https",
+            "access_url": {"url": "https://example.org/test.txt"},
+        },
+    ],
+}

tests/test_streaming.py

@@ -2,28 +2,79 @@
 import pytest
 
 from aioresponses import aioresponses
+from bento_lib.drs.resolver import DrsResolver
 from bento_lib.streaming import exceptions as se
 from fastapi import HTTPException, status
 
-from bento_reference_service import config as c, drs as d, streaming as s
+from bento_reference_service import config as c, streaming as s
+
+from .shared_data import TEST_DRS_REPLY_NO_ACCESS, TEST_DRS_REPLY
 
 HTTP_TEST_URI = "https://test.local/file.txt"
 
 logger = logging.getLogger(__name__)
 
 
 @pytest.mark.asyncio()
-async def test_uri_streaming_bad_uri():
-    config = c.get_config()
+async def test_drs_bytes_url_from_uri(aioresponse: aioresponses, config: c.Config, drs_resolver: DrsResolver):
+    aioresponse.get("https://example.org/ga4gh/drs/v1/objects/abc", payload=TEST_DRS_REPLY)
+    assert (
+        await s.drs_bytes_url_from_uri(config, drs_resolver, logger, "drs://example.org/abc")
+        == TEST_DRS_REPLY["access_methods"][1]["access_url"]["url"]
+    )
+
+
+@pytest.mark.asyncio()
+async def test_drs_bytes_url_from_uri_not_found(aioresponse: aioresponses, config: c.Config, drs_resolver: DrsResolver):
+    aioresponse.get(
+        "https://example.org/ga4gh/drs/v1/objects/abc",
+        status=status.HTTP_404_NOT_FOUND,
+        payload={"message": "Not Found"},
+    )
+
+    with pytest.raises(HTTPException) as e:
+        await s.drs_bytes_url_from_uri(config, drs_resolver, logger, "drs://example.org/abc")
+
+    assert e.value.status_code == status.HTTP_500_INTERNAL_SERVER_ERROR
+    assert "Not Found error" in e.value.detail
+
+
+@pytest.mark.asyncio()
+async def test_drs_bytes_url_from_uri_500(aioresponse: aioresponses, config: c.Config, drs_resolver: DrsResolver):
+    aioresponse.get(
+        "https://example.org/ga4gh/drs/v1/objects/abc",
+        status=status.HTTP_500_INTERNAL_SERVER_ERROR,
+        payload={"message": "Internal Server Error"},
+    )
+
+    with pytest.raises(HTTPException) as e:
+        await s.drs_bytes_url_from_uri(config, drs_resolver, logger, "drs://example.org/abc")
+
+    assert e.value.status_code == status.HTTP_500_INTERNAL_SERVER_ERROR
+    assert "while accessing DRS record" in e.value.detail
+
+
+@pytest.mark.asyncio()
+async def test_drs_bytes_url_from_uri_no_access(aioresponse: aioresponses, config: c.Config, drs_resolver: DrsResolver):
+    aioresponse.get("https://example.org/ga4gh/drs/v1/objects/abc", payload=TEST_DRS_REPLY_NO_ACCESS)
+
+    with pytest.raises(HTTPException) as e:
+        await s.drs_bytes_url_from_uri(config, drs_resolver, logger, "drs://example.org/abc")
+
+    assert e.value.status_code == status.HTTP_500_INTERNAL_SERVER_ERROR
+    assert "HTTPS access method" in e.value.detail
+
+
+@pytest.mark.asyncio()
+async def test_uri_streaming_bad_uri(config: c.Config, drs_resolver: DrsResolver):
     with pytest.raises(se.StreamingBadURI):
-        await s.stream_from_uri(config, d.get_drs_resolver(config), logger, "http://[.com", None, False)
+        await s.stream_from_uri(config, drs_resolver, logger, "http://[.com", None, False)
 
 
 @pytest.mark.asyncio()
-async def test_uri_streaming_bad_scheme():
-    config = c.get_config()
+async def test_uri_streaming_bad_scheme(config: c.Config, drs_resolver: DrsResolver):
     with pytest.raises(se.StreamingUnsupportedURIScheme):
-        await s.stream_from_uri(config, d.get_drs_resolver(config), logger, "asdf://example.org", None, False)
+        await s.stream_from_uri(config, drs_resolver, logger, "asdf://example.org", None, False)
 
 
 @pytest.mark.asyncio()
@@ -75,22 +126,21 @@ async def test_http_streaming_404_1(aioresponse: aioresponses):
 
 
 @pytest.mark.asyncio()
-async def test_http_streaming_404_2(aioresponse: aioresponses):
+async def test_http_streaming_404_2(aioresponse: aioresponses, config: c.Config, drs_resolver: DrsResolver):
     aioresponse.get(HTTP_TEST_URI, status=status.HTTP_404_NOT_FOUND, body=b"Not Found")
     with pytest.raises(se.StreamingProxyingError):
-        config = c.get_config()
-        _, _, stream = await s.stream_from_uri(config, d.get_drs_resolver(config), logger, HTTP_TEST_URI, None, False)
+        _, _, stream = await s.stream_from_uri(config, drs_resolver, logger, HTTP_TEST_URI, None, False)
         await anext(stream)
 
 
 @pytest.mark.asyncio()
-async def test_http_streaming_404_3(aioresponse: aioresponses):
+async def test_http_streaming_404_3(aioresponse: aioresponses, config: c.Config, drs_resolver: DrsResolver):
     aioresponse.get(HTTP_TEST_URI, status=status.HTTP_404_NOT_FOUND, body=b"Not Found")
     with pytest.raises(HTTPException):
         config = c.get_config()
         res = await s.generate_uri_streaming_response(
             config,
-            d.get_drs_resolver(config),
+            drs_resolver,
             logger,
             HTTP_TEST_URI,
             None,