♻️ maintenance: fixes scicrunch tests and set as integration tests (ITISFoundation#3018)

* split scicrunch into unit and integration tests

* doc

* adapts tests to pass

Author: pcrespov

packages/dask-task-models-library/src/dask_task_models_library/container_tasks/docker.py

@@ -13,7 +13,7 @@ class Config:
                 {
                     "server_address": "docker.io",
                     "username": "admin",
-                    "password": "sfjlskdjoiw",
+                    "password": "123456",
                 }
             ]
         }

packages/pytest-simcore/src/pytest_simcore/helpers/utils_scrunch_citations.py

@@ -28,11 +28,19 @@ def _split(citation: str) -> Tuple[str, str]:
 # https://www.addgene.org/44362/
 PLAMID_CITATIONS = split_citations(["(RRID:Addgene_44362)"])
 
-#  MMRRC, catalog https://www.mmrrc.org/catalog/cellLineSDS.php?mmrrc_id=26409
-ORGANISM_CITATIONS = split_citations(["(MMRRC Cat# 026409-UCD, RRID:MMRRC_026409-UCD)"])
+#  MMRRC,
+# catalog https://www.mmrrc.org/catalog/cellLineSDS.php?mmrrc_id=26409
+#         https://scicrunch.org/resolver/RRID:MMRRC_026409-UCD.json
+#
+# As of May 2022, changed proper_citation change from
+#  '(MMRRC Cat# 026409-UCD, RRID:MMRRC_026409-UCD)' to
+#  'RRID:MMRRC_026409-UCD'
+#
+ORGANISM_CITATIONS = split_citations(["(RRID:MMRRC_026409-UCD)"])
 
 # https://web.expasy.org/cellosaurus/CVCL_0033
-CELL_LINE_CITATIONS = split_citations(["(ATCC Cat# HTB-30, RRID:CVCL_0033)"])
+# As of May 2022, name changed from 'ATCC Cat# HTB-30' to 'AddexBio Cat# C0006007/65'
+CELL_LINE_CITATIONS = split_citations(["(AddexBio Cat# C0006007/65, RRID:CVCL_0033)"])
 
 #
 #  WARNING: Since Sep.2021, the order of the resolved hits list returned by

services/web/server/tests/integration/02/scicrunch/conftest.py

@@ -0,0 +1,12 @@
+# pylint: disable=redefined-outer-name
+# pylint: disable=unused-argument
+# pylint: disable=unused-variable
+
+
+import pytest
+from simcore_service_webserver.scicrunch.settings import SciCrunchSettings
+
+
+@pytest.fixture
+async def settings() -> SciCrunchSettings:
+    return SciCrunchSettings(SCICRUNCH_API_KEY="fake-secret-key")

services/web/server/tests/unit/isolated/scicrunch/test_scicrunch__resolver.py renamed to services/web/server/tests/integration/02/scicrunch/test_scicrunch__resolver.py

@@ -10,6 +10,7 @@
 # FIXME: PC check the CELL_LINE_CITATIONS test please
 from pytest_simcore.helpers.utils_scrunch_citations import (  # CELL_LINE_CITATIONS,
     ANTIBODY_CITATIONS,
+    CELL_LINE_CITATIONS,
     ORGANISM_CITATIONS,
     PLAMID_CITATIONS,
     TOOL_CITATIONS,
@@ -20,18 +21,27 @@
 
 @pytest.mark.parametrize(
     "name,rrid",
-    TOOL_CITATIONS + ANTIBODY_CITATIONS + PLAMID_CITATIONS + ORGANISM_CITATIONS,
+    TOOL_CITATIONS
+    + ANTIBODY_CITATIONS
+    + PLAMID_CITATIONS
+    + ORGANISM_CITATIONS
+    + CELL_LINE_CITATIONS,
 )
 async def test_scicrunch_resolves_all_valid_rrids(
     name: str, rrid: str, settings: SciCrunchSettings
 ):
+    # NOTE: this test run against https://scicrunch.org/resolver/{SCR_018997}.json
+    # which is an open API (no auth required). Any change in the responses of that
+    # service might cause a failure on this test
+    # This tests checks some of the structure "deduced" from the responses so far.
+
     async with ClientSession(timeout=ClientTimeout(total=30)) as client:
-        resolved = await resolve_rrid(rrid, client, settings)
+        resolved = await resolve_rrid(identifier=rrid, client=client, settings=settings)
 
         assert resolved
         assert isinstance(resolved, ResolvedItem)
 
-        if resolved.is_unique:
+        if resolved.is_unique and name:
             assert name in resolved.proper_citation
 
         assert rrid in resolved.proper_citation
@@ -42,7 +52,7 @@ async def test_scicrunch_resolves_all_valid_rrids(
             # only rrid with a prefix
             assert resolved.proper_citation == f"RRID:{rrid}"
         else:
-            # includes name and rrid
+            # proper_citation includes both 'name' and 'rrid' but in different formats!
 
             #
             # NOTE: why CELL_LINE_CITATIONS are removed from test parametrization ?

services/web/server/tests/unit/isolated/scicrunch/test_scicrunch__rest.py renamed to services/web/server/tests/integration/02/scicrunch/test_scicrunch__rest.py

@@ -0,0 +1,127 @@
+# pylint:disable=unused-variable
+# pylint:disable=unused-argument
+# pylint:disable=redefined-outer-name
+
+"""
+    Use this test to emulate situations with scicrunch service API
+
+"""
+import json
+import os
+from pathlib import Path
+
+import pytest
+from aioresponses.core import aioresponses
+from servicelib.aiohttp.application import create_safe_application
+from servicelib.aiohttp.client_session import get_client_session
+from simcore_service_webserver.application_settings import setup_settings
+from simcore_service_webserver.scicrunch.plugin import setup_scicrunch
+from simcore_service_webserver.scicrunch.service_client import (
+    ResearchResource,
+    SciCrunch,
+)
+
+
+@pytest.fixture
+async def mock_scicrunch_service_api(fake_data_dir: Path, mock_env_devel_environment):
+    assert mock_env_devel_environment["SCICRUNCH_API_KEY"] == os.environ.get(
+        "SCICRUNCH_API_KEY"
+    )
+
+    API_KEY = os.environ.get("SCICRUNCH_API_KEY")
+    assert os.environ.get("SCICRUNCH_API_BASE_URL") == "https://scicrunch.org/api/1"
+
+    with aioresponses() as mock:
+        # curl -X GET "https://scicrunch.org/api/1/resource/fields/autocomplete?field=Resource%20Name&value=octave" -H "accept: application/json
+        mock.get(
+            f"https://scicrunch.org/api/1/resource/fields/autocomplete?field=Resource%20Name&value=octave&key={API_KEY}",
+            status=200,
+            payload={
+                "data": [
+                    {
+                        "rid": "SCR_000860",
+                        "original_id": "nlx_155680",
+                        "name": "cbiNifti: Matlab/Octave Nifti library",
+                    },
+                    {
+                        "rid": "SCR_009637",
+                        "original_id": "nlx_155924",
+                        "name": "Pipeline System for Octave and Matlab",
+                    },
+                    {
+                        "rid": "SCR_014398",
+                        "original_id": "SCR_014398",
+                        "name": "GNU Octave",
+                    },
+                ],
+                "success": "true",
+            },
+        )
+        # curl -X GET "https://scicrunch.org/api/1/resource/fields/view/SCR_018997" -H "accept: application/json"
+        mock.get(
+            f"https://scicrunch.org/api/1/resource/fields/view/SCR_018997?key={API_KEY}",
+            status=200,
+            payload=json.loads(
+                (fake_data_dir / "get_osparc_resource_payload.json").read_text()
+            ),
+        )
+        # curl -X GET "https://scicrunch.org/api/1/resource/versions/all/SCR_018997" -H "accept: application/json"
+        mock.get(
+            f"https://scicrunch.org/api/1/resource/versions/all/SCR_018997?key={API_KEY}",
+            status=200,
+            payload=json.loads(
+                '{"data":[{"version":2,"status":"Curated","time":1598984801,"uid":34739,"username":"Edyta Vieth","cid":null},{"version":1,"status":"Pending","time":1598898249,"uid":43,"username":"Anita Bandrowski","cid":30}],"success":true}'
+            ),
+        )
+
+        yield mock
+
+
+@pytest.fixture
+async def mock_scicrunch_service_resolver(
+    fake_data_dir: Path, mock_env_devel_environment, aioresponses_mocker
+):
+    aioresponses_mocker.get(
+        "https://scicrunch.org/resolver/SCR_018997.json",
+        status=200,
+        payload=json.loads(
+            (fake_data_dir / "get_scicrunch_resolver_response.json").read_text()
+        ),
+    )
+
+
+@pytest.fixture
+async def fake_app(mock_env_devel_environment):
+    # By using .env-devel we ensure all needed variables are at
+    # least defined there
+    print("app's environment variables", format(mock_env_devel_environment))
+
+    app = create_safe_application()
+
+    setup_settings(app)
+    setup_scicrunch(app)
+
+    yield app
+
+    client = get_client_session(app)
+    await client.close()
+
+
+## TESTS -------------------------------------------------------
+
+
+def test_setup_scicrunch_submodule(fake_app):
+    # scicruch should be init
+    scicrunch = SciCrunch.get_instance(fake_app)
+    assert scicrunch
+    assert scicrunch.client == get_client_session(fake_app)
+
+
+async def test_get_research_resource(fake_app, mock_scicrunch_service_resolver):
+    # mock_scicrunch_service_api):
+    scicrunch = SciCrunch.get_instance(fake_app)
+    resource: ResearchResource = await scicrunch.get_resource_fields(rrid="SCR_018997")
+
+    assert resource.rrid == "RRID:SCR_018997"
+    assert resource.name == "o²S²PARC"
+    assert "Simulation platform" in resource.description

services/web/server/tests/integration/02/scicrunch/test_scicrunch_service_client.py

@@ -64,7 +64,3 @@ def test_research_resource_model(name, rrid_tag):
     )
 
     assert re.match(STRICT_RRID_PATTERN, resource.rrid)
-
-
-def test_models_conversion():
-    assert True