Merge branch 'extending-nodeports' of github.com:GitHK/osparc-simcore-forked into extending-nodeports

Author: Andrei Neagu

packages/simcore-sdk/src/simcore_sdk/node_data/data_manager.py

@@ -78,4 +78,4 @@ async def is_file_present_in_storage(file_path: Path) -> bool:
     return await filemanager.entry_exists(
         store_id=0,  # this is for simcore.s3
         s3_object=_create_s3_object(file_path),
-    )
+    )

services/web/server/src/simcore_service_webserver/groups_classifiers.py

@@ -31,10 +31,10 @@
 
 class ClassifierItem(BaseModel):
     classifier: str = Field(
-        ..., description="Unique identifier used to tag studies or services", example=""
+        ..., description="Unique identifier used to tag studies or services"
     )
     display_name: str
-    short_description: Optional[str]  # TODO: truncate
+    short_description: Optional[str]
     url: Optional[HttpUrl] = Field(
         None,
         description="Link to more information",
@@ -44,7 +44,7 @@ class ClassifierItem(BaseModel):
     @validator("short_description", pre=True)
     @classmethod
     def truncate_to_short(cls, v):
-        if len(v) >= MAX_SIZE_SHORT_MSG:
+        if v and len(v) >= MAX_SIZE_SHORT_MSG:
             return v[:MAX_SIZE_SHORT_MSG] + "…"
         return v
 
@@ -70,21 +70,21 @@ class GroupClassifierRepository:
     def __init__(self, app: web.Application):
         self.engine = app[APP_DB_ENGINE_KEY]
 
-    async def get_bundle(self, gid: int) -> Dict[str, Any]:
+    async def _get_bundle(self, gid: int) -> Optional[RowProxy]:
         async with self.engine.acquire() as conn:
-            bundle = await conn.scalar(
+            bundle: Optional[RowProxy] = await conn.scalar(
                 sa.select([group_classifiers.c.bundle]).where(
                     group_classifiers.c.gid == gid
                 )
             )
-            return bundle or {}
+            return bundle
 
     async def get_classifiers_from_bundle(self, gid: int) -> Dict[str, Any]:
-        bundle = await self.get_bundle(gid)
+        bundle = await self._get_bundle(gid)
         if bundle:
             try:
                 # truncate bundle to what is needed and drop the rest
-                bundle = Classifiers(**bundle).dict(exclude_unset=True)
+                return Classifiers(**bundle).dict(exclude_unset=True, exclude_none=True)
             except ValidationError as err:
                 logger.error(
                     "DB corrupt data in 'groups_classifiers' table. "
@@ -93,7 +93,7 @@ async def get_classifiers_from_bundle(self, gid: int) -> Dict[str, Any]:
                     gid,
                     err,
                 )
-        return bundle
+        return {}
 
     async def group_uses_scicrunch(self, gid: int) -> bool:
         async with self.engine.acquire() as conn:

services/web/server/tests/unit/with_dbs/fast/test_groups_classifiers.py

@@ -0,0 +1,57 @@
+# pylint:disable=unused-argument
+# pylint:disable=redefined-outer-name
+# pylint:disable=no-name-in-module
+
+from typing import Dict
+
+import pytest
+import sqlalchemy as sa
+from servicelib.aiopg_utils import DataSourceName, create_pg_engine
+from simcore_service_webserver.constants import APP_DB_ENGINE_KEY
+from simcore_service_webserver.groups_classifiers import GroupClassifierRepository
+from sqlalchemy.sql import text
+
+
+@pytest.fixture
+def inject_tables(postgres_db: sa.engine.Engine):
+
+    stmt = text(
+        """\
+    INSERT INTO "group_classifiers" ("id", "bundle", "created", "modified", "gid", "uses_scicrunch") VALUES
+    (2,	'{"vcs_ref": "asdfasdf", "vcs_url": "https://foo.classifiers.git", "build_date": "2021-01-20T15:19:30Z", "classifiers": {"project::dak": {"url": null, "logo": null, "aliases": [], "related": [], "markdown": "", "released": null, "classifier": "project::dak", "created_by": "Nicolas Chavannes", "github_url": null, "display_name": "DAK", "wikipedia_url": null, "short_description": null}, "organization::zmt": {"url": "https://zmt.swiss/", "logo": null, "aliases": ["Zurich MedTech AG"], "related": [], "markdown": "Zurich MedTech AG (ZMT) offers tools and best practices for targeted life sciences applications to simulate, analyze, and predict complex and dynamic biological processes and interactions. ZMT is a member of Zurich43", "released": null, "classifier": "organization::zmt", "created_by": "crespo", "github_url": null, "display_name": "ZMT", "wikipedia_url": null, "short_description": "ZMT is a member of Zurich43"}}, "collections": {"jupyterlab-math": {"items": ["crespo/osparc-demo"], "markdown": "Curated collection of repositories with examples of notebooks to run in jupyter-python-octave-math service", "created_by": "crespo", "display_name": "jupyterlab-math"}}}',	'2021-03-04 23:17:43.373258',	'2021-03-04 23:17:43.373258',	1,	'0');
+    """
+    )
+    with postgres_db.connect() as conn:
+        conn.execute(stmt)
+
+
+@pytest.fixture
+async def app(loop, postgres_dsn: Dict, inject_tables):
+
+    dsn = DataSourceName(
+        user=postgres_dsn["user"],
+        password=postgres_dsn["password"],
+        database=postgres_dsn["database"],
+        host=postgres_dsn["host"],
+        port=postgres_dsn["port"],
+    )
+
+    async with create_pg_engine(dsn) as engine:
+        fake_app = {APP_DB_ENGINE_KEY: engine}
+        yield fake_app
+
+
+async def test_classfiers_from_bundle(app):
+
+    repo = GroupClassifierRepository(app)
+
+    assert not await repo.group_uses_scicrunch(gid=1)
+
+    bundle = await repo.get_classifiers_from_bundle(gid=1)
+    assert bundle
+
+    # Prunes extras and excludes unset and nones
+    assert bundle["classifiers"]["project::dak"] == {
+        "classifier": "project::dak",
+        "display_name": "DAK",
+    }