Update Permitted Licenses

alembic/versions/68a0ec57694e_add_active_column_to_licenses.py

@@ -0,0 +1,29 @@
+"""Add active column to licenses
+
+Revision ID: 68a0ec57694e
+Revises: 2b6f40ea2fb6
+Create Date: 2024-10-22 15:36:41.868909
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "68a0ec57694e"
+down_revision = "2b6f40ea2fb6"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("licenses", sa.Column("active", sa.Boolean(), nullable=False, server_default=sa.true()))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("licenses", "active")
+    # ### end Alembic commands ###

src/mavedb/models/license.py

@@ -1,6 +1,6 @@
 from datetime import date
 
-from sqlalchemy import Column, Date, Integer, String
+from sqlalchemy import Boolean, Column, Date, Integer, String
 
 from mavedb.db.base import Base
 
@@ -16,3 +16,4 @@ class License(Base):
     version = Column(String, nullable=True, unique=False)
     creation_date = Column(Date, nullable=False, default=date.today)
     modification_date = Column(Date, nullable=False, default=date.today, onupdate=date.today)
+    active = Column(Boolean, nullable=False)

src/mavedb/routers/licenses.py

@@ -23,6 +23,19 @@ def list_licenses(
     return items
 
 
+@router.get("/active", status_code=200, response_model=List[license.ShortLicense], responses={404: {}})
+def list_active_licenses(
+    *,
+    db: Session = Depends(deps.get_db),
+) -> Any:
+    """
+    List active licenses.
+    """
+
+    items = db.query(License).where(License.active.is_(True)).order_by(License.short_name).all()
+    return items
+
+
 @router.get("/{item_id}", status_code=200, response_model=license.License, responses={404: {}})
 def fetch_license(
     *,

src/mavedb/routers/score_sets.py

@@ -348,6 +348,11 @@ async def create_score_set(
     if not license_:
         logger.info(msg="Failed to create score set; The requested license does not exist.", extra=logging_context())
         raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="Unknown license")
+    elif not license_.active:
+        logger.info(
+            msg="Failed to create score set; The requested license is no longer active.", extra=logging_context()
+        )
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="Invalid license")
 
     save_to_logging_context({"requested_superseded_score_set": item_create.superseded_score_set_urn})
     if item_create.superseded_score_set_urn is not None:
@@ -698,6 +703,14 @@ async def update_score_set(
             )
             raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="Unknown license")
 
+            # Allow in-active licenses to be retained on update if they already exist on the item.
+        elif not license_.active and item.licence_id != item_update.license_id:
+            logger.info(
+                msg="Failed to update score set license; The requested license is no longer active.",
+                extra=logging_context(),
+            )
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="Invalid license")
+
         item.license = license_
 
     item.doi_identifiers = [

src/mavedb/view_models/license.py

@@ -10,6 +10,7 @@ class LicenseBase(BaseModel):
 
     long_name: str
     short_name: str
+    active: bool
     link: Optional[str]
     version: Optional[str]
 

tests/helpers/constants.py

@@ -14,6 +14,7 @@
 VALID_GENE = "BRCA1"
 
 SAVED_PUBMED_PUBLICATION = {
+    "recordType": "PublicationIdentifier",
     "identifier": "20711194",
     "dbName": "PubMed",
     "title": "None",
@@ -28,6 +29,7 @@
 }
 
 SAVED_DOI_IDENTIFIER = {
+    "recordType": "DoiIdentifier",
     "identifier": TEST_CROSSREF_IDENTIFIER,
     "url": f"https://doi.org/{TEST_CROSSREF_IDENTIFIER}",
     "id": 1,
@@ -51,6 +53,7 @@
 }
 
 SAVED_CONTRIBUTOR = {
+    "recordType": "Contributor",
     "orcidId": TEST_USER["username"],
     "givenName": TEST_USER["first_name"],
     "familyName": TEST_USER["last_name"],
@@ -80,6 +83,7 @@
 }
 
 SAVED_EXTRA_CONTRIBUTOR = {
+    "recordType": "Contributor",
     "orcidId": EXTRA_USER["username"],
     "givenName": EXTRA_USER["first_name"],
     "familyName": EXTRA_USER["last_name"],
@@ -347,14 +351,17 @@
     "text": "Don't be evil.",
     "link": "localhost",
     "version": "1.0",
+    "active": True,
 }
 
 SAVED_SHORT_TEST_LICENSE = {
+    "recordType": "ShortLicense",
     "id": TEST_LICENSE["id"],
     "shortName": TEST_LICENSE["short_name"],
     "longName": TEST_LICENSE["long_name"],
     "link": TEST_LICENSE["link"],
     "version": TEST_LICENSE["version"],
+    "active": TEST_LICENSE["active"],
 }
 
 EXTRA_LICENSE = {
@@ -364,14 +371,37 @@
     "text": "Don't be tooooo evil.",
     "link": "localhost",
     "version": "1.0",
+    "active": True,
 }
 
 SAVED_SHORT_EXTRA_LICENSE = {
+    "recordType": "ShortLicense",
     "id": EXTRA_LICENSE["id"],
     "shortName": EXTRA_LICENSE["short_name"],
     "longName": EXTRA_LICENSE["long_name"],
     "link": EXTRA_LICENSE["link"],
     "version": EXTRA_LICENSE["version"],
+    "active": EXTRA_LICENSE["active"],
+}
+
+TEST_INACTIVE_LICENSE = {
+    "id": 3,
+    "short_name": "Long",
+    "long_name": "Short",
+    "text": "Be evil.",
+    "link": "localhost",
+    "version": "1.0",
+    "active": False,
+}
+
+SAVED_SHORT_INACTIVE_LICENSE = {
+    "recordType": "ShortLicense",
+    "id": TEST_INACTIVE_LICENSE["id"],
+    "shortName": TEST_INACTIVE_LICENSE["short_name"],
+    "longName": TEST_INACTIVE_LICENSE["long_name"],
+    "link": TEST_INACTIVE_LICENSE["link"],
+    "version": TEST_INACTIVE_LICENSE["version"],
+    "active": TEST_INACTIVE_LICENSE["active"],
 }
 
 TEST_SEQ_SCORESET = {

tests/helpers/util.py

@@ -12,6 +12,7 @@
 from mavedb.models.contributor import Contributor
 from mavedb.models.enums.processing_state import ProcessingState
 from mavedb.models.score_set import ScoreSet as ScoreSetDbModel
+from mavedb.models.license import License
 from mavedb.models.user import User
 from mavedb.view_models.experiment import Experiment, ExperimentCreate
 from mavedb.view_models.score_set import ScoreSet, ScoreSetCreate
@@ -52,6 +53,17 @@ def change_ownership(db, urn, model):
     db.commit()
 
 
+def change_to_inactive_license(db, urn):
+    """Change the license of the score set with given urn to an inactive license."""
+    item = db.query(ScoreSetDbModel).filter(ScoreSetDbModel.urn == urn).one_or_none()
+    assert item is not None
+    license = db.query(License).filter(License.active.is_(False)).first()
+    assert license is not None
+    item.license_id = license.id
+    db.add(item)
+    db.commit()
+
+
 def create_experiment(client, update=None):
     experiment_payload = deepcopy(TEST_MINIMAL_EXPERIMENT)
     if update is not None:

tests/lib/conftest.py

@@ -5,7 +5,14 @@
 from mavedb.models.role import Role
 from mavedb.models.taxonomy import Taxonomy
 from mavedb.models.user import User
-from tests.helpers.constants import ADMIN_USER, EXTRA_USER, TEST_LICENSE, TEST_TAXONOMY, TEST_USER
+from tests.helpers.constants import (
+    ADMIN_USER,
+    EXTRA_USER,
+    TEST_LICENSE,
+    TEST_INACTIVE_LICENSE,
+    TEST_TAXONOMY,
+    TEST_USER,
+)
 
 
 @pytest.fixture
@@ -20,4 +27,5 @@ def setup_lib_db(session):
     db.add(User(**ADMIN_USER, role_objs=[Role(name=UserRole.admin)]))
     db.add(Taxonomy(**TEST_TAXONOMY))
     db.add(License(**TEST_LICENSE))
+    db.add(License(**TEST_INACTIVE_LICENSE))
     db.commit()

tests/routers/conftest.py

@@ -19,6 +19,7 @@
     TEST_CDOT_TRANSCRIPT,
     TEST_DB_KEYWORDS,
     TEST_LICENSE,
+    TEST_INACTIVE_LICENSE,
     EXTRA_LICENSE,
     TEST_TAXONOMY,
     TEST_USER,
@@ -44,6 +45,7 @@ def setup_router_db(session):
     db.add(User(**ADMIN_USER, role_objs=[Role(name=UserRole.admin)]))
     db.add(Taxonomy(**TEST_TAXONOMY))
     db.add(License(**TEST_LICENSE))
+    db.add(License(**TEST_INACTIVE_LICENSE))
     db.add(License(**EXTRA_LICENSE))
     db.add(Contributor(**EXTRA_CONTRIBUTOR))
     db.bulk_save_objects([ControlledKeyword(**keyword_obj) for keyword_obj in TEST_DB_KEYWORDS])

tests/routers/test_licenses.py

@@ -0,0 +1,47 @@
+import pytest
+
+from tests.helpers.constants import TEST_LICENSE
+from tests.helpers.dependency_overrider import DependencyOverrider
+
+
+@pytest.mark.parametrize("user_overrides", [None, "anonymous_app_overrides", "admin_app_overrides"])
+def test_can_list_licenses_as_any_user_class(setup_router_db, client, user_overrides, request):
+    if user_overrides is not None:
+        dep_overrides = request.getfixturevalue(user_overrides)
+        with DependencyOverrider(dep_overrides):
+            response = client.get("/api/v1/licenses/")
+    else:
+        response = client.get("/api/v1/licenses/")
+
+    assert response.status_code == 200
+    response_value = response.json()
+    assert len(response_value) == 3
+
+
+@pytest.mark.parametrize("user_overrides", [None, "anonymous_app_overrides", "admin_app_overrides"])
+def test_can_list_active_licenses_as_any_user_class(setup_router_db, client, user_overrides, request):
+    if user_overrides is not None:
+        dep_overrides = request.getfixturevalue(user_overrides)
+        with DependencyOverrider(dep_overrides):
+            response = client.get("/api/v1/licenses/active")
+    else:
+        response = client.get("/api/v1/licenses/active")
+
+    assert response.status_code == 200
+    response_value = response.json()
+    assert len(response_value) == 2
+    license_state = [_license["active"] for _license in response_value]
+    assert all(license_state)
+
+
+def test_can_fetch_arbitrary_license(setup_router_db, client):
+    response = client.get("/api/v1/licenses/1")
+
+    assert response.status_code == 200
+    response_value = response.json()
+    response_value["text"] == TEST_LICENSE["text"]
+
+
+def test_cannot_fetch_nonexistent_license(setup_router_db, client):
+    response = client.get("/api/v1/licenses/100")
+    assert response.status_code == 404

tests/routers/test_score_set.py

@@ -29,6 +29,7 @@
     TEST_SAVED_SCORESET_RANGE,
     TEST_MINIMAL_ACC_SCORESET_RESPONSE,
     TEST_USER,
+    TEST_INACTIVE_LICENSE,
     SAVED_DOI_IDENTIFIER,
     SAVED_EXTRA_CONTRIBUTOR,
     SAVED_PUBMED_PUBLICATION,
@@ -38,6 +39,7 @@
 from tests.helpers.util import (
     add_contributor,
     change_ownership,
+    change_to_inactive_license,
     create_experiment,
     create_seq_score_set,
     create_seq_score_set_with_variants,
@@ -1525,3 +1527,33 @@ def test_contributor_can_add_score_set_to_others_public_experiment(
     score_set_post_payload["experimentUrn"] = published_score_set["experiment"]["urn"]
     response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
     assert response.status_code == 200
+
+
+def test_cannot_create_score_set_with_inactive_license(session, client, setup_router_db):
+    experiment = create_experiment(client)
+    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
+    score_set_post_payload["experimentUrn"] = experiment["urn"]
+    score_set_post_payload["licenseId"] = TEST_INACTIVE_LICENSE["id"]
+    response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
+    assert response.status_code == 400
+
+
+def test_cannot_modify_score_set_to_inactive_license(session, client, setup_router_db):
+    experiment = create_experiment(client)
+    score_set = create_seq_score_set(client, experiment["urn"])
+    score_set_post_payload = score_set.copy()
+    score_set_post_payload.update({"licenseId": TEST_INACTIVE_LICENSE["id"], "urn": score_set["urn"]})
+    response = client.put(f"/api/v1/score-sets/{score_set['urn']}", json=score_set_post_payload)
+    assert response.status_code == 400
+
+
+def test_can_modify_metadata_for_score_set_with_inactive_license(session, client, setup_router_db):
+    experiment = create_experiment(client)
+    score_set = create_seq_score_set(client, experiment["urn"])
+    change_to_inactive_license(session, score_set["urn"])
+    score_set_post_payload = score_set.copy()
+    score_set_post_payload.update({"title": "Update title", "urn": score_set["urn"]})
+    response = client.put(f"/api/v1/score-sets/{score_set['urn']}", json=score_set_post_payload)
+    assert response.status_code == 200
+    response_data = response.json()
+    assert ("title", response_data["title"]) == ("title", "Update title")

tests/worker/conftest.py

@@ -6,7 +6,7 @@
 from mavedb.models.license import License
 from mavedb.models.taxonomy import Taxonomy
 from mavedb.models.user import User
-from tests.helpers.constants import EXTRA_USER, TEST_LICENSE, TEST_TAXONOMY, TEST_USER
+from tests.helpers.constants import EXTRA_USER, TEST_LICENSE, TEST_INACTIVE_LICENSE, TEST_TAXONOMY, TEST_USER
 from tests.helpers.util import create_experiment, create_seq_score_set
 
 
@@ -17,6 +17,7 @@ def setup_worker_db(session):
     db.add(User(**EXTRA_USER))
     db.add(Taxonomy(**TEST_TAXONOMY))
     db.add(License(**TEST_LICENSE))
+    db.add(License(**TEST_INACTIVE_LICENSE))
     db.commit()