feat: Add external links property to experiments

alembic/versions/00dab0f5f498_add_external_links_property_to_.py

@@ -0,0 +1,33 @@
+"""add external links property to experiments
+
+Revision ID: 00dab0f5f498
+Revises: b22b450d409c
+Create Date: 2025-12-16 12:06:15.265947
+
+"""
+
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "00dab0f5f498"
+down_revision = "b22b450d409c"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column(
+        "experiments",
+        sa.Column("external_links", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("experiments", "external_links")
+    # ### end Alembic commands ###

src/mavedb/models/experiment.py

@@ -73,6 +73,7 @@ class Experiment(Base):
     abstract_text = Column(String, nullable=False)
     method_text = Column(String, nullable=False)
     extra_metadata = Column(JSONB, nullable=False)
+    external_links = Column(JSONB, nullable=False, default={})
 
     private = Column(Boolean, nullable=False, default=True)
     approved = Column(Boolean, nullable=False, default=False)

src/mavedb/view_models/collection.py

@@ -1,5 +1,5 @@
 from datetime import date
-from typing import Any, Sequence, Optional
+from typing import Any, Optional, Sequence
 
 from pydantic import Field, model_validator
 
@@ -132,3 +132,14 @@ class Collection(SavedCollection):
 # NOTE: Coupled to ContributionRole enum
 class AdminCollection(Collection):
     pass
+
+
+# Properties to return for official collections
+class OfficialCollection(BaseModel):
+    badge_name: str
+    name: str
+    urn: str
+
+    class Config:
+        arbitrary_types_allowed = True
+        from_attributes = True

src/mavedb/view_models/components/external_link.py

@@ -0,0 +1,15 @@
+from typing import Optional
+
+from mavedb.view_models.base.base import BaseModel
+
+
+class ExternalLink(BaseModel):
+    """
+    Represents an external hyperlink for view models.
+
+    Attributes:
+        url (Optional[str]): Fully qualified URL for the external resource.
+            May be None if no link is available or applicable.
+    """
+
+    url: Optional[str] = None

src/mavedb/view_models/experiment.py

@@ -1,18 +1,20 @@
 from datetime import date
 from typing import Any, Collection, Optional, Sequence
 
-from pydantic import field_validator, model_validator, ValidationInfo
+from pydantic import ValidationInfo, field_validator, model_validator
 
+from mavedb.lib.validation import urn_re
 from mavedb.lib.validation.exceptions import ValidationError
 from mavedb.lib.validation.transform import (
     transform_experiment_set_to_urn,
-    transform_score_set_list_to_urn_list,
     transform_record_publication_identifiers,
+    transform_score_set_list_to_urn_list,
 )
-from mavedb.lib.validation import urn_re
 from mavedb.lib.validation.utilities import is_null
 from mavedb.view_models import record_type_validator, set_record_type
 from mavedb.view_models.base.base import BaseModel
+from mavedb.view_models.collection import OfficialCollection
+from mavedb.view_models.components.external_link import ExternalLink
 from mavedb.view_models.contributor import Contributor, ContributorCreate
 from mavedb.view_models.doi_identifier import (
     DoiIdentifier,
@@ -37,16 +39,6 @@
 from mavedb.view_models.user import SavedUser, User
 
 
-class OfficialCollection(BaseModel):
-    badge_name: str
-    name: str
-    urn: str
-
-    class Config:
-        arbitrary_types_allowed = True
-        from_attributes = True
-
-
 class ExperimentBase(BaseModel):
     title: str
     short_description: str
@@ -115,6 +107,7 @@ class SavedExperiment(ExperimentBase):
     contributors: list[Contributor]
     keywords: Sequence[SavedExperimentControlledKeyword]
     score_set_urns: list[str]
+    external_links: dict[str, ExternalLink]
 
     _record_type_factory = record_type_validator()(set_record_type)
 

src/mavedb/view_models/score_set.py

@@ -19,6 +19,8 @@
 from mavedb.models.enums.processing_state import ProcessingState
 from mavedb.view_models import record_type_validator, set_record_type
 from mavedb.view_models.base.base import BaseModel
+from mavedb.view_models.collection import OfficialCollection
+from mavedb.view_models.components.external_link import ExternalLink
 from mavedb.view_models.contributor import Contributor, ContributorCreate
 from mavedb.view_models.doi_identifier import (
     DoiIdentifier,
@@ -49,20 +51,6 @@
 UnboundedRange = tuple[Union[float, None], Union[float, None]]
 
 
-class ExternalLink(BaseModel):
-    url: Optional[str] = None
-
-
-class OfficialCollection(BaseModel):
-    badge_name: str
-    name: str
-    urn: str
-
-    class Config:
-        arbitrary_types_allowed = True
-        from_attributes = True
-
-
 class ScoreSetBase(BaseModel):
     """Base class for score set view models."""
 

tests/conftest.py

@@ -1,7 +1,7 @@
 import logging  # noqa: F401
+import sys
 from datetime import datetime
 from unittest import mock
-import sys
 
 import email_validator
 import pytest
@@ -11,35 +11,33 @@
 from sqlalchemy.pool import NullPool
 
 from mavedb.db.base import Base
+from mavedb.models import *  # noqa: F403
+from mavedb.models.experiment import Experiment
 from mavedb.models.experiment_set import ExperimentSet
-from mavedb.models.score_set_publication_identifier import ScoreSetPublicationIdentifierAssociation
-from mavedb.models.user import User, UserRole, Role
 from mavedb.models.license import License
-from mavedb.models.taxonomy import Taxonomy
-from mavedb.models.publication_identifier import PublicationIdentifier
-from mavedb.models.experiment import Experiment
-from mavedb.models.variant import Variant
 from mavedb.models.mapped_variant import MappedVariant
+from mavedb.models.publication_identifier import PublicationIdentifier
 from mavedb.models.score_set import ScoreSet
-
-from mavedb.models import *  # noqa: F403
-
+from mavedb.models.score_set_publication_identifier import ScoreSetPublicationIdentifierAssociation
+from mavedb.models.taxonomy import Taxonomy
+from mavedb.models.user import Role, User, UserRole
+from mavedb.models.variant import Variant
 from tests.helpers.constants import (
     ADMIN_USER,
     EXTRA_USER,
-    TEST_LICENSE,
+    TEST_BRNICH_SCORE_CALIBRATION,
     TEST_INACTIVE_LICENSE,
+    TEST_LICENSE,
+    TEST_PATHOGENICITY_SCORE_CALIBRATION,
+    TEST_PUBMED_IDENTIFIER,
     TEST_SAVED_TAXONOMY,
     TEST_USER,
-    VALID_VARIANT_URN,
-    VALID_SCORE_SET_URN,
-    VALID_EXPERIMENT_URN,
-    VALID_EXPERIMENT_SET_URN,
-    TEST_PUBMED_IDENTIFIER,
     TEST_VALID_POST_MAPPED_VRS_ALLELE_VRS2_X,
     TEST_VALID_PRE_MAPPED_VRS_ALLELE_VRS2_X,
-    TEST_BRNICH_SCORE_CALIBRATION,
-    TEST_PATHOGENICITY_SCORE_CALIBRATION,
+    VALID_EXPERIMENT_SET_URN,
+    VALID_EXPERIMENT_URN,
+    VALID_SCORE_SET_URN,
+    VALID_VARIANT_URN,
 )
 
 sys.path.append(".")
@@ -56,7 +54,7 @@
 assert pytest_postgresql.factories
 
 # Allow the @test domain name through our email validator.
-email_validator.SPECIAL_USE_DOMAIN_NAMES.remove("test")
+email_validator.TEST_ENVIRONMENT = True
 
 
 @pytest.fixture()

tests/helpers/constants.py

@@ -540,6 +540,7 @@
     "primaryPublicationIdentifiers": [],
     "secondaryPublicationIdentifiers": [],
     "rawReadIdentifiers": [],
+    "externalLinks": {},
     # keys to be set after receiving response
     "urn": None,
     "experimentSetUrn": None,
@@ -580,6 +581,7 @@
     "primaryPublicationIdentifiers": [],
     "secondaryPublicationIdentifiers": [],
     "rawReadIdentifiers": [],
+    "externalLinks": {},
     # keys to be set after receiving response
     "urn": None,
     "experimentSetUrn": None,
@@ -630,6 +632,7 @@
     "primaryPublicationIdentifiers": [],
     "secondaryPublicationIdentifiers": [],
     "rawReadIdentifiers": [],
+    "externalLinks": {},
     # keys to be set after receiving response
     "urn": None,
     "experimentSetUrn": None,