feat: add external links property to Experiment model and view model

Author: bencap

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/experiment.py

@@ -1,15 +1,15 @@
 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
@@ -37,6 +37,10 @@
 from mavedb.view_models.user import SavedUser, User
 
 
+class ExternalLink(BaseModel):
+    url: Optional[str] = None
+
+
 class OfficialCollection(BaseModel):
     badge_name: str
     name: str
@@ -115,6 +119,7 @@ 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)
 

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,