feat(urns): forward URNs retired by publication to the published record

alembic/versions/c4b18d0f7a92_add_urn_redirects.py

@@ -0,0 +1,35 @@
+"""Add urn_redirects, forwarding URNs that publication has retired
+
+Revision ID: c4b18d0f7a92
+Revises: a7f3c2e9b104
+Create Date: 2026-09-01 00:00:00.000000
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "c4b18d0f7a92"
+down_revision = "a7f3c2e9b104"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # Not backfilled: publication overwrote each record's temporary URN in place and kept no history of
+    # it, so the URNs retired before this table existed cannot be recovered.
+    op.create_table(
+        "urn_redirects",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("old_urn", sa.String(length=64), nullable=False),
+        sa.Column("new_urn", sa.String(length=64), nullable=False),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index("ix_urn_redirects_old_urn", "urn_redirects", ["old_urn"], unique=True)
+
+
+def downgrade():
+    op.drop_index("ix_urn_redirects_old_urn", table_name="urn_redirects")
+    op.drop_table("urn_redirects")

src/mavedb/lib/urn_redirects.py

@@ -0,0 +1,172 @@
+"""Forwarding of URNs that publication has retired.
+
+A dataset is created with a ``tmp:<uuid>`` URN and keeps it until it is published, at which point
+:func:`mavedb.routers.score_sets.publish_score_set` overwrites the URN in place with a permanent one.
+Any link already shared to the unpublished record then stops resolving, which is what
+https://github.com/VariantEffect/mavedb-ui/issues/617 reports: the record is still there, under a name
+the caller has no way to guess.
+
+Publication records what each retired URN became, and every read is checked here before it reaches its
+route. A request naming a retired URN is answered with ``308 Permanent Redirect`` to the same path
+under the record's current URN.
+
+Three limits:
+
+  - Only a public target is forwarded to. A ``Location`` header names the record it points at, and
+    forwarding happens before any route checks a permission, so the header would disclose that URN to
+    an anonymous caller. See _target_is_public.
+  - Forwarding is one hop. Nothing in the application renames a published record, so a chain cannot
+    arise; if one ever could, resolution here would need to follow it.
+  - URNs retired before this was added are unrecoverable. Publication overwrote them and no history of
+    them was kept, so links to records published earlier stay broken.
+"""
+
+import logging
+from typing import Optional
+from urllib.parse import quote
+
+from fastapi import Depends, HTTPException
+from sqlalchemy import select
+from sqlalchemy.orm import Session
+from starlette.requests import Request
+
+from mavedb.deps import get_db
+from mavedb.lib.logging.context import logging_context, save_to_logging_context
+from mavedb.lib.permissions.actions import Action
+from mavedb.lib.permissions.core import has_permission
+from mavedb.lib.validation.urn_re import (
+    MAVEDB_EXPERIMENT_SET_URN_RE,
+    MAVEDB_EXPERIMENT_URN_RE,
+    MAVEDB_SCORE_SET_URN_RE,
+    MAVEDB_TMP_URN_RE,
+)
+from mavedb.models.experiment import Experiment
+from mavedb.models.experiment_set import ExperimentSet
+from mavedb.models.score_set import ScoreSet
+from mavedb.models.urn_redirect import UrnRedirect
+
+logger = logging.getLogger(__name__)
+
+# Methods whose requests are forwarded. See forward_retired_urns for why a write is not.
+SAFE_METHODS = frozenset({"GET", "HEAD"})
+
+
+def record_urn_redirect(db: Session, old_urn: Optional[str], new_urn: str) -> None:
+    """
+    Record that a record's URN has changed, so that requests naming the old one can be forwarded.
+
+    Staged on the session rather than committed, so that a caller which reassigns several URNs -- as
+    publication does, across an experiment set, an experiment and a score set -- commits the redirects
+    together with the renames they describe.
+
+    :param db: An active database session.
+    :param old_urn: The URN being retired. A record that never had one, or a rename that is not a
+        change, is not worth a row and is ignored.
+    :param new_urn: The URN replacing it.
+    """
+    if not old_urn or old_urn == new_urn:
+        return
+
+    db.add(UrnRedirect(old_urn=old_urn, new_urn=new_urn))  # type: ignore[call-arg]
+
+
+def _target_is_public(db: Session, urn: str) -> bool:
+    """
+    Report whether the record a redirect points to is one that may be named to any caller.
+
+    A ``Location`` header discloses the URN it carries, to whoever asked -- including an anonymous
+    caller, since forwarding happens before a route checks anything. Publication only ever records a
+    redirect onto a record it is making public, and nothing in the application returns a published
+    record to private, so a private target should not arise; a row written out of band, or by some
+    later feature, would be enough for one to. Deferring to ``Action.READ`` with no user keeps that
+    from becoming a disclosure, and keeps this answer in step with the rules a route would apply.
+
+    A target that no longer exists is likewise not public: a deleted record leaves its redirect row
+    behind, and forwarding to it would answer a permanent redirect with a 404.
+
+    :param db: An active database session.
+    :param urn: The URN a redirect points to.
+    :return: True only if a record under this URN exists and an anonymous caller may read it.
+    """
+    target: Optional[ScoreSet | Experiment | ExperimentSet] = None
+    if MAVEDB_SCORE_SET_URN_RE.fullmatch(urn):
+        target = db.query(ScoreSet).filter(ScoreSet.urn == urn).one_or_none()
+    elif MAVEDB_EXPERIMENT_URN_RE.fullmatch(urn):
+        target = db.query(Experiment).filter(Experiment.urn == urn).one_or_none()
+    elif MAVEDB_EXPERIMENT_SET_URN_RE.fullmatch(urn):
+        target = db.query(ExperimentSet).filter(ExperimentSet.urn == urn).one_or_none()
+
+    return target is not None and has_permission(None, target, Action.READ).permitted
+
+
+def forwarded_path(db: Session, path: str) -> Optional[str]:
+    """
+    Rewrite a request path so that any retired URN in it names the record's current URN instead.
+
+    Substitution is by substring, not by path segment, so a variant URN -- ``{score_set_urn}#{n}`` --
+    is carried along by its score set's redirect.
+
+    :param db: An active database session.
+    :param path: The decoded request path.
+    :return: The rewritten path, or None if the path should be served as it is: it names no retired URN,
+        or one whose target this caller must not be told about. See _target_is_public.
+    """
+    # A live temporary URN belongs to an unpublished record and matches nothing in the table, so the
+    # lookup below distinguishes the two cases and no separate check for publication is needed.
+    candidate_urns = set(MAVEDB_TMP_URN_RE.findall(path))
+    if not candidate_urns:
+        return None
+
+    redirects = db.execute(
+        select(UrnRedirect.old_urn, UrnRedirect.new_urn).where(UrnRedirect.old_urn.in_(candidate_urns))
+    ).all()
+    if not redirects:
+        return None
+
+    forwarded = path
+    for old_urn, new_urn in redirects:
+        if not _target_is_public(db, new_urn):
+            return None
+        forwarded = forwarded.replace(old_urn, new_urn)
+
+    return forwarded
+
+
+def forward_retired_urns(request: Request, db: Session = Depends(get_db)) -> None:
+    """
+    Forward a request that names a retired URN to the same resource under its current URN.
+
+    Installed as an application-wide dependency in :mod:`mavedb.server_main`, which is what makes one
+    implementation cover every route that takes a URN, sub-resources included: a stale link to a score
+    set's scores CSV or mapped variants is forwarded on the same terms as a link to the score set.
+
+    Only reads are forwarded. A write to a retired URN keeps getting the 404 it gets today, which
+    tells the client to look the record up again.
+    """
+    if request.scope["method"] not in SAFE_METHODS:
+        return
+
+    # The ASGI scope rather than request.url: Starlette builds request.url by re-parsing the decoded
+    # path, so a variant URN's '#' starts a fragment there and everything after it -- the variant
+    # number, the sub-resource, the query -- is silently dropped.
+    path = request.scope["path"]
+    query = request.scope.get("query_string", b"").decode("ascii")
+
+    forwarded = forwarded_path(db, path)
+    if forwarded is None:
+        return
+
+    # The scope's path is percent-decoded, so a '#' in it has to be re-encoded or it would open a
+    # fragment in the header. Relative, so that a proxy's scheme and host survive.
+    location = quote(forwarded, safe="/:")
+    if query:
+        location = f"{location}?{query}"
+
+    save_to_logging_context({"requested_resource": path, "forwarded_to": forwarded})
+    logger.info(msg="Forwarding a request that named a retired URN.", extra=logging_context())
+
+    raise HTTPException(
+        status_code=308,
+        detail="This URN was replaced when the record was published; the record has moved permanently.",
+        headers={"Location": location},
+    )

src/mavedb/models/__init__.py

@@ -35,6 +35,7 @@
     "taxonomy",
     "uniprot_identifier",
     "uniprot_offset",
+    "urn_redirect",
     "user",
     "variant_annotation_status",
     "variant",

src/mavedb/models/urn_redirect.py

@@ -0,0 +1,36 @@
+"""
+SQLAlchemy model for URNs that publication has retired.
+"""
+
+from datetime import datetime
+
+from sqlalchemy import DateTime, Integer, String, func
+from sqlalchemy.orm import Mapped, mapped_column
+
+from mavedb.db.base import Base
+
+
+class UrnRedirect(Base):
+    """
+    Records that a record's URN was replaced, and by what.
+
+    Publishing a dataset overwrites the ``tmp:<uuid>`` URN it was created with, so every link already
+    shared to the unpublished record stops resolving. One row is written here per URN publication
+    retires, and requests naming a retired URN are forwarded to its replacement.
+
+    Only experiment sets, experiments and score sets get rows. A variant's URN is
+    ``{score_set_urn}#{n}``, so forwarding replaces the retired URN wherever it appears in a request
+    path and a variant follows its score set without a row of its own.
+    """
+
+    __tablename__ = "urn_redirects"
+
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+
+    old_urn: Mapped[str] = mapped_column(String(64), nullable=False, unique=True, index=True)
+    new_urn: Mapped[str] = mapped_column(String(64), nullable=False)
+
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+
+    def __repr__(self) -> str:
+        return f"<UrnRedirect(old_urn='{self.old_urn}', new_urn='{self.new_urn}')>"

src/mavedb/routers/score_sets.py

@@ -77,6 +77,7 @@
 from mavedb.lib.target_genes import find_or_create_target_gene_by_accession, find_or_create_target_gene_by_sequence
 from mavedb.lib.taxonomies import find_or_create_taxonomy
 from mavedb.lib.types.authentication import UserData
+from mavedb.lib.urn_redirects import record_urn_redirect
 from mavedb.lib.urns import (
     generate_experiment_set_urn,
     generate_experiment_urn,
@@ -2530,6 +2531,13 @@ async def publish_score_set(
 
     assert_permission(user_data, item, Action.PUBLISH)
 
+    if not item.private:
+        logger.info(
+            msg="Failed to publish score set; The requested score set has already been published.",
+            extra=logging_context(),
+        )
+        raise HTTPException(status_code=409, detail="This score set has already been published.")
+
     if not item.experiment:
         logger.info(
             msg="Failed to publish score set; The requested score set does not belong to an experiment.",
@@ -2563,26 +2571,33 @@ async def publish_score_set(
     published_date = date.today()
 
     if item.experiment.experiment_set.private or not item.experiment.experiment_set.published_date:
+        retired_experiment_set_urn = item.experiment.experiment_set.urn
         item.experiment.experiment_set.urn = generate_experiment_set_urn(db)
+        record_urn_redirect(db, retired_experiment_set_urn, item.experiment.experiment_set.urn)
         item.experiment.experiment_set.private = False
         item.experiment.experiment_set.published_date = published_date
         db.add(item.experiment.experiment_set)
 
     save_to_logging_context({"experiment_set": item.experiment.experiment_set.urn})
 
     if item.experiment.private or not item.experiment.published_date:
+        retired_experiment_urn = item.experiment.urn
         item.experiment.urn = generate_experiment_urn(
             db,
             item.experiment.experiment_set,
             experiment_is_meta_analysis=len(item.meta_analyzes_score_sets) > 0,
         )
+        record_urn_redirect(db, retired_experiment_urn, item.experiment.urn)
         item.experiment.private = False
         item.experiment.published_date = published_date
         db.add(item.experiment)
 
     save_to_logging_context({"experiment": item.experiment.urn})
 
+    retired_score_set_urn = item.urn
     item.urn = generate_score_set_urn(db, item.experiment)
+    # Variant URNs are rewritten below from the score set's, so this one redirect forwards them too.
+    record_urn_redirect(db, retired_score_set_urn, item.urn)
     item.private = False
     item.published_date = published_date
     refresh_variant_urns(db, item)

src/mavedb/server_main.py

@@ -3,7 +3,7 @@
 
 import uvicorn
 from eutils._internal.exceptions import EutilsRequestError  # type: ignore
-from fastapi import FastAPI
+from fastapi import Depends, FastAPI
 from fastapi.encoders import jsonable_encoder
 from fastapi.exceptions import RequestValidationError
 from fastapi.middleware.cors import CORSMiddleware
@@ -37,6 +37,7 @@
 from mavedb.lib.middleware import CatchAllErrorMiddleware
 from mavedb.lib.permissions.exceptions import PermissionException
 from mavedb.lib.slack import send_slack_error
+from mavedb.lib.urn_redirects import forward_retired_urns
 from mavedb.models import *  # noqa: F403
 from mavedb.routers import (
     access_keys,
@@ -75,7 +76,9 @@
 # an instance of the related class has been created.
 configure_mappers()
 
-app = FastAPI()
+# forward_retired_urns is applied to every route, so that one implementation forwards a read of a URN
+# publication has retired wherever that URN points: a record, or any of its sub-resources.
+app = FastAPI(dependencies=[Depends(forward_retired_urns)])
 # `add_middleware` inserts at the head of the stack, so the *first* call here is the innermost layer.
 # CatchAllErrorMiddleware must sit inside both CORSMiddleware and the context middleware: CORS has to
 # decorate the 500 it produces, and the correlation id it returns comes from the context.