Migrate direct raw-S3 bbop-sqlite consumers to the semanticsql CDN

[kltm]

[bot] Opened by a Claude Code agent on behalf of @kltm. Body updated 2026-08-18 (2nd revision): every entry below is now verified against fetched default-branch file content (literal-match), not code-search hits — search tokenizes on hyphens and produced several false positives, now removed. Verdicts also cross-checked against raw-bucket access logs (2026-07-08 → 2026-08-18) and per-file git history.

Companion to #112 (remove raw-bucket access). These projects hardcode the raw bucket URL directly, so they will not auto-migrate via oaklib/ODK bumps; they need to repoint to https://semanticsql.berkeleybop.io (drop-in, same paths) before raw access is removed.

Gotcha RETIRED 2026-08-18: the CDN no longer 403s Python-urllib/* User-Agents (host-scoped Browser Integrity Check exemption, verified). All client types work; the swap is a plain one-line change.

Verified still-present (literal raw URL in current default-branch runtime code)

• monarch-initiative/monarch-ingest — src/monarch_ingest/download.yaml L28 — outreach Repoint hardcoded bbop-sqlite S3 URLs to the semanticsql CDN before raw-bucket access is retired monarch-initiative/monarch-ingest#711 (open, no engagement) — phenio pulls also confirmed in access logs
• Knowledge-Graph-Hub/kg-alzheimers — src/kg_alzheimers/download.yaml L186/L255 — outreach Repoint hardcoded bbop-sqlite S3 URLs to the semanticsql CDN before raw-bucket access is retired Knowledge-Graph-Hub/kg-alzheimers#78 (open, no engagement) — traffic-confirmed
• monarch-initiative/dictybase-ingest — download.yaml L10; ⚠️ src/versions.py filters on contains=["bbop-sqlite"], so the URL fix must also update that selector or version-tracking silently breaks — outreach Repoint hardcoded bbop-sqlite S3 URLs to the semanticsql CDN before raw-bucket access is retired monarch-initiative/dictybase-ingest#3 (open, no engagement) — traffic-confirmed
• biobricks-ai/semsql — stages/01_download.sh (URL generator); ⚠️ stages/00_invalidate.sh does anonymous aws s3 ls (bucket-listing dependency, see below); .bb/source.jsonld metadata — outreach Repoint hardcoded bbop-sqlite S3 URLs to the semanticsql CDN before raw-bucket access is retired biobricks-ai/semsql#1 (open, no engagement)
• Knowledge-Graph-Hub/universalizer — universalizer/oak_utils.py L48 (note: fetches uncompressed .db objects) — outreach Repoint hardcoded bbop-sqlite S3 URLs to the semanticsql CDN before raw-bucket access is retired Knowledge-Graph-Hub/universalizer#41 (open, no engagement)
• microbiomedata/ontology-loader — src/ontology_loader/ontology_processor.py L100 — outreach Repoint hardcoded bbop-sqlite S3 URLs to the semanticsql CDN before raw-bucket access is retired microbiomedata/ontology-loader#59 (open, no engagement). Covers microbiomedata/nmdc-runtime too (its notebook just calls this library).
• ccb-hms/NHANES-metadata — code/generate_ontology_tables.py L30 — outreach Repoint hardcoded bbop-sqlite S3 URLs to the semanticsql CDN before raw-bucket access is retired ccb-hms/NHANES-metadata#37 (open, no engagement)
• waldronlab/bioanalyzer-backend — app/normalization/grounding/seed.py L57 (SEMANTIC_SQL_BASE_URL) — outreach [bot] Repoint semantic-sql base URL to the semanticsql CDN before raw-bucket retirement waldronlab/bioanalyzer-backend#124
• seandavi/metacurator — src/metacurator/grounding/local_duckdb.py L26 (single base-URL constant; cleanest possible migration) — outreach [bot] Repoint SEMSQL_BASE_URL to the semanticsql CDN before raw-bucket retirement seandavi/metacurator#29 — hancestro pulls confirmed in access logs
• seandavi/cdsci-lake — src/cdsci/lake/config.py L141 + sources/ontology/ingest.py; ⚠️ its registry IS the bucket listing (paginated ListObjectsV2) — outreach via comment on Ontologies: register+run the existing ontology source, extend to BioPortal coverage + mappings seandavi/cdsci-lake#40
• CultureBotAI/MediaIngredientMech — scripts/check_chebi_currency.py L53 — outreach via comment on check-chebi-currency infers 'a refresh would help' from byte size, not release CultureBotAI/MediaIngredientMech#206
• microbiomedata/external-metadata-awareness — notebooks/environmental_context_value_sets/generate_voting_sheet.ipynb (source cell) + ⚠️ notebooks/multi-lexmatch/interleave_s3_catalog_yaml_registry_bioportal_obo.ipynb calls the S3 ListBucket XML API; 2 docs files — outreach [bot] semsql pulls reference the retiring raw bbop-sqlite bucket (URL swap + one ListBucket dependency) microbiomedata/external-metadata-awareness#553
• Knowledge-Graph-Hub/kg-registry — resource/reactome/reactome*.md product_url: frontmatter — machine-consumable registry metadata, not prose; directs downstream users to the raw URL — outreach [bot] reactome product_url points at the retiring raw bbop-sqlite bucket — repoint to the semanticsql CDN Knowledge-Graph-Hub/kg-registry#701

⚠️ Bucket-LISTING dependents (URL swap alone does not migrate these)

Four verified consumers enumerate the bucket rather than (only) fetching objects: ontoProc2 (post-migration code parses ListBucket XML from the CDN root), cdsci-lake (ListObjectsV2 registry), biobricks 00_invalidate.sh (aws s3 ls), external-metadata-awareness (ListBucket XML notebook). Live probes 2026-08-18: the CDN root currently proxies the bucket's V1 listing (works only while the bucket stays public), and CloudFront strips query strings, so V2/pagination params are silently ignored (fine at ~332 keys; breaks at 1,000). #112 must decide a listing strategy: grant s3:ListBucket to the CDN origin access at lockdown, or publish a manifest file and migrate these four to it.

Migrated (verified in current code — done or nearly)

• Knowledge-Graph-Hub/kg-microbe — repointed to the CDN 2026-07-21 (9c8ddcad, via #595). Residual raw-log traffic through 2026-08-18 attributed to stale checkouts/deployments, not master.
• vjcitn/ontoProc2 — runtime repointed 2026-07-29 (1d4df64d, via Repoint hardcoded bbop-sqlite S3 URLs to the semanticsql CDN before raw-bucket access is retired vjcitn/ontoProc2#11, still open): remaining items are the README aws s3 ls s3://bbop-sqlite/ example and the listing caveat above. vjcitn/op2workshop README carries the same example.
• monarch-initiative/dismech, ai4curation/ai-gene-review — oaklib lock bumps landed 2026-08-07 / 2026-08-12; verified in traffic.

Docs/examples only (verified literals, prose/log context; fix opportunistically)

• cthoyt/pystow — docstring examples (api.py, impl.py)
• berkeleybop/metpo — 3 docs files (its script uses sqlite:obo: selectors — migrates with oaklib); turbomam/metpo-attic — 4 docs files incl. a copy-pasteable curl example
• brad-usredoxlabs/computable-lab — 1 doc
• monarch-initiative/ontogpt-experiments — committed stdout log of an old run (evidence, not config)

Removed after verification (false positives of hyphen-tokenized code search)

monarch-initiative/rare-disease-identification (docstring prose only; runtime uses a local OBO), monarch-initiative/mondo notebook (URL only in saved output cells; source uses sqlite:obo: selectors), several name-only doc mentions elsewhere. Selector-based (sqlite:obo:) consumers are out of scope here — they migrate via oaklib ≥0.7.2, with the standing caveat that pinned lockfiles do not auto-migrate (three CI consumers to date required manual lock bumps).

Coordination notes

• Outreach-by-issue has had near-zero engagement: of the 2026-07-14 wave, only kg-microbe (silent fix) and ontoProc2 (same-day author response) acted; the other six issues have zero comments after five weeks. Minimal PRs are likely the higher-yield instrument for the remaining repos.
• [bot] Cut a semsql release including the semanticsql.berkeleybop.io default #114 remains the blocker for semsql download / library-default users: semsql on PyPI is still 0.4.0 (2025-02-05).
• The other ecosystem-wide unlock is an ODK release: the bundled-oaklib bump ([bot] Bump bundled oaklib to 0.7.2 so sqlite:obo CI downloads use the semanticsql CDN ontology-development-kit#1354) is merged but unreleased — the newest stable image (odkfull:v1.6.1) still bundles oaklib 0.6.23, so every ODK-based ontology repo's CI pulls from the raw bucket and cannot migrate by its own action until ODK ships (verified 2026-08-18: only odkfull:dev carries the fix). Release request filed: [bot] Released odkfull images bundle pre-CDN oaklib (0.6.23) — ODK-based repos cannot migrate off the retiring bbop-sqlite bucket until a release ships the #1354 bump ontology-development-kit#1368.
• Populations with no discoverable repo (cloud notebooks, one-shot users, private code) remain reachable only via release notes / announcements before Eliminate S3 bucket access #112.

— Posted by Claude Code agent on behalf of @kltm.

[github-actions]

Summary + live status check (2026-07-14)

This is a tracking issue in a chain:

• Provide sqlite via a different URL #110 (closed) — established the vendor-neutral semanticsql.berkeleybop.io CDN URL.
• Eliminate S3 bucket access #112 (open) — plan to eliminate raw S3 (bbop-sqlite) bucket access once traffic has shifted to the CDN.
• [bot] Cut a semsql release including the semanticsql.berkeleybop.io default #114 (open) — blocker: the CDN-default change landed on master but hasn't been released to PyPI yet (semsql is still 0.4.0, from 2025-02-05, as of this check). Anyone relying on semsql download / the library default (rather than a hardcoded URL) won't get the CDN switch until that release ships.
• Migrate direct raw-S3 bbop-sqlite consumers to the semanticsql CDN #115 (this issue) — the subset of consumers that bypass both OAK's selector and the semsql package entirely by hardcoding the raw S3 URL, so neither Eliminate S3 bucket access #112's traffic-shift nor [bot] Cut a semsql release including the semanticsql.berkeleybop.io default #114's release will fix them.

Verified current state of the checklist

I fetched each listed file directly (as of 2026-07-14) to confirm none have migrated yet — all 9 repos / 10 files are still unmigrated:

Repo	File	Status
biobricks-ai/semsql	stages/01_download.sh	❌ still https://s3.amazonaws.com/bbop-sqlite/${onto}.db.gz (loops full catalog — highest-traffic consumer)
Knowledge-Graph-Hub/kg-alzheimers	src/kg_alzheimers/download.yaml	❌ still S3 (e.g. ddpheno.db, phenio.db.gz)
Knowledge-Graph-Hub/kg-microbe	download.yaml (default branch is master, not main)	❌ still S3 (ncit.db.gz, bto.db.gz, po.db.gz, ...)
Knowledge-Graph-Hub/universalizer	universalizer/oak_utils.py	❌ still f"https://s3.amazonaws.com/bbop-sqlite/{db}.db"
microbiomedata/ontology-loader	src/ontology_loader/ontology_processor.py	❌ still ontology_db_url_prefix = "https://s3.amazonaws.com/bbop-sqlite/"
ccb-hms/NHANES-metadata	code/generate_ontology_tables.py	❌ still "https://s3.amazonaws.com/bbop-sqlite/%s.db.gz"
vjcitn/ontoProc2	R/semsql_url.R	❌ still "https://s3.amazonaws.com/bbop-sqlite/%s.db.gz" (default ontology "efo")
vjcitn/ontoProc2	R/bbop_sqlite_db_gz.R	❌ still url = "https://s3.amazonaws.com/bbop-sqlite" default arg
monarch-initiative/monarch-ingest	src/monarch_ingest/download.yaml	❌ still S3 (phenio.db.gz)
monarch-initiative/dictybase-ingest	download.yaml	❌ still S3 (ddpheno.db)

I also searched all 9 downstream repos for any existing issue/PR mentioning semanticsql.berkeleybop.io or bbop-sqlite — none found. So outreach to these external maintainers hasn't started yet; this checklist accurately reflects zero progress so far.

Notes for whoever actions this

• The CDN's 403-to-default-User-Agent behavior (noted in the issue body) will bite non-Python clients too — worth flagging explicitly for vjcitn/ontoProc2 (R's download.file/httr also send a default UA that could be blocked) and biobricks-ai/semsql (shell curl/wget).
• biobricks-ai/semsql is worth prioritizing given it "loops the whole catalog on push" — it's the single heaviest hardcoded consumer of the raw bucket by request volume.
• Since none of these 9 repos yet have an issue opened against them, and this tracking issue only coordinates (doesn't action), consider whether outreach issues should be filed in each downstream repo — e.g. via @dragon-ai-agent please open an issue in each of the 9 downstream repos listed here, linking back to INCATools/semantic-sql#115, asking maintainers to repoint their hardcoded bbop-sqlite S3 URLs to https://semanticsql.berkeleybop.io (with a non-default User-Agent) before the raw bucket is retired per #112.
• Recommend not closing raw-bucket access (Eliminate S3 bucket access #112) until (a) [bot] Cut a semsql release including the semanticsql.berkeleybop.io default #114's release ships and (b) at least the high-traffic items here (biobricks-ai/semsql, kg-microbe, monarch-ingest) have migrated — the S3 access logs mentioned in Eliminate S3 bucket access #112 should make it easy to confirm before flipping the switch.

[caufieldjh]

Downstream outreach filed (2026-07-14)

Opened repointing issues in the downstream repos listed above. Each links back here and to #112, cites the specific hardcoded file(s), gives the s3.amazonaws.com/bbop-sqlite/ → semanticsql.berkeleybop.io/ swap, and flags the 403-to-default-User-Agent gotcha (tailored per client: shell curl/wget, Python urllib/requests, R download.file/httr).

Repo	File(s)	Outreach issue
biobricks-ai/semsql	stages/01_download.sh	biobricks-ai/semsql#1
Knowledge-Graph-Hub/kg-alzheimers	src/kg_alzheimers/download.yaml	Knowledge-Graph-Hub/kg-alzheimers#78
Knowledge-Graph-Hub/kg-microbe	download.yaml (master)	Knowledge-Graph-Hub/kg-microbe#595
Knowledge-Graph-Hub/universalizer	universalizer/oak_utils.py	Knowledge-Graph-Hub/universalizer#41
ccb-hms/NHANES-metadata	code/generate_ontology_tables.py	ccb-hms/NHANES-metadata#37
vjcitn/ontoProc2	R/semsql_url.R, R/bbop_sqlite_db_gz.R	vjcitn/ontoProc2#11
monarch-initiative/monarch-ingest	src/monarch_ingest/download.yaml	monarch-initiative/monarch-ingest#711
monarch-initiative/dictybase-ingest	download.yaml	monarch-initiative/dictybase-ingest#3
microbiomedata/ontology-loader	src/ontology_loader/ontology_processor.py	⚠️ not filed — see below

⚠️ microbiomedata/ontology-loader could not be filed automatically

The microbiomedata org rejects classic personal access tokens for API writes:

microbiomedata forbids access via a personal access token (classic). Please use a GitHub App, OAuth App, or a personal access token with fine-grained permissions.

So this one needs to be opened manually (or with a fine-grained token / GitHub App that the org allows). The target is src/ontology_loader/ontology_processor.py — ontology_db_url_prefix = "https://s3.amazonaws.com/bbop-sqlite/" → "https://semanticsql.berkeleybop.io/", plus the non-default User-Agent requirement.

[caufieldjh]

Opened the issue in microbiomedata/ontology-loader manually: microbiomedata/ontology-loader#59