From 946e0df1a0e2951e39170205171d82a1ac58eaed Mon Sep 17 00:00:00 2001 From: Manish Kumar Date: Tue, 11 Aug 2026 21:24:18 -0500 Subject: [PATCH] fix: wire DB_HOST/DB_PORT/DB_NAME/DB_USER/DB_PASSWORD into tes service TES's run_store.py (Mode B Phase 1A/1B) has its own DB_* defaults (DB_USER=DB_PASSWORD="omnibioai") that never matched any real MySQL grant -- that PR's own code comment flagged this exact gap as a known TODO ("this repo's own docker-compose environment block still needs that same DB_* set added... omnibioai-studio is a different repo, out of scope for this change") and it was never followed up on. Confirmed live: every real /api/runs/submit has been crashing on RunStore.create()'s MySQL connect this whole time -- "Access denied for user 'omnibioai'@... (using password: YES)". Wires the same shared DB (mysql/omnibioai) and the same DB_USER=root / MYSQL_ROOT_PASSWORD credential every other service in this file already uses -- not a new database, not guessed credentials. Mirrors workflow-bundles' own existing entry in this same file exactly. Found and fixed while verifying omnibioai-workbench#196 end-to-end (TES call sites routed through api-gateway) -- unrelated concern (gateway routing vs. TES's own persistence layer), kept as its own commit/branch rather than bundled into #196's GATEWAY_URL change. Co-Authored-By: Claude Sonnet 5 --- docker-compose.yml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/docker-compose.yml b/docker-compose.yml index a9449c6..479b0f9 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -101,6 +101,22 @@ services: SENTRY_RELEASE: "0.7.0" DOCKER_HOST: unix:///var/run/docker.sock PYTHONPATH: /workspace/src + # Mode B Phase 1A/1B run_store.py's own DB_* defaults (DB_USER= + # DB_PASSWORD="omnibioai") never matched any real MySQL grant -- + # this block was flagged as a known TODO in that PR's own code + # comment ("this repo's own docker-compose environment block still + # needs that same DB_* set added... out of scope for this change") + # and never followed up on, so every real submit() has been + # crashing on RunStore.create()'s MySQL connect this whole time + # (confirmed live: "Access denied for user 'omnibioai'@..."). + # Same shared DB, same DB_USER=root/DB_PASSWORD credential every + # other service here already uses -- mirrors workflow-bundles' + # own entry in this file exactly, not a new/guessed credential. + DB_HOST: mysql + DB_PORT: "3306" + DB_NAME: omnibioai + DB_USER: root + DB_PASSWORD: ${MYSQL_ROOT_PASSWORD:-omnibioai} TOOLSERVER_BASE_URL: http://toolserver:9090 TES_TOOLS: /workspace/configs/tools TES_SERVERS: /workspace/configs/servers