Skip to content

Rebuild elb-openapi 4.22 so the finalizer preserves the outfmt 7 '# Fields:' header

Motivation

Issue #31: the dashboard fix for sharded outfmt 7 taxid / scientific-name columns has two halves with different rollout paths. The parser alias half ships in the elb-api image via the normal Container App deploy (already covered). The finalizer # Fields:-preservation half is baked into the elb-openapi image, because the finalizer + merge scripts are delivered to the cluster as a ConfigMap built from that image. The deployed elb-openapi:4.21 predated the finalizer change (terminal/patch_elastic_blast.py: awk '!/^#/' → awk '/^# Fields:/ || !/^#/'), so the merged merged_results.out.gz carried a std-12 # Fields: header over 14-column data rows and the dashboard Scientific Name column stayed blank for OpenAPI-plane runs.

User-facing change

  • elb-openapi is rebuilt to 4.22 from the dashboard-patched local sibling build context (scripts/dev/patch-openapi-build-context.py support files refreshed from terminal/), so the in-cluster finalizer now runs awk '/^# Fields:/ || !/^#/' and keeps the per-shard # Fields: line.
  • The merged result's # Fields: header now lists the extended columns (... bit score, subject tax ids, subject sci names), so the BLAST Results Scientific Name column + Taxonomy tab populate for sharded OpenAPI-plane runs instead of showing blank / "Unknown".
  • The same rebuild also carries the multi-token -outfmt argv patch (blast-run-aks.sh rebuilds ELB_BLAST_ARGV and rejoins the -outfmt tokens), so an unquoted extended layout survives the YAML→env→shell→blastn path (issue #29 runtime half).

API / IaC diff summary

  • api/services/image_tags.py — IMAGE_TAGS["elb-openapi"] 4.21 → 4.22.
  • ~/dev/elastic-blast-azure/docker-openapi/patch_elastic_blast.py refreshed from terminal/patch_elastic_blast.py (build-context support file; not committed to this repo).
  • No Bicep / Container App template change.

Rollout order (charter)

Build + push the sibling image to ACR FIRST, then move the pin:

  1. cp terminal/patch_elastic_blast.py ~/dev/elastic-blast-azure/docker-openapi/ (sync the finalizer fix into the build context).
  2. az acr build -r acrelbdashboard3abp67bppe -t elb-openapi:4.22 -f ~/dev/elastic-blast-azure/docker-openapi/Dockerfile ~/dev/elastic-blast-azure/docker-openapi — ACR run defw Succeeded.
  3. Bump IMAGE_TAGS["elb-openapi"] 4.21 → 4.22 (this commit).
  4. Redeploy the pod: kubectl set image deployment/elb-openapi openapi=…/elb-openapi:4.22.

Validation evidence

  • New pod elb-openapi-567675dbb7-… runs acrelbdashboard3abp67bppe.azurecr.io/elb-openapi:4.22.
  • Finalizer patch live in the pod's installed elastic-blast: /opt/venv/lib/python3.11/site-packages/elastic_blast/templates/scripts/elb-finalizer-aks.sh:164 → if ! zcat "$f" | awk '/^# Fields:/ || !/^#/' >> "$MERGE_INPUT"; then.
  • argv patch live: blast-run-aks.sh carries ELB_BLAST_ARGV rebuild (lines 86-130).
  • Live sharded core_nt -outfmt 7 std staxids sscinames submit on elb-cluster-01 (OpenAPI plane, job a4a2ee33aeee, core_nt_precise → 5 shards):
  • The batch pod rendered the multi-token specifier as a single blastn argument: blastn -db core_nt_shard_00 … -outfmt 7 std staxids sscinames -searchsp … (argv patch works — no YAML break, no shell word-split).
  • merged_results.out.gz # Fields: header carries the extended columns: … bit score, subject tax ids, subject sci names.
  • Data rows are 14-column with the taxid + scientific name populated, e.g. NR_024570.1 … 998 562 Escherichia coli (taxid 562).
  • merge-report.json resolved columns by name: qseqid=0, subject=1, evalue=10, bitscore=11 (std-first keeps qseqid leading → single query group, not collapsed).
  • The dashboard results parser (api/services/blast/results_parser.py) already aliases subject tax ids → staxids and subject sci names → sscinames, so the Scientific Name column + Taxonomy tab populate from this header.