Sync fork with IHTSDO/master (resolves #10)

[MattCordell]

Summary

Brings aehrc/master up to date with IHTSDO/release-validation-framework@master, which it had fallen ~232 commits / ~2 years behind.

The fork had diverged but with zero net custom content — its 13 unique commits are entirely self-canceling: four commit+revert pairs (M1 build helpers, an RC test-run script, "pre-requisite SQL" support, and a varchar widening attempt 4d28428 reverted by 82c1ba0) plus three older IHTSDO merge commits. The merge_base...aehrc/master net file diff was empty, so this merge applied with no conflicts and the resulting tree is identical to IHTSDO/master.

Resolves #10

Issue #10 asked to widen the description term column so full-length SNOMED terms aren't truncated. IHTSDO already shipped this in MAINT-2526 (e0ad400):

• description_f, description_s, description_d term columns are now varchar(4096) collate utf8_bin (was varchar(256));
• the idx_term(term) indexes were dropped — required because all tables are MyISAM (1000-byte index-key cap; varchar(4096) utf8 = 12,288 bytes would fail CREATE TABLE). This is exactly why the fork's earlier widen-only attempt (4d28428) was reverted.

Syncing therefore resolves the issue the correct way (widen and drop the index), without re-introducing the original failure. Closes #10.

Verification

• git diff origin/master --stat (origin = IHTSDO) is empty — synced tree matches IHTSDO/master exactly.
• All term columns in src/main/resources/sql/create-tables-mysql.sql are varchar(4096) collate utf8_bin; no idx_term remains.

Notes / follow-ups

• The fork's previously-reverted features (pre-requisite-SQL support, M1 build helpers, RC test-run script) are not resurrected. If still wanted, re-apply them as fresh PRs on top of the synced master.
• Downstream aehrc/rvf cleanup (per Widen description term column to support full-length SNOMED terms (varchar 4100) #10): bump the RVF image tag, delete testscripts/fix-long-terms.sh, and remove its invocation in testscripts/run-test.sh.

🤖 Generated with Claude Code

[MattCordell]

Status / where we're up to — ⏸️ HOLD merge until after this week's production release

TL;DR: the sync itself is verified clean and mergeable, but the resulting image is not a drop-in for the existing aehrc/rvf deployment harness. Several downstream changes (entrypoint, auth model, JVM flags) would break rvf if the new image were deployed as-is. Given a production release this week, we're holding the merge until the downstream rvf adaptation is done and tested against a non-:latest test image.

✅ Verified on this PR (safe)

• Merged tree is byte-identical to IHTSDO/master (c90f12d9^{tree} == origin/master^{tree}).
• Fork's 13 unique commits are self-cancelling — net diff merge-base(88b15112)..aehrc/master is empty.
• Proper 2-parent merge; history preserved.
• Issue Widen description term column to support full-length SNOMED terms (varchar 4100) #10 resolved correctly: all term columns are varchar(4096) collate utf8_bin, idx_term removed (required under MyISAM's 1000-byte index-key cap).

Merging the PR is low-risk in isolation — it does not touch rvf. The risk is purely in deploying the new image. Do not let anything auto-deploy :latest off the back of this merge during release week.

⚠️ Downstream aehrc/rvf impact (must be done before deploying the new image)

Analysis below; rvf-side line refs are from that repo and not yet re-verified here. Framework-side items marked ✔ are confirmed against this repo.

Change	Source	Impact on rvf (templates/job.yaml, run-test.sh)
No Dockerfile — now built via jib-maven-plugin ✔	RAP-93	Image entrypoint is mainClass org.ihtsdo.rvf.App (no rvf-api.jar). The -jar rvf-api.jar line in job.yaml:60 will fail. New launch is jib's classpath form.
JVM flags ✔	RAP-93 / VAL-405	--add-opens=java.base/java.lang=ALL-UNNAMED is baked into the image (pom.xml), but any hand-rolled java invocation in job.yaml:60 must include it. AWS region is set via spring.cloud.aws.region.static=us-east-1 in the image; the AWS SDK v2 default-region chain may still want AWS_REGION/-Daws.region if cloud storage is enabled (not for a local useCloud=false test).
Auth model changed — SSO header, NOT Basic Auth ✔	SecurityConfig	Sharper than first thought. New SecurityConfig wires only RequestHeaderAuthenticationDecorator (IHTSDO SSO header auth) with anyRequest().authenticated(); no httpBasic. run-test.sh:7-8 Basic-Auth (RVF_USER/RVF_PASSWORD) will get a JSON 401 regardless of spring.security.user.*. Fix requires either re-adding httpBasic() (fork patch to SecurityConfig) or supplying the SSO header — setting matching env vars alone is not sufficient.
Module Storage Coordinator ✔	VAL-405 / VAL-493	New module.storage.* props. Defaults are sane for a quick test (useCloud=false, local.path=store/local/, application.properties:56-62) — should work without cloud config.
rvf.empty-release-file=empty-rf2-snapshot.zip ✔	RAP-13	Confirmed at application.properties:50. Used as placeholder when no previous release is supplied; must ship in image or be mounted.
MySQL 8	PIP-521	rvf already on mysql:8.0.28 (job.yaml:41) — no change.
fix-long-terms.sh	local	Now redundant (schema accepts 4096, so the length >= 255 awk path never trips). Harmless to leave for first test; delete in a cleanup commit.

🧪 Building a test image locally (notes for whoever picks this up)

Target: ontoserver.azurecr.io/aehrc-rvf/release-validation-framework:sync-ihtsdo (non-:latest). Three local Windows build-env gotchas found:

1. checkout-resources.sh fails on Windows — .gitattributes * text=auto gives it CRLF endings, breaking bash. (Linux CI is unaffected.)
2. The script shells out to a nested mvn, which needs JAVA_HOME (only java on PATH locally).
3. az (Azure CLI) not installed — needed to auth the ACR push.

Workaround that sidesteps 1 & 2: pre-clone the two resource repos (snomed-drools-rules, snomed-release-validation-assertions @ master) and build with -Dexec.skip=true. To push only the :sync-ihtsdo tag (and not also :8.3.1, which the pom's <tags> block would otherwise push and could overwrite a release tag in the registry):

mvn clean package jib:build -DskipTests -Pdocker-amd64 -Dexec.skip=true \
  -Dimage=ontoserver.azurecr.io/aehrc-rvf/release-validation-framework:sync-ihtsdo \
  -Djib.to.tags=

Next steps

1. Hold this PR until after the production release.
2. Branch rvf and adapt: job.yaml entrypoint → jib launch form; resolve the auth model change (decide: re-add httpBasic upstream-side, or switch the test harness to SSO header); confirm module-storage + empty-release defaults.
3. Build the :sync-ihtsdo test image, point the rvf branch at it, run the pipeline end-to-end.
4. Only then merge this PR and roll the image forward. Clean up fix-long-terms.sh separately.

See also: See also : https://github.com/aehrc/rvf/issues/25