PR8/15: import six services verbatim (subtree, full history)#267
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Gcolon021 wants to merge 1764 commits into
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PR8/15: import six services verbatim (subtree, full history)#267Gcolon021 wants to merge 1764 commits into
Gcolon021 wants to merge 1764 commits into
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* ALS-4643: Add integration tests using 1k genome dataset * ALS-6564: Allow searching by old variant coords
Enhance code documentation by adding Javadoc comments to Ga4ghVisaV1, Ga4ghPassportV1, RasDbgapPermission, Passport, and User classes. These comments provide a clearer understanding of the purpose and structure of each class.
[ALS-7575] Added new endpoints for cache inspection and introduced CacheEvictionService to handle cache eviction for users. Security configuration was updated to allow access to cache endpoints, and several services were modified to utilize the new cache eviction mechanisms.
) * Set token 'active' field to false on invalid token scenarios Ensure the 'active' field in tokenInspection is marked false whenever a token is invalid or user not found. This improves the clarity and consistency of token status checks throughout the service. * Remove custom key generator from cache eviction Removed the custom key generator from cache eviction in AccessRuleService for streamlined annotation usage. Added null and blank subject checks in CacheEvictionService to prevent errors, and removed unnecessary blank line in FENCEAuthenticationService.
* Remove obsolete Maven deploy workflow Deleted the `github-actions-deploy-snapshots.yml` file as it was redundant. Renamed the `github-actions-test.yml` for consistency, updating the directory from `workflow` to `workflows`. * Update .github/workflows/github-actions-test.yml
* Remove duplicate and unused test classes * Switch project parent to Spring Boot and update dependencies. Updated the project parent to `spring-boot-starter-parent` with version `3.3.5`. Consolidated and streamlined dependencies to align with Spring Boot configurations, ensuring compatibility and removing redundant entries. * Refactor tests to use JUnit 5 and Spring Boot Test Migrated test classes from JUnit 4 to JUnit 5, replacing @before with @beforeeach, @test(expected) with assertThrows, and @RunWith with @SpringBootTest/@ContextConfiguration annotations. Updated Mockito annotations to @MockBean where appropriate and used dependency injection with @Autowired to initialize services. * Add unit tests for caching mechanisms in auth services Introduced `CacheTest` to validate caching behavior in `AccessRuleService` and `UserService`. These tests ensure the correct usage of caches like `mergedRulesCache`, `preProcessedAccessRules`, and `mergedTemplateCache`, and verify proper eviction mechanisms. * Update Dockerfiles for dynamic JAR filename handling Changed the Dockerfile COPY commands to use a wildcard for JAR filenames, ensuring compatibility with differing build outputs. Additionally, added the packaging type as 'jar' in the pom.xml to standardize project packaging. * Add AWS Secrets Manager dependency to pom.xml Included the `aws-secretsmanager-jdbc` dependency in the pom.xml to support secure secrets management with AWS Secrets Manager. This change aims to enhance security by integrating Secrets Manager into the authentication services.
* [ALS-5000] Update maven compiler plugin Maven compiler plugin has a dependency on log4j. * [ALS-5053] Add error pages to web.xml * [ALS-5053] Add value to server.xml This value will intercept request processed by tomcat. I have disabled reports and show server information. This information should not be returned to the client. (cherry picked from commit cf108c9687bf76b9eb889781d806ffff6e549a00)
(cherry picked from commit 428eacc6e15cd182c58018ec860eb311d27a3e08)
(cherry picked from commit 55732233977b9b110b06571bfbd422d92e8ce3f3)
- Create service for writing out to file - Add configuration to specify where to write - Add PIC-SURE uuid to query object - This is how we namespace file writes - Make abstract processor intersect ID sets more proactively - Memory issues - Most of this work will be done by another service, but
- In GIC land, we get queries that have a concept path that is present in some other site, but not the one the query is getting run in - The TimeseriesProcessor needs to not explode when this happens (cherry picked from commit d3d039d6834a1bb71e5a79372536c1d003f92cbc)
(cherry picked from commit 2c550655801f51cdf8771f9634be075f85956d49)
(cherry picked from commit c34a1a4cf0f13e27e1c83e6c2461c9a9a382a384)
(cherry picked from commit 25d0d01d53c5cb4eae5cbc40501bd3a22912e56f)
- Make service that does this - Isolate time series logic a bit more - Tests (cherry picked from commit 5aea45b35964602debb49b8fca4e9e67f10cf5e0)
(cherry picked from commit 35d59ede482a45b52af478de5808acc8adb27fc6)
(cherry picked from commit 369086bb990d5df4b90305c94af0030e3b049cc8)
…#109) V7 and V10 referenced concept_node, concept_node_meta, and facet__concept_node without the dict schema prefix, relying on the session search_path resolving to dict. Qualify every table, trigger target, and index target with dict. so the migrations are correct regardless of search_path, matching V5/V6/V8/V9. V8 and V9 were already fully qualified and are unchanged.
* Emit caller as a top-level audit field Add caller to the AuditEvent model and emit it as a top-level field in AuditLogService
…or (Phase 3) Adds spring-boot-starter-actuator to the service module and a custom HpdsReadinessHealthIndicator that reports UP only when phenotype or genomic data is actually loaded (AbstractProcessor.getDictionary() / getInfoStoreColumns() non-empty), since HPDS has no DataSource for the built-in db indicator to key off of. Enables health details and probes via management.endpoint properties; no port or existing behavior changes.
…ust not report DOWN)
* feat(auth): segment-aware HPDS-v3 consent-skip (keep legacy /v3 until Phase 7) * feat(health): expose Actuator /actuator/health with db indicator (Phase 3 Task 4) * fix(health): disable actuator mail indicator (SMTP-unreachable envs must not report DOWN)
The resource registry is gone, so hpdsResourceUUID no longer arrives from clients (the path-routed frontend omits it) and cannot drive access selection. The gateway owns X-User-Id (strips client-supplied values, injects it only after successful introspection), so its presence proves an authenticated caller and its absence means the request passed open-access validation -- unlike the body field, it cannot be spoofed to obtain unobfuscated counts. hpdsResourceUUID stays accepted as an optional legacy field and is passed through to HPDS request bodies (HPDS ignores it); the AUTH/OPEN_HPDS_RESOURCE_UUID env vars are now optional fallbacks rather than required startup config.
Found by live smoke: with no configured fallback UUIDs and no body UUID (the production shape after the registry removal), audit metadata NPE'd on resourceUUID.toString(). VisualizationIntegrationTest now runs with blank UUID properties to pin the production shape.
HPDS ignores the body field entirely; with the registry gone and no configured fallbacks the UUID is legitimately null. Replaces the require-UUID tests with one pinning that a null UUID still queries HPDS. Found by live smoke (second layer behind the audit NPE).
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ramari16
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Verbatim, history-preserving imports of the six remaining services, replayed from the original
subtree imports. None of these is in the reactor yet — the root build is unchanged; each
service joins the reactor in its own adoption PR (PR9–PR14), which is where the actual refactor
diff lives. Review here = provenance check.
Part of the monorepo consolidation stack (PR1–PR14). Verified: each
services/<name>/tree isbyte-identical to the original import;
mvn validategreen; gitleaks scanned (new commits clean).