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fix(brain): unwedge suggestion approval and refresh knowledge counts live (#77)
Follow-up to #74. That PR made the failure *visible* (bulk decide now returns `failures[]`, and the UI renders a partial/zero success as an error) but the approval itself still threw — its diagnosis, a `schema_documentation_source_check` missing `CODE_DERIVED`, did not apply to the reporting install, where the CHECK was already correct and the log said something else entirely. ## What was actually failing ``` WARN CodeScanService : bulk decide skipped e2011614-…: Query did not return a unique result: 2 results were returned WARN CodeScanService : bulk decide skipped f3689e0e-…: Query did not return a unique result: 2 results were returned ``` `schema_documentation` carried no unique constraint on `(connection_id, object_type, object_name, parent_object, source)` and `CodeSuggestionApplier.approve` took no row lock, so **one bulk approve submitted twice concurrently wrote 219 duplicate pairs** (pairs ~3s apart; in every group the older row is an orphan and the newer one holds the `applied_doc_id`). Every later approve landing on such a key threw out of the `Optional`-returning upsert finder, and bulk-decide swallowed it per item. The duplicate never self-heals, so **all 198 pending SCHEMA_DOC suggestions were permanently unapprovable**. ## Fix **1. Duplicate-tolerant upsert.** The three finders now return `List`, so the compiler forces every caller to handle N matches. `SchemaDocumentationDeduplicator` keeps the newest row, repoints any `applied_doc_id` off the rows it deletes (a loose reference, not an FK — a dangling value fails silently), and drops their RAG embeddings. Applied at all four call sites, including `SchemaDriftListener`, which would have thrown identically the first time one of 17 duplicated tables was dropped. **2. Data repair + constraint.** `V116__dedupe_schema_documentation.sql`, applied by `SchemaDocumentationDedupeInitializer` — there is no Flyway runtime here, so a SQL file alone would never run. Idempotent: it returns before touching a row once the index exists. `coalesce(parent_object,'')` in the key because Postgres treats NULLs as distinct. **3. The root cause.** `approve`/`reject` load the suggestion `FOR UPDATE`, so the concurrent double-submit blocks and the second caller sees `APPROVED`. ## Also fixed (reported after the first fix landed) - **Counts stale until reload.** An approval also writes `schema_documentation`, served by `brain/notes`, which backs the Write-notes tab and its coverage counts. The decide hooks invalidated only `codeScan` + `companyKnowledge`. `invalidateAfterDecision` now covers `brain` and `schemaContext` too. - **Newest notes sorted last.** `@PreUpdate` never fires on insert, so a new note has a null `updatedAt`; sorting on it alone with nulls last sent every brand-new note to the *bottom*. Now `COALESCE(updatedAt, createdAt)`, matching `CompanyKnowledgeEntryRepository`. - **Fresh approvals buried in the Approved view.** `listSuggestions` sorted every status by confidence. PENDING stays confidence-first (it is a work queue); decided statuses now sort by `decidedAt DESC NULLS LAST`. ## Two bugs in #74's own test tooling - Both scripts hardcoded `sudo -u postgres psql`, which does not exist on the Compose deployment `install.sh` produces — the verify command in #74's description failed before testing anything. Now resolved through `scripts/self-host/vaultdb.py`. - **`e2e-review-approvals.py` step 10 rewrote every real `CODE_DERIVED` row to `source='USER'` and never restored it.** Running it against a live install silently relabelled 339 approved docs, and post-V116 it would collide with the unique index. It now parks rows in a scratch table and restores them with a verified count, and its cleanup deletes the planted row only while nothing references it. ## Verification Run against the live self-host stack, not just unit tests. - Initializer on the affected install: `removed 219 duplicate rows, 219 orphaned embeddings`; 7068 → 6849 doc rows, 8190 → 7971 RAG rows, **0 duplicate groups, 0 dangling `applied_doc_id`**. Skipped cleanly on restart. - The two originally stuck suggestions: `{"requested": 2, "succeeded": 2, "failed": 0}`. - Ordering, approving the three *lowest*-confidence items so the two sorts disagree — all three land above older `conf=0.97` rows. - `brain/notes` 4607 → 4608 on a first-time doc (the count that never refreshed), and the just-approved `crm.customers` now sorts first. - 21 backend unit tests green (4 new on collapse, 2 new on note ordering). 184 related tests run; the 6 failures in `TrainingServiceBusinessTermTest` / `BrainInitStageExecutorTest` reproduce identically on pristine `main` and are unrelated. - **E2E suite: 30/30 pass**, including duplicate collapse, `applied_doc_id` repointing, the unique index rejecting a second row, and two genuinely concurrent approves writing exactly one row. ```bash python3 scripts/self-host/seed-review-suggestions.py <connectionId> --count 20 python3 scripts/self-host/e2e-review-approvals.py <connectionId> # ✓ All review-approval edge cases passed ``` Note: the suite consumes its own fixtures, so re-run the seed before each run. 🤖 Generated with [Claude Code](https://claude.com/claude-code) https://claude.ai/code/session_018mG2xj9gWJ8WzfDP2fDePP Co-authored-by: Krishna Sasank Talasila <606482+geekypunk@users.noreply.github.com> Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com> Co-authored-by: Venkat SF <venkatesh.sakamuri@stayflexi.com>
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‎.gitignore‎

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@@ -104,3 +104,7 @@ optd-sidecar/target/
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*.iml
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.local-admin-credentials
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.local-mcp-token
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# Python bytecode from scripts/
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__pycache__/
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*.pyc

‎CLAUDE.md‎

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@@ -296,6 +296,16 @@ broken. Assert the *outcome*, never the attempt:
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- **Mocks hide SDK breaks.** `tests/tools/test_mcp_structured_content.py` uses a
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`_FakeCallToolResult` with a hardcoded `.isError`, so it kept passing precisely when
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the real SDK stopped matching. Pin the dependency; a fake cannot catch this.
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- **A self-host verification script must reach the DB the way the install does.**
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`seed-review-suggestions.py` / `e2e-review-approvals.py` hardcoded
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`sudo -u postgres psql`, which only exists on a bare-metal install — on the Compose
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deployment `install.sh` actually produces, the documented verify command died before
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testing anything. Both now resolve the path through `scripts/self-host/vaultdb.py`.
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- **A test that mutates shared state must restore it, and only what it created.** The
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same e2e suite parked every real `CODE_DERIVED` row by rewriting `source` to `USER`
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and never restored it, so a run against a live install silently relabelled the user's
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approved docs. It now copies rows to a scratch table and restores them, and its
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cleanup deletes the planted row only while nothing references it.
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- **Never claim a check you did not run.** `install.sh` reported "up to date" when it
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could not reach npm; it now says it could not check.
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- **`set -e` + `read` at EOF aborts silently.** Prompts in `install.sh` use
@@ -384,6 +394,53 @@ it against a real database — not a theoretical hardening pass.
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`POST /users/admin/reset` on every install that had run `setup-agent.sh`, since that
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mints an admin MCP token on each run.
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- **An `Optional`-returning derived finder is an assertion that the key is unique.**
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Spring Data throws `IncorrectResultSizeDataAccessException` ("Query did not return a
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unique result: N results were returned") the moment it is not, and the row that broke
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it never repairs itself, so the failure is permanent rather than transient.
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`schema_documentation` had no unique constraint on
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`(connection_id, object_type, object_name, parent_object, source)` and
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`CodeSuggestionApplier.approve` took no row lock, so one bulk approve submitted twice
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concurrently wrote 219 duplicate pairs. Every later approve touching one of those keys
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threw, `CodeScanService.bulkDecide` swallowed it per item, and the Review queue
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reported "Approved 0 of 2" — with all 198 pending SCHEMA_DOC suggestions wedged.
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Three-part fix, and all three are load-bearing:
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1. `V116__dedupe_schema_documentation.sql` + `SchemaDocumentationDedupeInitializer`
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(no Flyway here, so the initializer is what actually applies it) collapse the
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duplicates and add `ux_schema_doc_target`, keyed on
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`coalesce(parent_object,'')` because Postgres treats NULLs as distinct.
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2. Those finders now return `List`, and `SchemaDocumentationDeduplicator.collapse`
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keeps the newest row, repoints any `applied_doc_id` off the rows it deletes, and
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drops their RAG embeddings. Do not restore an `Optional` variant — legacy installs
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still carry duplicates until the initializer runs.
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3. `approve`/`reject` load the suggestion via `findByIdForUpdate` (`PESSIMISTIC_WRITE`)
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so the concurrent double-submit that created the duplicates blocks instead of racing.
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- **`applied_doc_id` is a loose reference, not an FK.** Deleting a `schema_documentation`
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row it points at raises nothing and dangles silently — repoint before deleting.
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- **Approve *updates* the row an earlier scan wrote**, so a "freshly approved" doc row
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carries a historical `created_at`. A test that plants an "old" duplicate with a
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hardcoded past date can easily plant the *newer* of the two and assert nothing; anchor
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fixture timestamps to the real row's `created_at`.
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- **A write's blast radius decides what to invalidate, not the endpoint you called.**
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Approving a code-scan suggestion writes `code_knowledge_suggestion` *and*
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`schema_documentation` (served by `brain/notes`, which backs the Write-notes tab
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and its coverage counts) *and* `rag_documents` *and*, for KNOWLEDGE_ENTRY, a
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company knowledge entry. The decide hooks invalidated only `codeScan` +
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`companyKnowledge`, so every schema-doc-derived count stayed stale until the user
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reloaded the page. `invalidateAfterDecision` in `useCodeScan.js` is the single
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place that lists them; add to it when an approval starts writing something new.
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- **`@PreUpdate` does not fire on insert, so `updatedAt` is null on a brand-new row.**
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Sorting "newest first" on `updatedAt` alone with nulls last therefore sends every
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freshly created row to the *bottom* — which is why a just-approved note did not
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appear at the top of the Write-notes list. Sort on
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`COALESCE(updatedAt, createdAt)` (`BrainNoteService.touchedAt`,
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`CompanyKnowledgeEntryRepository.findByConnectionIdOrderByRecency`).
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- **Suggestion list order depends on the status being viewed.** PENDING is a work
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queue → `confidence DESC`. APPROVED/REJECTED are history → `decidedAt DESC NULLS
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LAST` so the decision you just made is at the top; confidence-sorting a decided
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list scattered fresh approvals among hundreds of older ones
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(`CodeScanService.sortFor`).
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### Endpoint Authorization Rules
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- **Authentication is not authorization.** `SecurityConfig` only asserts

‎backend/src/main/java/com/dbaagent/config/SchemaDocumentationDedupeInitializer.java‎

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package com.dbaagent.config;
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import lombok.extern.slf4j.Slf4j;
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import org.springframework.context.annotation.Bean;
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import org.springframework.context.annotation.Configuration;
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import org.springframework.context.annotation.DependsOn;
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import org.springframework.jdbc.core.JdbcTemplate;
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import org.springframework.transaction.support.TransactionTemplate;
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import org.springframework.transaction.PlatformTransactionManager;
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import javax.sql.DataSource;
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/**
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* Applies {@code V116__dedupe_schema_documentation.sql} at startup: collapses
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* duplicate {@code schema_documentation} rows and adds the unique index on the
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* logical key.
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*
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* <p>This repo has no Flyway runtime — {@code db/migration} is a hand-maintained
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* changelog and Hibernate {@code ddl-auto=update} never adds an index the entity
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* does not declare. Without this, self-host installs carrying duplicates from a
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* double-submitted bulk approve stay wedged: every SCHEMA_DOC approve throws
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* {@code Query did not return a unique result}. Mirrors
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* {@link SchemaDocumentationSourceCompatibilityInitializer}.
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*
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* <p>Idempotent and cheap on a clean install: the index exists, so it returns
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* before touching a row.
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*/
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@Configuration
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@Slf4j
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public class SchemaDocumentationDedupeInitializer {
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private static final String TABLE = "schema_documentation";
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private static final String INDEX = "ux_schema_doc_target";
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@Bean("schemaDocumentationDedupeBootstrap")
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@DependsOn("entityManagerFactory")
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public Object schemaDocumentationDedupeBootstrap(DataSource dataSource,
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PlatformTransactionManager txManager) {
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JdbcTemplate jdbc = new JdbcTemplate(dataSource);
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if (!tableExists(jdbc, TABLE)) {
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return new Object();
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}
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if (indexExists(jdbc, INDEX)) {
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return new Object();
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}
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// One transaction: a half-applied dedupe (rows deleted, index missing)
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// would silently re-accumulate duplicates until the next boot.
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new TransactionTemplate(txManager).executeWithoutResult(status -> {
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int repointed = jdbc.update("""
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UPDATE code_knowledge_suggestion s
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SET applied_doc_id = l.keep_id
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FROM (%s) l
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WHERE s.applied_doc_id = l.id
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""".formatted(LOSERS));
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int embeddings = jdbc.update(
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"DELETE FROM rag_documents WHERE id IN (SELECT id FROM (%s) l)".formatted(LOSERS));
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int removed = jdbc.update(
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"DELETE FROM schema_documentation WHERE id IN (SELECT id FROM (%s) l)".formatted(LOSERS));
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jdbc.execute("""
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CREATE UNIQUE INDEX IF NOT EXISTS %s
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ON %s (connection_id, object_type, object_name, coalesce(parent_object, ''), source)
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""".formatted(INDEX, TABLE));
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if (removed > 0) {
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log.warn("Deduped {}: removed {} duplicate rows, {} orphaned embeddings, "
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+ "repointed {} applied_doc_id references",
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TABLE, removed, embeddings, repointed);
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}
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log.info("Ensured unique index {} on {}", INDEX, TABLE);
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});
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return new Object();
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}
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/**
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* Every row but the newest within each logical key. Newest wins because it is
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* the row existing {@code applied_doc_id} references point at; {@code id}
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* breaks ties for rows written in the same clock tick. {@code coalesce} on
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* {@code parent_object} because Postgres treats NULLs as distinct, so TABLE
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* rows would otherwise never group together.
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*/
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private static final String LOSERS = """
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SELECT id, keep_id FROM (
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SELECT id,
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first_value(id) OVER w AS keep_id,
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row_number() OVER w AS rn
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FROM schema_documentation
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WINDOW w AS (
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PARTITION BY connection_id, object_type, object_name,
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coalesce(parent_object, ''), source
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ORDER BY created_at DESC NULLS LAST, id DESC
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)
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) ranked WHERE rn > 1
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""";
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private boolean tableExists(JdbcTemplate jdbc, String tableName) {
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Integer count = jdbc.queryForObject("""
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SELECT COUNT(*)
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FROM information_schema.tables
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WHERE table_schema = 'public' AND table_name = ?
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""", Integer.class, tableName);
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return count != null && count > 0;
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}
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private boolean indexExists(JdbcTemplate jdbc, String indexName) {
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Integer count = jdbc.queryForObject("""
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SELECT COUNT(*)
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FROM pg_indexes
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WHERE schemaname = 'public' AND indexname = ?
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""", Integer.class, indexName);
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return count != null && count > 0;
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}
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}

‎backend/src/main/java/com/dbaagent/repository/CodeKnowledgeSuggestionRepository.java‎

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import com.dbaagent.model.code.CodeKnowledgeSuggestion;
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import org.springframework.data.domain.Page;
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import org.springframework.data.domain.Pageable;
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import jakarta.persistence.LockModeType;
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import org.springframework.data.jpa.repository.JpaRepository;
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import org.springframework.data.jpa.repository.Lock;
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import org.springframework.data.jpa.repository.Modifying;
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import org.springframework.data.jpa.repository.Query;
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import org.springframework.data.repository.query.Param;
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import org.springframework.stereotype.Repository;
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import java.util.Collection;
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import java.util.List;
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import java.util.Optional;
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@Repository
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public interface CodeKnowledgeSuggestionRepository extends JpaRepository<CodeKnowledgeSuggestion, String> {
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/**
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* Row-locking load used by approve/reject. Without it two concurrent bulk
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* decides both read the same suggestion as PENDING and both materialize a
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* {@code schema_documentation} row — the duplicate-row bug that
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* {@code V116__dedupe_schema_documentation.sql} had to clean up. The second
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* caller now blocks, then sees APPROVED and returns early.
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*/
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@Lock(LockModeType.PESSIMISTIC_WRITE)
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@Query("SELECT s FROM CodeKnowledgeSuggestion s WHERE s.id = :id")
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Optional<CodeKnowledgeSuggestion> findByIdForUpdate(@Param("id") String id);
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/**
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* Repoints approvals at the surviving row when duplicate schema_documentation
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* rows are collapsed. {@code applied_doc_id} is a loose reference, not an FK,
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* so deleting a duplicate would otherwise leave a suggestion pointing at a row
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* that no longer exists — silently, since nothing enforces it.
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*/
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@Modifying(flushAutomatically = true)
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@Query("UPDATE CodeKnowledgeSuggestion s SET s.appliedDocId = :keepId "
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+ "WHERE s.appliedDocId IN :staleIds")
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int repointAppliedDocId(@Param("keepId") String keepId,
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@Param("staleIds") Collection<String> staleIds);
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Page<CodeKnowledgeSuggestion> findByConnectionIdAndStatus(
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String connectionId,
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CodeKnowledgeSuggestion.Status status,

‎backend/src/main/java/com/dbaagent/repository/SchemaDocumentationRepository.java‎

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SchemaDocumentation.DocumentationType objectType
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);
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Optional<SchemaDocumentation> findByConnectionIdAndObjectTypeAndObjectName(
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/**
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* Returns a {@link List}, never an {@link Optional} — the logical key is not
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* unique in data written before {@code V116__dedupe_schema_documentation.sql}
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* added the constraint, and an {@code Optional} finder throws
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* {@code IncorrectResultSizeDataAccessException} on a legacy duplicate rather
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* than letting the caller repair it. Collapse matches with
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* {@link com.dbaagent.service.SchemaDocumentationDeduplicator}.
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*/
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List<SchemaDocumentation> findByConnectionIdAndObjectTypeAndObjectName(
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String connectionId,
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SchemaDocumentation.DocumentationType objectType,
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String objectName
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""")
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long countWithBusinessTerms(@Param("connectionId") String connectionId);
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// Upsert support: find existing AI doc to update instead of creating duplicates
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Optional<SchemaDocumentation> findByConnectionIdAndObjectTypeAndObjectNameAndSource(
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// Upsert support: find existing doc to update instead of creating duplicates.
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// List-returning for the same reason as findByConnectionIdAndObjectTypeAndObjectName above.
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List<SchemaDocumentation> findByConnectionIdAndObjectTypeAndObjectNameAndSource(
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String connectionId, SchemaDocumentation.DocumentationType objectType,
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String objectName, DocumentationSource source);
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Optional<SchemaDocumentation> findByConnectionIdAndObjectTypeAndObjectNameAndParentObjectAndSource(
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List<SchemaDocumentation> findByConnectionIdAndObjectTypeAndObjectNameAndParentObjectAndSource(
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String connectionId, SchemaDocumentation.DocumentationType objectType,
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String objectName, String parentObject, DocumentationSource source);
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‎backend/src/main/java/com/dbaagent/service/SchemaDescriptionService.java‎

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private final ColumnProfileRepository columnProfileRepo;
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private final InferredTableRelationshipRepository inferredRelationshipRepository;
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private final TrainingService trainingService;
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private final SchemaDocumentationDeduplicator schemaDocDeduplicator;
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private final ConnectionService connectionService;
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private final DatabaseProviderRegistry providerRegistry;
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private final ObjectMapper objectMapper = new ObjectMapper();
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ColumnProfileRepository columnProfileRepo,
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InferredTableRelationshipRepository inferredRelationshipRepository,
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TrainingService trainingService,
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SchemaDocumentationDeduplicator schemaDocDeduplicator,
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ConnectionService connectionService,
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DatabaseProviderRegistry providerRegistry,
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@Value("${brain.description.ai-concurrency:4}") int aiConcurrency) {
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this.columnProfileRepo = columnProfileRepo;
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this.inferredRelationshipRepository = inferredRelationshipRepository;
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this.trainingService = trainingService;
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this.schemaDocDeduplicator = schemaDocDeduplicator;
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this.connectionService = connectionService;
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this.providerRegistry = providerRegistry;
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this.aiConcurrency = Math.max(1, aiConcurrency);
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: desc.getTableName();
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// Upsert table-level doc (find existing AI doc or create new)
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var existingTableDoc = schemaDocRepo
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.findByConnectionIdAndObjectTypeAndObjectNameAndSource(
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var existingTableDoc = schemaDocDeduplicator.collapse(
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schemaDocRepo.findByConnectionIdAndObjectTypeAndObjectNameAndSource(
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connectionId, DocumentationType.TABLE, objectName,
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DocumentationSource.AI_GENERATED);
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DocumentationSource.AI_GENERATED),
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objectName + " (TABLE, AI_GENERATED)");
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SchemaDocumentation tableDoc;
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if (existingTableDoc.isPresent()) {
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tableDoc = existingTableDoc.get();
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if (existingTableDoc != null) {
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tableDoc = existingTableDoc;
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tableDoc.setDescription(desc.getTableDescription());
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tableDoc.setBusinessTerms(desc.getBusinessTerms());
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tableDoc.setConfidence(desc.getConfidence());
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// Upsert column-level docs
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for (var col : desc.getColumns()) {
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if (col.getDescription() == null || col.getDescription().isBlank()) continue;
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var existingColDoc = schemaDocRepo
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.findByConnectionIdAndObjectTypeAndObjectNameAndParentObjectAndSource(
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var existingColDoc = schemaDocDeduplicator.collapse(
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schemaDocRepo.findByConnectionIdAndObjectTypeAndObjectNameAndParentObjectAndSource(
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connectionId, DocumentationType.COLUMN, col.getName(),
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objectName, DocumentationSource.AI_GENERATED);
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objectName, DocumentationSource.AI_GENERATED),
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objectName + "." + col.getName() + " (COLUMN, AI_GENERATED)");
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SchemaDocumentation colDoc;
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if (existingColDoc.isPresent()) {
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colDoc = existingColDoc.get();
458+
if (existingColDoc != null) {
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colDoc = existingColDoc;
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colDoc.setDescription(col.getDescription());
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colDoc.setConfidence(col.getConfidence());
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} else {

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