fix: use fully qualified name to resolve DuckDB ambiguous reference error

[jerome-ng]

No description provided.

[Copilot]

Pull request overview

This PR fixes a DuckDB ambiguous reference error by using fully qualified names. However, the diff is extremely broad — it appears to be a large-scale repository restructuring that: renames the root package, reorganizes extensions and plugins into new paths, introduces a new core/server application (with MCP server, plugin system, auth, etc.), adds extensive integration tests, and adds several new plugin examples and infrastructure files.

Changes:

• Renames and restructures the root package from @ohdsi/trex to @trexsql/ext, reorganizing plugin paths and CI workflows
• Introduces a new core/server TypeScript/Deno application with auth, MCP server, plugin management, and transform/migration support
• Adds a comprehensive suite of integration tests for distributed DB, pgwire, ETL, migration, FHIR/CQL, AI, and more

Reviewed changes

Copilot reviewed 1 out of 1 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
core/server/auth.ts	New BetterAuth-based auth module with SSO provider management
core/server/plugin/transform.ts	New transform plugin handler with endpoint registration and DuckDB query execution
core/server/plugin/migration.ts	New migration plugin runner using trex_migration_run_schema
core/server/plugin/utils.ts	Plugin directory scanner and utility functions
core/server/mcp/tools/trexdb.ts	MCP tools for querying the trexsql engine
core/server/lib/sql.ts	SQL escaping/validation utilities
integration-tests/	New integration test suite for all extension modules
package.json	Renamed package and updated dependencies
docker-compose.yml	Restructured service definitions
Dockerfile	Replaced edge-runtime build with trexsql-based build

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[Copilot]

The query SELECT COUNT(*)::int AS count FROM "user" does not include a schema qualifier. Given that this pool is configured with search_path=trex,public, the query will resolve against the trex schema at runtime, but it is inconsistent with all other queries in this file which explicitly use trex."user". If search_path ever changes or this code is reused in a different context, the query could silently target the wrong table. It should use FROM trex."user" for consistency and correctness.

[Copilot]

Same as above — UPDATE "user" lacks the trex. schema prefix. This is inconsistent with all other queries in the file that use trex."user" and is exactly the kind of ambiguous reference the PR title says it's fixing. This should be UPDATE trex."user".

Suggested change

	'UPDATE trex."user" SET role = $1 WHERE id = $2',

[Copilot]

The function name waitfor should follow camelCase conventions and be renamed to waitFor to match standard TypeScript naming conventions used elsewhere in the codebase (e.g., wait_for in Python tests, and camelCase style in the TS files).

[Copilot]

These two imports from the same module should be combined into a single import statement: import { pool, reloadAuthProviders } from "../../auth.ts";

Suggested change

	import { pool, reloadAuthProviders } from "../../auth.ts";

[Copilot]

A hardcoded password (Toor1234) is committed in the Docker Compose file for the HANA service. Even for a test/development environment, this is a poor practice since the password is publicly visible in the repository. Consider using an environment variable (e.g., ${HANA_MASTER_PASSWORD:-Toor1234}) so it can be overridden without changing source code.

Suggested change

	- ${HANA_MASTER_PASSWORD:-Toor1234}

[Copilot]

The pg-trex-up target is missing a blank line separator after the test-etl-db rule. This is a formatting inconsistency compared to other target separations in the Makefile (e.g., test-pg-trex and check-migration are similarly missing a blank line on line 138/139). These should have blank lines for readability.