Fix code quality errors and warnings

[alicia-koh]

Merge Checklist

Please cross check this list if additions / modifications needs to be done on top of your core changes and tick them off. Reviewer can as well glance through and help the developer if something is missed out.

• Automated Tests (Jasmine integration tests, Unit tests, and/or Performance tests)
• Updated Manual tests / Demo Config
• Documentation (Application guide, Admin guide, Markdown, Readme and/or Wiki)
• Verified that local development environment is working with latest changes (integrated with latest develop branch)
• following best practices in code review doc

[Copilot]

Pull request overview

This pull request addresses various code quality errors and warnings across TypeScript, JavaScript, and Python files. The changes include bug fixes, code style improvements, and best practice implementations.

Changes:

• Fixed off-by-one loop boundary errors and added missing async/await keywords
• Improved resource management using context managers for file operations
• Removed redundant code (pass statements, unused variables) and improved exception handling specificity

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
ui/apps/vue-mri-ui-lib/src/utils/IfrToExtCohortDeps/cdmConfigUtils.ts	Fixed loop condition to prevent array out-of-bounds access
ui/apps/gateway-proxy/src/index.js	Fixed const variable reassignment by introducing intermediate variable
ui/alp-libs/python/pyqe/pyqe/api/result.py	Replaced manual file handling with context manager
ui/alp-libs/python/pyodidepyqe/test/test_pa_config.py	Added missing function parameter to match signature
ui/alp-libs/python/pyodidepyqe/samples/python/phekb_hypothyroidism.py	Moved Query instantiation closer to usage point
ui/alp-libs/python/pyodidepyqe/samples/python/phekb_diabetic_retinopathy.py	Moved Query instantiation closer to usage point
ui/alp-libs/python/pyodidepyqe/pyqe/api/result.py	Replaced manual file handling with context manager
ui/alp-libs/python/pyodidepyqe/pyqe/api/query.py	Added missing function parameter to match signature
ui/alp-libs/python/pyodidepyqe/pyqe/api/base.py	Added async/await keywords for proper async function handling
services/enterprise-gateway/kernels/R_ohdsi_docker/server_listener.py	Removed redundant pass statement
functions/query-gen-svc/src/svc/QueryGenSvc.ts	Changed Object.keys to Object.entries with destructuring
functions/files-manager/src/files-manager/files-manager.router.ts	Added missing await keywords for async function calls
functions/cdw-svc/spec/qe/config/cdm_config_integrationtest.ts	Stored connection reference before use
functions/analytics-svc/src/ifr-to-extcohort/cdmConfigUtils.ts	Fixed loop condition to prevent array out-of-bounds access
flows/hades/strategus_plugin/flow.py	Made exception handling more specific
flows/data_transformation/ner_extract_plugin/nel.py	Removed redundant pass statement
flows/data_transformation/dicom_etl_plugin/tasks.py	Removed unused variable
flows/data_transformation/dataflow_ui_plugin/nodes.py	Added missing constructor parameter
flows/data_transformation/dataflow_ui_plugin/flowutils.py	Made exception handling more specific
flows/base/omop_cdm_plugin/flow.py	Removed redundant logger declaration
flows/base/create_cachedb_file_plugin/types.py	Removed unused constant

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