BDMS-432-Migrate-Radionucleides

[jirhiker]

This PR tightens transfer/migration behavior, adds Radionuclides admin support, and improves legacy transfer reliability with explicit logging and updated schema details (notably HydraulicsData UUIDs
and columns).

What changed

• Added Radionuclides admin view and registration, updated HydraulicsData admin view for new fields.
• Updated HydraulicsData migration/model/transfer to include WellID (UUID), GlobalID (UUID), and OBJECTID (plus indexes).
• ChemistrySampleInfo transfer now normalizes SamplePointID (suffix/case) to match Things and logs lookup misses.
• Radionuclides and MinorTraceChemistry moved out of the parallel transfer group to run after ChemistrySampleInfo.
• Transfer logging now includes start/end for all transfers (base Transferer + functional transfers).
• Alembic env now:
  • creates app_read role outside the migration transaction
  • keeps existing loggers enabled post-migration
  • applies GRANT SELECT and default privileges with explicit logs.
• Added default transfer flags to .env and .env.example.

Why

• Ensure dependent transfers (Radionuclides, MinorTraceChemistry) do not run before ChemistrySampleInfo.
• Fix missing HydraulicsData columns/types and align with NM_Aquifer_Dev_DB.
• Make transfer progress visible and avoid logging being silenced by Alembic.
• Keep app_read role provisioning safe for Postgres (no CREATE ROLE in transaction).

Behavior changes

• Radionuclides and MinorTraceChemistry no longer run in parallel group 1.
• ChemistrySampleInfo Thing matching is now normalized (suffix-stripped + uppercase).

Testing

• pytest (full suite) — previously green after changes; re-run as needed for this PR.

Notes

• .env now explicitly lists transfer flags; adjust as needed for local runs.

[Copilot]

Pull request overview

This PR migrates the Radionuclides and MinorTraceChemistry transfers from parallel execution to sequential execution, and adds comprehensive logging throughout the transfer process.

Changes:

• Moved Radionuclides and MinorTraceChemistry transfers from parallel execution to sequential execution after other transfers complete
• Added consistent "Starting transfer" and "Completed transfer" logging messages across all transfer modules
• Fixed Alembic migration logging to prevent logger conflicts and improved grant execution handling

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
transfers/transfer.py	Moved Radionuclides and MinorTraceChemistry to sequential execution; added logging for schema rebuild steps
transfers/transferer.py	Added helper method for DataFrame length checks and transfer lifecycle logging
transfers/thing_transfer.py	Added start/complete logging for Things transfer
transfers/stratigraphy_transfer.py	Standardized logging format and added completion log
transfers/permissions_transfer.py	Added transfer logging and record count tracking
transfers/logger.py	Set explicit INFO level and added force=True to prevent logger conflicts
transfers/geologic_formation_transfer.py	Standardized logging format and added completion log
transfers/chemistry_sampleinfo.py	Added Thing ID normalization and lookup miss logging
transfers/aquifer_system_transfer.py	Standardized logging format and added completion log
alembic/env.py	Fixed logger configuration and separated grant statements for better logging
.env.example	Added environment variable documentation for all transfer flags

[Copilot]

Pull request overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 1 comment.

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