Katalyst: SDF import of many compounds fails in Katalyst (data integrity concern)

Description

• A user attempts to import an SDF file with many unique compounds (e.g., ~350 structures) into Katalyst.
• Import fails with an error message in the Katalyst UI, and the user is concerned about partial imports and data integrity.
• The SDF file is believed to be valid, but Katalyst may not process it correctly under current settings.

Solution

• First, confirm SDF file integrity:
  • Open the SDF in a structure editor or viewer and verify that:
    • All records contain valid structures or identifiers.
    • Key fields (e.g., IDs, names) are present and consistent.
• In Katalyst:
  • Check SDF import configuration (field mappings, uniqueness rules, maximum record limits).
  • Look at server logs for detailed errors during import (e.g., invalid records, bad SMILES, DB constraint violations).
• Common remediation steps:
  • Remove or correct any clearly invalid records from the SDF.
  • Break a very large SDF into smaller batches to see if a specific subset triggers the error.
  • Adjust de‑duplication or uniqueness criteria if multiple entries are intentionally similar (e.g., same base structure but different solutions).
• After import succeeds in a test environment:
  • Repeat the same steps in production.
  • Confirm that all expected records appear correctly and that no partial/duplicated entries exist.
• If logs show an internal error without clear root cause, contact Technical Support and provide with:
  • The SDF file (or sanitized sample).
  • Exact Katalyst version and environment details.