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Supported Inputs

This page documents the current file and directory structures that PreFlight UI should accept and validate before handoff to core analysis.

Supported root structure​

PreFlight UI should validate the same runner contract used by the deployed pipeline:

<input-root>/<project_id>/01_sources/

The required file at that location is:

<input-root>/<project_id>/01_sources/sources.json

Required inputs​

The minimum valid package contains:

  1. sources.json
  2. portfolio_selected.csv

The selection file must be resolvable through sources.json.

Optional supported inputs​

PreFlight UI should recognize, validate, and classify these as optional rather than required:

  • assays.csv
  • compounds.csv
  • targets.csv
  • structures/*.pdb

Optional inputs can unlock additional downstream analysis depth, but their absence should not be treated as an automatic submission failure unless a selected workflow explicitly depends on them.

Supported file expectations​

sources.json​

The manifest should point only to files that exist under 01_sources/. Common keys include:

  • portfolio_selected_csv
  • primary_candidate_id
  • assays_csv
  • compounds_csv
  • targets_csv
  • pdbs

portfolio_selected.csv​

The selected portfolio file must include one of:

  • smiles
  • canonical_smiles

Recommended identifiers and metadata:

  • candidate_id
  • compound_id
  • name
  • Customer metadata columns that should flow into analysis context

Structure files​

When structure files are included, they should be staged as .pdb files under a structure directory referenced by the manifest.

What PreFlight should check exactly​

At a minimum, the validator should confirm:

  • The <project_id> folder exists
  • The 01_sources directory exists
  • sources.json exists and is parseable
  • portfolio_selected.csv resolves from the manifest
  • The portfolio file contains at least one supported structure column for molecules
  • Referenced optional files exist when listed in the manifest

Known limitations​

  • The validator can confirm structural readiness, but it does not guarantee scientific sufficiency for every module family.
  • Missing optional files may be acceptable for ingestion but can still reduce module coverage later.
  • Support for formats other than the current CSV and PDB-centric contract should be documented explicitly before being presented as supported.

For the analysis-side interpretation of these constraints, see Prepare Inputs.