CHESS-ID3A-FAST

FOXDEN is a collection of services intended to facilitate the capture, curation, and dissemination of sample and dataset metadata and provenance. The FOXDEN homepage can be found at https://foxden.classe.cornell.edu:8344.

Sample-level metadata records can be constructed and, if desired, injected directly into FOXDEN directly from SPEC during data collection. To set up FOXDEN record automation, in SPEC run foxden_setup. In the menu that comes up, configure options as desired:

• Metadata service records on/off: if on, will construct a sample-level metadata record when newsample is run from SPEC, and inject to FOXDEN or just save the record .json according to the setting chosen under “record submission location” below.
• SpecScans service records on/off: if on, will construct a SPEC Scan Service record .json after each SPEC scan and submit to the FOXDEN SPEC Scan Service https://foxden.classe.cornell.edu:8344/info/specscans
• Manual metadata input enable/disable:
  • if enabled, SPEC will construct a sample-level metadata record according to how newsample is run:
    • if no arguments are used with newsample, SPEC will prompt for metadata values interactively, and save the resulting composite .json in /nfs/chess/aux/cycles/[cycle ID]/id3a/[btr ID]/[sample ID]/[sample ID.json]
    • if you wish to upload a .json file with pre-populated sample-level metadata, run newsample [sample name] [sample .json with full path], for example: newsample lshr-1 /nfs/chess/aux/cycles/2026-1/shanks-4838-a/example_sample_json.json SPEC will combine the information in the specified .json file with BTR-level metadata specified during newuserid, and save the resulting composite .json in /nfs/chess/aux/cycles/[cycle ID]/id3a/[btr ID]/[sample ID]/[sample ID.json]
  • If disabled, an incomplete record .json will be created in /nfs/chess/aux/[cycle ID]/ID3A/[btr ID]/[sample ID]/metadata/[sample ID.json] containing only the raw data location.
• Record submission location prod services/file only/dev services:
  • if prod services: records will be submitted to the production server https://foxden.classe.cornell.edu:8344
  • if file only: metadata .json will be created, but will not be injected into FOXDEN
  • if dev services: records will be submitted to the development server https://foxden-dev.classe.cornell.edu:8344

FOXDEN records can also be created manually via webform at https://foxden.classe.cornell.edu:8344/meta. In the dropdown menu labeled “Beamlines” on the left side of that page, choose a beamline schema (probably 3A if you’re reading this guide!) to use the ID3A schema for a record describing sample-level data collected at the beamline, or choose “user” to define your own schema.