{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "title": "mzPeak file index JSON",
  "description": "Describe the JSON format of the file index",
  "required": ["files", "metadata"],
  "type": "object",
  "properties": {
    "files": {
      "type": "array",
      "items": { "$ref": "#/definitions/file" },
      "description": "The files described in the index"
    },
    "metadata": {
      "type": "object",
      "additionalProperties": true,
      "required": [
        "version"
      ],
      "properties": {
        "version": {
          "type": "string",
          "description": "The mzPeak file format version"
        },
        "id": {
          "type": "string",
          "description": "An optional id for the mzPeak archive used for referencing from external files. It is recommended to use LSIDs when possible."
        },
        "accession": {
          "type": "string",
          "description": "An optional accession number for the mzPeak archive used for storage, e.g. in PRIDE."
        },
        "file_description": {
          "$ref": "https://raw.githubusercontent.com/HUPO-PSI/mzPeak-specification/refs/heads/main/schema/file_description.json"
        },
        "instrument_configuration_list": {
          "$ref": "https://raw.githubusercontent.com/HUPO-PSI/mzPeak-specification/refs/heads/main/schema/instrument_configuration.json"
        },
        "data_processing_method_list": {
          "$ref": "https://raw.githubusercontent.com/HUPO-PSI/mzPeak-specification/refs/heads/main/schema/data_processing.json"
        },
        "software_list": {
          "$ref": "https://raw.githubusercontent.com/HUPO-PSI/mzPeak-specification/refs/heads/main/schema/software.json"
        },
        "sample_list": {
          "$ref": "https://raw.githubusercontent.com/HUPO-PSI/mzPeak-specification/refs/heads/main/schema/sample.json"
        },
        "cv_list": {
          "$ref": "https://raw.githubusercontent.com/HUPO-PSI/mzPeak-specification/refs/heads/main/schema/cv_list.json"
        },
        "run": {
          "$ref": "https://raw.githubusercontent.com/HUPO-PSI/mzPeak-specification/refs/heads/main/schema/ms_run.json"
        }
      }
    }
  },
  "definitions": {
    "file": {
      "type": "object",
      "description": "A single file in the mzPeak archive of a certain type",
      "properties": {
        "name": {
          "type": "string",
          "description": "The name of the file, relative to the root of the archive"
        },
        "entity_type": {
          "type": "string",
          "examples": ["spectrum", "chromatogram", "other", "proprietary"],
          "description": "The things being described in one facet or another by this file"
        },
        "data_kind": {
          "type": "string",
          "examples": [
            "data arrays",
            "metadata",
            "peaks",
            "other",
            "proprietary"
          ],
          "description": "The facet of the thing being described in this file"
        }
      }
    }
  }
}