<commit_before>{
    "title": "Human Individual",
    "description": "Schema for submitting a human individual.",
    "id": "/profiles/individual_human.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": ["award", "lab"],
    "identifyingProperties": ["uuid", "accession", "aliases"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/status" },
        { "$ref": "individual.json#/properties" },
        { "$ref": "mixins.json#/accession" },
        { "$ref": "mixins.json#/aliases" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/modified" },
        { "$ref": "mixins.json#/release_dates" },
        { "$ref": "mixins.json#/documents" },
        { "$ref": "mixins.json#/tags" },
        { "$ref": "mixins.json#/notes" },
        { "$ref": "mixins.json#/static_embeds" }
    ],
    "mixinFacets" : [
        { "$ref": "mixins.json#/facets_common" }
    ],
    "dependencies": {
      "age": ["age_units"]
    },
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "ethnicity": {
            "title": "Ethnicity",
            "type": "string",
            "lookup": 30
        },
        "health_status": {
            "title": "Individual Health Status",
            "type": "string",
            "lookup": 40
        },
        "life_stage": {
            "title": "Life stage",
            "type": "string",
            "lookup": 20,
            "enum": [
                "fetal",
                "newborn",
                "child",
                "adult",
                "unknown",
                "embryonic",
                "postnatal"
            ]
        },
        "organism": {
            "default": "7745b647-ff15-4ff3-9ced-b897d4e2983c",
            "exclude_from": ["submit4dn", "FFedit-create"],
            "lookup": 2,
            "linkEnum": ["7745b647-ff15-4ff3-9ced-b897d4e2983c"]
        },
        "individual_relation": {
            "exclude_from": ["submit4dn", "FFedit-create"]
        },
        "dbxrefs": {
            "@type": "@id",
            "rdfs:subPropertyOf": "rdfs:seeAlso",
            "title": "External identifiers",
            "description": "Unique identifiers from external resources.",
            "type": "array",
            "lookup": 1000,
            "uniqueItems": true,
            "items": {
                "title": "External identifier",
                "description": "A unique identifier from external resource.",
                "type":  "string",
                "pattern": "^((PGP:hu[\\S\\s\\d]+)|(GTEx:[a-zA-Z0-9\\-_]+)|(GEO:SAMN\\d+))$"
            }
        }<commit_msg>add protected_data to individual<commit_after>{
    "title": "Human Individual",
    "description": "Schema for submitting a human individual.",
    "id": "/profiles/individual_human.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": ["award", "lab"],
    "identifyingProperties": ["uuid", "accession", "aliases"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/status" },
        { "$ref": "individual.json#/properties" },
        { "$ref": "mixins.json#/accession" },
        { "$ref": "mixins.json#/aliases" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/modified" },
        { "$ref": "mixins.json#/release_dates" },
        { "$ref": "mixins.json#/documents" },
        { "$ref": "mixins.json#/tags" },
        { "$ref": "mixins.json#/notes" },
        { "$ref": "mixins.json#/static_embeds" }
    ],
    "mixinFacets" : [
        { "$ref": "mixins.json#/facets_common" }
    ],
    "dependencies": {
      "age": ["age_units"]
    },
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "ethnicity": {
            "title": "Ethnicity",
            "type": "string",
            "lookup": 30
        },
        "health_status": {
            "title": "Individual Health Status",
            "type": "string",
            "lookup": 40
        },
        "life_stage": {
            "title": "Life stage",
            "type": "string",
            "lookup": 20,
            "enum": [
                "fetal",
                "newborn",
                "child",
                "adult",
                "unknown",
                "embryonic",
                "postnatal"
            ]
        },
        "protected_data": {
            "title": "Protected Data",
            "description": "A flag to indicate whether consent to publish sequence files from this individual is not available. If true, fastq and bam files are subject to restricted access.",
            "type": "boolean",
            "default": false,
            "lookup": 50
        },
        "organism": {
            "default": "7745b647-ff15-4ff3-9ced-b897d4e2983c",
            "exclude_from": ["submit4dn", "FFedit-create"],
            "lookup": 2,
            "linkEnum": ["7745b647-ff15-4ff3-9ced-b897d4e2983c"]
        },
        "individual_relation": {
            "exclude_from": ["submit4dn", "FFedit-create"]
        },
        "dbxrefs": {
            "@type": "@id",
            "rdfs:subPropertyOf": "rdfs:seeAlso",
            "title": "External identifiers",
            "description": "Unique identifiers from external resources.",
            "type": "array",
            "lookup": 1000,
            "uniqueItems": true,
            "items": {
                "title": "External identifier",
                "description": "A unique identifier from external resource.",
                "type":  "string",
                "pattern": "^((PGP:hu[\\S\\s\\d]+)|(GTEx:[a-zA-Z0-9\\-_]+)|(GEO:SAMN\\d+))$"
            }
        }
{'fraction_non_alphanumeric': 0.18906455862977603, 'fraction_numerical': 0.019433465085639, 'mean_word_length': 1.7208781362007168, 'pattern_counts': {'":': 130, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6707735', 'n_tokens_mistral': 1988, 'n_tokens_neox': 1848, 'n_words': 333}